From cda8dcf43a0867342bd68715521c03d84f162f49 Mon Sep 17 00:00:00 2001 From: xnought Date: Fri, 9 Feb 2024 12:08:19 -0800 Subject: [PATCH] feat: instead of fork jsut cp entire venome --- .gitmodules | 3 - frontend/venome-molstar | 1 - frontend/venome-molstar/.eslintrc.json | 118 + frontend/venome-molstar/.gitattributes | 1 + .../venome-molstar/.github/workflows/node.yml | 19 + frontend/venome-molstar/.gitignore | 10 + frontend/venome-molstar/.npmignore | 3 + frontend/venome-molstar/CHANGELOG.md | 50 + frontend/venome-molstar/LICENSE | 201 + frontend/venome-molstar/README.md | 26 + frontend/venome-molstar/component-demo.html | 232 + frontend/venome-molstar/example/.gitignore | 24 + .../example/.vscode/extensions.json | 3 + frontend/venome-molstar/example/README.md | 47 + frontend/venome-molstar/example/index.html | 13 + frontend/venome-molstar/example/package.json | 21 + .../venome-molstar/example/public/vite.svg | 1 + .../venome-molstar/example/src/App.svelte | 69 + frontend/venome-molstar/example/src/app.css | 0 .../example/src/assets/svelte.svg | 1 + frontend/venome-molstar/example/src/main.ts | 8 + .../venome-molstar/example/src/vite-env.d.ts | 2 + .../venome-molstar/example/svelte.config.js | 7 + frontend/venome-molstar/example/tsconfig.json | 20 + .../venome-molstar/example/tsconfig.node.json | 9 + .../venome-molstar/example/vite.config.ts | 7 + frontend/venome-molstar/example/yarn.lock | 865 ++ frontend/venome-molstar/favicon.ico | Bin 0 -> 16958 bytes frontend/venome-molstar/index.html | 259 + .../lib/alphafold-transparency.d.ts | 6 + .../lib/alphafold-transparency.js | 98 + .../venome-molstar/lib/custom-events.d.ts | 4 + frontend/venome-molstar/lib/custom-events.js | 68 + .../lib/domain-annotations/behavior.d.ts | 5 + .../lib/domain-annotations/behavior.js | 39 + .../lib/domain-annotations/color.d.ts | 10 + .../lib/domain-annotations/color.js | 81 + .../lib/domain-annotations/prop.d.ts | 35 + .../lib/domain-annotations/prop.js | 142 + frontend/venome-molstar/lib/helpers.d.ts | 106 + frontend/venome-molstar/lib/helpers.js | 389 + frontend/venome-molstar/lib/index.d.ts | 98 + frontend/venome-molstar/lib/index.js | 928 ++ frontend/venome-molstar/lib/labels.d.ts | 2 + frontend/venome-molstar/lib/labels.js | 46 + frontend/venome-molstar/lib/loci-details.d.ts | 27 + frontend/venome-molstar/lib/loci-details.js | 141 + frontend/venome-molstar/lib/overlay.d.ts | 16 + frontend/venome-molstar/lib/overlay.js | 50 + frontend/venome-molstar/lib/overlay.scss | 46 + .../lib/plugin-custom-state.d.ts | 84 + .../venome-molstar/lib/plugin-custom-state.js | 5 + .../venome-molstar/lib/sifts-mapping.d.ts | 16 + frontend/venome-molstar/lib/sifts-mapping.js | 83 + .../lib/sifts-mappings-behaviour.d.ts | 5 + .../lib/sifts-mappings-behaviour.js | 54 + .../venome-molstar/lib/spec-from-html.d.ts | 3 + frontend/venome-molstar/lib/spec-from-html.js | 109 + frontend/venome-molstar/lib/spec.d.ts | 122 + frontend/venome-molstar/lib/spec.js | 124 + .../venome-molstar/lib/subscribe-events.d.ts | 1 + .../venome-molstar/lib/subscribe-events.js | 190 + .../lib/superposition-export.d.ts | 4 + .../lib/superposition-export.js | 130 + .../superposition-focus-representation.d.ts | 16 + .../lib/superposition-focus-representation.js | 148 + .../lib/superposition-sifts-mapping.d.ts | 22 + .../lib/superposition-sifts-mapping.js | 155 + .../venome-molstar/lib/superposition.d.ts | 7 + frontend/venome-molstar/lib/superposition.js | 727 + .../lib/ui/alphafold-superposition.d.ts | 56 + .../lib/ui/alphafold-superposition.js | 149 + .../lib/ui/alphafold-tranparency.d.ts | 21 + .../lib/ui/alphafold-tranparency.js | 45 + .../lib/ui/annotation-controls.d.ts | 27 + .../lib/ui/annotation-controls.js | 151 + .../lib/ui/annotation-row-controls.d.ts | 26 + .../lib/ui/annotation-row-controls.js | 36 + .../lib/ui/export-superposition.d.ts | 6 + .../lib/ui/export-superposition.js | 49 + .../lib/ui/pdbe-left-panel.d.ts | 18 + .../venome-molstar/lib/ui/pdbe-left-panel.js | 129 + .../lib/ui/pdbe-screenshot-controls.d.ts | 20 + .../lib/ui/pdbe-screenshot-controls.js | 65 + .../lib/ui/pdbe-structure-controls.d.ts | 18 + .../lib/ui/pdbe-structure-controls.js | 48 + .../lib/ui/pdbe-viewport-controls.d.ts | 5 + .../lib/ui/pdbe-viewport-controls.js | 26 + .../venome-molstar/lib/ui/segment-tree.d.ts | 18 + .../venome-molstar/lib/ui/segment-tree.js | 652 + .../lib/ui/superposition-components.d.ts | 9 + .../lib/ui/superposition-components.js | 364 + .../lib/ui/superposition-viewport.d.ts | 4 + .../lib/ui/superposition-viewport.js | 12 + .../lib/ui/symmetry-annotation-controls.d.ts | 46 + .../lib/ui/symmetry-annotation-controls.js | 213 + frontend/venome-molstar/package-lock.json | 11725 ++++++++++++++++ frontend/venome-molstar/package.json | 82 + frontend/venome-molstar/portfolio.html | 415 + frontend/venome-molstar/scripts.js | 91 + .../src/app/alphafold-transparency.ts | 191 + .../venome-molstar/src/app/custom-events.ts | 99 + .../src/app/domain-annotations/behavior.ts | 68 + .../src/app/domain-annotations/color.ts | 122 + .../src/app/domain-annotations/prop.ts | 198 + frontend/venome-molstar/src/app/helpers.ts | 588 + frontend/venome-molstar/src/app/index.ts | 1255 ++ frontend/venome-molstar/src/app/labels.ts | 58 + .../venome-molstar/src/app/loci-details.ts | 227 + frontend/venome-molstar/src/app/overlay.ts | 59 + .../src/app/plugin-custom-state.ts | 74 + .../venome-molstar/src/app/sifts-mapping.ts | 116 + .../src/app/sifts-mappings-behaviour.ts | 84 + .../venome-molstar/src/app/spec-from-html.ts | 125 + frontend/venome-molstar/src/app/spec.ts | 267 + .../src/app/subscribe-events.ts | 209 + .../src/app/superposition-export.ts | 157 + .../app/superposition-focus-representation.ts | 213 + .../src/app/superposition-sifts-mapping.ts | 250 + .../venome-molstar/src/app/superposition.ts | 1006 ++ .../src/app/ui/alphafold-superposition.tsx | 236 + .../src/app/ui/alphafold-tranparency.tsx | 52 + .../src/app/ui/annotation-controls.tsx | 199 + .../src/app/ui/annotation-row-controls.tsx | 74 + .../src/app/ui/export-superposition.tsx | 63 + .../src/app/ui/pdbe-left-panel.tsx | 205 + .../src/app/ui/pdbe-screenshot-controls.tsx | 109 + .../src/app/ui/pdbe-structure-controls.tsx | 77 + .../src/app/ui/pdbe-viewport-controls.tsx | 40 + .../src/app/ui/segment-tree.tsx | 785 ++ .../src/app/ui/superposition-components.tsx | 498 + .../src/app/ui/superposition-viewport.tsx | 25 + .../app/ui/symmetry-annotation-controls.tsx | 250 + frontend/venome-molstar/src/overlay.scss | 46 + .../venome-molstar/src/web-component/index.js | 19 + frontend/venome-molstar/tsconfig.json | 27 + .../webpack.config.development.js | 21 + .../webpack.config.production.js | 140 + 138 files changed, 29116 insertions(+), 4 deletions(-) delete mode 100644 .gitmodules delete mode 160000 frontend/venome-molstar create mode 100644 frontend/venome-molstar/.eslintrc.json create mode 100644 frontend/venome-molstar/.gitattributes create mode 100644 frontend/venome-molstar/.github/workflows/node.yml create mode 100644 frontend/venome-molstar/.gitignore create mode 100644 frontend/venome-molstar/.npmignore create mode 100644 frontend/venome-molstar/CHANGELOG.md create mode 100644 frontend/venome-molstar/LICENSE create mode 100644 frontend/venome-molstar/README.md create mode 100644 frontend/venome-molstar/component-demo.html create mode 100644 frontend/venome-molstar/example/.gitignore create mode 100644 frontend/venome-molstar/example/.vscode/extensions.json create mode 100644 frontend/venome-molstar/example/README.md create mode 100644 frontend/venome-molstar/example/index.html create mode 100644 frontend/venome-molstar/example/package.json create mode 100644 frontend/venome-molstar/example/public/vite.svg create mode 100644 frontend/venome-molstar/example/src/App.svelte create mode 100644 frontend/venome-molstar/example/src/app.css create mode 100644 frontend/venome-molstar/example/src/assets/svelte.svg create mode 100644 frontend/venome-molstar/example/src/main.ts create mode 100644 frontend/venome-molstar/example/src/vite-env.d.ts create mode 100644 frontend/venome-molstar/example/svelte.config.js create mode 100644 frontend/venome-molstar/example/tsconfig.json create mode 100644 frontend/venome-molstar/example/tsconfig.node.json create mode 100644 frontend/venome-molstar/example/vite.config.ts create mode 100644 frontend/venome-molstar/example/yarn.lock create mode 100644 frontend/venome-molstar/favicon.ico create mode 100644 frontend/venome-molstar/index.html create mode 100644 frontend/venome-molstar/lib/alphafold-transparency.d.ts create mode 100644 frontend/venome-molstar/lib/alphafold-transparency.js create mode 100644 frontend/venome-molstar/lib/custom-events.d.ts create mode 100644 frontend/venome-molstar/lib/custom-events.js create mode 100644 frontend/venome-molstar/lib/domain-annotations/behavior.d.ts create mode 100644 frontend/venome-molstar/lib/domain-annotations/behavior.js create mode 100644 frontend/venome-molstar/lib/domain-annotations/color.d.ts create mode 100644 frontend/venome-molstar/lib/domain-annotations/color.js create mode 100644 frontend/venome-molstar/lib/domain-annotations/prop.d.ts create mode 100644 frontend/venome-molstar/lib/domain-annotations/prop.js create mode 100644 frontend/venome-molstar/lib/helpers.d.ts create mode 100644 frontend/venome-molstar/lib/helpers.js create mode 100644 frontend/venome-molstar/lib/index.d.ts create mode 100644 frontend/venome-molstar/lib/index.js create mode 100644 frontend/venome-molstar/lib/labels.d.ts create mode 100644 frontend/venome-molstar/lib/labels.js create mode 100644 frontend/venome-molstar/lib/loci-details.d.ts create mode 100644 frontend/venome-molstar/lib/loci-details.js create mode 100644 frontend/venome-molstar/lib/overlay.d.ts create mode 100644 frontend/venome-molstar/lib/overlay.js create mode 100644 frontend/venome-molstar/lib/overlay.scss create mode 100644 frontend/venome-molstar/lib/plugin-custom-state.d.ts create mode 100644 frontend/venome-molstar/lib/plugin-custom-state.js create mode 100644 frontend/venome-molstar/lib/sifts-mapping.d.ts create mode 100644 frontend/venome-molstar/lib/sifts-mapping.js create mode 100644 frontend/venome-molstar/lib/sifts-mappings-behaviour.d.ts create mode 100644 frontend/venome-molstar/lib/sifts-mappings-behaviour.js create mode 100644 frontend/venome-molstar/lib/spec-from-html.d.ts create mode 100644 frontend/venome-molstar/lib/spec-from-html.js create mode 100644 frontend/venome-molstar/lib/spec.d.ts create mode 100644 frontend/venome-molstar/lib/spec.js create mode 100644 frontend/venome-molstar/lib/subscribe-events.d.ts create mode 100644 frontend/venome-molstar/lib/subscribe-events.js create mode 100644 frontend/venome-molstar/lib/superposition-export.d.ts create mode 100644 frontend/venome-molstar/lib/superposition-export.js create mode 100644 frontend/venome-molstar/lib/superposition-focus-representation.d.ts create mode 100644 frontend/venome-molstar/lib/superposition-focus-representation.js create mode 100644 frontend/venome-molstar/lib/superposition-sifts-mapping.d.ts create mode 100644 frontend/venome-molstar/lib/superposition-sifts-mapping.js create mode 100644 frontend/venome-molstar/lib/superposition.d.ts create mode 100644 frontend/venome-molstar/lib/superposition.js create mode 100644 frontend/venome-molstar/lib/ui/alphafold-superposition.d.ts create mode 100644 frontend/venome-molstar/lib/ui/alphafold-superposition.js create mode 100644 frontend/venome-molstar/lib/ui/alphafold-tranparency.d.ts create mode 100644 frontend/venome-molstar/lib/ui/alphafold-tranparency.js create mode 100644 frontend/venome-molstar/lib/ui/annotation-controls.d.ts create mode 100644 frontend/venome-molstar/lib/ui/annotation-controls.js create mode 100644 frontend/venome-molstar/lib/ui/annotation-row-controls.d.ts create mode 100644 frontend/venome-molstar/lib/ui/annotation-row-controls.js create mode 100644 frontend/venome-molstar/lib/ui/export-superposition.d.ts create mode 100644 frontend/venome-molstar/lib/ui/export-superposition.js create mode 100644 frontend/venome-molstar/lib/ui/pdbe-left-panel.d.ts create mode 100644 frontend/venome-molstar/lib/ui/pdbe-left-panel.js create mode 100644 frontend/venome-molstar/lib/ui/pdbe-screenshot-controls.d.ts create mode 100644 frontend/venome-molstar/lib/ui/pdbe-screenshot-controls.js create mode 100644 frontend/venome-molstar/lib/ui/pdbe-structure-controls.d.ts create mode 100644 frontend/venome-molstar/lib/ui/pdbe-structure-controls.js create mode 100644 frontend/venome-molstar/lib/ui/pdbe-viewport-controls.d.ts create mode 100644 frontend/venome-molstar/lib/ui/pdbe-viewport-controls.js create mode 100644 frontend/venome-molstar/lib/ui/segment-tree.d.ts create mode 100644 frontend/venome-molstar/lib/ui/segment-tree.js create mode 100644 frontend/venome-molstar/lib/ui/superposition-components.d.ts create mode 100644 frontend/venome-molstar/lib/ui/superposition-components.js create mode 100644 frontend/venome-molstar/lib/ui/superposition-viewport.d.ts create mode 100644 frontend/venome-molstar/lib/ui/superposition-viewport.js create mode 100644 frontend/venome-molstar/lib/ui/symmetry-annotation-controls.d.ts create mode 100644 frontend/venome-molstar/lib/ui/symmetry-annotation-controls.js create mode 100644 frontend/venome-molstar/package-lock.json create mode 100644 frontend/venome-molstar/package.json create mode 100644 frontend/venome-molstar/portfolio.html create mode 100644 frontend/venome-molstar/scripts.js create mode 100644 frontend/venome-molstar/src/app/alphafold-transparency.ts create mode 100644 frontend/venome-molstar/src/app/custom-events.ts create mode 100644 frontend/venome-molstar/src/app/domain-annotations/behavior.ts create mode 100644 frontend/venome-molstar/src/app/domain-annotations/color.ts create mode 100644 frontend/venome-molstar/src/app/domain-annotations/prop.ts create mode 100644 frontend/venome-molstar/src/app/helpers.ts create mode 100644 frontend/venome-molstar/src/app/index.ts create mode 100644 frontend/venome-molstar/src/app/labels.ts create mode 100644 frontend/venome-molstar/src/app/loci-details.ts create mode 100644 frontend/venome-molstar/src/app/overlay.ts create mode 100644 frontend/venome-molstar/src/app/plugin-custom-state.ts create mode 100644 frontend/venome-molstar/src/app/sifts-mapping.ts create mode 100644 frontend/venome-molstar/src/app/sifts-mappings-behaviour.ts create mode 100644 frontend/venome-molstar/src/app/spec-from-html.ts create mode 100644 frontend/venome-molstar/src/app/spec.ts create mode 100644 frontend/venome-molstar/src/app/subscribe-events.ts create mode 100644 frontend/venome-molstar/src/app/superposition-export.ts create mode 100644 frontend/venome-molstar/src/app/superposition-focus-representation.ts create mode 100644 frontend/venome-molstar/src/app/superposition-sifts-mapping.ts create mode 100644 frontend/venome-molstar/src/app/superposition.ts create mode 100644 frontend/venome-molstar/src/app/ui/alphafold-superposition.tsx create mode 100644 frontend/venome-molstar/src/app/ui/alphafold-tranparency.tsx create mode 100644 frontend/venome-molstar/src/app/ui/annotation-controls.tsx create mode 100644 frontend/venome-molstar/src/app/ui/annotation-row-controls.tsx create mode 100644 frontend/venome-molstar/src/app/ui/export-superposition.tsx create mode 100644 frontend/venome-molstar/src/app/ui/pdbe-left-panel.tsx create mode 100644 frontend/venome-molstar/src/app/ui/pdbe-screenshot-controls.tsx create mode 100644 frontend/venome-molstar/src/app/ui/pdbe-structure-controls.tsx create mode 100644 frontend/venome-molstar/src/app/ui/pdbe-viewport-controls.tsx create mode 100644 frontend/venome-molstar/src/app/ui/segment-tree.tsx create mode 100644 frontend/venome-molstar/src/app/ui/superposition-components.tsx create mode 100644 frontend/venome-molstar/src/app/ui/superposition-viewport.tsx create mode 100644 frontend/venome-molstar/src/app/ui/symmetry-annotation-controls.tsx create mode 100644 frontend/venome-molstar/src/overlay.scss create mode 100644 frontend/venome-molstar/src/web-component/index.js create mode 100644 frontend/venome-molstar/tsconfig.json create mode 100644 frontend/venome-molstar/webpack.config.development.js create mode 100644 frontend/venome-molstar/webpack.config.production.js diff --git a/.gitmodules b/.gitmodules deleted file mode 100644 index 83d64a11..00000000 --- a/.gitmodules +++ /dev/null @@ -1,3 +0,0 @@ -[submodule "frontend/venome-molstar"] - path = frontend/venome-molstar - url = git@github.com:xnought/venome-molstar.git diff --git a/frontend/venome-molstar b/frontend/venome-molstar deleted file mode 160000 index 885b180d..00000000 --- a/frontend/venome-molstar +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 885b180d35cb977a1bb442dfdb1dd5fe53b9ad9c diff --git a/frontend/venome-molstar/.eslintrc.json b/frontend/venome-molstar/.eslintrc.json new file mode 100644 index 00000000..e5c62c5e --- /dev/null +++ b/frontend/venome-molstar/.eslintrc.json @@ -0,0 +1,118 @@ +{ + "env": { + "browser": true, + "node": true + }, + "parserOptions": { + "ecmaVersion": 2018, + "sourceType": "module", + "ecmaFeatures": { + "impliedStrict": true + } + }, + "rules": { + "indent": "off", + "arrow-parens": [ + "off", + "as-needed" + ], + "brace-style": "off", + "comma-spacing": "off", + "space-infix-ops": "off", + "comma-dangle": "off", + "eqeqeq": [ + "error", + "smart" + ], + "import/order": "off", + "no-eval": "warn", + "no-new-wrappers": "warn", + "no-trailing-spaces": "warn", + "no-unsafe-finally": "warn", + "no-var": "error", + "spaced-comment": "warn", + "semi": "warn", + "no-throw-literal": "error", + "key-spacing": "warn", + "object-curly-spacing": ["warn", "always"], + "array-bracket-spacing": "warn", + "space-in-parens": "warn", + "computed-property-spacing": "error", + "prefer-const": ["warn", { + "destructuring": "all", + "ignoreReadBeforeAssign": false + }], + "space-before-function-paren": "off", + "func-call-spacing": "off", + "no-multi-spaces": "warn", + "block-spacing": "warn", + "keyword-spacing": "off", + "space-before-blocks": "warn", + "semi-spacing": "warn" + }, + "overrides": [ + { + "files": ["**/*.ts", "**/*.tsx"], + "parser": "@typescript-eslint/parser", + "parserOptions": { + "project": ["tsconfig.json", "tsconfig.commonjs.json"], + "sourceType": "module" + }, + "plugins": [ + "@typescript-eslint" + ], + "rules": { + "@typescript-eslint/ban-types": "off", + "@typescript-eslint/class-name-casing": "off", + "@typescript-eslint/indent": [ + "error", + 4, + { + "ignoredNodes": ["TypeExpression"], + "SwitchCase": 1 + } + ], + "@typescript-eslint/member-delimiter-style": [ + "off", + { + "multiline": { + "delimiter": "none", + "requireLast": true + }, + "singleline": { + "delimiter": "semi", + "requireLast": false + } + } + ], + "@typescript-eslint/prefer-namespace-keyword": "warn", + "@typescript-eslint/quotes": [ + "error", + "single", + { + "avoidEscape": true, + "allowTemplateLiterals": true + } + ], + "@typescript-eslint/semi": [ + "off", + null + ], + "@typescript-eslint/type-annotation-spacing": "error", + "@typescript-eslint/brace-style": [ + "error", + "1tbs", { "allowSingleLine": true } + ], + "@typescript-eslint/comma-spacing": "warn", + "@typescript-eslint/space-infix-ops": "warn", + "@typescript-eslint/space-before-function-paren": ["warn", { + "anonymous": "always", + "named": "never", + "asyncArrow": "always" + }], + "@typescript-eslint/func-call-spacing": ["warn"], + "@typescript-eslint/keyword-spacing": ["warn"] + } + } + ] +} \ No newline at end of file diff --git a/frontend/venome-molstar/.gitattributes b/frontend/venome-molstar/.gitattributes new file mode 100644 index 00000000..20eac601 --- /dev/null +++ b/frontend/venome-molstar/.gitattributes @@ -0,0 +1 @@ +package-lock.json binary \ No newline at end of file diff --git a/frontend/venome-molstar/.github/workflows/node.yml b/frontend/venome-molstar/.github/workflows/node.yml new file mode 100644 index 00000000..ecf223a2 --- /dev/null +++ b/frontend/venome-molstar/.github/workflows/node.yml @@ -0,0 +1,19 @@ +name: Build + +on: + push: + pull_request: + +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - uses: actions/setup-node@v2 + with: + node-version: 16 + - run: npm ci + - name: Lint + run: npm run lint + - name: Build + run: npm run build diff --git a/frontend/venome-molstar/.gitignore b/frontend/venome-molstar/.gitignore new file mode 100644 index 00000000..f95a82de --- /dev/null +++ b/frontend/venome-molstar/.gitignore @@ -0,0 +1,10 @@ +build/ + +node_modules/ +debug.log +npm-debug.log +tsconfig.tsbuildinfo + +*.sublime-workspace +.idea +.DS_Store diff --git a/frontend/venome-molstar/.npmignore b/frontend/venome-molstar/.npmignore new file mode 100644 index 00000000..f6314701 --- /dev/null +++ b/frontend/venome-molstar/.npmignore @@ -0,0 +1,3 @@ +!build/ +src/ +lib/ \ No newline at end of file diff --git a/frontend/venome-molstar/CHANGELOG.md b/frontend/venome-molstar/CHANGELOG.md new file mode 100644 index 00000000..5f6ec55d --- /dev/null +++ b/frontend/venome-molstar/CHANGELOG.md @@ -0,0 +1,50 @@ +# Change Log +All notable changes to this project will be documented in this file, following the suggestions of [Keep a CHANGELOG](http://keepachangelog.com/). This project adheres to [Semantic Versioning](http://semver.org/) for its most widely used - and defacto - public interfaces. + +## [Unreleased] + +- Mol* core dependency updated to 3.44.0 +- Removed Assembly Symmetry hack (now will hide assembly symmetry section for non-biological assemblies) +- Manual testing via `portfolio.html` +- Fixed hideStructure.nonStandard option +- hideStructure.het option also hides ions +- Removed loadCartoonsOnly option +- Setting highlight and selection color (by `.visual.setColor()`) includes the outline color +- Web-component attributes renamed to `ligand-auth-asym-id` and `ligand-struct-asym-id` (lowercase i) + +## [v3.1.3] +- Added ``Assembly Symmetry`` to structure controls, requires setting ``symmetryAnnotation`` in initialization parameters +- Keep sequence panel in settings even when initially hidden +- Changed `tsconfig.json` to place `tsconfig.tsbuildinfo` correctly (for incremental build) +- Fixed coloring after annotation is switched off (revert to `chain-id`, not `polymer-id`) +- Loading overlay with animated PDBe logo (requires initParam `loadingOverlay`) +- Use linting to keep code nice +- Correctly handle numeric value 0 in selections +- Fetch structures from static files when possible, instead of using ModelServer + +## [v3.1.2] +- Added PDBe Sifts Mappings module to solve UniPort mappings issue +- Split Webpack config file into separate files for Production and Development + +## [v3.1.1] +- Controls menu visible for AlphaFold view +- ``Reactive`` parameter addition for better responsive layout support + +## [v3.1.0] +- Mol* core dependency updated to V3.15.0 +- Superposition view - added option to superpose AlphaFold model +- UniPort residue numbering param addition to higlight and selection helper methods +- New param to display Sequence panel [62](https://github.com/molstar/lib/pdbe-molstar/lib/issues/62) + +## [v1.2.1] - 2021-12-03 +- Selection helper method ``representationColor`` param issue fix + +## [v1.2.0] - 2021-09-20 +- Add parameters to support AlphaFold Protein Structure DB view +- Add parameters to customize mouse events, issues [#8](https://github.com/PDBeurope/pdbe-molstar/lib/issues/8) +- Add parameter to customize ``lighting`` setting +- Extend ``Selection / highlight`` helper methods to support ``label_atom_id`` list, issues [#32](https://github.com/PDBeurope/pdbe-molstar/lib/issues/32) +- Extend helper methods support for multiple structures +- Extend ``hideCanvasControls`` +- Fix Frame rate drop issue while rotating the canvas +- Fix RGB color issue for params starting with r:0 \ No newline at end of file diff --git a/frontend/venome-molstar/LICENSE b/frontend/venome-molstar/LICENSE new file mode 100644 index 00000000..261eeb9e --- /dev/null +++ b/frontend/venome-molstar/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/frontend/venome-molstar/README.md b/frontend/venome-molstar/README.md new file mode 100644 index 00000000..016f9a86 --- /dev/null +++ b/frontend/venome-molstar/README.md @@ -0,0 +1,26 @@ +# PDBe Molstar + +PDBe implementation of [Mol\* (/'mol-star/)](https://github.com/molstar/lib/molstar) + +**Refer [PDBe Molstar Wiki](https://github.com/PDBeurope/pdbe-molstar/lib/wiki) for detailed documentation and examples** + +## Building & Running locally + +```sh +npm install +npm run build +# npm run rebuild # for a clean build +npm run serve +``` + +## Build automatically on file save: + +```sh +npm run watch +``` + +## Manual testing + +- Run locally by `npm run serve` +- Go to and check the viewer with various different setting (some of these reflect the actual setting on PDBe pages) +- If you want to tweak the options, go to "Frame URL" and change the options in the URL diff --git a/frontend/venome-molstar/component-demo.html b/frontend/venome-molstar/component-demo.html new file mode 100644 index 00000000..799f1046 --- /dev/null +++ b/frontend/venome-molstar/component-demo.html @@ -0,0 +1,232 @@ + + + + + + + PDBe Molstar Component Demo + + + + + + + + + + + + + + + +

PDBe Molstar Component

+ +
+
+

Canvas/ layout methods

+
+

Set Background

+ + + +

Toggle controls menu

+ + + + +

Toggle Fullscreen

+ +
+ +

Visual Methods

+
+

Change representation visibility

+ + + +

Toggle Spin

+ + + + +

Focus

+ + +

Highlight

+ + + +

Selection

+ +
+ +
+ +
+ +
+ +
+ + +

Set highlight / selection colour

+ + +
+ + + +

Reset Visual

+ + + + +

Update data

+ + +
+
+ +
+

PDBe Mol* Web-component Demo

+ +
+ + +
+ +
+
+ + + + + + \ No newline at end of file diff --git a/frontend/venome-molstar/example/.gitignore b/frontend/venome-molstar/example/.gitignore new file mode 100644 index 00000000..a547bf36 --- /dev/null +++ b/frontend/venome-molstar/example/.gitignore @@ -0,0 +1,24 @@ +# Logs +logs +*.log +npm-debug.log* +yarn-debug.log* +yarn-error.log* +pnpm-debug.log* +lerna-debug.log* + +node_modules +dist +dist-ssr +*.local + +# Editor directories and files +.vscode/* +!.vscode/extensions.json +.idea +.DS_Store +*.suo +*.ntvs* +*.njsproj +*.sln +*.sw? diff --git a/frontend/venome-molstar/example/.vscode/extensions.json b/frontend/venome-molstar/example/.vscode/extensions.json new file mode 100644 index 00000000..bdef8201 --- /dev/null +++ b/frontend/venome-molstar/example/.vscode/extensions.json @@ -0,0 +1,3 @@ +{ + "recommendations": ["svelte.svelte-vscode"] +} diff --git a/frontend/venome-molstar/example/README.md b/frontend/venome-molstar/example/README.md new file mode 100644 index 00000000..e6cd94fc --- /dev/null +++ b/frontend/venome-molstar/example/README.md @@ -0,0 +1,47 @@ +# Svelte + TS + Vite + +This template should help get you started developing with Svelte and TypeScript in Vite. + +## Recommended IDE Setup + +[VS Code](https://code.visualstudio.com/) + [Svelte](https://marketplace.visualstudio.com/items?itemName=svelte.svelte-vscode). + +## Need an official Svelte framework? + +Check out [SvelteKit](https://github.com/sveltejs/kit#readme), which is also powered by Vite. Deploy anywhere with its serverless-first approach and adapt to various platforms, with out of the box support for TypeScript, SCSS, and Less, and easily-added support for mdsvex, GraphQL, PostCSS, Tailwind CSS, and more. + +## Technical considerations + +**Why use this over SvelteKit?** + +- It brings its own routing solution which might not be preferable for some users. +- It is first and foremost a framework that just happens to use Vite under the hood, not a Vite app. + +This template contains as little as possible to get started with Vite + TypeScript + Svelte, while taking into account the developer experience with regards to HMR and intellisense. It demonstrates capabilities on par with the other `create-vite` templates and is a good starting point for beginners dipping their toes into a Vite + Svelte project. + +Should you later need the extended capabilities and extensibility provided by SvelteKit, the template has been structured similarly to SvelteKit so that it is easy to migrate. + +**Why `global.d.ts` instead of `compilerOptions.types` inside `jsconfig.json` or `tsconfig.json`?** + +Setting `compilerOptions.types` shuts out all other types not explicitly listed in the configuration. Using triple-slash references keeps the default TypeScript setting of accepting type information from the entire workspace, while also adding `svelte` and `vite/client` type information. + +**Why include `.vscode/extensions.json`?** + +Other templates indirectly recommend extensions via the README, but this file allows VS Code to prompt the user to install the recommended extension upon opening the project. + +**Why enable `allowJs` in the TS template?** + +While `allowJs: false` would indeed prevent the use of `.js` files in the project, it does not prevent the use of JavaScript syntax in `.svelte` files. In addition, it would force `checkJs: false`, bringing the worst of both worlds: not being able to guarantee the entire codebase is TypeScript, and also having worse typechecking for the existing JavaScript. In addition, there are valid use cases in which a mixed codebase may be relevant. + +**Why is HMR not preserving my local component state?** + +HMR state preservation comes with a number of gotchas! It has been disabled by default in both `svelte-hmr` and `@sveltejs/vite-plugin-svelte` due to its often surprising behavior. You can read the details [here](https://github.com/rixo/svelte-hmr#svelte-hmr). + +If you have state that's important to retain within a component, consider creating an external store which would not be replaced by HMR. + +```ts +// store.ts +// An extremely simple external store +import { writable } from 'svelte/store' +export default writable(0) +``` diff --git a/frontend/venome-molstar/example/index.html b/frontend/venome-molstar/example/index.html new file mode 100644 index 00000000..b6c5f0af --- /dev/null +++ b/frontend/venome-molstar/example/index.html @@ -0,0 +1,13 @@ + + + + + + + Vite + Svelte + TS + + +
+ + + diff --git a/frontend/venome-molstar/example/package.json b/frontend/venome-molstar/example/package.json new file mode 100644 index 00000000..97841b33 --- /dev/null +++ b/frontend/venome-molstar/example/package.json @@ -0,0 +1,21 @@ +{ + "name": "test", + "private": true, + "version": "0.0.0", + "type": "module", + "scripts": { + "dev": "vite", + "build": "vite build", + "preview": "vite preview", + "check": "svelte-check --tsconfig ./tsconfig.json" + }, + "devDependencies": { + "@sveltejs/vite-plugin-svelte": "^3.0.1", + "@tsconfig/svelte": "^5.0.2", + "svelte": "^4.2.8", + "svelte-check": "^3.6.2", + "tslib": "^2.6.2", + "typescript": "^5.2.2", + "vite": "^5.0.8" + } +} diff --git a/frontend/venome-molstar/example/public/vite.svg b/frontend/venome-molstar/example/public/vite.svg new file mode 100644 index 00000000..e7b8dfb1 --- /dev/null +++ b/frontend/venome-molstar/example/public/vite.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/frontend/venome-molstar/example/src/App.svelte b/frontend/venome-molstar/example/src/App.svelte new file mode 100644 index 00000000..df6f9844 --- /dev/null +++ b/frontend/venome-molstar/example/src/App.svelte @@ -0,0 +1,69 @@ + + +
+ + + + + + diff --git a/frontend/venome-molstar/example/src/app.css b/frontend/venome-molstar/example/src/app.css new file mode 100644 index 00000000..e69de29b diff --git a/frontend/venome-molstar/example/src/assets/svelte.svg b/frontend/venome-molstar/example/src/assets/svelte.svg new file mode 100644 index 00000000..c5e08481 --- /dev/null +++ b/frontend/venome-molstar/example/src/assets/svelte.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/frontend/venome-molstar/example/src/main.ts b/frontend/venome-molstar/example/src/main.ts new file mode 100644 index 00000000..8a909a15 --- /dev/null +++ b/frontend/venome-molstar/example/src/main.ts @@ -0,0 +1,8 @@ +import './app.css' +import App from './App.svelte' + +const app = new App({ + target: document.getElementById('app'), +}) + +export default app diff --git a/frontend/venome-molstar/example/src/vite-env.d.ts b/frontend/venome-molstar/example/src/vite-env.d.ts new file mode 100644 index 00000000..4078e747 --- /dev/null +++ b/frontend/venome-molstar/example/src/vite-env.d.ts @@ -0,0 +1,2 @@ +/// +/// diff --git a/frontend/venome-molstar/example/svelte.config.js b/frontend/venome-molstar/example/svelte.config.js new file mode 100644 index 00000000..b0683fd2 --- /dev/null +++ b/frontend/venome-molstar/example/svelte.config.js @@ -0,0 +1,7 @@ +import { vitePreprocess } from '@sveltejs/vite-plugin-svelte' + +export default { + // Consult https://svelte.dev/docs#compile-time-svelte-preprocess + // for more information about preprocessors + preprocess: vitePreprocess(), +} diff --git a/frontend/venome-molstar/example/tsconfig.json b/frontend/venome-molstar/example/tsconfig.json new file mode 100644 index 00000000..5fb548f2 --- /dev/null +++ b/frontend/venome-molstar/example/tsconfig.json @@ -0,0 +1,20 @@ +{ + "extends": "@tsconfig/svelte/tsconfig.json", + "compilerOptions": { + "target": "ESNext", + "useDefineForClassFields": true, + "module": "ESNext", + "resolveJsonModule": true, + /** + * Typecheck JS in `.svelte` and `.js` files by default. + * Disable checkJs if you'd like to use dynamic types in JS. + * Note that setting allowJs false does not prevent the use + * of JS in `.svelte` files. + */ + "allowJs": true, + "checkJs": true, + "isolatedModules": true + }, + "include": ["src/**/*.ts", "src/**/*.js", "src/**/*.svelte"], + "references": [{ "path": "./tsconfig.node.json" }] +} diff --git a/frontend/venome-molstar/example/tsconfig.node.json b/frontend/venome-molstar/example/tsconfig.node.json new file mode 100644 index 00000000..494bfe08 --- /dev/null +++ b/frontend/venome-molstar/example/tsconfig.node.json @@ -0,0 +1,9 @@ +{ + "compilerOptions": { + "composite": true, + "skipLibCheck": true, + "module": "ESNext", + "moduleResolution": "bundler" + }, + "include": ["vite.config.ts"] +} diff --git a/frontend/venome-molstar/example/vite.config.ts b/frontend/venome-molstar/example/vite.config.ts new file mode 100644 index 00000000..d7019694 --- /dev/null +++ b/frontend/venome-molstar/example/vite.config.ts @@ -0,0 +1,7 @@ +import { defineConfig } from 'vite' +import { svelte } from '@sveltejs/vite-plugin-svelte' + +// https://vitejs.dev/config/ +export default defineConfig({ + plugins: [svelte()], +}) diff --git a/frontend/venome-molstar/example/yarn.lock b/frontend/venome-molstar/example/yarn.lock new file mode 100644 index 00000000..cc3f075d --- /dev/null +++ b/frontend/venome-molstar/example/yarn.lock @@ -0,0 +1,865 @@ +# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY. +# yarn lockfile v1 + + +"@ampproject/remapping@^2.2.1": + version "2.2.1" + resolved "https://registry.yarnpkg.com/@ampproject/remapping/-/remapping-2.2.1.tgz#99e8e11851128b8702cd57c33684f1d0f260b630" + integrity sha512-lFMjJTrFL3j7L9yBxwYfCq2k6qqwHyzuUl/XBnif78PWTJYyL/dfowQHWE3sp6U6ZzqWiiIZnpTMO96zhkjwtg== + dependencies: + "@jridgewell/gen-mapping" "^0.3.0" + "@jridgewell/trace-mapping" "^0.3.9" + +"@esbuild/aix-ppc64@0.19.12": + version "0.19.12" + resolved "https://registry.yarnpkg.com/@esbuild/aix-ppc64/-/aix-ppc64-0.19.12.tgz#d1bc06aedb6936b3b6d313bf809a5a40387d2b7f" + integrity sha512-bmoCYyWdEL3wDQIVbcyzRyeKLgk2WtWLTWz1ZIAZF/EGbNOwSA6ew3PftJ1PqMiOOGu0OyFMzG53L0zqIpPeNA== + +"@esbuild/android-arm64@0.19.12": + version "0.19.12" + resolved "https://registry.yarnpkg.com/@esbuild/android-arm64/-/android-arm64-0.19.12.tgz#7ad65a36cfdb7e0d429c353e00f680d737c2aed4" + integrity 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PDBe Molstar

+ +
+
+

Canvas/ layout methods

+
+

Set Background

+ + + +

Toggle controls menu

+ + + + +

Toggle Fullscreen

+ +
+ +

Visual Methods

+
+

Change representation visibility

+ + + +

Toggle Spin

+ + + + +

Focus

+ + +

Highlight

+ + + +

Selection

+ +
+ +
+ +
+ +
+ +
+ + +

Set highlight / selection colour

+ + +
+ + + +

Reset Visual

+ + + + +

Update data

+ + +
+ +
+

Options

+
+ 

+                

+            

+        

+
+        

+            
PDBe Mol* JS Plugin Demo

+            
+            

+        

+    

+
+
+    
+
+
+
\ No newline at end of file
diff --git a/frontend/venome-molstar/lib/alphafold-transparency.d.ts b/frontend/venome-molstar/lib/alphafold-transparency.d.ts
new file mode 100644
index 00000000..5196db37
--- /dev/null
+++ b/frontend/venome-molstar/lib/alphafold-transparency.d.ts
@@ -0,0 +1,6 @@
+import { StructureElement } from "molstar/lib/mol-model/structure";
+import { PluginContext } from "molstar/lib/mol-plugin/context";
+import { StructureComponentRef, StructureRef } from "molstar/lib/mol-plugin-state/manager/structure/hierarchy-state";
+export declare function applyAFTransparency(plugin: PluginContext, structure: Readonly, transparency: number, pLDDT?: number): Promise;
+export declare function setStructureTransparency(plugin: PluginContext, components: StructureComponentRef[], value: number, loci: StructureElement.Loci, types?: string[]): Promise;
+export declare function clearStructureTransparency(plugin: PluginContext, components: StructureComponentRef[], types?: string[]): Promise;
diff --git a/frontend/venome-molstar/lib/alphafold-transparency.js b/frontend/venome-molstar/lib/alphafold-transparency.js
new file mode 100644
index 00000000..46710f0d
--- /dev/null
+++ b/frontend/venome-molstar/lib/alphafold-transparency.js
@@ -0,0 +1,98 @@
+import { StructureElement } from "molstar/lib/mol-model/structure";
+import { StateTransforms } from "molstar/lib/mol-plugin-state/transforms";
+import { StateSelection, } from "molstar/lib/mol-state";
+import { isEmptyLoci, Loci } from "molstar/lib/mol-model/loci";
+import { Transparency } from "molstar/lib/mol-theme/transparency";
+import { MolScriptBuilder as MS } from "molstar/lib/mol-script/language/builder";
+import { QualityAssessment } from "molstar/lib/extensions/model-archive/quality-assessment/prop";
+import { compile } from "molstar/lib/mol-script/runtime/query/compiler";
+import { StructureSelection, QueryContext, } from "molstar/lib/mol-model/structure";
+const TransparencyManagerTag = "transparency-controls";
+function getLociByPLDDT(score, contextData) {
+    const queryExp = MS.struct.modifier.union([
+        MS.struct.modifier.wholeResidues([
+            MS.struct.modifier.union([
+                MS.struct.generator.atomGroups({
+                    "chain-test": MS.core.rel.eq([
+                        MS.ammp("objectPrimitive"),
+                        "atomistic",
+                    ]),
+                    "residue-test": MS.core.rel.lte([
+                        QualityAssessment.symbols.pLDDT.symbol(),
+                        score,
+                    ]),
+                }),
+            ]),
+        ]),
+    ]);
+    const query = compile(queryExp);
+    const sel = query(new QueryContext(contextData));
+    return StructureSelection.toLociWithSourceUnits(sel);
+}
+export async function applyAFTransparency(plugin, structure, transparency, pLDDT = 70) {
+    return plugin.dataTransaction(async (ctx) => {
+        const loci = getLociByPLDDT(pLDDT, structure.cell.obj.data);
+        await setStructureTransparency(plugin, structure.components, transparency, loci);
+    }, { canUndo: "Apply Transparency" });
+}
+export async function setStructureTransparency(plugin, components, value, loci, types) {
+    await eachRepr(plugin, components, async (update, repr, transparencyCell) => {
+        if (types &&
+            types.length > 0 &&
+            !types.includes(repr.params.values.type.name))
+            return;
+        const structure = repr.obj.data.sourceData;
+        if (Loci.isEmpty(loci) || isEmptyLoci(loci))
+            return;
+        const layer = {
+            bundle: StructureElement.Bundle.fromLoci(loci),
+            value,
+        };
+        if (transparencyCell) {
+            const bundleLayers = [
+                ...transparencyCell.params.values.layers,
+                layer,
+            ];
+            const filtered = getFilteredBundle(bundleLayers, structure);
+            update
+                .to(transparencyCell)
+                .update(Transparency.toBundle(filtered));
+        }
+        else {
+            const filtered = getFilteredBundle([layer], structure);
+            update
+                .to(repr.transform.ref)
+                .apply(StateTransforms.Representation
+                .TransparencyStructureRepresentation3DFromBundle, Transparency.toBundle(filtered), { tags: TransparencyManagerTag });
+        }
+    });
+}
+export async function clearStructureTransparency(plugin, components, types) {
+    await eachRepr(plugin, components, async (update, repr, transparencyCell) => {
+        if (types &&
+            types.length > 0 &&
+            !types.includes(repr.params.values.type.name))
+            return;
+        if (transparencyCell) {
+            update.delete(transparencyCell.transform.ref);
+        }
+    });
+}
+async function eachRepr(plugin, components, callback) {
+    const state = plugin.state.data;
+    const update = state.build();
+    for (const c of components) {
+        for (const r of c.representations) {
+            const transparency = state.select(StateSelection.Generators.ofTransformer(StateTransforms.Representation
+                .TransparencyStructureRepresentation3DFromBundle, r.cell.transform.ref).withTag(TransparencyManagerTag));
+            await callback(update, r.cell, transparency[0]);
+        }
+    }
+    return update.commit({ doNotUpdateCurrent: true });
+}
+/** filter transparency layers for given structure */
+function getFilteredBundle(layers, structure) {
+    const transparency = Transparency.ofBundle(layers, structure.root);
+    const merged = Transparency.merge(transparency);
+    return Transparency.filter(merged, structure);
+}
diff --git a/frontend/venome-molstar/lib/custom-events.d.ts b/frontend/venome-molstar/lib/custom-events.d.ts
new file mode 100644
index 00000000..9366968d
--- /dev/null
+++ b/frontend/venome-molstar/lib/custom-events.d.ts
@@ -0,0 +1,4 @@
+import { PluginContext } from "molstar/lib/mol-plugin/context";
+export declare namespace CustomEvents {
+    function add(plugin: PluginContext, targetElement: HTMLElement): void;
+}
diff --git a/frontend/venome-molstar/lib/custom-events.js b/frontend/venome-molstar/lib/custom-events.js
new file mode 100644
index 00000000..3af52bc3
--- /dev/null
+++ b/frontend/venome-molstar/lib/custom-events.js
@@ -0,0 +1,68 @@
+import { lociDetails } from "./loci-details";
+import { debounceTime } from "rxjs/operators";
+export var CustomEvents;
+(function (CustomEvents) {
+    function create(eventTypeArr) {
+        const eventObj = {};
+        for (let ei = 0, el = eventTypeArr.length; ei < el; ei++) {
+            const eventType = eventTypeArr[ei];
+            let event;
+            if (typeof MouseEvent == "function") {
+                // current standard
+                event = new MouseEvent(eventType, {
+                    view: window,
+                    bubbles: true,
+                    cancelable: true,
+                });
+            }
+            else if (typeof document.createEvent == "function") {
+                // older standard
+                event = document.createEvent("MouseEvents");
+                event.initEvent(eventType, true /* bubbles */, true /* cancelable */);
+            }
+            eventObj[eventType] = event;
+        }
+        return eventObj;
+    }
+    function dispatchCustomEvent(event, eventData, targetElement) {
+        if (typeof eventData !== "undefined") {
+            eventData["residueNumber"] = eventData.seq_id;
+            event["eventData"] = eventData;
+            event.eventData.residueNumber = eventData.seq_id;
+            targetElement.dispatchEvent(event);
+        }
+    }
+    function add(plugin, targetElement) {
+        const pdbevents = create([
+            "PDB.molstar.click",
+            "PDB.molstar.mouseover",
+            "PDB.molstar.mouseout",
+        ]);
+        plugin.behaviors.interaction.click.subscribe((e) => {
+            if (e.button === 1 &&
+                e.current &&
+                e.current.loci.kind !== "empty-loci") {
+                const evData = lociDetails(e.current.loci);
+                if (evData)
+                    dispatchCustomEvent(pdbevents["PDB.molstar.click"], evData, targetElement);
+            }
+        });
+        plugin.behaviors.interaction.hover
+            .pipe(debounceTime(100))
+            .subscribe((e) => {
+            if (e.current &&
+                e.current.loci &&
+                e.current.loci.kind !== "empty-loci") {
+                const evData = lociDetails(e.current.loci);
+                if (evData)
+                    dispatchCustomEvent(pdbevents["PDB.molstar.mouseover"], evData, targetElement);
+            }
+            if (e.current &&
+                e.current.loci &&
+                e.current.loci.kind === "empty-loci") {
+                dispatchCustomEvent(pdbevents["PDB.molstar.mouseout"], {}, targetElement);
+            }
+        });
+    }
+    CustomEvents.add = add;
+})(CustomEvents || (CustomEvents = {}));
diff --git a/frontend/venome-molstar/lib/domain-annotations/behavior.d.ts b/frontend/venome-molstar/lib/domain-annotations/behavior.d.ts
new file mode 100644
index 00000000..3eb05ed7
--- /dev/null
+++ b/frontend/venome-molstar/lib/domain-annotations/behavior.d.ts
@@ -0,0 +1,5 @@
+import { PluginBehavior } from "molstar/lib/mol-plugin/behavior";
+export declare const PDBeDomainAnnotations: import("molstar/lib/mol-state/transformer").StateTransformer;
diff --git a/frontend/venome-molstar/lib/domain-annotations/behavior.js b/frontend/venome-molstar/lib/domain-annotations/behavior.js
new file mode 100644
index 00000000..74dc9920
--- /dev/null
+++ b/frontend/venome-molstar/lib/domain-annotations/behavior.js
@@ -0,0 +1,39 @@
+import { DomainAnnotationsProvider } from "./prop";
+import { DomainAnnotationsColorThemeProvider } from "./color";
+import { ParamDefinition as PD } from "molstar/lib/mol-util/param-definition";
+import { PluginBehavior } from "molstar/lib/mol-plugin/behavior";
+export const PDBeDomainAnnotations = PluginBehavior.create({
+    name: "pdbe-domain-annotations-prop",
+    category: "custom-props",
+    display: {
+        name: "Domain annotations",
+        description: "Data for domain annotations, obtained via PDBe.",
+    },
+    ctor: class extends PluginBehavior.Handler {
+        provider = DomainAnnotationsProvider;
+        labelDomainAnnotations = {
+            label: (loci) => void 0,
+        };
+        register() {
+            this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
+            this.ctx.managers.lociLabels.addProvider(this.labelDomainAnnotations);
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(DomainAnnotationsColorThemeProvider);
+        }
+        update(p) {
+            const updated = this.params.autoAttach !== p.autoAttach;
+            this.params.autoAttach = p.autoAttach;
+            this.params.showTooltip = p.showTooltip;
+            this.ctx.customModelProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach);
+            return updated;
+        }
+        unregister() {
+            this.ctx.customModelProperties.unregister(DomainAnnotationsProvider.descriptor.name);
+            this.ctx.managers.lociLabels.removeProvider(this.labelDomainAnnotations);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(DomainAnnotationsColorThemeProvider);
+        }
+    },
+    params: () => ({
+        autoAttach: PD.Boolean(false),
+        showTooltip: PD.Boolean(true),
+    }),
+});
diff --git a/frontend/venome-molstar/lib/domain-annotations/color.d.ts b/frontend/venome-molstar/lib/domain-annotations/color.d.ts
new file mode 100644
index 00000000..f4f34182
--- /dev/null
+++ b/frontend/venome-molstar/lib/domain-annotations/color.d.ts
@@ -0,0 +1,10 @@
+import { ColorTheme } from "molstar/lib/mol-theme/color";
+import { ThemeDataContext } from "molstar/lib/mol-theme/theme";
+import { ParamDefinition as PD } from "molstar/lib/mol-util/param-definition";
+export declare const DomainAnnotationsColorThemeParams: {
+    type: PD.Mapped, "">>;
+};
+type Params = any;
+export declare function DomainAnnotationsColorTheme(ctx: ThemeDataContext, props: PD.Values): ColorTheme;
+export declare const DomainAnnotationsColorThemeProvider: ColorTheme.Provider;
+export {};
diff --git a/frontend/venome-molstar/lib/domain-annotations/color.js b/frontend/venome-molstar/lib/domain-annotations/color.js
new file mode 100644
index 00000000..e1256f08
--- /dev/null
+++ b/frontend/venome-molstar/lib/domain-annotations/color.js
@@ -0,0 +1,81 @@
+import { DomainAnnotations, DomainAnnotationsProvider } from "./prop";
+import { StructureElement } from "molstar/lib/mol-model/structure";
+import { ColorTheme } from "molstar/lib/mol-theme/color";
+import { Color } from "molstar/lib/mol-util/color";
+import { ParamDefinition as PD } from "molstar/lib/mol-util/param-definition";
+const DomainColors = [
+    Color.fromRgb(170, 170, 170),
+    Color.fromRgb(255, 112, 3),
+];
+export const DomainAnnotationsColorThemeParams = {
+    type: PD.MappedStatic("", {
+        "": PD.EmptyGroup(),
+    }),
+};
+export function DomainAnnotationsColorTheme(ctx, props) {
+    let color;
+    if (ctx.structure &&
+        !ctx.structure.isEmpty &&
+        ctx.structure.models[0].customProperties.has(DomainAnnotationsProvider.descriptor)) {
+        const getDomains = DomainAnnotations.getDomains;
+        const issue = props.type.params.kind;
+        color = (location) => {
+            if (StructureElement.Location.is(location) &&
+                getDomains(location).indexOf(issue) >= 0) {
+                return DomainColors[1];
+            }
+            return DomainColors[0];
+        };
+    }
+    else {
+        color = () => DomainColors[0];
+    }
+    return {
+        factory: DomainAnnotationsColorTheme,
+        granularity: "group",
+        color: color,
+        props: props,
+        description: "Highlights Sequnece and Structure Domain Annotations. Data obtained via PDBe.",
+    };
+}
+export const DomainAnnotationsColorThemeProvider = {
+    name: "pdbe-domain-annotations",
+    label: "Domain annotations",
+    category: ColorTheme.Category.Misc,
+    factory: DomainAnnotationsColorTheme,
+    getParams: (ctx) => {
+        const domainNames = DomainAnnotations.getDomainNames(ctx.structure);
+        const domainTypes = DomainAnnotations.getDomainTypes(ctx.structure);
+        const optionObj = {};
+        domainTypes.forEach((tp, index) => {
+            if (domainNames[index].length > 0) {
+                optionObj[tp] = PD.Group({
+                    kind: PD.Select(domainNames[index][0], PD.arrayToOptions(domainNames[index])),
+                }, { isFlat: true });
+            }
+        });
+        if (Object.keys(optionObj).length > 0) {
+            return {
+                type: PD.MappedStatic(optionObj[0], optionObj),
+            };
+        }
+        else {
+            return {
+                type: PD.MappedStatic("", {
+                    "": PD.EmptyGroup(),
+                }),
+            };
+        }
+    },
+    defaultValues: PD.getDefaultValues(DomainAnnotationsColorThemeParams),
+    isApplicable: (ctx) => DomainAnnotations.isApplicable(ctx.structure?.models[0]),
+    ensureCustomProperties: {
+        attach: (ctx, data) => {
+            return data.structure
+                ? DomainAnnotationsProvider.attach(ctx, data.structure.models[0], void 0, true)
+                : Promise.resolve();
+        },
+        detach: (data) => data.structure &&
+            data.structure.models[0].customProperties.reference(DomainAnnotationsProvider.descriptor, false),
+    },
+};
diff --git a/frontend/venome-molstar/lib/domain-annotations/prop.d.ts b/frontend/venome-molstar/lib/domain-annotations/prop.d.ts
new file mode 100644
index 00000000..b1985456
--- /dev/null
+++ b/frontend/venome-molstar/lib/domain-annotations/prop.d.ts
@@ -0,0 +1,35 @@
+import { Model, IndexedCustomProperty } from "molstar/lib/mol-model/structure";
+import { StructureElement, Structure } from "molstar/lib/mol-model/structure/structure";
+import { PropertyWrapper } from "molstar/lib/mol-model-props/common/wrapper";
+import { CustomModelProperty } from "molstar/lib/mol-model-props/common/custom-model-property";
+import { ParamDefinition as PD } from "molstar/lib/mol-util/param-definition";
+import { CustomProperty } from "molstar/lib/mol-model-props/common/custom-property";
+export { DomainAnnotations };
+type DomainAnnotations = PropertyWrapper<{
+    domains: IndexedCustomProperty.Residue;
+    domainNames: string[][];
+    domainTypes: string[];
+} | undefined>;
+declare namespace DomainAnnotations {
+    const DefaultServerUrl = "https://www.ebi.ac.uk/pdbe/api/mappings";
+    function getEntryUrl(pdbId: string, serverUrl: string): string;
+    function isApplicable(model?: Model): boolean;
+    function fromJson(model: Model, data: any): {
+        info: PropertyWrapper.Info;
+        data: {
+            domains: IndexedCustomProperty.Residue;
+            domainNames: string[][];
+            domainTypes: string[];
+        } | undefined;
+    };
+    function fromServer(ctx: CustomProperty.Context, model: Model, props: DomainAnnotationsProps): Promise>;
+    function getDomains(e: StructureElement.Location): string[];
+    function getDomainTypes(structure?: Structure): string[];
+    function getDomainNames(structure?: Structure): string[] | string[][];
+}
+export declare const DomainAnnotationsParams: {
+    serverUrl: PD.Text;
+};
+export type DomainAnnotationsParams = typeof DomainAnnotationsParams;
+export type DomainAnnotationsProps = PD.Values;
+export declare const DomainAnnotationsProvider: CustomModelProperty.Provider;
diff --git a/frontend/venome-molstar/lib/domain-annotations/prop.js b/frontend/venome-molstar/lib/domain-annotations/prop.js
new file mode 100644
index 00000000..3573daa1
--- /dev/null
+++ b/frontend/venome-molstar/lib/domain-annotations/prop.js
@@ -0,0 +1,142 @@
+import { Model, Unit, IndexedCustomProperty, } from "molstar/lib/mol-model/structure";
+import { PropertyWrapper } from "molstar/lib/mol-model-props/common/wrapper";
+import { CustomModelProperty } from "molstar/lib/mol-model-props/common/custom-model-property";
+import { ParamDefinition as PD } from "molstar/lib/mol-util/param-definition";
+import { arraySetAdd } from "molstar/lib/mol-util/array";
+import { Asset } from "molstar/lib/mol-util/assets";
+import { CustomPropertyDescriptor } from "molstar/lib/mol-model/custom-property";
+export { DomainAnnotations };
+var DomainAnnotations;
+(function (DomainAnnotations) {
+    DomainAnnotations.DefaultServerUrl = "https://www.ebi.ac.uk/pdbe/api/mappings";
+    function getEntryUrl(pdbId, serverUrl) {
+        return `${serverUrl}/${pdbId.toLowerCase()}`;
+    }
+    DomainAnnotations.getEntryUrl = getEntryUrl;
+    function isApplicable(model) {
+        return !!model && Model.hasPdbId(model);
+    }
+    DomainAnnotations.isApplicable = isApplicable;
+    function fromJson(model, data) {
+        const info = PropertyWrapper.createInfo();
+        const domainMap = createdomainMapFromJson(model, data);
+        return { info, data: domainMap };
+    }
+    DomainAnnotations.fromJson = fromJson;
+    async function fromServer(ctx, model, props) {
+        const url = Asset.getUrlAsset(ctx.assetManager, getEntryUrl(model.entryId, props.serverUrl));
+        const json = await ctx.assetManager
+            .resolve(url, "json")
+            .runInContext(ctx.runtime);
+        const data = json.data[model.entryId.toLowerCase()];
+        if (!data)
+            throw new Error("missing data");
+        return { value: fromJson(model, data), assets: [json] };
+    }
+    DomainAnnotations.fromServer = fromServer;
+    const _emptyArray = [];
+    function getDomains(e) {
+        if (!Unit.isAtomic(e.unit))
+            return _emptyArray;
+        const prop = DomainAnnotationsProvider.get(e.unit.model).value;
+        if (!prop || !prop.data)
+            return _emptyArray;
+        const rI = e.unit.residueIndex[e.element];
+        return prop.data.domains.has(rI)
+            ? prop.data.domains.get(rI)
+            : _emptyArray;
+    }
+    DomainAnnotations.getDomains = getDomains;
+    function getDomainTypes(structure) {
+        if (!structure)
+            return _emptyArray;
+        const prop = DomainAnnotationsProvider.get(structure.models[0]).value;
+        if (!prop || !prop.data)
+            return _emptyArray;
+        return prop.data.domainTypes;
+    }
+    DomainAnnotations.getDomainTypes = getDomainTypes;
+    function getDomainNames(structure) {
+        if (!structure)
+            return _emptyArray;
+        const prop = DomainAnnotationsProvider.get(structure.models[0]).value;
+        if (!prop || !prop.data)
+            return _emptyArray;
+        return prop.data.domainNames;
+    }
+    DomainAnnotations.getDomainNames = getDomainNames;
+})(DomainAnnotations || (DomainAnnotations = {}));
+export const DomainAnnotationsParams = {
+    serverUrl: PD.Text(DomainAnnotations.DefaultServerUrl, {
+        description: "JSON API Server URL",
+    }),
+};
+export const DomainAnnotationsProvider = CustomModelProperty.createProvider({
+    label: "Domain annotations",
+    descriptor: CustomPropertyDescriptor({
+        name: "domain_annotations",
+    }),
+    type: "static",
+    defaultParams: DomainAnnotationsParams,
+    getParams: (data) => DomainAnnotationsParams,
+    isApplicable: (data) => DomainAnnotations.isApplicable(data),
+    obtain: async (ctx, data, props) => {
+        const p = { ...PD.getDefaultValues(DomainAnnotationsParams), ...props };
+        return await DomainAnnotations.fromServer(ctx, data, p);
+    },
+});
+function findChainLabel(map, label_entity_id, label_asym_id) {
+    const entityIndex = map.entities.getEntityIndex;
+    const eI = entityIndex(label_entity_id);
+    if (eI < 0 || !map.entity_index_label_asym_id.has(eI))
+        return -1;
+    const cm = map.entity_index_label_asym_id.get(eI);
+    if (!cm)
+        return -1;
+    return cm.has(label_asym_id) ? cm.get(label_asym_id) : -1;
+}
+function findResidue(modelData, map, label_entity_id, label_asym_id, label_seq_id) {
+    const cI = findChainLabel(map, label_entity_id, label_asym_id);
+    if (cI < 0)
+        return -1;
+    const rm = map.chain_index_auth_seq_id.get(cI);
+    return rm.has(label_seq_id) ? rm.get(label_seq_id) : -1;
+}
+function createdomainMapFromJson(modelData, data) {
+    const domainTypes = [];
+    const domainNames = [];
+    const ret = new Map();
+    const defaultDomains = ["Pfam", "InterPro", "CATH", "SCOP"];
+    for (const db_name of Object.keys(data)) {
+        if (defaultDomains.indexOf(db_name) === -1)
+            continue;
+        const tempDomains = [];
+        domainTypes.push(db_name);
+        const db = data[db_name];
+        for (const db_code of Object.keys(db)) {
+            const domain = db[db_code];
+            for (const map of domain.mappings) {
+                arraySetAdd(tempDomains, domain.identifier);
+                const indexData = modelData.atomicHierarchy.index;
+                const indexMap = indexData.map;
+                for (let i = map.start.residue_number; i <= map.end.residue_number; i++) {
+                    const seq_id = i;
+                    const idx = findResidue(modelData, indexMap, map.entity_id + "", map.chain_id, seq_id);
+                    let addVal = [domain.identifier];
+                    const prevVal = ret.get(idx);
+                    if (prevVal) {
+                        prevVal.push(domain.identifier);
+                        addVal = prevVal;
+                    }
+                    ret.set(idx, addVal);
+                }
+            }
+        }
+        domainNames.push(tempDomains);
+    }
+    return {
+        domains: IndexedCustomProperty.fromResidueMap(ret),
+        domainNames,
+        domainTypes,
+    };
+}
diff --git a/frontend/venome-molstar/lib/helpers.d.ts b/frontend/venome-molstar/lib/helpers.d.ts
new file mode 100644
index 00000000..0fe7bd6d
--- /dev/null
+++ b/frontend/venome-molstar/lib/helpers.d.ts
@@ -0,0 +1,106 @@
+import { Model, Structure } from "molstar/lib/mol-model/structure";
+import { BuiltInTrajectoryFormat } from "molstar/lib/mol-plugin-state/formats/trajectory";
+import { PluginContext } from "molstar/lib/mol-plugin/context";
+import Expression from "molstar/lib/mol-script/language/expression";
+import { InitParams } from "./spec";
+export type SupportedFormats = "mmcif" | "bcif" | "cif" | "pdb" | "sdf";
+export type LoadParams = {
+    url: string;
+    format?: BuiltInTrajectoryFormat;
+    assemblyId?: string;
+    isHetView?: boolean;
+    isBinary?: boolean;
+    progressMessage?: string;
+};
+export type MapParams = {
+    em?: MapStyle;
+    "2fo-fc"?: MapStyle;
+    "fo-fc(+ve)"?: MapStyle;
+    "fo-fc(-ve)"?: MapStyle;
+};
+interface MapStyle {
+    opacity?: number;
+    wireframe?: boolean;
+}
+export declare namespace PDBeVolumes {
+    function mapParams(defaultParams: any, mapParams?: MapParams, ref?: string | number): any;
+    function displayUsibilityMessage(plugin: PluginContext): void;
+    function toggle(plugin: PluginContext): void;
+}
+export declare namespace AlphafoldView {
+    function getLociByPLDDT(score: number, contextData: Structure): import("molstar/lib/mol-model/structure/structure/element/loci").Loci;
+}
+export type LigandQueryParam = {
+    label_comp_id_list?: any;
+    auth_asym_id?: string;
+    struct_asym_id?: string;
+    label_comp_id?: string;
+    auth_seq_id?: number;
+    show_all?: boolean;
+};
+export declare namespace LigandView {
+    function query(ligandViewParams: LigandQueryParam): {
+        core: Expression.Expression;
+        surroundings: Expression.Expression;
+    };
+    function branchedQuery(params: any): {
+        core: Expression.Expression;
+        surroundings: Expression.Expression;
+    };
+}
+export type QueryParam = {
+    auth_seq_id?: number;
+    entity_id?: string;
+    auth_asym_id?: string;
+    struct_asym_id?: string;
+    residue_number?: number;
+    start_residue_number?: number;
+    end_residue_number?: number;
+    auth_residue_number?: number;
+    auth_ins_code_id?: string;
+    start_auth_residue_number?: number;
+    start_auth_ins_code_id?: string;
+    end_auth_residue_number?: number;
+    end_auth_ins_code_id?: string;
+    atoms?: string[];
+    label_comp_id?: string;
+    color?: any;
+    sideChain?: boolean;
+    representation?: string;
+    representationColor?: any;
+    focus?: boolean;
+    tooltip?: string;
+    start?: any;
+    end?: any;
+    atom_id?: number[];
+    uniprot_accession?: string;
+    uniprot_residue_number?: number;
+    start_uniprot_residue_number?: number;
+    end_uniprot_residue_number?: number;
+};
+export declare namespace QueryHelper {
+    function getQueryObject(params: QueryParam[], contextData: any): Expression.Expression;
+    function getInteractivityLoci(params: any, contextData: any): import("molstar/lib/mol-model/structure/structure/element/loci").Loci;
+    function getHetLoci(queryExp: Expression.Expression, contextData: any): import("molstar/lib/mol-model/structure/structure/element/loci").Loci;
+}
+export interface ModelInfo {
+    hetNames: string[];
+    carbEntityCount: number;
+}
+export declare namespace ModelInfo {
+    function get(model: Model, structures: any): Promise;
+}
+/** Run `action` with showing a message in the bottom-left corner of the plugin UI */
+export declare function runWithProgressMessage(plugin: PluginContext, progressMessage: string | undefined, action: () => any): Promise;
+/** Parameters for a request to ModelServer */
+export interface ModelServerRequest {
+    pdbId: string;
+    queryType: "full" | "residueSurroundings" | "atoms";
+    queryParams?: Record;
+}
+/** Return URL for a ModelServer request.
+ * If `queryType` is 'full' and `lowPrecisionCoords` is false, return URL of the static file instead (updated mmCIF or bCIF). */
+export declare function getStructureUrl(initParams: InitParams, request: ModelServerRequest): string;
+/** Create a copy of object `object`, fill in missing/undefined keys using `defaults` */
+export declare function addDefaults(object: Partial | undefined, defaults: T): T;
+export {};
diff --git a/frontend/venome-molstar/lib/helpers.js b/frontend/venome-molstar/lib/helpers.js
new file mode 100644
index 00000000..cccbc7d6
--- /dev/null
+++ b/frontend/venome-molstar/lib/helpers.js
@@ -0,0 +1,389 @@
+import { QualityAssessment } from "molstar/lib/extensions/model-archive/quality-assessment/prop";
+import { Queries, QueryContext, StructureProperties, StructureSelection, } from "molstar/lib/mol-model/structure";
+import { StructureQuery } from "molstar/lib/mol-model/structure/query/query";
+import { CreateVolumeStreamingInfo } from "molstar/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers";
+import { PluginCommands } from "molstar/lib/mol-plugin/commands";
+import { MolScriptBuilder as MS } from "molstar/lib/mol-script/language/builder";
+import { compile } from "molstar/lib/mol-script/runtime/query/compiler";
+import { StateSelection } from "molstar/lib/mol-state";
+import { Task } from "molstar/lib/mol-task";
+import { SIFTSMapping } from "./sifts-mapping";
+export var PDBeVolumes;
+(function (PDBeVolumes) {
+    function mapParams(defaultParams, mapParams, ref) {
+        const pdbeParams = { ...defaultParams };
+        pdbeParams.options.behaviorRef =
+            "volume-streaming" +
+                "" +
+                Math.floor(Math.random() * Math.floor(100));
+        pdbeParams.options.emContourProvider = "pdbe";
+        pdbeParams.options.serverUrl =
+            "https://www.ebi.ac.uk/pdbe/volume-server";
+        const MAIN_MAP_DEFAULTS = { opacity: 0.49, wireframe: false };
+        const DIFF_MAP_DEFAULTS = { opacity: 0.3, wireframe: true };
+        pdbeParams.options.channelParams["em"] = addDefaults(mapParams?.["em"], MAIN_MAP_DEFAULTS);
+        pdbeParams.options.channelParams["2fo-fc"] = addDefaults(mapParams?.["2fo-fc"], MAIN_MAP_DEFAULTS);
+        pdbeParams.options.channelParams["fo-fc(+ve)"] = addDefaults(mapParams?.["fo-fc(+ve)"], DIFF_MAP_DEFAULTS);
+        pdbeParams.options.channelParams["fo-fc(-ve)"] = addDefaults(mapParams?.["fo-fc(-ve)"], DIFF_MAP_DEFAULTS);
+        return pdbeParams;
+    }
+    PDBeVolumes.mapParams = mapParams;
+    function displayUsibilityMessage(plugin) {
+        PluginCommands.Toast.Show(plugin, {
+            title: "Volume",
+            message: "Streaming enabled, click on a residue or an atom to view the data.",
+            key: "toast-1",
+            timeoutMs: 7000,
+        });
+    }
+    PDBeVolumes.displayUsibilityMessage = displayUsibilityMessage;
+    function toggle(plugin) {
+        const state = plugin.state.data;
+        const streamingState = state.select(StateSelection.Generators.ofTransformer(CreateVolumeStreamingInfo))[0];
+        if (streamingState) {
+            PluginCommands.State.ToggleVisibility(plugin, {
+                state: state,
+                ref: streamingState.transform.ref,
+            });
+            return;
+        }
+    }
+    PDBeVolumes.toggle = toggle;
+})(PDBeVolumes || (PDBeVolumes = {}));
+export var AlphafoldView;
+(function (AlphafoldView) {
+    function getLociByPLDDT(score, contextData) {
+        const queryExp = MS.struct.modifier.union([
+            MS.struct.modifier.wholeResidues([
+                MS.struct.modifier.union([
+                    MS.struct.generator.atomGroups({
+                        "chain-test": MS.core.rel.eq([
+                            MS.ammp("objectPrimitive"),
+                            "atomistic",
+                        ]),
+                        "residue-test": MS.core.rel.gr([
+                            QualityAssessment.symbols.pLDDT.symbol(),
+                            score,
+                        ]),
+                    }),
+                ]),
+            ]),
+        ]);
+        const query = compile(queryExp);
+        const sel = query(new QueryContext(contextData));
+        return StructureSelection.toLociWithSourceUnits(sel);
+    }
+    AlphafoldView.getLociByPLDDT = getLociByPLDDT;
+})(AlphafoldView || (AlphafoldView = {}));
+export var LigandView;
+(function (LigandView) {
+    function query(ligandViewParams) {
+        const atomGroupsParams = {
+            "group-by": MS.core.str.concat([
+                MS.struct.atomProperty.core.operatorName(),
+                MS.struct.atomProperty.macromolecular.residueKey(),
+            ]),
+        };
+        // Residue Param
+        let residueParam;
+        if (ligandViewParams.auth_seq_id !== undefined) {
+            residueParam = MS.core.rel.eq([
+                MS.struct.atomProperty.macromolecular.auth_seq_id(),
+                ligandViewParams.auth_seq_id,
+            ]);
+        }
+        else if (ligandViewParams.label_comp_id) {
+            residueParam = MS.core.rel.eq([
+                MS.struct.atomProperty.macromolecular.label_comp_id(),
+                ligandViewParams.label_comp_id,
+            ]);
+        }
+        if (residueParam)
+            atomGroupsParams["residue-test"] = residueParam;
+        // Chain Param
+        if (ligandViewParams.auth_asym_id) {
+            atomGroupsParams["chain-test"] = MS.core.rel.eq([
+                MS.struct.atomProperty.macromolecular.auth_asym_id(),
+                ligandViewParams.auth_asym_id,
+            ]);
+        }
+        else if (ligandViewParams.struct_asym_id) {
+            atomGroupsParams["chain-test"] = MS.core.rel.eq([
+                MS.struct.atomProperty.macromolecular.label_asym_id(),
+                ligandViewParams.struct_asym_id,
+            ]);
+        }
+        // Construct core query
+        const core = ligandViewParams.show_all
+            ? MS.struct.generator.atomGroups(atomGroupsParams)
+            : MS.struct.filter.first([
+                MS.struct.generator.atomGroups(atomGroupsParams),
+            ]);
+        // Construct surroundings query
+        const surroundings = MS.struct.modifier.includeSurroundings({
+            0: core,
+            radius: 5,
+            "as-whole-residues": true,
+        });
+        return {
+            core,
+            surroundings,
+        };
+    }
+    LigandView.query = query;
+    function branchedQuery(params) {
+        const entityObjArray = [];
+        params.atom_site.forEach((param) => {
+            const qEntities = {
+                "group-by": MS.core.str.concat([
+                    MS.struct.atomProperty.core.operatorName(),
+                    MS.struct.atomProperty.macromolecular.residueKey(),
+                ]),
+                "residue-test": MS.core.rel.eq([
+                    MS.struct.atomProperty.macromolecular.auth_seq_id(),
+                    param.auth_seq_id,
+                ]),
+            };
+            entityObjArray.push(qEntities);
+        });
+        const atmGroupsQueries = [];
+        entityObjArray.forEach((entityObj) => {
+            atmGroupsQueries.push(MS.struct.generator.atomGroups(entityObj));
+        });
+        const core = MS.struct.modifier.union([
+            atmGroupsQueries.length === 1
+                ? atmGroupsQueries[0]
+                : // Need to union before merge for fast performance
+                    MS.struct.combinator.merge(atmGroupsQueries.map((q) => MS.struct.modifier.union([q]))),
+        ]);
+        // Construct surroundings query
+        const surroundings = MS.struct.modifier.includeSurroundings({
+            0: core,
+            radius: 5,
+            "as-whole-residues": true,
+        });
+        return {
+            core,
+            surroundings,
+        };
+    }
+    LigandView.branchedQuery = branchedQuery;
+})(LigandView || (LigandView = {}));
+export var QueryHelper;
+(function (QueryHelper) {
+    function getQueryObject(params, contextData) {
+        const selections = [];
+        let siftMappings;
+        let currentAccession;
+        params.forEach((param) => {
+            const selection = {};
+            // entity
+            if (param.entity_id)
+                selection["entityTest"] = (l) => StructureProperties.entity.id(l.element) ===
+                    param.entity_id;
+            // chain
+            if (param.struct_asym_id) {
+                selection["chainTest"] = (l) => StructureProperties.chain.label_asym_id(l.element) ===
+                    param.struct_asym_id;
+            }
+            else if (param.auth_asym_id) {
+                selection["chainTest"] = (l) => StructureProperties.chain.auth_asym_id(l.element) ===
+                    param.auth_asym_id;
+            }
+            // residues
+            if (param.label_comp_id) {
+                selection["residueTest"] = (l) => StructureProperties.atom.label_comp_id(l.element) ===
+                    param.label_comp_id;
+            }
+            else if (param.uniprot_accession &&
+                param.uniprot_residue_number !== undefined) {
+                selection["residueTest"] = (l) => {
+                    if (!siftMappings ||
+                        currentAccession !== param.uniprot_accession) {
+                        siftMappings = SIFTSMapping.Provider.get(contextData.models[0]).value;
+                        currentAccession = param.uniprot_accession;
+                    }
+                    const rI = StructureProperties.residue.key(l.element);
+                    return (!!siftMappings &&
+                        param.uniprot_accession ===
+                            siftMappings.accession[rI] &&
+                        param.uniprot_residue_number === +siftMappings.num[rI]);
+                };
+            }
+            else if (param.uniprot_accession &&
+                param.start_uniprot_residue_number !== undefined &&
+                param.end_uniprot_residue_number !== undefined) {
+                selection["residueTest"] = (l) => {
+                    if (!siftMappings ||
+                        currentAccession !== param.uniprot_accession) {
+                        siftMappings = SIFTSMapping.Provider.get(contextData.models[0]).value;
+                        currentAccession = param.uniprot_accession;
+                    }
+                    const rI = StructureProperties.residue.key(l.element);
+                    return (!!siftMappings &&
+                        param.uniprot_accession ===
+                            siftMappings.accession[rI] &&
+                        param.start_uniprot_residue_number <=
+                            +siftMappings.num[rI] &&
+                        param.end_uniprot_residue_number >=
+                            +siftMappings.num[rI]);
+                };
+            }
+            else if (param.residue_number !== undefined) {
+                selection["residueTest"] = (l) => StructureProperties.residue.label_seq_id(l.element) ===
+                    param.residue_number;
+            }
+            else if (param.start_residue_number !== undefined &&
+                param.end_residue_number !== undefined &&
+                param.end_residue_number > param.start_residue_number) {
+                selection["residueTest"] = (l) => {
+                    const labelSeqId = StructureProperties.residue.label_seq_id(l.element);
+                    return (labelSeqId >= param.start_residue_number &&
+                        labelSeqId <= param.end_residue_number);
+                };
+            }
+            else if (param.start_residue_number !== undefined &&
+                param.end_residue_number !== undefined &&
+                param.end_residue_number === param.start_residue_number) {
+                selection["residueTest"] = (l) => StructureProperties.residue.label_seq_id(l.element) ===
+                    param.start_residue_number;
+            }
+            else if (param.auth_seq_id !== undefined) {
+                selection["residueTest"] = (l) => StructureProperties.residue.auth_seq_id(l.element) ===
+                    param.auth_seq_id;
+            }
+            else if (param.auth_residue_number !== undefined &&
+                !param.auth_ins_code_id) {
+                selection["residueTest"] = (l) => StructureProperties.residue.auth_seq_id(l.element) ===
+                    param.auth_residue_number;
+            }
+            else if (param.auth_residue_number !== undefined &&
+                param.auth_ins_code_id) {
+                selection["residueTest"] = (l) => StructureProperties.residue.auth_seq_id(l.element) ===
+                    param.auth_residue_number;
+            }
+            else if (param.start_auth_residue_number !== undefined &&
+                param.end_auth_residue_number !== undefined &&
+                param.end_auth_residue_number > param.start_auth_residue_number) {
+                selection["residueTest"] = (l) => {
+                    const authSeqId = StructureProperties.residue.auth_seq_id(l.element);
+                    return (authSeqId >= param.start_auth_residue_number &&
+                        authSeqId <= param.end_auth_residue_number);
+                };
+            }
+            else if (param.start_auth_residue_number !== undefined &&
+                param.end_auth_residue_number !== undefined &&
+                param.end_auth_residue_number ===
+                    param.start_auth_residue_number) {
+                selection["residueTest"] = (l) => StructureProperties.residue.auth_seq_id(l.element) ===
+                    param.start_auth_residue_number;
+            }
+            // atoms
+            if (param.atoms) {
+                selection["atomTest"] = (l) => param.atoms.includes(StructureProperties.atom.label_atom_id(l.element));
+            }
+            if (param.atom_id) {
+                selection["atomTest"] = (l) => param.atom_id.includes(StructureProperties.atom.id(l.element));
+            }
+            selections.push(selection);
+        });
+        const atmGroupsQueries = [];
+        selections.forEach((selection) => {
+            atmGroupsQueries.push(Queries.generators.atoms(selection));
+        });
+        return Queries.combinators.merge(atmGroupsQueries);
+    }
+    QueryHelper.getQueryObject = getQueryObject;
+    function getInteractivityLoci(params, contextData) {
+        const sel = StructureQuery.run(QueryHelper.getQueryObject(params, contextData), contextData);
+        return StructureSelection.toLociWithSourceUnits(sel);
+    }
+    QueryHelper.getInteractivityLoci = getInteractivityLoci;
+    function getHetLoci(queryExp, contextData) {
+        const query = compile(queryExp);
+        const sel = query(new QueryContext(contextData));
+        return StructureSelection.toLociWithSourceUnits(sel);
+    }
+    QueryHelper.getHetLoci = getHetLoci;
+})(QueryHelper || (QueryHelper = {}));
+export var ModelInfo;
+(function (ModelInfo) {
+    async function get(model, structures) {
+        const { _rowCount: residueCount } = model.atomicHierarchy.residues;
+        const { offsets: residueOffsets } = model.atomicHierarchy.residueAtomSegments;
+        const chainIndex = model.atomicHierarchy.chainAtomSegments.index;
+        const hetNames = [];
+        let carbEntityCount = 0;
+        for (let rI = 0; rI < residueCount; rI++) {
+            const cI = chainIndex[residueOffsets[rI]];
+            const eI = model.atomicHierarchy.index.getEntityFromChain(cI);
+            const entityType = model.entities.data.type.value(eI);
+            if (entityType !== "non-polymer" && entityType !== "branched")
+                continue;
+            // const comp_id = model.atomicHierarchy.atoms.label_comp_id.value(rI);
+            const comp_id = model.atomicHierarchy.atoms.label_comp_id.value(residueOffsets[rI]);
+            if (entityType === "branched") {
+                carbEntityCount++;
+            }
+            else {
+                if (hetNames.indexOf(comp_id) === -1)
+                    hetNames.push(comp_id);
+            }
+        }
+        return {
+            hetNames,
+            carbEntityCount,
+        };
+    }
+    ModelInfo.get = get;
+})(ModelInfo || (ModelInfo = {}));
+/** Run `action` with showing a message in the bottom-left corner of the plugin UI */
+export async function runWithProgressMessage(plugin, progressMessage, action) {
+    const task = Task.create(progressMessage ?? "Task", async (ctx) => {
+        let done = false;
+        try {
+            if (progressMessage) {
+                setTimeout(() => {
+                    if (!done)
+                        ctx.update(progressMessage);
+                }, 1000); // Delay the first update to force showing message in UI
+            }
+            await action();
+        }
+        finally {
+            done = true;
+        }
+    });
+    await plugin.runTask(task);
+}
+/** Return URL for a ModelServer request.
+ * If `queryType` is 'full' and `lowPrecisionCoords` is false, return URL of the static file instead (updated mmCIF or bCIF). */
+export function getStructureUrl(initParams, request) {
+    const pdbeUrl = initParams.pdbeUrl.replace(/\/$/, ""); // without trailing slash
+    const useStaticFile = request.queryType === "full" && !initParams.lowPrecisionCoords;
+    if (useStaticFile) {
+        const suffix = initParams.encoding === "bcif" ? ".bcif" : "_updated.cif";
+        return `${pdbeUrl}/entry-files/download/${request.pdbId}${suffix}`;
+    }
+    else {
+        const queryParams = {
+            ...request.queryParams,
+            encoding: initParams.encoding,
+            lowPrecisionCoords: initParams.lowPrecisionCoords ? 1 : undefined,
+        };
+        const queryString = Object.entries(queryParams)
+            .filter(([key, value]) => value !== undefined)
+            .map(([key, value]) => `${key}=${value}`)
+            .join("&");
+        const url = `${pdbeUrl}/model-server/v1/${request.pdbId}/${request.queryType}`;
+        return queryString !== "" ? `${url}?${queryString}` : url;
+    }
+}
+/** Create a copy of object `object`, fill in missing/undefined keys using `defaults` */
+export function addDefaults(object, defaults) {
+    const result = { ...object };
+    for (const key in defaults) {
+        result[key] ??= defaults[key];
+    }
+    return result;
+}
diff --git a/frontend/venome-molstar/lib/index.d.ts b/frontend/venome-molstar/lib/index.d.ts
new file mode 100644
index 00000000..1c697733
--- /dev/null
+++ b/frontend/venome-molstar/lib/index.d.ts
@@ -0,0 +1,98 @@
+import { Canvas3DProps } from "molstar/lib/mol-canvas3d/canvas3d";
+import { PluginContext } from "molstar/lib/mol-plugin/context";
+import { Color } from "molstar/lib/mol-util/color/color";
+import { LoadParams, QueryParam } from "./helpers";
+import { ColorParams, InitParams } from "./spec";
+import "molstar/lib/mol-plugin-ui/skin/dark.scss";
+import "./overlay.scss";
+export declare class PDBeMolstarPlugin {
+    private _ev;
+    readonly events: {
+        loadComplete: import("rxjs").Subject;
+    };
+    plugin: PluginContext;
+    initParams: InitParams;
+    targetElement: HTMLElement;
+    assemblyRef: string;
+    selectedParams: any;
+    defaultRendererProps: Canvas3DProps["renderer"];
+    defaultMarkingProps: Canvas3DProps["marking"];
+    isHighlightColorUpdated: boolean;
+    isSelectedColorUpdated: boolean;
+    /** Extract InitParams from attributes of an HTML element */
+    static initParamsFromHtmlAttributes(element: HTMLElement): Partial;
+    render(target: string | HTMLElement, options: Partial): Promise;
+    getMoleculeSrcUrl(): {
+        url: string;
+        format: string;
+        isBinary: boolean;
+    };
+    screenshotData(): Promise | undefined;
+    get state(): import("molstar/lib/mol-state/state").State;
+    createLigandStructure(isBranched: boolean): Promise;
+    load({ url, format, isBinary, assemblyId, progressMessage, }: LoadParams, fullLoad?: boolean): Promise;
+    applyVisualParams: () => void;
+    canvas: {
+        toggleControls: (isVisible?: boolean) => void;
+        toggleExpanded: (isExpanded?: boolean) => void;
+        setBgColor: (color?: {
+            r: number;
+            g: number;
+            b: number;
+        }) => Promise;
+        applySettings: (settings?: {
+            color?: {
+                r: number;
+                g: number;
+                b: number;
+            };
+            lighting?: string;
+        }) => Promise;
+    };
+    getLociForParams(params: QueryParam[], structureNumber?: number): import("molstar/lib/mol-model/structure/structure/element/loci").Loci | {
+        kind: "empty-loci";
+    };
+    getLociByPLDDT(score: number, structureNumber?: number): import("molstar/lib/mol-model/structure/structure/element/loci").Loci | {
+        kind: "empty-loci";
+    };
+    normalizeColor(colorVal: any, defaultColor?: Color): Color;
+    visual: {
+        highlight: (params: {
+            data: QueryParam[];
+            color?: any;
+            focus?: boolean;
+            structureNumber?: number;
+        }) => void;
+        clearHighlight: () => Promise;
+        select: (params: {
+            data: QueryParam[];
+            nonSelectedColor?: any;
+            addedRepr?: boolean;
+            structureNumber?: number;
+        }) => Promise;
+        clearSelection: (structureNumber?: number) => Promise;
+        update: (options: Partial, fullLoad?: boolean) => Promise;
+        visibility: (data: {
+            [key: string]: any;
+            polymer?: boolean | undefined;
+            het?: boolean | undefined;
+            water?: boolean | undefined;
+            carbs?: boolean | undefined;
+            nonStandard?: boolean | undefined;
+            maps?: boolean | undefined;
+        }) => Promise;
+        toggleSpin: (isSpinning?: boolean, resetCamera?: boolean) => Promise;
+        focus: (params: QueryParam[], structureNumber?: number) => Promise;
+        setColor: (param: {
+            highlight?: ColorParams;
+            select?: ColorParams;
+        }) => Promise;
+        reset: (params: {
+            camera?: boolean;
+            theme?: boolean;
+            highlightColor?: boolean;
+            selectColor?: boolean;
+        }) => Promise;
+    };
+    clear(): Promise;
+}
diff --git a/frontend/venome-molstar/lib/index.js b/frontend/venome-molstar/lib/index.js
new file mode 100644
index 00000000..051e2e80
--- /dev/null
+++ b/frontend/venome-molstar/lib/index.js
@@ -0,0 +1,928 @@
+import { GeometryExport } from "molstar/lib/extensions/geo-export";
+import { MAQualityAssessment } from "molstar/lib/extensions/model-archive/quality-assessment/behavior";
+import { Mp4Export } from "molstar/lib/extensions/mp4-export";
+import { PDBeStructureQualityReport } from "molstar/lib/extensions/pdbe";
+import { RCSBAssemblySymmetry, RCSBAssemblySymmetryConfig, } from "molstar/lib/extensions/rcsb/assembly-symmetry/behavior";
+import { EmptyLoci, Loci } from "molstar/lib/mol-model/loci";
+import { AnimateAssemblyUnwind } from "molstar/lib/mol-plugin-state/animation/built-in/assembly-unwind";
+import { AnimateCameraRock } from "molstar/lib/mol-plugin-state/animation/built-in/camera-rock";
+import { AnimateCameraSpin } from "molstar/lib/mol-plugin-state/animation/built-in/camera-spin";
+import { AnimateModelIndex } from "molstar/lib/mol-plugin-state/animation/built-in/model-index";
+import { AnimateStructureSpin } from "molstar/lib/mol-plugin-state/animation/built-in/spin-structure";
+import { AnimateStateInterpolation } from "molstar/lib/mol-plugin-state/animation/built-in/state-interpolation";
+import { AnimateStateSnapshots } from "molstar/lib/mol-plugin-state/animation/built-in/state-snapshots";
+import { clearStructureOverpaint } from "molstar/lib/mol-plugin-state/helpers/structure-overpaint";
+import { createStructureRepresentationParams } from "molstar/lib/mol-plugin-state/helpers/structure-representation-params";
+import { StructureComponentManager } from "molstar/lib/mol-plugin-state/manager/structure/component";
+import { createPluginUI } from "molstar/lib/mol-plugin-ui/react18";
+import { FocusLoci } from "molstar/lib/mol-plugin/behavior/dynamic/camera";
+import { SelectLoci } from "molstar/lib/mol-plugin/behavior/dynamic/representation";
+import { StructureFocusRepresentation } from "molstar/lib/mol-plugin/behavior/dynamic/selection/structure-focus-representation";
+import { InitVolumeStreaming } from "molstar/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers";
+import { PluginCommands } from "molstar/lib/mol-plugin/commands";
+import { PluginConfig } from "molstar/lib/mol-plugin/config";
+import { PluginLayoutStateParams } from "molstar/lib/mol-plugin/layout";
+import { PluginSpec } from "molstar/lib/mol-plugin/spec";
+import { StateSelection, StateTransform } from "molstar/lib/mol-state";
+import { ElementSymbolColorThemeParams } from "molstar/lib/mol-theme/color/element-symbol";
+import { Asset } from "molstar/lib/mol-util/assets";
+import { Color } from "molstar/lib/mol-util/color/color";
+import { ParamDefinition } from "molstar/lib/mol-util/param-definition";
+import { RxEventHelper } from "molstar/lib/mol-util/rx-event-helper";
+import { CustomEvents } from "./custom-events";
+import { PDBeDomainAnnotations } from "./domain-annotations/behavior";
+import { AlphafoldView, LigandView, PDBeVolumes, QueryHelper, addDefaults, getStructureUrl, runWithProgressMessage, } from "./helpers";
+import { LoadingOverlay } from "./overlay";
+import { PluginCustomState } from "./plugin-custom-state";
+import { DefaultParams, DefaultPluginUISpec, validateInitParams, } from "./spec";
+import { initParamsFromHtmlAttributes } from "./spec-from-html";
+import { subscribeToComponentEvents } from "./subscribe-events";
+import { initSuperposition } from "./superposition";
+import { SuperpositionFocusRepresentation } from "./superposition-focus-representation";
+import { LeftPanelControls } from "./ui/pdbe-left-panel";
+import { PDBeLigandViewStructureTools, PDBeStructureTools, PDBeSuperpositionStructureTools, } from "./ui/pdbe-structure-controls";
+import { PDBeViewportControls } from "./ui/pdbe-viewport-controls";
+import { SuperpostionViewport } from "./ui/superposition-viewport";
+import "molstar/lib/mol-plugin-ui/skin/dark.scss";
+import "./overlay.scss";
+export class PDBeMolstarPlugin {
+    _ev = RxEventHelper.create();
+    events = {
+        loadComplete: this._ev(),
+    };
+    plugin;
+    initParams;
+    targetElement;
+    assemblyRef = "";
+    selectedParams;
+    defaultRendererProps;
+    defaultMarkingProps;
+    isHighlightColorUpdated = false;
+    isSelectedColorUpdated = false;
+    /** Extract InitParams from attributes of an HTML element */
+    static initParamsFromHtmlAttributes(element) {
+        return initParamsFromHtmlAttributes(element);
+    }
+    async render(target, options) {
+        console.debug("Rendering PDBeMolstarPlugin instance with options:", options);
+        // Validate options
+        if (!options) {
+            console.error("Missing `options` argument to `PDBeMolstarPlugin.render");
+            return;
+        }
+        const validationIssues = validateInitParams(options);
+        if (validationIssues) {
+            console.error("Invalid PDBeMolstarPlugin options:", options);
+            return;
+        }
+        this.initParams = addDefaults(options, DefaultParams);
+        // Set PDBe Plugin Spec
+        const pdbePluginSpec = DefaultPluginUISpec();
+        pdbePluginSpec.config ??= [];
+        if (!this.initParams.ligandView &&
+            !this.initParams.superposition &&
+            this.initParams.selectInteraction) {
+            pdbePluginSpec.behaviors.push(PluginSpec.Behavior(StructureFocusRepresentation));
+        }
+        if (this.initParams.superposition) {
+            pdbePluginSpec.behaviors.push(PluginSpec.Behavior(SuperpositionFocusRepresentation), PluginSpec.Behavior(MAQualityAssessment, {
+                autoAttach: true,
+                showTooltip: true,
+            }));
+        }
+        // Add custom properties
+        if (this.initParams.domainAnnotation) {
+            pdbePluginSpec.behaviors.push(PluginSpec.Behavior(PDBeDomainAnnotations, {
+                autoAttach: true,
+                showTooltip: false,
+            }));
+        }
+        if (this.initParams.validationAnnotation) {
+            pdbePluginSpec.behaviors.push(PluginSpec.Behavior(PDBeStructureQualityReport, {
+                autoAttach: true,
+                showTooltip: false,
+            }));
+        }
+        if (this.initParams.symmetryAnnotation) {
+            pdbePluginSpec.behaviors.push(PluginSpec.Behavior(RCSBAssemblySymmetry));
+            pdbePluginSpec.config.push([RCSBAssemblySymmetryConfig.DefaultServerType, "pdbe"], [
+                RCSBAssemblySymmetryConfig.DefaultServerUrl,
+                "https://www.ebi.ac.uk/pdbe/aggregated-api/pdb/symmetry",
+            ], [RCSBAssemblySymmetryConfig.ApplyColors, false]);
+        }
+        pdbePluginSpec.layout = {
+            initial: {
+                isExpanded: this.initParams.expanded,
+                showControls: !this.initParams.hideControls,
+                regionState: {
+                    left: "full",
+                    right: "full",
+                    top: this.initParams.sequencePanel ? "full" : "hidden",
+                    bottom: "full",
+                },
+                controlsDisplay: this.initParams.reactive
+                    ? "reactive"
+                    : this.initParams.landscape
+                        ? "landscape"
+                        : PluginLayoutStateParams.controlsDisplay.defaultValue,
+            },
+        };
+        pdbePluginSpec.components = {
+            controls: {
+                left: LeftPanelControls,
+                // right: DefaultStructureTools,
+                // top: 'none',
+                bottom: "none",
+            },
+            viewport: {
+                controls: PDBeViewportControls,
+                view: this.initParams.superposition
+                    ? SuperpostionViewport
+                    : void 0,
+            },
+            remoteState: "none",
+            structureTools: this.initParams.superposition
+                ? PDBeSuperpositionStructureTools
+                : this.initParams.ligandView
+                    ? PDBeLigandViewStructureTools
+                    : PDBeStructureTools,
+        };
+        if (this.initParams.alphafoldView) {
+            pdbePluginSpec.behaviors.push(PluginSpec.Behavior(MAQualityAssessment, {
+                autoAttach: true,
+                showTooltip: true,
+            }));
+        }
+        pdbePluginSpec.config.push([
+            PluginConfig.Structure.DefaultRepresentationPresetParams,
+            {
+                theme: {
+                    globalName: this.initParams.alphafoldView
+                        ? "plddt-confidence"
+                        : undefined,
+                    carbonColor: { name: "element-symbol", params: {} },
+                    focus: {
+                        name: "element-symbol",
+                        params: {
+                            carbonColor: { name: "element-symbol", params: {} },
+                        },
+                    },
+                },
+            },
+        ]);
+        ElementSymbolColorThemeParams.carbonColor.defaultValue = {
+            name: "element-symbol",
+            params: {},
+        };
+        // Add animation props
+        if (!this.initParams.ligandView && !this.initParams.superposition) {
+            pdbePluginSpec.animations = [
+                AnimateModelIndex,
+                AnimateCameraSpin,
+                AnimateCameraRock,
+                AnimateStateSnapshots,
+                AnimateAssemblyUnwind,
+                AnimateStructureSpin,
+                AnimateStateInterpolation,
+            ];
+            pdbePluginSpec.behaviors.push(PluginSpec.Behavior(Mp4Export));
+            pdbePluginSpec.behaviors.push(PluginSpec.Behavior(GeometryExport));
+        }
+        if (this.initParams.hideCanvasControls.includes("expand"))
+            pdbePluginSpec.config.push([
+                PluginConfig.Viewport.ShowExpand,
+                false,
+            ]);
+        if (this.initParams.hideCanvasControls.includes("selection"))
+            pdbePluginSpec.config.push([
+                PluginConfig.Viewport.ShowSelectionMode,
+                false,
+            ]);
+        if (this.initParams.hideCanvasControls.includes("animation"))
+            pdbePluginSpec.config.push([
+                PluginConfig.Viewport.ShowAnimation,
+                false,
+            ]);
+        if (this.initParams.hideCanvasControls.includes("controlToggle"))
+            pdbePluginSpec.config.push([
+                PluginConfig.Viewport.ShowControls,
+                false,
+            ]);
+        if (this.initParams.hideCanvasControls.includes("controlInfo"))
+            pdbePluginSpec.config.push([
+                PluginConfig.Viewport.ShowSettings,
+                false,
+            ]);
+        // override default event bindings
+        if (this.initParams.selectBindings) {
+            pdbePluginSpec.behaviors.push(PluginSpec.Behavior(SelectLoci, {
+                bindings: this.initParams.selectBindings,
+            }));
+        }
+        if (this.initParams.focusBindings) {
+            pdbePluginSpec.behaviors.push(PluginSpec.Behavior(FocusLoci, {
+                bindings: this.initParams.focusBindings,
+            }));
+        }
+        this.targetElement =
+            typeof target === "string"
+                ? document.getElementById(target)
+                : target;
+        this.targetElement.viewerInstance = this;
+        // Create/ Initialise Plugin
+        this.plugin = await createPluginUI(this.targetElement, pdbePluginSpec);
+        PluginCustomState(this.plugin).initParams = { ...this.initParams };
+        PluginCustomState(this.plugin).events = {
+            segmentUpdate: this._ev(),
+            superpositionInit: this._ev(),
+            isBusy: this._ev(),
+        };
+        // Set background colour
+        if (this.initParams.bgColor || this.initParams.lighting) {
+            this.canvas.applySettings({
+                color: this.initParams.bgColor,
+                lighting: this.initParams.lighting,
+            });
+        }
+        // Set selection granularity
+        if (this.initParams.granularity) {
+            this.plugin.managers.interactivity.setProps({
+                granularity: this.initParams.granularity,
+            });
+        }
+        // Set default highlight and selection colors
+        if (this.initParams.highlightColor || this.initParams.selectColor) {
+            this.visual.setColor({
+                highlight: this.initParams.highlightColor,
+                select: this.initParams.selectColor,
+            });
+        }
+        // Save renderer defaults
+        this.defaultRendererProps = { ...this.plugin.canvas3d.props.renderer };
+        this.defaultMarkingProps = { ...this.plugin.canvas3d.props.marking };
+        if (this.initParams.superposition) {
+            // Set left panel tab
+            this.plugin.behaviors.layout.leftPanelTabName.next("segments");
+            // Initialise superposition
+            if (this.initParams.loadingOverlay) {
+                new LoadingOverlay(this.targetElement, {
+                    resize: this.plugin?.canvas3d?.resized,
+                    hide: this.events.loadComplete,
+                }).show();
+            }
+            initSuperposition(this.plugin, this.events.loadComplete);
+        }
+        else {
+            // Collapse left panel and set left panel tab to none
+            PluginCommands.Layout.Update(this.plugin, {
+                state: {
+                    regionState: {
+                        ...this.plugin.layout.state.regionState,
+                        left: "collapsed",
+                    },
+                },
+            });
+            this.plugin.behaviors.layout.leftPanelTabName.next("none");
+            // Load Molecule CIF or coordQuery and Parse
+            const dataSource = this.getMoleculeSrcUrl();
+            if (dataSource) {
+                if (this.initParams.loadingOverlay) {
+                    new LoadingOverlay(this.targetElement, {
+                        resize: this.plugin?.canvas3d?.resized,
+                        hide: this.events.loadComplete,
+                    }).show();
+                }
+                this.load({
+                    url: dataSource.url,
+                    format: dataSource.format,
+                    assemblyId: this.initParams.assemblyId,
+                    isBinary: dataSource.isBinary,
+                    progressMessage: `Loading ${this.initParams.moleculeId ?? ""} ...`,
+                });
+            }
+            // Binding to other PDB Component events
+            if (this.initParams.subscribeEvents) {
+                subscribeToComponentEvents(this);
+            }
+            // Event handling
+            CustomEvents.add(this.plugin, this.targetElement);
+        }
+    }
+    getMoleculeSrcUrl() {
+        if (this.initParams.customData) {
+            let { url, format, binary } = this.initParams.customData;
+            if (!url || !format) {
+                throw new Error(`Provide all custom data parameters`);
+            }
+            if (format === "cif" || format === "bcif")
+                format = "mmcif";
+            // Validate supported format
+            const supportedFormats = ["mmcif", "pdb", "sdf"];
+            if (!supportedFormats.includes(format)) {
+                throw new Error(`${format} not supported.`);
+            }
+            return {
+                url: url,
+                format: format,
+                isBinary: binary,
+            };
+        }
+        if (this.initParams.moleculeId) {
+            const request = {
+                pdbId: this.initParams.moleculeId,
+                queryType: "full",
+                queryParams: {},
+            };
+            if (this.initParams.ligandView) {
+                request.queryType = "residueSurroundings";
+                request.queryParams["data_source"] = "pdb-h";
+                if (!this.initParams.ligandView.label_comp_id_list) {
+                    request.queryParams["label_comp_id"] =
+                        this.initParams.ligandView.label_comp_id;
+                    request.queryParams["auth_seq_id"] =
+                        this.initParams.ligandView.auth_seq_id;
+                    request.queryParams["auth_asym_id"] =
+                        this.initParams.ligandView.auth_asym_id;
+                }
+            }
+            return {
+                url: getStructureUrl(this.initParams, request),
+                format: "mmcif",
+                isBinary: this.initParams.encoding === "bcif",
+            };
+        }
+        throw new Error(`Mandatory parameters missing! (customData or moleculeId must be defined)`);
+    }
+    screenshotData() {
+        return this.plugin.helpers.viewportScreenshot?.getImageDataUri();
+    }
+    get state() {
+        return this.plugin.state.data;
+    }
+    async createLigandStructure(isBranched) {
+        if (this.assemblyRef === "")
+            return;
+        for await (const comp of this.plugin.managers.structure.hierarchy
+            .currentComponentGroups) {
+            await PluginCommands.State.RemoveObject(this.plugin, {
+                state: comp[0].cell.parent,
+                ref: comp[0].cell.transform.ref,
+                removeParentGhosts: true,
+            });
+        }
+        const structure = this.state.select(this.assemblyRef)[0];
+        let ligandQuery;
+        if (isBranched) {
+            ligandQuery = LigandView.branchedQuery(this.initParams.ligandView?.label_comp_id_list);
+        }
+        else {
+            ligandQuery = LigandView.query(this.initParams.ligandView);
+        }
+        const ligandVis = await this.plugin.builders.structure.tryCreateComponentFromExpression(structure, ligandQuery.core, "pivot", { label: "Ligand" });
+        if (ligandVis)
+            await this.plugin.builders.structure.representation.addRepresentation(ligandVis, {
+                type: "ball-and-stick",
+                color: "element-symbol",
+                colorParams: {
+                    carbonColor: { name: "element-symbol", params: {} },
+                },
+                size: "uniform",
+                sizeParams: { value: 2.5 },
+            }, { tag: "ligand-vis" });
+        const ligandSurr = await this.plugin.builders.structure.tryCreateComponentFromExpression(structure, ligandQuery.surroundings, "rest", { label: "Surroundings" });
+        if (ligandSurr)
+            await this.plugin.builders.structure.representation.addRepresentation(ligandSurr, {
+                type: "ball-and-stick",
+                color: "element-symbol",
+                colorParams: {
+                    carbonColor: { name: "element-symbol", params: {} },
+                },
+                size: "uniform",
+                sizeParams: { value: 0.8 },
+            });
+        // Focus ligand
+        const ligRef = StateSelection.findTagInSubtree(this.plugin.state.data.tree, StateTransform.RootRef, "ligand-vis");
+        if (!ligRef)
+            return;
+        const cell = this.plugin.state.data.cells.get(ligRef);
+        if (cell?.obj) {
+            const repr = cell.obj.data.repr;
+            const ligLoci = repr.getAllLoci()[0]; // getAllLoci returns multiple copies of the same loci (one per representation visual)
+            this.plugin.managers.structure.focus.setFromLoci(ligLoci);
+            // focus-add is not handled in camera behavior, doing it here
+            const current = this.plugin.managers.structure.focus.current?.loci;
+            if (current)
+                this.plugin.managers.camera.focusLoci(current);
+        }
+    }
+    async load({ url, format = "mmcif", isBinary = false, assemblyId = "", progressMessage, }, fullLoad = true) {
+        await runWithProgressMessage(this.plugin, progressMessage, async () => {
+            let success = false;
+            try {
+                if (fullLoad)
+                    await this.clear();
+                const isHetView = this.initParams.ligandView ? true : false;
+                let downloadOptions = void 0;
+                let isBranchedView = false;
+                if (this.initParams.ligandView &&
+                    this.initParams.ligandView.label_comp_id_list) {
+                    isBranchedView = true;
+                    downloadOptions = {
+                        body: JSON.stringify(this.initParams.ligandView.label_comp_id_list),
+                        headers: [["Content-type", "application/json"]],
+                    };
+                }
+                const data = await this.plugin.builders.data.download({ url: Asset.Url(url, downloadOptions), isBinary }, { state: { isGhost: true } });
+                const trajectory = await this.plugin.builders.structure.parseTrajectory(data, format);
+                if (!isHetView) {
+                    await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, this.initParams.defaultPreset, {
+                        structure: assemblyId
+                            ? assemblyId === "preferred"
+                                ? void 0
+                                : {
+                                    name: "assembly",
+                                    params: { id: assemblyId },
+                                }
+                            : { name: "model", params: {} },
+                        showUnitcell: false,
+                        representationPreset: "auto",
+                    });
+                    if (this.initParams.hideStructure.length > 0 ||
+                        this.initParams.visualStyle) {
+                        this.applyVisualParams();
+                    }
+                }
+                else {
+                    const model = await this.plugin.builders.structure.createModel(trajectory);
+                    await this.plugin.builders.structure.createStructure(model, { name: "model", params: {} });
+                }
+                // show selection if param is set
+                if (this.initParams.selection) {
+                    this.visual.select(this.initParams.selection);
+                }
+                // Store assembly ref
+                const pivotIndex = this.plugin.managers.structure.hierarchy.selection
+                    .structures.length - 1;
+                const pivot = this.plugin.managers.structure.hierarchy.selection
+                    .structures[pivotIndex];
+                if (pivot && pivot.cell.parent)
+                    this.assemblyRef = pivot.cell.transform.ref;
+                // Load Volume
+                if (this.initParams.loadMaps) {
+                    if (this.assemblyRef === "")
+                        return;
+                    const asm = this.state.select(this.assemblyRef)[0].obj;
+                    const defaultMapParams = InitVolumeStreaming.createDefaultParams(asm, this.plugin);
+                    const pdbeMapParams = PDBeVolumes.mapParams(defaultMapParams, this.initParams.mapSettings, "");
+                    if (pdbeMapParams) {
+                        await this.plugin.runTask(this.state.applyAction(InitVolumeStreaming, pdbeMapParams, this.assemblyRef));
+                        if (pdbeMapParams.method !== "em" &&
+                            !this.initParams.ligandView)
+                            PDBeVolumes.displayUsibilityMessage(this.plugin);
+                    }
+                }
+                // Create Ligand Representation
+                if (isHetView) {
+                    await this.createLigandStructure(isBranchedView);
+                }
+                success = true;
+            }
+            finally {
+                this.events.loadComplete.next(success);
+            }
+        });
+    }
+    applyVisualParams = () => {
+        const componentGroups = this.plugin.managers.structure.hierarchy.currentComponentGroups;
+        for (const compGroup of componentGroups) {
+            const compRef = compGroup[compGroup.length - 1];
+            const tag = compRef.key ?? "";
+            const remove = this.initParams.hideStructure.some((type) => StructureComponentTags[type]?.includes(tag));
+            if (remove) {
+                this.plugin.managers.structure.hierarchy.remove([compRef]);
+            }
+            if (!remove && this.initParams.visualStyle) {
+                if (compRef && compRef.representations) {
+                    compRef.representations.forEach((rep) => {
+                        const currentParams = createStructureRepresentationParams(this.plugin, void 0, { type: this.initParams.visualStyle });
+                        this.plugin.managers.structure.component.updateRepresentations([compRef], rep, currentParams);
+                    });
+                }
+            }
+        }
+    };
+    canvas = {
+        toggleControls: (isVisible) => {
+            if (typeof isVisible === "undefined")
+                isVisible = !this.plugin.layout.state.showControls;
+            PluginCommands.Layout.Update(this.plugin, {
+                state: { showControls: isVisible },
+            });
+        },
+        toggleExpanded: (isExpanded) => {
+            if (typeof isExpanded === "undefined")
+                isExpanded = !this.plugin.layout.state.isExpanded;
+            PluginCommands.Layout.Update(this.plugin, {
+                state: { isExpanded: isExpanded },
+            });
+        },
+        setBgColor: async (color) => {
+            if (!color)
+                return;
+            await this.canvas.applySettings({ color });
+        },
+        applySettings: async (settings) => {
+            if (!settings)
+                return;
+            if (!this.plugin.canvas3d)
+                return;
+            const renderer = { ...this.plugin.canvas3d.props.renderer };
+            if (settings.color) {
+                renderer.backgroundColor = Color.fromRgb(settings.color.r, settings.color.g, settings.color.b);
+            }
+            if (settings.lighting) {
+                renderer.style = { name: settings.lighting }; // I don't think this does anything and I don't see how it could ever have worked
+            }
+            await PluginCommands.Canvas3D.SetSettings(this.plugin, {
+                settings: { renderer },
+            });
+        },
+    };
+    getLociForParams(params, structureNumber) {
+        let assemblyRef = this.assemblyRef;
+        if (structureNumber) {
+            assemblyRef =
+                this.plugin.managers.structure.hierarchy.current.structures[structureNumber - 1].cell.transform.ref;
+        }
+        if (assemblyRef === "")
+            return EmptyLoci;
+        const data = this.plugin.state.data.select(assemblyRef)[0]
+            .obj.data;
+        if (!data)
+            return EmptyLoci;
+        return QueryHelper.getInteractivityLoci(params, data);
+    }
+    getLociByPLDDT(score, structureNumber) {
+        let assemblyRef = this.assemblyRef;
+        if (structureNumber) {
+            assemblyRef =
+                this.plugin.managers.structure.hierarchy.current.structures[structureNumber - 1].cell.transform.ref;
+        }
+        if (assemblyRef === "")
+            return EmptyLoci;
+        const data = this.plugin.state.data.select(assemblyRef)[0]
+            .obj.data;
+        if (!data)
+            return EmptyLoci;
+        return AlphafoldView.getLociByPLDDT(score, data);
+    }
+    normalizeColor(colorVal, defaultColor) {
+        let color = Color.fromRgb(170, 170, 170);
+        try {
+            if (typeof colorVal.r !== "undefined") {
+                color = Color.fromRgb(colorVal.r, colorVal.g, colorVal.b);
+            }
+            else if (colorVal[0] === "#") {
+                color = Color(Number(`0x${colorVal.substr(1)}`));
+            }
+            else {
+                color = Color(colorVal);
+            }
+        }
+        catch (e) {
+            if (defaultColor)
+                color = defaultColor;
+        }
+        return color;
+    }
+    visual = {
+        highlight: (params) => {
+            const loci = this.getLociForParams(params.data, params.structureNumber);
+            if (Loci.isEmpty(loci))
+                return;
+            if (params.color) {
+                this.visual.setColor({ highlight: params.color });
+            }
+            this.plugin.managers.interactivity.lociHighlights.highlightOnly({
+                loci,
+            });
+            if (params.focus)
+                this.plugin.managers.camera.focusLoci(loci);
+        },
+        clearHighlight: async () => {
+            this.plugin.managers.interactivity.lociHighlights.highlightOnly({
+                loci: EmptyLoci,
+            });
+            if (this.isHighlightColorUpdated)
+                this.visual.reset({ highlightColor: true });
+        },
+        select: async (params) => {
+            // clear prvious selection
+            if (this.selectedParams) {
+                await this.visual.clearSelection(params.structureNumber);
+            }
+            // Structure list to apply selection
+            let structureData = this.plugin.managers.structure.hierarchy.current.structures;
+            if (params.structureNumber) {
+                structureData = [
+                    this.plugin.managers.structure.hierarchy.current.structures[params.structureNumber - 1],
+                ];
+            }
+            // set non selected theme color
+            if (params.nonSelectedColor) {
+                for await (const s of structureData) {
+                    await this.plugin.managers.structure.component.updateRepresentationsTheme(s.components, {
+                        color: "uniform",
+                        colorParams: {
+                            value: this.normalizeColor(params.nonSelectedColor),
+                        },
+                    });
+                }
+            }
+            // apply individual selections
+            for await (const param of params.data) {
+                // get loci from param
+                const loci = this.getLociForParams([param], params.structureNumber);
+                if (Loci.isEmpty(loci))
+                    return;
+                // set default selection color to minimise change display
+                this.visual.setColor({
+                    select: param.color
+                        ? param.color
+                        : { r: 255, g: 112, b: 3 },
+                });
+                // apply selection
+                this.plugin.managers.interactivity.lociSelects.selectOnly({
+                    loci,
+                });
+                // create theme param values and apply them to create overpaint
+                const themeParams = StructureComponentManager.getThemeParams(this.plugin, this.plugin.managers.structure.component.pivotStructure);
+                const colorValue = ParamDefinition.getDefaultValues(themeParams);
+                colorValue.action.params = {
+                    color: param.color
+                        ? this.normalizeColor(param.color)
+                        : Color.fromRgb(255, 112, 3),
+                    opacity: 1,
+                };
+                await this.plugin.managers.structure.component.applyTheme(colorValue, structureData);
+                // add new representations
+                if (param.sideChain || param.representation) {
+                    let repr = "ball-and-stick";
+                    if (param.representation)
+                        repr = param.representation;
+                    const defaultParams = StructureComponentManager.getAddParams(this.plugin, {
+                        allowNone: false,
+                        hideSelection: true,
+                        checkExisting: true,
+                    });
+                    const defaultValues = ParamDefinition.getDefaultValues(defaultParams);
+                    defaultValues.options = {
+                        label: "selection-by-script",
+                        checkExisting: params.structureNumber ? false : true,
+                    };
+                    const values = {
+                        ...defaultValues,
+                        ...{ representation: repr },
+                    };
+                    const structures = this.plugin.managers.structure.hierarchy.getStructuresWithSelection();
+                    await this.plugin.managers.structure.component.add(values, structures);
+                    // Apply uniform theme
+                    if (param.representationColor) {
+                        let updatedStructureData = this.plugin.managers.structure.hierarchy.current
+                            .structures;
+                        if (params.structureNumber) {
+                            updatedStructureData = [
+                                this.plugin.managers.structure.hierarchy.current
+                                    .structures[params.structureNumber - 1],
+                            ];
+                        }
+                        const comps = updatedStructureData[0].components;
+                        const lastCompsIndex = comps.length - 1;
+                        const recentRepComp = [comps[lastCompsIndex]];
+                        const uniformColor = param.representationColor
+                            ? this.normalizeColor(param.representationColor)
+                            : Color.fromRgb(255, 112, 3);
+                        this.plugin.managers.structure.component.updateRepresentationsTheme(recentRepComp, {
+                            color: "uniform",
+                            colorParams: { value: uniformColor },
+                        });
+                    }
+                    params.addedRepr = true;
+                }
+                // focus loci
+                if (param.focus)
+                    this.plugin.managers.camera.focusLoci(loci);
+                // remove selection
+                this.plugin.managers.interactivity.lociSelects.deselect({
+                    loci,
+                });
+            }
+            // reset selection color
+            this.visual.reset({ selectColor: true });
+            // save selection params to optimise clear
+            this.selectedParams = params;
+        },
+        clearSelection: async (structureNumber) => {
+            const structIndex = structureNumber ? structureNumber - 1 : 0;
+            this.plugin.managers.interactivity.lociSelects.deselectAll();
+            // reset theme to default
+            if (this.selectedParams && this.selectedParams.nonSelectedColor) {
+                this.visual.reset({ theme: true });
+            }
+            // remove overpaints
+            await clearStructureOverpaint(this.plugin, this.plugin.managers.structure.hierarchy.current.structures[structIndex].components);
+            // remove selection representations
+            if (this.selectedParams && this.selectedParams.addedRepr) {
+                const selReprCells = [];
+                for (const c of this.plugin.managers.structure.hierarchy.current
+                    .structures[structIndex].components) {
+                    if (c.cell &&
+                        c.cell.params &&
+                        c.cell.params.values &&
+                        c.cell.params.values.label === "selection-by-script")
+                        selReprCells.push(c.cell);
+                }
+                if (selReprCells.length > 0) {
+                    for await (const selReprCell of selReprCells) {
+                        await PluginCommands.State.RemoveObject(this.plugin, {
+                            state: selReprCell.parent,
+                            ref: selReprCell.transform.ref,
+                        });
+                    }
+                }
+            }
+            this.selectedParams = undefined;
+        },
+        update: async (options, fullLoad) => {
+            console.debug("Updating PDBeMolstarPlugin instance with options:", options);
+            // Validate options
+            if (!options) {
+                console.error("Missing `options` argument to `PDBeMolstarPlugin.visual.update");
+                return;
+            }
+            const validationIssues = validateInitParams(options);
+            if (validationIssues) {
+                console.error("Invalid PDBeMolstarPlugin options:", options);
+                return;
+            }
+            this.initParams = addDefaults(options, DefaultParams);
+            if (!this.initParams.moleculeId && !this.initParams.customData)
+                return false;
+            if (this.initParams.customData &&
+                this.initParams.customData.url &&
+                !this.initParams.customData.format)
+                return false;
+            PluginCustomState(this.plugin).initParams = this.initParams;
+            // Show/hide buttons in the viewport control panel
+            this.plugin.config.set(PluginConfig.Viewport.ShowExpand, !this.initParams.hideCanvasControls.includes("expand"));
+            this.plugin.config.set(PluginConfig.Viewport.ShowSelectionMode, !this.initParams.hideCanvasControls.includes("selection"));
+            this.plugin.config.set(PluginConfig.Viewport.ShowAnimation, !this.initParams.hideCanvasControls.includes("animation"));
+            this.plugin.config.set(PluginConfig.Viewport.ShowControls, !this.initParams.hideCanvasControls.includes("controlToggle"));
+            this.plugin.config.set(PluginConfig.Viewport.ShowSettings, !this.initParams.hideCanvasControls.includes("controlInfo"));
+            // Set background colour
+            if (this.initParams.bgColor || this.initParams.lighting) {
+                await this.canvas.applySettings({
+                    color: this.initParams.bgColor,
+                    lighting: this.initParams.lighting,
+                });
+            }
+            // Load Molecule CIF or coordQuery and Parse
+            const dataSource = this.getMoleculeSrcUrl();
+            if (dataSource) {
+                await this.load({
+                    url: dataSource.url,
+                    format: dataSource.format,
+                    assemblyId: this.initParams.assemblyId,
+                    isBinary: dataSource.isBinary,
+                }, fullLoad);
+            }
+        },
+        visibility: async (data) => {
+            if (!data)
+                return;
+            for (const visual in data) {
+                const tags = StructureComponentTags[visual] ?? [];
+                for (const tag of tags) {
+                    const componentRef = StateSelection.findTagInSubtree(this.plugin.state.data.tree, StateTransform.RootRef, tag);
+                    if (componentRef) {
+                        const compVisual = this.plugin.state.data.select(componentRef)[0];
+                        if (compVisual && compVisual.obj) {
+                            const currentlyVisible = compVisual.state && compVisual.state.isHidden
+                                ? false
+                                : true;
+                            if (data[visual] !== currentlyVisible) {
+                                await PluginCommands.State.ToggleVisibility(this.plugin, { state: this.state, ref: componentRef });
+                            }
+                        }
+                    }
+                }
+            }
+        },
+        toggleSpin: async (isSpinning, resetCamera) => {
+            if (!this.plugin.canvas3d)
+                return;
+            const trackball = this.plugin.canvas3d.props.trackball;
+            let toggleSpinParam = trackball.animate.name === "spin"
+                ? { name: "off", params: {} }
+                : { name: "spin", params: { speed: 1 } };
+            if (typeof isSpinning !== "undefined") {
+                toggleSpinParam = { name: "off", params: {} };
+                if (isSpinning)
+                    toggleSpinParam = { name: "spin", params: { speed: 1 } };
+            }
+            await PluginCommands.Canvas3D.SetSettings(this.plugin, {
+                settings: {
+                    trackball: { ...trackball, animate: toggleSpinParam },
+                },
+            });
+            if (resetCamera)
+                await PluginCommands.Camera.Reset(this.plugin, {});
+        },
+        focus: async (params, structureNumber) => {
+            const loci = this.getLociForParams(params, structureNumber);
+            this.plugin.managers.camera.focusLoci(loci);
+        },
+        setColor: async (param) => {
+            if (!this.plugin.canvas3d)
+                return;
+            if (!param.highlight && !param.select)
+                return;
+            const renderer = { ...this.plugin.canvas3d.props.renderer };
+            const marking = { ...this.plugin.canvas3d.props.marking };
+            if (param.highlight) {
+                renderer.highlightColor = this.normalizeColor(param.highlight);
+                marking.highlightEdgeColor = Color.darken(this.normalizeColor(param.highlight), 1);
+                this.isHighlightColorUpdated = true;
+            }
+            if (param.select) {
+                renderer.selectColor = this.normalizeColor(param.select);
+                marking.selectEdgeColor = Color.darken(this.normalizeColor(param.select), 1);
+                this.isSelectedColorUpdated = true;
+            }
+            await PluginCommands.Canvas3D.SetSettings(this.plugin, {
+                settings: { renderer, marking },
+            });
+        },
+        reset: async (params) => {
+            if (params.camera)
+                await PluginCommands.Camera.Reset(this.plugin, {
+                    durationMs: 250,
+                });
+            if (params.theme) {
+                const defaultTheme = {
+                    color: this.initParams.alphafoldView
+                        ? "plddt-confidence"
+                        : "default",
+                };
+                const componentGroups = this.plugin.managers.structure.hierarchy
+                    .currentComponentGroups;
+                for (const compGrp of componentGroups) {
+                    await this.plugin.managers.structure.component.updateRepresentationsTheme(compGrp, defaultTheme);
+                }
+            }
+            if (params.highlightColor || params.selectColor) {
+                if (!this.plugin.canvas3d)
+                    return;
+                const renderer = { ...this.plugin.canvas3d.props.renderer };
+                const marking = { ...this.plugin.canvas3d.props.marking };
+                if (params.highlightColor) {
+                    renderer.highlightColor =
+                        this.defaultRendererProps.highlightColor;
+                    marking.highlightEdgeColor =
+                        this.defaultMarkingProps.highlightEdgeColor;
+                    this.isHighlightColorUpdated = false;
+                }
+                if (params.selectColor) {
+                    renderer.selectColor =
+                        this.defaultRendererProps.selectColor;
+                    marking.selectEdgeColor =
+                        this.defaultMarkingProps.selectEdgeColor;
+                    this.isSelectedColorUpdated = false;
+                }
+                await PluginCommands.Canvas3D.SetSettings(this.plugin, {
+                    settings: { renderer, marking },
+                });
+            }
+        },
+    };
+    async clear() {
+        await this.plugin.clear();
+        this.assemblyRef = "";
+        this.selectedParams = void 0;
+        this.isHighlightColorUpdated = false;
+        this.isSelectedColorUpdated = false;
+    }
+}
+const StructureComponentTags = {
+    polymer: ["structure-component-static-polymer"],
+    het: [
+        "structure-component-static-ligand",
+        "structure-component-static-ion",
+    ],
+    water: ["structure-component-static-water"],
+    carbs: ["structure-component-static-branched"],
+    nonStandard: ["structure-component-static-non-standard"],
+    coarse: ["structure-component-static-coarse"],
+    maps: ["volume-streaming-info"],
+};
+window.PDBeMolstarPlugin = PDBeMolstarPlugin;
diff --git a/frontend/venome-molstar/lib/labels.d.ts b/frontend/venome-molstar/lib/labels.d.ts
new file mode 100644
index 00000000..e6f58abb
--- /dev/null
+++ b/frontend/venome-molstar/lib/labels.d.ts
@@ -0,0 +1,2 @@
+import { PluginBehavior } from "molstar/lib/mol-plugin/behavior";
+export declare const PDBeLociLabelProvider: import("molstar/lib/mol-state/transformer").StateTransformer;
diff --git a/frontend/venome-molstar/lib/labels.js b/frontend/venome-molstar/lib/labels.js
new file mode 100644
index 00000000..7de23978
--- /dev/null
+++ b/frontend/venome-molstar/lib/labels.js
@@ -0,0 +1,46 @@
+import { PluginBehavior } from "molstar/lib/mol-plugin/behavior";
+import { StructureElement, StructureProperties, } from "molstar/lib/mol-model/structure";
+import { lociLabel } from "molstar/lib/mol-theme/label";
+import { PluginCustomState } from "./plugin-custom-state";
+export const PDBeLociLabelProvider = PluginBehavior.create({
+    name: "pdbe-loci-label-provider",
+    category: "interaction",
+    ctor: class {
+        ctx;
+        f = {
+            label: (loci) => {
+                const superpositionView = PluginCustomState(this.ctx)
+                    .initParams.superposition;
+                const label = [];
+                if (!superpositionView &&
+                    StructureElement.Loci.is(loci) &&
+                    loci.elements.length === 1) {
+                    const entityNames = new Set();
+                    for (const { unit: u } of loci.elements) {
+                        const l = StructureElement.Location.create(loci.structure, u, u.elements[0]);
+                        const name = StructureProperties.entity
+                            .pdbx_description(l)
+                            .join(", ");
+                        entityNames.add(name);
+                    }
+                    if (entityNames.size === 1)
+                        entityNames.forEach((name) => label.push(name));
+                }
+                label.push(lociLabel(loci));
+                return label.filter((l) => !!l).join("
");
+            },
+            group: (label) => label.toString().replace(/Model [0-9]+/g, "Models"),
+            priority: 100,
+        };
+        register() {
+            this.ctx.managers.lociLabels.addProvider(this.f);
+        }
+        unregister() {
+            this.ctx.managers.lociLabels.removeProvider(this.f);
+        }
+        constructor(ctx) {
+            this.ctx = ctx;
+        }
+    },
+    display: { name: "Provide PDBe Loci Label" },
+});
diff --git a/frontend/venome-molstar/lib/loci-details.d.ts b/frontend/venome-molstar/lib/loci-details.d.ts
new file mode 100644
index 00000000..73ca739e
--- /dev/null
+++ b/frontend/venome-molstar/lib/loci-details.d.ts
@@ -0,0 +1,27 @@
+import { Bond } from "molstar/lib/mol-model/structure";
+import { Loci } from "molstar/lib/mol-model/loci";
+export type EventDetail = {
+    models?: string[];
+    entity_id?: string;
+    label_asym_id?: string;
+    asym_id?: string;
+    auth_asym_id?: string;
+    unp_accession?: string;
+    unp_seq_id?: number;
+    seq_id?: number;
+    auth_seq_id?: number;
+    ins_code?: string;
+    comp_id?: string;
+    atom_id?: string[];
+    alt_id?: string;
+    micro_het_comp_ids?: string[];
+    seq_id_begin?: number;
+    seq_id_end?: number;
+    button?: number;
+    modifiers?: any;
+};
+type LabelGranularity = "element" | "conformation" | "residue" | "chain" | "structure";
+export declare function lociDetails(loci: Loci): EventDetail | undefined;
+export declare function bondLabel(bond: Bond.Location, granularity: LabelGranularity): any;
+export declare function _bundleLabel(bundle: Loci.Bundle, granularity: LabelGranularity): EventDetail | (EventDetail | undefined)[];
+export {};
diff --git a/frontend/venome-molstar/lib/loci-details.js b/frontend/venome-molstar/lib/loci-details.js
new file mode 100644
index 00000000..e0404b8d
--- /dev/null
+++ b/frontend/venome-molstar/lib/loci-details.js
@@ -0,0 +1,141 @@
+import { Unit, StructureElement, StructureProperties as Props, } from "molstar/lib/mol-model/structure";
+import { OrderedSet } from "molstar/lib/mol-data/int";
+import { SIFTSMapping as BestDatabaseSequenceMappingProp } from "molstar/lib/mol-model-props/sequence/sifts-mapping";
+export function lociDetails(loci) {
+    switch (loci.kind) {
+        case "structure-loci":
+            return {
+                models: loci.structure.models
+                    .map((m) => m.entry)
+                    .filter((l) => !!l),
+            };
+        case "element-loci":
+            return structureElementStatsDetail(StructureElement.Stats.ofLoci(loci));
+        case "bond-loci":
+            const bond = loci.bonds[0];
+            return bond ? bondLabel(bond, "element") : "";
+        default:
+            return void 0;
+    }
+}
+function structureElementStatsDetail(stats) {
+    const { chainCount, residueCount, elementCount } = stats;
+    if (elementCount === 1 && residueCount === 0 && chainCount === 0) {
+        return getElementDetails(stats.firstElementLoc, "element");
+    }
+    else if (elementCount === 0 && residueCount === 1 && chainCount === 0) {
+        return getElementDetails(stats.firstResidueLoc, "residue");
+    }
+    else {
+        return void 0;
+    }
+}
+function getElementDetails(location, granularity = "element") {
+    const basicDetails = {};
+    let entry = location.unit.model.entry;
+    if (entry.length > 30)
+        entry = entry.substr(0, 27) + "\u2026"; // ellipsis
+    basicDetails["entry_id"] = entry; // entry
+    if (granularity !== "structure") {
+        basicDetails["model"] = location.unit.model.modelNum; // model
+        basicDetails["instance"] = location.unit.conformation.operator.name; // instance
+    }
+    let elementDetails;
+    if (Unit.isAtomic(location.unit)) {
+        elementDetails = atomicElementDetails(location, granularity);
+    }
+    else if (Unit.isCoarse(location.unit)) {
+        elementDetails = coarseElementDetails(location, granularity);
+    }
+    return { ...basicDetails, ...elementDetails };
+}
+function atomicElementDetails(location, granularity) {
+    const elementDetails = {
+        entity_id: Props.chain.label_entity_id(location),
+        label_asym_id: Props.chain.label_asym_id(location),
+        auth_asym_id: Props.chain.auth_asym_id(location),
+        unp_accession: undefined,
+        unp_seq_id: undefined,
+        seq_id: Props.residue.label_seq_id(location),
+        auth_seq_id: Props.residue.auth_seq_id(location),
+        ins_code: Props.residue.pdbx_PDB_ins_code(location),
+        comp_id: Props.atom.label_comp_id(location),
+        atom_id: [Props.atom.label_atom_id(location)],
+        alt_id: Props.atom.label_alt_id(location),
+    };
+    const unpLabel = BestDatabaseSequenceMappingProp.getLabel(location);
+    if (unpLabel) {
+        const unpLabelDetails = unpLabel.split(" ");
+        if (unpLabelDetails[0] === "UNP") {
+            elementDetails.unp_accession = unpLabelDetails[1];
+            elementDetails.unp_seq_id = +unpLabelDetails[2];
+        }
+    }
+    const microHetCompIds = Props.residue.microheterogeneityCompIds(location);
+    elementDetails["micro_het_comp_ids"] =
+        granularity === "residue" && microHetCompIds.length > 1
+            ? microHetCompIds
+            : [elementDetails["comp_id"]];
+    return elementDetails;
+}
+function coarseElementDetails(location, granularity) {
+    const elementDetails = {
+        asym_id: Props.coarse.asym_id(location),
+        seq_id_begin: Props.coarse.seq_id_begin(location),
+        seq_id_end: Props.coarse.seq_id_end(location),
+    };
+    if (granularity === "residue") {
+        if (elementDetails.seq_id_begin === elementDetails.seq_id_end) {
+            const entityIndex = Props.coarse.entityKey(location);
+            const seq = location.unit.model.sequence.byEntityKey[entityIndex];
+            elementDetails["comp_id"] = seq.sequence.compId.value(elementDetails.seq_id_begin - 1); // 1-indexed
+        }
+    }
+    return elementDetails;
+}
+export function bondLabel(bond, granularity) {
+    return _bundleLabel({
+        loci: [
+            StructureElement.Loci(bond.aStructure, [
+                {
+                    unit: bond.aUnit,
+                    indices: OrderedSet.ofSingleton(bond.aIndex),
+                },
+            ]),
+            StructureElement.Loci(bond.bStructure, [
+                {
+                    unit: bond.bUnit,
+                    indices: OrderedSet.ofSingleton(bond.bIndex),
+                },
+            ]),
+        ],
+    }, granularity);
+}
+export function _bundleLabel(bundle, granularity) {
+    let isSingleElements = true;
+    for (const l of bundle.loci) {
+        if (!StructureElement.Loci.is(l) ||
+            StructureElement.Loci.size(l) !== 1) {
+            isSingleElements = false;
+            break;
+        }
+    }
+    if (isSingleElements) {
+        const locations = bundle.loci.map((l) => {
+            const { unit, indices } = l.elements[0];
+            return StructureElement.Location.create(l.structure, unit, unit.elements[OrderedSet.start(indices)]);
+        });
+        const elementDetailsArr = locations.map((l) => getElementDetails(l, granularity));
+        const atomIds = [
+            elementDetailsArr[0].atom_id[0],
+            elementDetailsArr[1].atom_id[0],
+        ];
+        const elementDetails = elementDetailsArr[0];
+        elementDetails["atom_id"] = atomIds;
+        return elementDetails;
+    }
+    else {
+        const elementDetails = bundle.loci.map((l) => lociDetails(l));
+        return elementDetails;
+    }
+}
diff --git a/frontend/venome-molstar/lib/overlay.d.ts b/frontend/venome-molstar/lib/overlay.d.ts
new file mode 100644
index 00000000..2adc5879
--- /dev/null
+++ b/frontend/venome-molstar/lib/overlay.d.ts
@@ -0,0 +1,16 @@
+import { Subject } from 'rxjs';
+type OverlayEvents = 'resize' | 'hide';
+/** Shows overlay layer with animated PDBe logo */
+export declare class LoadingOverlay {
+    private readonly target;
+    private readonly subjects;
+    private readonly overlayHtml;
+    private readonly subscriptions;
+    constructor(target: HTMLElement, subjects?: {
+        readonly [key in OverlayEvents]?: Subject;
+    }, overlayHtml?: string);
+    private getOverlayParent;
+    show(): void;
+    hide(): void;
+}
+export {};
diff --git a/frontend/venome-molstar/lib/overlay.js b/frontend/venome-molstar/lib/overlay.js
new file mode 100644
index 00000000..c63ba9c3
--- /dev/null
+++ b/frontend/venome-molstar/lib/overlay.js
@@ -0,0 +1,50 @@
+const PdbeAnimatedLogoSvg = '';
+const OverlayBox = `
${PdbeAnimatedLogoSvg}
`;
+/** Shows overlay layer with animated PDBe logo */
+export class LoadingOverlay {
+    target;
+    subjects;
+    overlayHtml;
+    subscriptions = {};
+    constructor(target, subjects = {}, overlayHtml = OverlayBox) {
+        this.target = target;
+        this.subjects = subjects;
+        this.overlayHtml = overlayHtml;
+    }
+    getOverlayParent() {
+        return this.target.parentElement ?? document.body;
+    }
+    show() {
+        this.hide();
+        const overlayParent = this.getOverlayParent();
+        const divOverlay = document.createElement('div');
+        divOverlay.classList.add('pdbemolstar-overlay');
+        // divOverlay.setAttribute('title', 'Loading...');
+        divOverlay.innerHTML = this.overlayHtml;
+        overlayParent.appendChild(divOverlay);
+        const resize = () => {
+            const viewerRect = this.target.getElementsByClassName('msp-layout-main').item(0)?.getBoundingClientRect();
+            if (viewerRect) {
+                const { left, top, width, height } = viewerRect;
+                const origin = this.target.offsetParent?.getBoundingClientRect() ?? { left: 0, top: 0 };
+                divOverlay.setAttribute('style', `position: absolute; left: ${left - origin?.left}px; top: ${top - origin.top}px; width: ${width}px; height: ${height}px;`);
+            }
+            else {
+                divOverlay.setAttribute('style', `position: fixed; top: 0px; bottom: 0px; left: 0px; right: 0px;`);
+            }
+        };
+        resize();
+        this.subscriptions.resize = this.subjects.resize?.subscribe(() => resize());
+        this.subscriptions.hide = this.subjects.hide?.subscribe(() => this.hide());
+    }
+    hide() {
+        const existingOverlays = this.getOverlayParent().getElementsByClassName('pdbemolstar-overlay');
+        for (let i = 0; i < existingOverlays.length; i++) {
+            existingOverlays.item(i)?.remove();
+        }
+        this.subscriptions.resize?.unsubscribe();
+        this.subscriptions.resize = undefined;
+        this.subscriptions.hide?.unsubscribe();
+        this.subscriptions.hide = undefined;
+    }
+}
diff --git a/frontend/venome-molstar/lib/overlay.scss b/frontend/venome-molstar/lib/overlay.scss
new file mode 100644
index 00000000..d47fb070
--- /dev/null
+++ b/frontend/venome-molstar/lib/overlay.scss
@@ -0,0 +1,46 @@
+.pdbemolstar-overlay {
+    z-index: 1000;
+    position: fixed;
+    top: 0px;
+    bottom: 0px;
+    left: 0px;
+    right: 0px;
+    display: flex;
+    justify-content: center;
+    align-items: center;
+    pointer-events: none;
+}
+
+.pdbemolstar-overlay-box {
+    width: 25%;
+    height: 25%;
+}
+
+svg.pdbe-animated-logo {
+    background-color: transparent;
+    width: 100%;
+    height: 100%;
+    opacity: 80%;
+
+    .path-fg {
+        stroke-dasharray: 1812 250;
+        stroke-dashoffset: -250;
+        animation: dash linear normal infinite;
+        animation-duration: 5s;
+        animation-delay: 1s;
+    }
+    @keyframes dash {
+        0% {
+            stroke-dashoffset: 1812;
+        }
+        80% {
+            stroke-dashoffset: -250;
+        }
+        100% {
+            stroke-dashoffset: -250;
+        }
+    }
+}
+.msp-plugin .msp-viewport-controls-buttons .msp-btn-link-toggle-off {
+	background: black !important;
+}
diff --git a/frontend/venome-molstar/lib/plugin-custom-state.d.ts b/frontend/venome-molstar/lib/plugin-custom-state.d.ts
new file mode 100644
index 00000000..2e909220
--- /dev/null
+++ b/frontend/venome-molstar/lib/plugin-custom-state.d.ts
@@ -0,0 +1,84 @@
+import { SymmetryOperator } from "molstar/lib/mol-math/geometry";
+import { Mat4 } from "molstar/lib/mol-math/linear-algebra";
+import { PluginContext } from "molstar/lib/mol-plugin/context";
+import { StateSelection, StateTransform } from "molstar/lib/mol-state";
+import { Subject } from "rxjs";
+import { InitParams } from "./spec";
+export interface PluginCustomState {
+    initParams?: InitParams;
+    events?: {
+        segmentUpdate: Subject;
+        superpositionInit: Subject;
+        isBusy: Subject;
+    };
+    superpositionState?: {
+        models: {
+            [molId: string]: string;
+        };
+        entries: {
+            [pdbId: string]: StateSelection.Selector;
+        };
+        refMaps: {
+            [ref: string]: string;
+        };
+        segmentData: Segment[] | undefined;
+        matrixData: {
+            [key: string]: {
+                matrix: number[][];
+            };
+        };
+        activeSegment: number;
+        loadedStructs: string[][];
+        visibleRefs: StateTransform.Ref[][];
+        invalidStruct: string[];
+        noMatrixStruct: string[];
+        hets: {
+            [key: string]: unknown[];
+        };
+        colorPalette: [
+            "dark-2",
+            "red-yellow-green",
+            "paired",
+            "set-1",
+            "accent",
+            "set-2",
+            "rainbow"
+        ];
+        colorState: {
+            palleteIndex: number;
+            colorIndex: number;
+        }[];
+        alphafold: {
+            apiData: {
+                cif: string;
+                pae: string;
+                length: number;
+            };
+            length: number;
+            ref: string;
+            traceOnly: boolean;
+            visibility: boolean[];
+            transforms: Mat4[];
+            rmsds: string[][];
+            coordinateSystems: (SymmetryOperator | undefined)[];
+        };
+    };
+    superpositionError?: string;
+}
+export interface ClusterMember {
+    pdb_id: string;
+    auth_asym_id: string;
+    struct_asym_id: string;
+    entity_id: number;
+    is_representative: boolean;
+}
+export interface Segment {
+    segment_start: number;
+    segment_end: number;
+    clusters: ClusterMember[][];
+    isHetView?: boolean;
+    isBinary?: boolean;
+}
+/** Access `plugin.customState` only through this function to get proper typing.
+ * Supports getting and setting properties. */
+export declare function PluginCustomState(plugin: PluginContext): PluginCustomState;
diff --git a/frontend/venome-molstar/lib/plugin-custom-state.js b/frontend/venome-molstar/lib/plugin-custom-state.js
new file mode 100644
index 00000000..65918a95
--- /dev/null
+++ b/frontend/venome-molstar/lib/plugin-custom-state.js
@@ -0,0 +1,5 @@
+/** Access `plugin.customState` only through this function to get proper typing.
+ * Supports getting and setting properties. */
+export function PluginCustomState(plugin) {
+    return (plugin.customState ??= {});
+}
diff --git a/frontend/venome-molstar/lib/sifts-mapping.d.ts b/frontend/venome-molstar/lib/sifts-mapping.d.ts
new file mode 100644
index 00000000..2fa430ba
--- /dev/null
+++ b/frontend/venome-molstar/lib/sifts-mapping.d.ts
@@ -0,0 +1,16 @@
+import { Model } from "molstar/lib/mol-model/structure";
+import { StructureElement } from "molstar/lib/mol-model/structure/structure";
+import { CustomModelProperty } from "molstar/lib/mol-model-props/common/custom-model-property";
+export { SIFTSMapping as SIFTSMapping };
+export interface SIFTSMappingMapping {
+    readonly dbName: string[];
+    readonly accession: string[];
+    readonly num: string[];
+    readonly residue: string[];
+}
+declare namespace SIFTSMapping {
+    const Provider: CustomModelProperty.Provider<{}, SIFTSMappingMapping>;
+    function isAvailable(model: Model): boolean;
+    function getKey(loc: StructureElement.Location): string;
+    function getLabel(loc: StructureElement.Location): string | undefined;
+}
diff --git a/frontend/venome-molstar/lib/sifts-mapping.js b/frontend/venome-molstar/lib/sifts-mapping.js
new file mode 100644
index 00000000..1442bb54
--- /dev/null
+++ b/frontend/venome-molstar/lib/sifts-mapping.js
@@ -0,0 +1,83 @@
+import { Column } from "molstar/lib/mol-data/db";
+import { MmcifFormat } from "molstar/lib/mol-model-formats/structure/mmcif";
+import { CustomPropertyDescriptor } from "molstar/lib/mol-model/custom-property";
+import { CustomModelProperty } from "molstar/lib/mol-model-props/common/custom-model-property";
+export { SIFTSMapping as SIFTSMapping };
+var SIFTSMapping;
+(function (SIFTSMapping) {
+    SIFTSMapping.Provider = CustomModelProperty.createProvider({
+        label: "SIFTS Mapping",
+        descriptor: CustomPropertyDescriptor({
+            name: "sifts_sequence_mapping",
+        }),
+        type: "static",
+        defaultParams: {},
+        getParams: () => ({}),
+        isApplicable: (data) => isAvailable(data),
+        obtain: async (ctx, data) => {
+            return { value: fromCif(data) };
+        },
+    });
+    function isAvailable(model) {
+        if (!MmcifFormat.is(model.sourceData))
+            return false;
+        const { pdbx_sifts_xref_db_name: db_name, pdbx_sifts_xref_db_acc: db_acc, pdbx_sifts_xref_db_num: db_num, pdbx_sifts_xref_db_res: db_res, } = model.sourceData.data.db.atom_site;
+        return (db_name.isDefined &&
+            db_acc.isDefined &&
+            db_num.isDefined &&
+            db_res.isDefined);
+    }
+    SIFTSMapping.isAvailable = isAvailable;
+    function getKey(loc) {
+        const model = loc.unit.model;
+        const data = SIFTSMapping.Provider.get(model).value;
+        if (!data)
+            return "";
+        const rI = model.atomicHierarchy.residueAtomSegments.index[loc.element];
+        return data.accession[rI];
+    }
+    SIFTSMapping.getKey = getKey;
+    function getLabel(loc) {
+        const model = loc.unit.model;
+        const data = SIFTSMapping.Provider.get(model).value;
+        if (!data)
+            return;
+        const rI = model.atomicHierarchy.residueAtomSegments.index[loc.element];
+        const dbName = data.dbName[rI];
+        if (!dbName)
+            return;
+        return `${dbName} ${data.accession[rI]} ${data.num[rI]} ${data.residue[rI]}`;
+    }
+    SIFTSMapping.getLabel = getLabel;
+    function fromCif(model) {
+        if (!MmcifFormat.is(model.sourceData))
+            return;
+        const { pdbx_sifts_xref_db_name: db_name, pdbx_sifts_xref_db_acc: db_acc, pdbx_sifts_xref_db_num: db_num, pdbx_sifts_xref_db_res: db_res, } = model.sourceData.data.db.atom_site;
+        if (!db_name.isDefined ||
+            !db_acc.isDefined ||
+            !db_num.isDefined ||
+            !db_res.isDefined)
+            return;
+        const { atomSourceIndex } = model.atomicHierarchy;
+        const { count, offsets: residueOffsets } = model.atomicHierarchy.residueAtomSegments;
+        const dbName = new Array(count);
+        const accession = new Array(count);
+        const num = new Array(count);
+        const residue = new Array(count);
+        for (let i = 0; i < count; i++) {
+            const row = atomSourceIndex.value(residueOffsets[i]);
+            if (db_name.valueKind(row) !== Column.ValueKind.Present) {
+                dbName[i] = "";
+                accession[i] = "";
+                num[i] = "";
+                residue[i] = "";
+                continue;
+            }
+            dbName[i] = db_name.value(row);
+            accession[i] = db_acc.value(row);
+            num[i] = db_num.value(row);
+            residue[i] = db_res.value(row);
+        }
+        return { dbName, accession, num, residue };
+    }
+})(SIFTSMapping || (SIFTSMapping = {}));
diff --git a/frontend/venome-molstar/lib/sifts-mappings-behaviour.d.ts b/frontend/venome-molstar/lib/sifts-mappings-behaviour.d.ts
new file mode 100644
index 00000000..b496adec
--- /dev/null
+++ b/frontend/venome-molstar/lib/sifts-mappings-behaviour.d.ts
@@ -0,0 +1,5 @@
+import { PluginBehavior } from "molstar/lib/mol-plugin/behavior";
+export declare const PDBeSIFTSMapping: import("molstar/lib/mol-state/transformer").StateTransformer;
diff --git a/frontend/venome-molstar/lib/sifts-mappings-behaviour.js b/frontend/venome-molstar/lib/sifts-mappings-behaviour.js
new file mode 100644
index 00000000..15249661
--- /dev/null
+++ b/frontend/venome-molstar/lib/sifts-mappings-behaviour.js
@@ -0,0 +1,54 @@
+import { OrderedSet } from "molstar/lib/mol-data/int";
+import { SIFTSMapping as BestDatabaseSequenceMappingProp } from "./sifts-mapping";
+import { SIFTSMappingColorThemeProvider } from "molstar/lib/mol-model-props/sequence/themes/sifts-mapping";
+import { StructureElement } from "molstar/lib/mol-model/structure";
+import { ParamDefinition as PD } from "molstar/lib/mol-util/param-definition";
+import { PluginBehavior } from "molstar/lib/mol-plugin/behavior";
+export const PDBeSIFTSMapping = PluginBehavior.create({
+    name: "pdbe-sifts-mapping-prop",
+    category: "custom-props",
+    display: { name: "PDBe SIFTS Mapping" },
+    ctor: class extends PluginBehavior.Handler {
+        provider = BestDatabaseSequenceMappingProp.Provider;
+        labelProvider = {
+            label: (loci) => {
+                if (!this.params.showTooltip)
+                    return;
+                return PDBeBestDatabaseSequenceMappingLabel(loci);
+            },
+        };
+        update(p) {
+            const updated = this.params.autoAttach !== p.autoAttach ||
+                this.params.showTooltip !== p.showTooltip;
+            this.params.autoAttach = p.autoAttach;
+            this.params.showTooltip = p.showTooltip;
+            this.ctx.customStructureProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach);
+            return updated;
+        }
+        register() {
+            this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(SIFTSMappingColorThemeProvider);
+            this.ctx.managers.lociLabels.addProvider(this.labelProvider);
+        }
+        unregister() {
+            this.ctx.customModelProperties.unregister(this.provider.descriptor.name);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(SIFTSMappingColorThemeProvider);
+            this.ctx.managers.lociLabels.removeProvider(this.labelProvider);
+        }
+    },
+    params: () => ({
+        autoAttach: PD.Boolean(true),
+        showTooltip: PD.Boolean(true),
+    }),
+});
+//
+function PDBeBestDatabaseSequenceMappingLabel(loci) {
+    if (loci.kind === "element-loci") {
+        if (loci.elements.length === 0)
+            return;
+        const e = loci.elements[0];
+        const u = e.unit;
+        const se = StructureElement.Location.create(loci.structure, u, u.elements[OrderedSet.getAt(e.indices, 0)]);
+        return BestDatabaseSequenceMappingProp.getLabel(se);
+    }
+}
diff --git a/frontend/venome-molstar/lib/spec-from-html.d.ts b/frontend/venome-molstar/lib/spec-from-html.d.ts
new file mode 100644
index 00000000..c6afcf10
--- /dev/null
+++ b/frontend/venome-molstar/lib/spec-from-html.d.ts
@@ -0,0 +1,3 @@
+import { InitParams } from './spec';
+/** Extract InitParams from attributes of an HTML element */
+export declare function initParamsFromHtmlAttributes(element: HTMLElement): Partial;
diff --git a/frontend/venome-molstar/lib/spec-from-html.js b/frontend/venome-molstar/lib/spec-from-html.js
new file mode 100644
index 00000000..c31237cb
--- /dev/null
+++ b/frontend/venome-molstar/lib/spec-from-html.js
@@ -0,0 +1,109 @@
+import { Encoding, Lighting, Preset, VisualStyle, validateInitParams } from './spec';
+/** Extract InitParams from attributes of an HTML element */
+export function initParamsFromHtmlAttributes(element) {
+    const params = loadHtmlAttributes(element, InitParamsLoadingActions, {});
+    const validationIssues = validateInitParams(params);
+    if (validationIssues)
+        console.error('Invalid PDBeMolstarPlugin options:', params);
+    return params;
+}
+/** Actions for loading individual HTML attributes into InitParams object */
+const InitParamsLoadingActions = {
+    'molecule-id': setString('moleculeId'),
+    'custom-data-url': (value, params) => { (params.customData ??= defaultCustomData()).url = value; },
+    'custom-data-format': (value, params) => { (params.customData ??= defaultCustomData()).format = value; },
+    'custom-data-binary': (value, params) => { (params.customData ??= defaultCustomData()).binary = parseBool(value); },
+    'assembly-id': setString('assemblyId'),
+    'default-preset': setLiteral(Preset, 'defaultPreset'),
+    'ligand-label-comp-id': (value, params) => { (params.ligandView ??= {}).label_comp_id = value; },
+    'ligand-auth-asym-id': (value, params) => { (params.ligandView ??= {}).auth_asym_id = value; },
+    'ligand-struct-asym-id': (value, params) => { (params.ligandView ??= {}).struct_asym_id = value; },
+    'ligand-auth-seq-id': (value, params) => { (params.ligandView ??= {}).auth_seq_id = Number(value); },
+    'ligand-show-all': (value, params) => { (params.ligandView ??= {}).show_all = parseBool(value); },
+    'alphafold-view': setBool('alphafoldView'),
+    'visual-style': setLiteral(VisualStyle, 'visualStyle'),
+    'hide-polymer': pushItem('hideStructure', 'polymer'),
+    'hide-water': pushItem('hideStructure', 'water'),
+    'hide-het': pushItem('hideStructure', 'het'),
+    'hide-carbs': pushItem('hideStructure', 'carbs'),
+    'hide-non-standard': pushItem('hideStructure', 'nonStandard'),
+    'hide-coarse': pushItem('hideStructure', 'coarse'),
+    'load-maps': setBool('loadMaps'),
+    'bg-color-r': setColorComponent('bgColor', 'r'),
+    'bg-color-g': setColorComponent('bgColor', 'g'),
+    'bg-color-b': setColorComponent('bgColor', 'b'),
+    'highlight-color-r': setColorComponent('highlightColor', 'r'),
+    'highlight-color-g': setColorComponent('highlightColor', 'g'),
+    'highlight-color-b': setColorComponent('highlightColor', 'b'),
+    'select-color-r': setColorComponent('selectColor', 'r'),
+    'select-color-g': setColorComponent('selectColor', 'g'),
+    'select-color-b': setColorComponent('selectColor', 'b'),
+    'lighting': setLiteral(Lighting, 'lighting'),
+    'validation-annotation': setBool('validationAnnotation'),
+    'domain-annotation': setBool('domainAnnotation'),
+    'symmetry-annotation': setBool('symmetryAnnotation'),
+    'pdbe-url': setString('pdbeUrl'),
+    'encoding': setLiteral(Encoding, 'encoding'),
+    'low-precision': setBool('lowPrecisionCoords'),
+    'select-interaction': setBool('selectInteraction'),
+    'subscribe-events': setBool('subscribeEvents'),
+    'hide-controls': setBool('hideControls'),
+    'hide-expand-icon': pushItem('hideCanvasControls', 'expand'),
+    'hide-selection-icon': pushItem('hideCanvasControls', 'selection'),
+    'hide-animation-icon': pushItem('hideCanvasControls', 'animation'),
+    'hide-control-toggle-icon': pushItem('hideCanvasControls', 'controlToggle'),
+    'hide-control-info-icon': pushItem('hideCanvasControls', 'controlInfo'),
+    'sequence-panel': setBool('sequencePanel'),
+    'pdbe-link': setBool('pdbeLink'),
+    'loading-overlay': setBool('loadingOverlay'),
+    'expanded': setBool('expanded'),
+    'landscape': setBool('landscape'),
+    'reactive': setBool('reactive'),
+};
+/** Load attributes of an HTML element into a context */
+function loadHtmlAttributes(element, actions, context) {
+    for (const attribute in actions) {
+        const value = element.getAttribute(attribute);
+        if (typeof value === 'string') {
+            actions[attribute](value, context);
+        }
+    }
+    return context;
+}
+function setString(key) {
+    return (value, obj) => { obj[key] = value; };
+}
+function setLiteral(allowedValues, key) {
+    return (value, ctx) => {
+        if (!allowedValues.includes(value))
+            console.error(`Value "${value}" is not valid for type ${allowedValues.map(s => `"${s}"`).join(' | ')}`);
+        ctx[key] = value;
+    };
+}
+function setBool(key) {
+    return (value, obj) => { obj[key] = parseBool(value); };
+}
+function setColorComponent(key, component) {
+    return (value, obj) => {
+        const color = obj[key] ??= { r: 0, g: 0, b: 0 };
+        color[component] = Number(value);
+    };
+}
+function pushItem(key, item) {
+    return (value, obj) => {
+        if (parseBool(value)) {
+            const array = obj[key] ??= [];
+            array.push(item);
+        }
+    };
+}
+/** Parse a string into a boolean.
+ * Consider strings like 'false', 'OFF', '0' as false; others as true.
+ * Empty string is parsed as true, because HTML attribute without value must be treated as truthy. */
+function parseBool(value) {
+    const FalseyStrings = ['false', 'off', '0'];
+    return !FalseyStrings.includes(value.toLowerCase());
+}
+function defaultCustomData() {
+    return { url: '', format: '', binary: false };
+}
diff --git a/frontend/venome-molstar/lib/spec.d.ts b/frontend/venome-molstar/lib/spec.d.ts
new file mode 100644
index 00000000..676c8a05
--- /dev/null
+++ b/frontend/venome-molstar/lib/spec.d.ts
@@ -0,0 +1,122 @@
+import { Loci } from "molstar/lib/mol-model/loci";
+import { PluginUISpec } from "molstar/lib/mol-plugin-ui/spec";
+import { DefaultFocusLociBindings } from "molstar/lib/mol-plugin/behavior/dynamic/camera";
+import { DefaultSelectLociBindings } from "molstar/lib/mol-plugin/behavior/dynamic/representation";
+import { PluginSpec } from "molstar/lib/mol-plugin/spec";
+import { LigandQueryParam, MapParams, QueryParam } from "./helpers";
+export declare const DefaultPluginSpec: () => PluginSpec;
+export declare const DefaultPluginUISpec: () => PluginUISpec;
+/** RGB color (r, g, b values 0-255) */
+export interface ColorParams {
+    r: number;
+    g: number;
+    b: number;
+}
+export declare const Preset: readonly ["default", "unitcell", "all-models", "supercell"];
+export type Preset = (typeof Preset)[number];
+export declare const Lighting: readonly ["flat", "matte", "glossy", "metallic", "plastic"];
+export type Lighting = (typeof Lighting)[number];
+export declare const VisualStyle: readonly ["cartoon", "ball-and-stick", "carbohydrate", "ellipsoid", "gaussian-surface", "molecular-surface", "point", "putty", "spacefill"];
+export type VisualStyle = (typeof VisualStyle)[number];
+export declare const Encoding: readonly ["cif", "bcif"];
+export type Encoding = (typeof Encoding)[number];
+/** Options for initializing `PDBeMolstarPlugin` */
+export interface InitParams {
+    /** PDB ID (example: '1cbs'), or UniProt ID if `superposition` is `true`. Leave `undefined` only when setting `customData` */
+    moleculeId?: string;
+    /** Load data from a specific data source.
+     * Example: `{ url: 'https://www.ebi.ac.uk/pdbe/model-server/v1/1cbs/atoms?label_entity_id=1&auth_asym_id=A&encoding=bcif', format: 'cif', binary: true }` */
+    customData?: {
+        url: string;
+        format: string;
+        binary: boolean;
+    };
+    /** Leave `undefined` to load deposited model structure. Use assembly identifier to load assembly structure. or 'preferred' to load default assembly (i.e. the first assembly). */
+    assemblyId?: string;
+    /** Specify type of structure to be loaded */
+    defaultPreset: Preset;
+    /** Use to display the PDBe ligand page 3D view like here (https://www.ebi.ac.uk/pdbe/entry/pdb/1cbs/bound/REA).
+     * Example: `{ label_comp_id: 'REA' }`. At least one is required of `label_comp_id` and `auth_seq_id` */
+    ligandView?: LigandQueryParam;
+    /** This applies AlphaFold confidence score colouring theme for AlphaFold model */
+    alphafoldView: boolean;
+    /** Display the superposed structures view like the one on the PDBe-KB pages. */
+    superposition: boolean;
+    /** Customize the superposed structures view. Example: `{ matrixAccession: 'P08684', segment: 1, ligandView: true, ligandColor: { r: 255, g: 255, b: 50} }`. */
+    superpositionParams?: {
+        matrixAccession?: string;
+        segment?: number;
+        cluster?: number[];
+        superposeCompleteCluster?: boolean;
+        ligandView?: boolean;
+        superposeAll?: boolean;
+        ligandColor?: ColorParams;
+    };
+    /** Specify parts of the structure to highlight with different colors */
+    selection?: {
+        data: QueryParam[];
+        nonSelectedColor?: ColorParams;
+        clearPrevious?: boolean;
+    };
+    /** Leave `undefined` to keep both cartoon and ball-and-sticks based on component type */
+    visualStyle?: VisualStyle;
+    /** Molstar renders multiple visuals (polymer, ligand, water...) visuals by default. This option is to exclude any of these default visuals */
+    hideStructure: ("polymer" | "het" | "water" | "carbs" | "nonStandard" | "coarse")[];
+    /** Load electron density (or EM) maps from Volume Server if value is set to true */
+    loadMaps: boolean;
+    /** Customize map style (opacity and solid/wireframe) */
+    mapSettings?: MapParams;
+    /** Canvas background color */
+    bgColor: ColorParams;
+    /** Color appearing on mouse-over */
+    highlightColor?: ColorParams;
+    /** Color for marking the selected part of structure (when Selection Mode is active) */
+    selectColor?: ColorParams;
+    /** Default lighting (I don't think it really works) */
+    lighting?: Lighting;
+    /** Load Validation Report Annotations. Adds 'Annotations' control in the menu */
+    validationAnnotation: boolean;
+    /** Load Domain Annotations. Adds 'Annotations' control in the menu */
+    domainAnnotation: boolean;
+    /** Load Assembly Symmetry Annotations. Adds 'Annotations' control in the menu */
+    symmetryAnnotation: boolean;
+    /** This option is to set the default base URL for the data source. Mostly used internally to test the plugin on different environments */
+    pdbeUrl: string;
+    /** Preferred encoding of input structural data */
+    encoding: Encoding;
+    /** Load low precision coordinates from Model Server */
+    lowPrecisionCoords: boolean;
+    /** Controls the action performed when clicking a residue. `true` (default) will zoom the residue
+     * and show ball-and-stick visual for its surroundings, `false` will only zoom the residue.
+     * If `ligandView` or `superposition` option is set, `selectInteraction` behaves as if `false`. */
+    selectInteraction: boolean;
+    /** Override mouse selection behavior */
+    selectBindings?: typeof DefaultSelectLociBindings;
+    /** Override mouse click focus behaviour */
+    focusBindings?: typeof DefaultFocusLociBindings;
+    /** Structure granularity level for interactions like highlight, focus, select.
+     * (Granularity levels ending with `Instances` treat multiple copies of the same element/residue/chain in an assembly as one object). */
+    granularity?: Loci.Granularity;
+    /** Subscribe to other PDB Web-components custom events */
+    subscribeEvents: boolean;
+    /** Hide all control panels by default (can be shown by the Toggle Controls Panel button (wrench icon)) */
+    hideControls: boolean;
+    /** Hide individual icon buttons in the top-right corner of the canvas */
+    hideCanvasControls: ("expand" | "selection" | "animation" | "controlToggle" | "controlInfo")[];
+    /** Display Sequence panel */
+    sequencePanel: boolean;
+    /** Display PDBe entry link in top right corner of the canvas */
+    pdbeLink: boolean;
+    /** Show overlay with PDBe logo while the initial structure is being loaded */
+    loadingOverlay: boolean;
+    /** Display full-screen by default on load */
+    expanded: boolean;
+    /** Set landscape layout (control panels on the sides instead of above and under the canvas) */
+    landscape: boolean;
+    /** Set reactive layout (switching between landscape and portrait based on the browser window size). Overrides `landscape`. */
+    reactive: boolean;
+}
+/** Default values for `InitParams` */
+export declare const DefaultParams: InitParams;
+/** Return `undefined` if `params` are valid, an error message otherwise. */
+export declare function validateInitParams(params: Partial): string | undefined;
diff --git a/frontend/venome-molstar/lib/spec.js b/frontend/venome-molstar/lib/spec.js
new file mode 100644
index 00000000..7dfefca8
--- /dev/null
+++ b/frontend/venome-molstar/lib/spec.js
@@ -0,0 +1,124 @@
+import { StateActions } from "molstar/lib/mol-plugin-state/actions";
+import { VolumeStreamingCustomControls } from "molstar/lib/mol-plugin-ui/custom/volume";
+import { PluginBehaviors } from "molstar/lib/mol-plugin/behavior";
+import { CreateVolumeStreamingBehavior } from "molstar/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers";
+import { PluginConfig } from "molstar/lib/mol-plugin/config";
+import { PluginSpec } from "molstar/lib/mol-plugin/spec";
+import { PDBeLociLabelProvider } from "./labels";
+import { PDBeSIFTSMapping } from "./sifts-mappings-behaviour";
+export const DefaultPluginSpec = () => ({
+    actions: [
+        PluginSpec.Action(StateActions.Structure.EnableStructureCustomProps),
+    ],
+    behaviors: [
+        PluginSpec.Behavior(PluginBehaviors.Representation.HighlightLoci),
+        PluginSpec.Behavior(PluginBehaviors.Representation.SelectLoci),
+        PluginSpec.Behavior(PDBeLociLabelProvider),
+        PluginSpec.Behavior(PluginBehaviors.Representation.FocusLoci),
+        PluginSpec.Behavior(PluginBehaviors.Camera.FocusLoci),
+        PluginSpec.Behavior(PluginBehaviors.Camera.CameraAxisHelper),
+        PluginSpec.Behavior(PluginBehaviors.CustomProps.StructureInfo),
+        PluginSpec.Behavior(PluginBehaviors.CustomProps.AccessibleSurfaceArea),
+        PluginSpec.Behavior(PDBeSIFTSMapping, {
+            autoAttach: true,
+            showTooltip: true,
+        }),
+        PluginSpec.Behavior(PluginBehaviors.CustomProps.Interactions),
+        PluginSpec.Behavior(PluginBehaviors.CustomProps.SecondaryStructure),
+        PluginSpec.Behavior(PluginBehaviors.CustomProps.ValenceModel),
+        PluginSpec.Behavior(PluginBehaviors.CustomProps.CrossLinkRestraint),
+    ],
+    // animations: [],
+    config: [
+        [
+            PluginConfig.VolumeStreaming.DefaultServer,
+            "https://www.ebi.ac.uk/pdbe/volume-server",
+        ],
+        [
+            PluginConfig.VolumeStreaming.EmdbHeaderServer,
+            "https://files.wwpdb.org/pub/emdb/structures",
+        ],
+    ],
+});
+export const DefaultPluginUISpec = () => ({
+    ...DefaultPluginSpec(),
+    customParamEditors: [
+        [CreateVolumeStreamingBehavior, VolumeStreamingCustomControls],
+    ],
+});
+export const Preset = [
+    "default",
+    "unitcell",
+    "all-models",
+    "supercell",
+];
+export const Lighting = [
+    "flat",
+    "matte",
+    "glossy",
+    "metallic",
+    "plastic",
+];
+export const VisualStyle = [
+    "cartoon",
+    "ball-and-stick",
+    "carbohydrate",
+    "ellipsoid",
+    "gaussian-surface",
+    "molecular-surface",
+    "point",
+    "putty",
+    "spacefill",
+];
+export const Encoding = ["cif", "bcif"];
+/** Default values for `InitParams` */
+export const DefaultParams = {
+    moleculeId: undefined,
+    customData: undefined,
+    assemblyId: undefined,
+    defaultPreset: "default",
+    ligandView: undefined,
+    alphafoldView: false,
+    superposition: false,
+    superpositionParams: undefined,
+    selection: undefined,
+    visualStyle: undefined,
+    hideStructure: [],
+    loadMaps: false,
+    mapSettings: undefined,
+    bgColor: { r: 0, g: 0, b: 0 },
+    highlightColor: undefined,
+    selectColor: undefined,
+    lighting: undefined,
+    validationAnnotation: false,
+    domainAnnotation: false,
+    symmetryAnnotation: false,
+    pdbeUrl: "https://www.ebi.ac.uk/pdbe/",
+    encoding: "bcif",
+    lowPrecisionCoords: false,
+    selectInteraction: true,
+    selectBindings: undefined,
+    focusBindings: undefined,
+    granularity: undefined,
+    subscribeEvents: false,
+    hideControls: false,
+    hideCanvasControls: [],
+    sequencePanel: false,
+    pdbeLink: true,
+    loadingOverlay: false,
+    expanded: false,
+    landscape: false,
+    reactive: false,
+};
+/** Return `undefined` if `params` are valid, an error message otherwise. */
+export function validateInitParams(params) {
+    if (!params.moleculeId && !params.customData?.url)
+        return "Option `moleculeId` or `customData` must be defined";
+    if (params.customData) {
+        if (!params.customData.url)
+            return "Option `customData.url` must be a non-empty string";
+        if (!params.customData.format)
+            return "Option `customData.format` must be a non-empty string";
+    }
+    return undefined;
+}
diff --git a/frontend/venome-molstar/lib/subscribe-events.d.ts b/frontend/venome-molstar/lib/subscribe-events.d.ts
new file mode 100644
index 00000000..438ca9bc
--- /dev/null
+++ b/frontend/venome-molstar/lib/subscribe-events.d.ts
@@ -0,0 +1 @@
+export declare function subscribeToComponentEvents(wrapperCtx: any): void;
diff --git a/frontend/venome-molstar/lib/subscribe-events.js b/frontend/venome-molstar/lib/subscribe-events.js
new file mode 100644
index 00000000..4637fbe7
--- /dev/null
+++ b/frontend/venome-molstar/lib/subscribe-events.js
@@ -0,0 +1,190 @@
+export function subscribeToComponentEvents(wrapperCtx) {
+    document.addEventListener('PDB.interactions.click', function (e) {
+        if (typeof e.detail !== 'undefined') {
+            const data = e.detail.interacting_nodes ? { data: e.detail.interacting_nodes } : { data: [e.detail.selected_node] };
+            data.data[0]['focus'] = true;
+            wrapperCtx.visual.select(data);
+        }
+    });
+    document.addEventListener('PDB.interactions.mouseover', function (e) {
+        if (typeof e.detail !== 'undefined') {
+            const data = e.detail.interacting_nodes ? { data: e.detail.interacting_nodes } : { data: [e.detail.selected_node] };
+            wrapperCtx.visual.highlight(data);
+        }
+    });
+    document.addEventListener('PDB.interactions.mouseout', function (e) {
+        wrapperCtx.visual.clearHighlight();
+    });
+    document.addEventListener('PDB.topologyViewer.click', function (e) {
+        if (typeof e.eventData !== 'undefined') {
+            // Create query object from event data
+            const highlightQuery = {
+                entity_id: e.eventData.entityId,
+                struct_asym_id: e.eventData.structAsymId,
+                start_residue_number: e.eventData.residueNumber,
+                end_residue_number: e.eventData.residueNumber,
+                sideChain: true,
+                focus: true
+            };
+            // Call highlightAnnotation
+            wrapperCtx.visual.select({ data: [highlightQuery] });
+        }
+    });
+    document.addEventListener('PDB.topologyViewer.mouseover', function (e) {
+        if (typeof e.eventData !== 'undefined') {
+            // Abort if entryid do not match or viewer type is unipdb
+            // if(e.eventData.entryId != scope.pdbId) return;
+            // Create query object from event data
+            const highlightQuery = {
+                entity_id: e.eventData.entityId,
+                struct_asym_id: e.eventData.structAsymId,
+                start_residue_number: e.eventData.residueNumber,
+                end_residue_number: e.eventData.residueNumber
+            };
+            // Call highlightAnnotation
+            wrapperCtx.visual.highlight({ data: [highlightQuery] });
+        }
+    });
+    document.addEventListener('PDB.topologyViewer.mouseout', function (e) {
+        wrapperCtx.visual.clearHighlight();
+    });
+    document.addEventListener('protvista-mouseover', function (e) {
+        if (typeof e.detail !== 'undefined') {
+            let highlightQuery = undefined;
+            // Create query object from event data
+            if (e.detail.start && e.detail.end) {
+                highlightQuery = {
+                    start_residue_number: parseInt(e.detail.start),
+                    end_residue_number: parseInt(e.detail.end)
+                };
+            }
+            if (e.detail.feature && e.detail.feature.entityId)
+                highlightQuery['entity_id'] = e.detail.feature.entityId + '';
+            if (e.detail.feature && e.detail.feature.bestChainId)
+                highlightQuery['struct_asym_id'] = e.detail.feature.bestChainId;
+            if (e.detail.feature && e.detail.feature.chainId)
+                highlightQuery['struct_asym_id'] = e.detail.feature.chainId;
+            if (highlightQuery)
+                wrapperCtx.visual.highlight({ data: [highlightQuery] });
+        }
+    });
+    document.addEventListener('protvista-mouseout', function (e) {
+        wrapperCtx.visual.clearHighlight();
+    });
+    document.addEventListener('protvista-click', function (e) {
+        if (typeof e.detail !== 'undefined') {
+            let showInteraction = false;
+            let highlightQuery = undefined;
+            // Create query object from event data
+            if (e.detail.start && e.detail.end) {
+                highlightQuery = {
+                    start_residue_number: parseInt(e.detail.start),
+                    end_residue_number: parseInt(e.detail.end)
+                };
+            }
+            if (e.detail.feature && e.detail.feature.entityId)
+                highlightQuery['entity_id'] = e.detail.feature.entityId + '';
+            if (e.detail.feature && e.detail.feature.bestChainId)
+                highlightQuery['struct_asym_id'] = e.detail.feature.bestChainId;
+            if (e.detail.feature && e.detail.feature.chainId)
+                highlightQuery['struct_asym_id'] = e.detail.feature.chainId;
+            if (e.detail.feature && e.detail.feature.accession && e.detail.feature.accession.split(' ')[0] === 'Chain' || e.detail.feature.tooltipContent === 'Ligand binding site') {
+                showInteraction = true;
+            }
+            if (e.detail.start === e.detail.end)
+                showInteraction = true;
+            if (highlightQuery) {
+                if (showInteraction) {
+                    highlightQuery['sideChain'] = true;
+                }
+                else {
+                    let selColor = undefined;
+                    if (e.detail.trackIndex > -1 && e.detail.feature.locations && e.detail.feature.locations[0].fragments[e.detail.trackIndex].color)
+                        selColor = e.detail.feature.locations[0].fragments[e.detail.trackIndex].color;
+                    if (typeof selColor == 'undefined' && e.detail.feature.color)
+                        selColor = e.detail.feature.color;
+                    if (typeof selColor == 'undefined' && e.detail.color)
+                        selColor = e.detail.color;
+                    if (typeof selColor == 'undefined') {
+                        selColor = { r: 65, g: 96, b: 91 };
+                    }
+                    else {
+                        const isRgb = /rgb/g;
+                        if (isRgb.test(selColor)) {
+                            const rgbArr = selColor.substring(4, selColor.length - 1).split(',');
+                            selColor = { r: rgbArr[0], g: rgbArr[1], b: rgbArr[2] };
+                        }
+                    }
+                    highlightQuery['color'] = selColor;
+                }
+                highlightQuery['focus'] = true;
+                wrapperCtx.visual.select({ data: [highlightQuery] });
+            }
+        }
+    });
+    const elementTypeArrForRange = ['uniprot', 'pfam', 'cath', 'scop', 'strand', 'helice'];
+    const elementTypeArrForSingle = ['chain', 'quality', 'quality_outlier', 'binding site', 'alternate conformer'];
+    document.addEventListener('PDB.seqViewer.click', function (e) {
+        if (typeof e.eventData !== 'undefined') {
+            // Abort if entryid and entityid do not match or viewer type is unipdb
+            // if(e.eventData.entryId != scope.pdbId) return;
+            if (typeof e.eventData.elementData !== 'undefined' && elementTypeArrForSingle.indexOf(e.eventData.elementData.elementType) > -1) {
+                // Create query object from event data
+                const highlightQuery = {
+                    entity_id: e.eventData.entityId,
+                    struct_asym_id: e.eventData.elementData.pathData.struct_asym_id,
+                    start_residue_number: e.eventData.residueNumber,
+                    end_residue_number: e.eventData.residueNumber,
+                    sideChain: true,
+                    focus: true
+                };
+                // Call highlightAnnotation
+                wrapperCtx.visual.select({ data: [highlightQuery] });
+            }
+            else if (typeof e.eventData.elementData !== 'undefined' && elementTypeArrForRange.indexOf(e.eventData.elementData.elementType) > -1) {
+                const seqColorArray = e.eventData.elementData.color;
+                // Create query object from event data
+                const highlightQuery = {
+                    entity_id: e.eventData.entityId,
+                    struct_asym_id: e.eventData.elementData.pathData.struct_asym_id,
+                    start_residue_number: e.eventData.elementData.pathData.start.residue_number,
+                    end_residue_number: e.eventData.elementData.pathData.end.residue_number,
+                    color: { r: seqColorArray[0], g: seqColorArray[1], b: seqColorArray[2] },
+                    focus: true
+                };
+                wrapperCtx.visual.select({ data: [highlightQuery] });
+            }
+        }
+    });
+    document.addEventListener('PDB.seqViewer.mouseover', function (e) {
+        if (typeof e.eventData !== 'undefined') {
+            // Abort if entryid and entityid do not match or viewer type is unipdb
+            // if(e.eventData.entryId != scope.pdbId) return;
+            if (typeof e.eventData.elementData !== 'undefined' && elementTypeArrForSingle.indexOf(e.eventData.elementData.elementType) > -1) {
+                // Create query object from event data
+                const highlightQuery = {
+                    entity_id: e.eventData.entityId,
+                    struct_asym_id: e.eventData.elementData.pathData.struct_asym_id,
+                    start_residue_number: e.eventData.residueNumber,
+                    end_residue_number: e.eventData.residueNumber,
+                    focus: true
+                };
+                wrapperCtx.visual.select({ data: [highlightQuery] });
+            }
+            else if (typeof e.eventData.elementData !== 'undefined' && elementTypeArrForRange.indexOf(e.eventData.elementData.elementType) > -1) {
+                // Create query object from event data
+                const highlightQuery = {
+                    entity_id: e.eventData.entityId,
+                    struct_asym_id: e.eventData.elementData.pathData.struct_asym_id,
+                    start_residue_number: e.eventData.elementData.pathData.start.residue_number,
+                    end_residue_number: e.eventData.elementData.pathData.end.residue_number
+                };
+                // Call highlightAnnotation
+                wrapperCtx.visual.highlight({ data: [highlightQuery] });
+            }
+        }
+    });
+    document.addEventListener('PDB.seqViewer.mouseout', function (e) {
+        wrapperCtx.visual.clearHighlight();
+    });
+}
diff --git a/frontend/venome-molstar/lib/superposition-export.d.ts b/frontend/venome-molstar/lib/superposition-export.d.ts
new file mode 100644
index 00000000..d8ae9240
--- /dev/null
+++ b/frontend/venome-molstar/lib/superposition-export.d.ts
@@ -0,0 +1,4 @@
+import { PluginContext } from "molstar/lib/mol-plugin/context";
+export declare function superpositionExportHierarchy(plugin: PluginContext, options?: {
+    format?: "cif" | "bcif";
+}): Promise;
diff --git a/frontend/venome-molstar/lib/superposition-export.js b/frontend/venome-molstar/lib/superposition-export.js
new file mode 100644
index 00000000..e708ee3e
--- /dev/null
+++ b/frontend/venome-molstar/lib/superposition-export.js
@@ -0,0 +1,130 @@
+import { utf8ByteCount, utf8Write } from "molstar/lib/mol-io/common/utf8";
+import { to_mmCIF, Unit } from "molstar/lib/mol-model/structure";
+import { Task } from "molstar/lib/mol-task";
+import { getFormattedTime } from "molstar/lib/mol-util/date";
+import { download } from "molstar/lib/mol-util/download";
+import { zip } from "molstar/lib/mol-util/zip/zip";
+import { PluginCommands } from "molstar/lib/mol-plugin/commands";
+import { PluginCustomState } from "./plugin-custom-state";
+export async function superpositionExportHierarchy(plugin, options) {
+    try {
+        await plugin.runTask(_superpositionExportHierarchy(plugin, options), {
+            useOverlay: true,
+        });
+    }
+    catch (e) {
+        console.error(e);
+        plugin.log.error(`Model export failed. See console for details.`);
+    }
+}
+function _superpositionExportHierarchy(plugin, options) {
+    return Task.create("Export", async (ctx) => {
+        await ctx.update({
+            message: "Exporting...",
+            isIndeterminate: true,
+            canAbort: false,
+        });
+        const format = options?.format ?? "cif";
+        //  const { structures } = plugin.managers.structure.hierarchy.current;
+        const customState = PluginCustomState(plugin);
+        if (!customState.initParams)
+            throw new Error("customState.initParams has not been initialized");
+        if (!customState.superpositionState)
+            throw new Error("customState.superpositionState has not been initialized");
+        const superpositionState = customState.superpositionState;
+        const segmentIndex = superpositionState.activeSegment - 1;
+        const files = [];
+        const entryMap = new Map();
+        const structures = superpositionState.loadedStructs[segmentIndex].slice();
+        if (!customState.initParams.moleculeId)
+            throw new Error("initParams.moleculeId is not defined");
+        if (superpositionState.alphafold.ref)
+            structures.push(`AF-${customState.initParams.moleculeId}`);
+        for (const molId of structures) {
+            const modelRef = superpositionState.models[molId];
+            if (!modelRef)
+                continue;
+            let isStrHidden = false;
+            const _s = plugin.managers.structure.hierarchy.current.refs.get(modelRef);
+            if (_s.cell.state.isHidden)
+                isStrHidden = true;
+            for (const strComp of _s.components) {
+                if (strComp.cell.state.isHidden)
+                    isStrHidden = true;
+            }
+            if (isStrHidden)
+                continue;
+            const s = _s.transform?.cell.obj?.data ?? _s.cell.obj?.data;
+            if (!s)
+                continue;
+            if (s.models.length > 1) {
+                plugin.log.warn(`[Export] Skipping ${_s.cell.obj?.label}: Multimodel exports not supported.`);
+                continue;
+            }
+            if (s.units.some((u) => !Unit.isAtomic(u))) {
+                plugin.log.warn(`[Export] Skipping ${_s.cell.obj?.label}: Non-atomic model exports not supported.`);
+                continue;
+            }
+            const name = entryMap.has(s.model.entryId)
+                ? `${s.model.entryId}_${entryMap.get(s.model.entryId) + 1}.${format}`
+                : `${s.model.entryId}.${format}`;
+            entryMap.set(s.model.entryId, (entryMap.get(s.model.entryId) ?? 0) + 1);
+            await ctx.update({
+                message: `Exporting ${s.model.entryId}...`,
+                isIndeterminate: true,
+                canAbort: false,
+            });
+            if (s.elementCount > 100000) {
+                // Give UI chance to update, only needed for larger structures.
+                await new Promise((res) => setTimeout(res, 50));
+            }
+            try {
+                files.push([
+                    name,
+                    to_mmCIF(s.model.entryId, s, format === "bcif", {
+                        copyAllCategories: true,
+                    }),
+                ]);
+            }
+            catch (e) {
+                if (format === "cif" && s.elementCount > 2000000) {
+                    plugin.log.warn(`[Export] The structure might be too big to be exported as Text CIF, consider using the BinaryCIF format instead.`);
+                }
+                throw e;
+            }
+        }
+        if (files.length === 0) {
+            PluginCommands.Toast.Show(plugin, {
+                title: "Export Models",
+                message: "No visible structure in the 3D view to export!",
+                key: "superposition-toast-1",
+                timeoutMs: 7000,
+            });
+            return;
+        }
+        if (files.length === 1) {
+            download(new Blob([files[0][1]]), files[0][0]);
+        }
+        else if (files.length > 1) {
+            const zipData = {};
+            for (const [fn, data] of files) {
+                if (data instanceof Uint8Array) {
+                    zipData[fn] = data;
+                }
+                else {
+                    const bytes = new Uint8Array(utf8ByteCount(data));
+                    utf8Write(bytes, 0, data);
+                    zipData[fn] = bytes;
+                }
+            }
+            await ctx.update({
+                message: `Compressing Data...`,
+                isIndeterminate: true,
+                canAbort: false,
+            });
+            const buffer = await zip(ctx, zipData);
+            download(new Blob([new Uint8Array(buffer, 0, buffer.byteLength)]), `structures_${getFormattedTime()}.zip`);
+        }
+        plugin.log.info(`[Export] Done.`);
+    });
+}
diff --git a/frontend/venome-molstar/lib/superposition-focus-representation.d.ts b/frontend/venome-molstar/lib/superposition-focus-representation.d.ts
new file mode 100644
index 00000000..aa6d2e7a
--- /dev/null
+++ b/frontend/venome-molstar/lib/superposition-focus-representation.d.ts
@@ -0,0 +1,16 @@
+import { PluginBehavior } from "molstar/lib/mol-plugin/behavior";
+import { ParamDefinition as PD } from "molstar/lib/mol-util/param-definition";
+import { PluginContext } from "molstar/lib/mol-plugin/context";
+declare const SuperpositionFocusRepresentationParams: (plugin: PluginContext) => {
+    expandRadius: PD.Numeric;
+    surroundingsParams: PD.Group>;
+};
+type SuperpositionFocusRepresentationProps = PD.ValuesFor>;
+export declare enum SuperpositionFocusRepresentationTags {
+    SurrSel = "superposition-focus-surr-sel",
+    SurrRepr = "superposition-focus-surr-repr"
+}
+export declare const SuperpositionFocusRepresentation: import("molstar/lib/mol-state/transformer").StateTransformer;
+export {};
diff --git a/frontend/venome-molstar/lib/superposition-focus-representation.js b/frontend/venome-molstar/lib/superposition-focus-representation.js
new file mode 100644
index 00000000..e4230bc2
--- /dev/null
+++ b/frontend/venome-molstar/lib/superposition-focus-representation.js
@@ -0,0 +1,148 @@
+import { StructureElement } from "molstar/lib/mol-model/structure";
+import { createStructureRepresentationParams } from "molstar/lib/mol-plugin-state/helpers/structure-representation-params";
+import { StateTransforms } from "molstar/lib/mol-plugin-state/transforms";
+import { PluginBehavior } from "molstar/lib/mol-plugin/behavior";
+import { MolScriptBuilder as MS } from "molstar/lib/mol-script/language/builder";
+import { StateSelection, StateTransform, } from "molstar/lib/mol-state";
+import { ParamDefinition as PD } from "molstar/lib/mol-util/param-definition";
+import { PluginCommands } from "molstar/lib/mol-plugin/commands";
+import { lociDetails } from "./loci-details";
+const SuperpositionFocusRepresentationParams = (plugin) => {
+    const reprParams = StateTransforms.Representation.StructureRepresentation3D
+        .definition.params(void 0, plugin);
+    return {
+        expandRadius: PD.Numeric(5, { min: 1, max: 10, step: 1 }),
+        surroundingsParams: PD.Group(reprParams, {
+            label: "Surroundings",
+            customDefault: createStructureRepresentationParams(plugin, void 0, {
+                type: "ball-and-stick",
+                size: "physical",
+                typeParams: { sizeFactor: 0.16 },
+                sizeParams: { scale: 0.3 },
+            }),
+        }),
+    };
+};
+export var SuperpositionFocusRepresentationTags;
+(function (SuperpositionFocusRepresentationTags) {
+    SuperpositionFocusRepresentationTags["SurrSel"] = "superposition-focus-surr-sel";
+    SuperpositionFocusRepresentationTags["SurrRepr"] = "superposition-focus-surr-repr";
+})(SuperpositionFocusRepresentationTags || (SuperpositionFocusRepresentationTags = {}));
+const TagSet = new Set([
+    SuperpositionFocusRepresentationTags.SurrSel,
+    SuperpositionFocusRepresentationTags.SurrRepr,
+]);
+class SuperpositionFocusRepresentationBehavior extends PluginBehavior.WithSubscribers {
+    get surrLabel() {
+        return `[Focus] Surroundings (${this.params.expandRadius} Å)`;
+    }
+    ensureShape(cell) {
+        const state = this.plugin.state.data, tree = state.tree;
+        const builder = state.build();
+        const refs = StateSelection.findUniqueTagsInSubtree(tree, cell.transform.ref, TagSet);
+        // Selections
+        if (!refs[SuperpositionFocusRepresentationTags.SurrSel]) {
+            refs[SuperpositionFocusRepresentationTags.SurrSel] = builder
+                .to(cell)
+                .apply(StateTransforms.Model.StructureSelectionFromExpression, {
+                expression: MS.struct.generator.empty(),
+                label: this.surrLabel,
+            }, { tags: SuperpositionFocusRepresentationTags.SurrSel }).ref;
+        }
+        // Representations
+        if (!refs[SuperpositionFocusRepresentationTags.SurrRepr]) {
+            refs[SuperpositionFocusRepresentationTags.SurrRepr] = builder
+                .to(refs[SuperpositionFocusRepresentationTags.SurrSel])
+                .apply(StateTransforms.Representation.StructureRepresentation3D, this.params.surroundingsParams, { tags: SuperpositionFocusRepresentationTags.SurrRepr }).ref;
+        }
+        return { state, builder, refs };
+    }
+    clear(root) {
+        const state = this.plugin.state.data;
+        const surrs = state.select(StateSelection.Generators.byRef(root)
+            .subtree()
+            .withTag(SuperpositionFocusRepresentationTags.SurrSel));
+        if (surrs.length === 0)
+            return;
+        const update = state.build();
+        const expression = MS.struct.generator.empty();
+        for (const s of surrs) {
+            update
+                .to(s)
+                .update(StateTransforms.Model.StructureSelectionFromExpression, (old) => ({ ...old, expression }));
+        }
+        return PluginCommands.State.Update(this.plugin, {
+            state,
+            tree: update,
+            options: { doNotLogTiming: true, doNotUpdateCurrent: true },
+        });
+    }
+    async focus(sourceLoci) {
+        const parent = this.plugin.helpers.substructureParent.get(sourceLoci.structure);
+        if (!parent || !parent.obj)
+            return;
+        const loci = StructureElement.Loci.remap(sourceLoci, parent.obj.data);
+        const residueLoci = StructureElement.Loci.extendToWholeResidues(loci);
+        const residueBundle = StructureElement.Bundle.fromLoci(residueLoci);
+        const target = StructureElement.Bundle.toExpression(residueBundle);
+        let surroundings = MS.struct.modifier.includeSurroundings({
+            0: target,
+            radius: this.params.expandRadius,
+            "as-whole-residues": true,
+        });
+        const lociDeatils = lociDetails(sourceLoci);
+        if (!lociDeatils) {
+            surroundings = MS.struct.modifier.exceptBy({
+                0: surroundings,
+                by: target,
+            });
+        }
+        const { state, builder, refs } = this.ensureShape(parent);
+        builder
+            .to(refs[SuperpositionFocusRepresentationTags.SurrSel])
+            .update(StateTransforms.Model.StructureSelectionFromExpression, (old) => ({
+            ...old,
+            expression: surroundings,
+            label: this.surrLabel,
+        }));
+        await PluginCommands.State.Update(this.plugin, {
+            state,
+            tree: builder,
+            options: { doNotLogTiming: true, doNotUpdateCurrent: true },
+        });
+    }
+    register(ref) {
+        this.subscribeObservable(this.plugin.managers.structure.focus.behaviors.current, (entry) => {
+            // if (entry) this.focus(entry.loci);
+            // else this.clear(StateTransform.RootRef);
+            this.clear(StateTransform.RootRef);
+            if (entry)
+                this.focus(entry.loci);
+        });
+    }
+    async update(params) {
+        const old = this.params;
+        this.params = params;
+        const state = this.plugin.state.data;
+        const builder = state.build();
+        const all = StateSelection.Generators.root.subtree();
+        for (const repr of state.select(all.withTag(SuperpositionFocusRepresentationTags.SurrRepr))) {
+            builder.to(repr).update(this.params.surroundingsParams);
+        }
+        await PluginCommands.State.Update(this.plugin, {
+            state,
+            tree: builder,
+            options: { doNotLogTiming: true, doNotUpdateCurrent: true },
+        });
+        if (params.expandRadius !== old.expandRadius)
+            await this.clear(StateTransform.RootRef);
+        return true;
+    }
+}
+export const SuperpositionFocusRepresentation = PluginBehavior.create({
+    name: "create-superposition-focus-representation",
+    display: { name: "Superposition Focus Representation" },
+    category: "interaction",
+    ctor: SuperpositionFocusRepresentationBehavior,
+    params: (_, plugin) => SuperpositionFocusRepresentationParams(plugin),
+});
diff --git a/frontend/venome-molstar/lib/superposition-sifts-mapping.d.ts b/frontend/venome-molstar/lib/superposition-sifts-mapping.d.ts
new file mode 100644
index 00000000..4e166ec5
--- /dev/null
+++ b/frontend/venome-molstar/lib/superposition-sifts-mapping.d.ts
@@ -0,0 +1,22 @@
+import { MinimizeRmsd } from "molstar/lib/mol-math/linear-algebra/3d/minimize-rmsd";
+import { ElementIndex, ResidueIndex } from "molstar/lib/mol-model/structure/model/indexing";
+import { StructureElement } from "molstar/lib/mol-model/structure/structure/element";
+import { Structure } from "molstar/lib/mol-model/structure";
+import { Unit } from "molstar/lib/mol-model/structure/structure/unit";
+export interface AlignmentResultEntry {
+    transform: MinimizeRmsd.Result;
+    pivot: number;
+    other: number;
+}
+export interface AlignmentResult {
+    entries: AlignmentResultEntry[];
+    zeroOverlapPairs: [number, number][];
+    failedPairs: [number, number][];
+}
+type IncludeResidueTest = (traceElementOrFirstAtom: StructureElement.Location, residueIndex: ResidueIndex, startIndex: ElementIndex, endIndex: ElementIndex) => boolean;
+export declare function alignAndSuperposeWithSIFTSMapping(structures: Structure[], options?: {
+    traceOnly?: boolean;
+    includeResidueTest?: IncludeResidueTest;
+    applyTestIndex?: number[];
+}): AlignmentResult;
+export {};
diff --git a/frontend/venome-molstar/lib/superposition-sifts-mapping.js b/frontend/venome-molstar/lib/superposition-sifts-mapping.js
new file mode 100644
index 00000000..dfefc819
--- /dev/null
+++ b/frontend/venome-molstar/lib/superposition-sifts-mapping.js
@@ -0,0 +1,155 @@
+import { Segmentation } from "molstar/lib/mol-data/int";
+import { MinimizeRmsd } from "molstar/lib/mol-math/linear-algebra/3d/minimize-rmsd";
+import { SIFTSMapping } from "./sifts-mapping";
+import { StructureElement } from "molstar/lib/mol-model/structure/structure/element";
+export function alignAndSuperposeWithSIFTSMapping(structures, options) {
+    const indexMap = new Map();
+    for (let i = 0; i < structures.length; i++) {
+        let includeResidueTest = options?.includeResidueTest ?? _includeAllResidues;
+        if (options?.applyTestIndex && !options.applyTestIndex.includes(i))
+            includeResidueTest = _includeAllResidues;
+        buildIndex(structures[i], indexMap, i, options?.traceOnly ?? true, includeResidueTest);
+    }
+    const index = Array.from(indexMap.values());
+    // TODO: support non-first structure pivots
+    const pairs = findPairs(structures.length, index);
+    const zeroOverlapPairs = [];
+    const failedPairs = [];
+    const entries = [];
+    for (const p of pairs) {
+        if (p.count === 0) {
+            zeroOverlapPairs.push([p.i, p.j]);
+        }
+        else {
+            const [a, b] = getPositionTables(index, p.i, p.j, p.count);
+            const transform = MinimizeRmsd.compute({ a, b });
+            if (Number.isNaN(transform.rmsd)) {
+                failedPairs.push([p.i, p.j]);
+            }
+            else {
+                entries.push({ transform, pivot: p.i, other: p.j });
+            }
+        }
+    }
+    return { entries, zeroOverlapPairs, failedPairs };
+}
+function getPositionTables(index, pivot, other, N) {
+    const xs = MinimizeRmsd.Positions.empty(N);
+    const ys = MinimizeRmsd.Positions.empty(N);
+    let o = 0;
+    for (const { pivots } of index) {
+        const a = pivots[pivot];
+        const b = pivots[other];
+        if (!a || !b)
+            continue;
+        const l = Math.min(a[2] - a[1], b[2] - b[1]);
+        // TODO: check if residue types match?
+        for (let i = 0; i < l; i++) {
+            let eI = (a[1] + i);
+            xs.x[o] = a[0].conformation.x(eI);
+            xs.y[o] = a[0].conformation.y(eI);
+            xs.z[o] = a[0].conformation.z(eI);
+            eI = (b[1] + i);
+            ys.x[o] = b[0].conformation.x(eI);
+            ys.y[o] = b[0].conformation.y(eI);
+            ys.z[o] = b[0].conformation.z(eI);
+            o++;
+        }
+    }
+    return [xs, ys];
+}
+function findPairs(N, index) {
+    const pairwiseCounts = [];
+    for (let i = 0; i < N; i++) {
+        pairwiseCounts[i] = [];
+        for (let j = 0; j < N; j++)
+            pairwiseCounts[i][j] = 0;
+    }
+    for (const { pivots } of index) {
+        for (let i = 0; i < N; i++) {
+            if (!pivots[i])
+                continue;
+            const lI = pivots[i][2] - pivots[i][1];
+            for (let j = i + 1; j < N; j++) {
+                if (!pivots[j])
+                    continue;
+                const lJ = pivots[j][2] - pivots[j][1];
+                pairwiseCounts[i][j] = pairwiseCounts[i][j] + Math.min(lI, lJ);
+            }
+        }
+    }
+    const ret = [];
+    for (let j = 1; j < N; j++) {
+        ret[j - 1] = { i: 0, j, count: pairwiseCounts[0][j] };
+    }
+    // TODO: support non-first structure pivots
+    // for (let i = 0; i < N - 1; i++) {
+    //     let max = 0, maxJ = i;
+    //     for (let j = i + 1; j < N; j++) {
+    //         if (pairwiseCounts[i][j] > max) {
+    //             maxJ = j;
+    //             max = pairwiseCounts[i][j];
+    //         }
+    //     }
+    //     ret[i] = { i, j: maxJ, count: max };
+    // }
+    return ret;
+}
+function _includeAllResidues() {
+    return true;
+}
+function buildIndex(structure, index, sI, traceOnly, includeTest) {
+    const loc = StructureElement.Location.create(structure);
+    for (const unit of structure.units) {
+        if (unit.kind !== 0 /* Unit.Kind.Atomic */)
+            continue;
+        const { elements, model } = unit;
+        loc.unit = unit;
+        const map = SIFTSMapping.Provider.get(model).value;
+        if (!map)
+            return;
+        const { dbName, accession, num } = map;
+        const chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
+        const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
+        const traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex;
+        while (chainsIt.hasNext) {
+            const chainSegment = chainsIt.move();
+            residuesIt.setSegment(chainSegment);
+            while (residuesIt.hasNext) {
+                const residueSegment = residuesIt.move();
+                const rI = residueSegment.index;
+                if (!dbName[rI])
+                    continue;
+                const traceElement = traceElementIndex[rI];
+                let start, end;
+                if (traceOnly) {
+                    start = traceElement;
+                    if (start === -1)
+                        continue;
+                    end = (start + 1);
+                }
+                else {
+                    start = elements[residueSegment.start];
+                    end = (elements[residueSegment.end - 1] +
+                        1);
+                }
+                loc.element = (traceElement >= 0 ? traceElement : start);
+                if (!includeTest(loc, rI, start, end))
+                    continue;
+                const key = `${dbName[rI]}-${accession[rI].split("-")[0]}-${num[rI]}`;
+                if (!index.has(key)) {
+                    index.set(key, {
+                        key,
+                        pivots: { [sI]: [unit, start, end] },
+                    });
+                }
+                else {
+                    const entry = index.get(key);
+                    if (!entry.pivots[sI]) {
+                        entry.pivots[sI] = [unit, start, end];
+                    }
+                }
+            }
+        }
+    }
+}
diff --git a/frontend/venome-molstar/lib/superposition.d.ts b/frontend/venome-molstar/lib/superposition.d.ts
new file mode 100644
index 00000000..7b100220
--- /dev/null
+++ b/frontend/venome-molstar/lib/superposition.d.ts
@@ -0,0 +1,7 @@
+import { PluginContext } from "molstar/lib/mol-plugin/context";
+import { Subject } from "rxjs";
+import { ClusterMember } from "./plugin-custom-state";
+export declare function initSuperposition(plugin: PluginContext, completeSubject?: Subject): Promise;
+export declare function loadAfStructure(plugin: PluginContext): Promise;
+export declare function superposeAf(plugin: PluginContext, traceOnly: boolean, segmentIndex?: number): Promise;
+export declare function renderSuperposition(plugin: PluginContext, segmentIndex: number, entryList: ClusterMember[]): Promise;
diff --git a/frontend/venome-molstar/lib/superposition.js b/frontend/venome-molstar/lib/superposition.js
new file mode 100644
index 00000000..78d21000
--- /dev/null
+++ b/frontend/venome-molstar/lib/superposition.js
@@ -0,0 +1,727 @@
+import { Mat4 } from "molstar/lib/mol-math/linear-algebra";
+import { StructureProperties } from "molstar/lib/mol-model/structure";
+import { StateTransforms } from "molstar/lib/mol-plugin-state/transforms";
+import { MolScriptBuilder as MS } from "molstar/lib/mol-script/language/builder";
+import { Script } from "molstar/lib/mol-script/script";
+import { StateObjectRef, } from "molstar/lib/mol-state";
+import { Task } from "molstar/lib/mol-task";
+import { Asset } from "molstar/lib/mol-util/assets";
+import { Color } from "molstar/lib/mol-util/color/color";
+import { ColorLists } from "molstar/lib/mol-util/color/lists";
+import { applyAFTransparency } from "./alphafold-transparency";
+import { ModelInfo, getStructureUrl } from "./helpers";
+import { PluginCustomState } from "./plugin-custom-state";
+import { alignAndSuperposeWithSIFTSMapping } from "./superposition-sifts-mapping";
+function getRandomColor(plugin, segmentIndex) {
+    const clList = ColorLists;
+    const spState = PluginCustomState(plugin).superpositionState;
+    if (!spState)
+        throw new Error("customState.superpositionState has not been initialized");
+    let palleteIndex = spState.colorState[segmentIndex].palleteIndex;
+    let colorIndex = spState.colorState[segmentIndex].colorIndex;
+    if (clList[spState.colorPalette[palleteIndex]].list[colorIndex + 1]) {
+        colorIndex += 1;
+    }
+    else {
+        colorIndex = 0;
+        palleteIndex = spState.colorPalette[palleteIndex + 1]
+            ? palleteIndex + 1
+            : 0;
+    }
+    const palleteName = spState.colorPalette[palleteIndex];
+    spState.colorState[segmentIndex].palleteIndex = palleteIndex;
+    spState.colorState[segmentIndex].colorIndex = colorIndex;
+    return clList[palleteName].list[colorIndex];
+}
+export async function initSuperposition(plugin, completeSubject) {
+    let success = false;
+    try {
+        await plugin.clear();
+        const customState = PluginCustomState(plugin);
+        customState.superpositionState = {
+            models: {},
+            entries: {},
+            refMaps: {},
+            segmentData: void 0,
+            matrixData: {},
+            activeSegment: 0,
+            loadedStructs: [],
+            visibleRefs: [],
+            invalidStruct: [],
+            noMatrixStruct: [],
+            hets: {},
+            colorPalette: [
+                "dark-2",
+                "red-yellow-green",
+                "paired",
+                "set-1",
+                "accent",
+                "set-2",
+                "rainbow",
+            ],
+            colorState: [],
+            alphafold: {
+                apiData: {
+                    cif: "",
+                    pae: "",
+                    length: 0,
+                },
+                length: 0,
+                ref: "",
+                traceOnly: true,
+                visibility: [],
+                transforms: [],
+                rmsds: [],
+                coordinateSystems: [],
+            },
+        };
+        // Get segment and cluster information for the given uniprot accession
+        await getSegmentData(plugin);
+        const segmentData = customState.superpositionState.segmentData;
+        if (!segmentData)
+            return;
+        // Load Matrix Data
+        await getMatrixData(plugin);
+        if (!customState.superpositionState.segmentData)
+            return;
+        if (!customState.initParams.moleculeId)
+            throw new Error("initParams.moleculeId is not defined");
+        const afStrUrls = await getAfUrl(plugin, customState.initParams.moleculeId);
+        if (afStrUrls)
+            customState.superpositionState.alphafold.apiData = afStrUrls;
+        segmentData.forEach(() => {
+            customState.superpositionState.loadedStructs.push([]);
+            customState.superpositionState.visibleRefs.push([]);
+            customState.superpositionState.colorState.push({
+                palleteIndex: 0,
+                colorIndex: -1,
+            });
+        });
+        // Set segment and cluster details from superPositionParams
+        const superpositionParams = customState.initParams.superpositionParams;
+        const segmentIndex = superpositionParams?.segment
+            ? superpositionParams.segment - 1
+            : 0;
+        customState.superpositionState.activeSegment = segmentIndex + 1;
+        const clusterIndexs = superpositionParams?.cluster
+            ? superpositionParams.cluster
+            : void 0;
+        // Emit segment API data load event
+        customState.events?.superpositionInit.next(true);
+        // Get entry list to load matrix data
+        let entryList = [];
+        const clusters = segmentData[segmentIndex].clusters;
+        clusters.forEach((cluster, clusterIndex) => {
+            // Validate for cluster index if provided in superPositionParams
+            if (clusterIndexs && clusterIndexs.indexOf(clusterIndex) === -1)
+                return;
+            // Add respresentative structure to the list
+            if (superpositionParams?.superposeAll) {
+                entryList = entryList.concat(cluster);
+            }
+            else {
+                entryList.push(cluster[0]);
+            }
+        });
+        await renderSuperposition(plugin, segmentIndex, entryList);
+        success = true;
+    }
+    finally {
+        completeSubject?.next(success);
+    }
+}
+function createCarbVisLabel(carbLigNamesAndCount) {
+    const compList = [];
+    for (const carbCompId in carbLigNamesAndCount) {
+        compList.push(`${carbCompId} (${carbLigNamesAndCount[carbCompId]})`);
+    }
+    return compList.join(", ");
+}
+async function getAfUrl(plugin, accession) {
+    let apiResponse;
+    let apiData;
+    await plugin.runTask(Task.create("Get AlphaFold URL", async (ctx) => {
+        try {
+            apiResponse = await plugin
+                .fetch({
+                url: `https://alphafold.ebi.ac.uk/api/prediction/${accession}`,
+                type: "json",
+            })
+                .runInContext(ctx);
+            if (apiResponse && apiResponse?.[0].bcifUrl) {
+                apiData = {
+                    cif: apiResponse?.[0].cifUrl,
+                    pae: apiResponse?.[0].paeImageUrl,
+                    length: apiResponse?.[0].uniprotEnd,
+                };
+            }
+        }
+        catch (e) {
+            // console.warn(e);
+        }
+    }));
+    return apiData;
+}
+export async function loadAfStructure(plugin) {
+    const customState = PluginCustomState(plugin);
+    if (!customState.superpositionState)
+        throw new Error("customState.superpositionState has not been initialized");
+    const { structure } = await loadStructure(plugin, customState.superpositionState.alphafold.apiData.cif, "mmcif", false);
+    const strInstance = structure;
+    if (!strInstance)
+        return false;
+    // Store Refs in state
+    const spState = customState.superpositionState;
+    spState.alphafold.ref = strInstance?.ref;
+    if (!customState.initParams?.moleculeId)
+        throw new Error("initParams.moleculeId is not defined");
+    spState.models[`AF-${customState.initParams.moleculeId}`] =
+        strInstance?.ref;
+    const chainSel = await plugin.builders.structure.tryCreateComponentStatic(strInstance, "polymer", {
+        label: `AlphaFold Structure`,
+        tags: [`alphafold-chain`, `superposition-sel`],
+    });
+    if (chainSel) {
+        await plugin.builders.structure.representation.addRepresentation(chainSel, {
+            type: "putty",
+            color: "plddt-confidence",
+            size: "uniform",
+            sizeParams: { value: 1.5 },
+        }, { tag: `af-superposition-visual` });
+        return strInstance?.ref;
+    }
+    return false;
+}
+export async function superposeAf(plugin, traceOnly, segmentIndex) {
+    const customState = PluginCustomState(plugin);
+    const spState = customState.superpositionState;
+    if (!spState?.segmentData)
+        return;
+    // Load AF structure
+    const afStrRef = spState.alphafold.ref || (await loadAfStructure(plugin));
+    if (!afStrRef)
+        return;
+    const afStr = plugin.managers.structure.hierarchy.current.refs.get(afStrRef);
+    const segmentNum = segmentIndex ? segmentIndex : spState.activeSegment - 1;
+    if (!spState.alphafold.transforms[segmentNum]) {
+        // Create representative list
+        const mappingResult = [];
+        const coordinateSystems = [];
+        const failedPairsResult = [];
+        const zeroOverlapPairsResult = [];
+        let minRmsd = 0;
+        let minIndex = 0;
+        const rmsdList = [];
+        const segmentClusters = spState.segmentData[segmentNum].clusters;
+        segmentClusters.forEach((cluster) => {
+            const modelRef = spState.models[`${cluster[0].pdb_id}_${cluster[0].struct_asym_id}`];
+            if (modelRef) {
+                const structHierarchy = plugin.managers.structure.hierarchy.current.refs.get(modelRef);
+                if (structHierarchy) {
+                    const input = [structHierarchy.components[0], afStr];
+                    const structures = input.map((s) => s.cell.obj?.data);
+                    let { entries, failedPairs, zeroOverlapPairs } = alignAndSuperposeWithSIFTSMapping(structures, {
+                        traceOnly,
+                        includeResidueTest: (loc) => StructureProperties.atom.B_iso_or_equiv(loc) >
+                            70,
+                        applyTestIndex: [1],
+                    });
+                    if (entries.length === 0 ||
+                        (entries &&
+                            entries[0] &&
+                            entries[0].transform.rmsd.toFixed(1) === "0.0")) {
+                        const alignWithoutPlddt = alignAndSuperposeWithSIFTSMapping(structures, {
+                            traceOnly,
+                        });
+                        entries = alignWithoutPlddt.entries;
+                    }
+                    if (entries && entries[0]) {
+                        mappingResult.push(entries[0]);
+                        coordinateSystems.push(input[0]?.transform?.cell.obj?.data.coordinateSystem);
+                        const totalMappings = mappingResult.length;
+                        if (totalMappings === 1 ||
+                            entries[0].transform.rmsd < minRmsd) {
+                            minRmsd = entries[0].transform.rmsd;
+                            minIndex =
+                                totalMappings === 1
+                                    ? 0
+                                    : mappingResult.length - 1;
+                        }
+                        rmsdList.push(`${cluster[0].pdb_id} chain ${cluster[0].struct_asym_id}:${entries[0].transform.rmsd.toFixed(2)}`);
+                    }
+                    else {
+                        if (failedPairs.length > 0)
+                            failedPairsResult.push(failedPairs);
+                        if (zeroOverlapPairs.length > 0)
+                            zeroOverlapPairsResult.push(zeroOverlapPairs);
+                        // rmsdList.push(`${cluster[0].pdb_id} ${cluster[0].struct_asym_id}:-`)
+                    }
+                }
+            }
+        });
+        // console.log(failedPairsResult);
+        // console.log(zeroOverlapPairsResult);
+        if (mappingResult.length > 0) {
+            spState.alphafold.visibility[segmentNum] = true;
+            spState.alphafold.transforms[segmentNum] =
+                mappingResult[minIndex].transform.bTransform;
+            spState.alphafold.coordinateSystems[segmentNum] =
+                coordinateSystems[minIndex];
+            spState.alphafold.rmsds[segmentNum] = rmsdList.sort((a, b) => parseFloat(a.split(":")[1]) - parseFloat(b.split(":")[1]));
+        }
+    }
+    await afTransform(plugin, afStr.cell, spState.alphafold.transforms[segmentNum], spState.alphafold.coordinateSystems[segmentNum]);
+    applyAFTransparency(plugin, afStr, 0.8, 70);
+    return true;
+}
+export async function renderSuperposition(plugin, segmentIndex, entryList) {
+    const customState = PluginCustomState(plugin);
+    const superpositionParams = customState.initParams.superpositionParams;
+    let busyFlagOn = false;
+    if (entryList.length > 1) {
+        busyFlagOn = true;
+        customState.events?.isBusy.next(true);
+    }
+    // Load Coordinates and render respresentations
+    return plugin.dataTransaction(async () => {
+        if (!customState.initParams)
+            throw new Error("customState.initParams has not been initialized");
+        if (!customState.superpositionState)
+            throw new Error("customState.superpositionState has not been initialized");
+        const spState = customState.superpositionState;
+        for await (const s of entryList) {
+            // validate matrix availability
+            if (!spState.matrixData[`${s.pdb_id}_${s.auth_asym_id}`]) {
+                spState.noMatrixStruct.push(`${s.pdb_id}_${s.struct_asym_id}`);
+                spState.invalidStruct.push(`${s.pdb_id}_${s.struct_asym_id}`);
+                continue;
+            }
+            spState.loadedStructs[segmentIndex].push(`${s.pdb_id}_${s.struct_asym_id}`);
+            // Set Coordinate server url
+            const request = superpositionParams && superpositionParams.ligandView
+                ? { pdbId: s.pdb_id, queryType: "full" }
+                : {
+                    pdbId: s.pdb_id,
+                    queryType: "atoms",
+                    queryParams: { auth_asym_id: s.auth_asym_id },
+                };
+            const strUrl = getStructureUrl(customState.initParams, request);
+            // Load Data
+            let strInstance;
+            let modelRef;
+            let clearOnFail = true;
+            if (superpositionParams &&
+                superpositionParams.ligandView &&
+                spState.entries[s.pdb_id]) {
+                const polymerInstance = plugin.state.data.select(spState.entries[s.pdb_id])[0];
+                modelRef = polymerInstance.transform.parent;
+                const modelInstance = plugin.state.data.select(modelRef)[0];
+                strInstance = await plugin.builders.structure.createStructure(modelInstance, { name: "model", params: {} });
+                clearOnFail = false;
+            }
+            else {
+                const isBinary = customState.initParams.encoding === "bcif" ? true : false;
+                const { model, structure } = await loadStructure(plugin, strUrl, "mmcif", isBinary);
+                strInstance = structure;
+                modelRef = model.ref;
+            }
+            if (!strInstance)
+                continue;
+            // Store Refs in state
+            if (!spState.models[`${s.pdb_id}_${s.struct_asym_id}`])
+                spState.models[`${s.pdb_id}_${s.struct_asym_id}`] =
+                    strInstance?.ref;
+            if (superpositionParams &&
+                superpositionParams.ligandView &&
+                !spState.entries[s.pdb_id])
+                spState.entries[s.pdb_id] = strInstance?.ref;
+            // Apply tranform matrix
+            const matrix = Mat4.ofRows(customState.superpositionState.matrixData[`${s.pdb_id}_${s.auth_asym_id}`].matrix);
+            await transform(plugin, strInstance, matrix);
+            // Create representations
+            let chainSel;
+            if (superpositionParams &&
+                superpositionParams.ligandView &&
+                s.is_representative) {
+                const uniformColor1 = getRandomColor(plugin, segmentIndex); // random color
+                chainSel =
+                    await plugin.builders.structure.tryCreateComponentFromExpression(strInstance, chainSelection(s.struct_asym_id), `Chain-${segmentIndex}`, { label: `Chain`, tags: [`superposition-sel`] });
+                if (chainSel) {
+                    await plugin.builders.structure.representation.addRepresentation(chainSel, {
+                        type: "putty",
+                        color: "uniform",
+                        colorParams: { value: uniformColor1 },
+                        size: "uniform",
+                    }, { tag: `superposition-visual` });
+                    spState.refMaps[chainSel.ref] = `${s.pdb_id}_${s.struct_asym_id}`;
+                }
+            }
+            else if (superpositionParams &&
+                superpositionParams.ligandView &&
+                !s.is_representative) {
+                // Do nothing
+            }
+            else {
+                const uniformColor2 = getRandomColor(plugin, segmentIndex); // random color
+                chainSel =
+                    await plugin.builders.structure.tryCreateComponentStatic(strInstance, "polymer", {
+                        label: `Chain`,
+                        tags: [
+                            `Chain-${segmentIndex}`,
+                            `superposition-sel`,
+                        ],
+                    });
+                if (chainSel) {
+                    await plugin.builders.structure.representation.addRepresentation(chainSel, {
+                        type: "putty",
+                        color: "uniform",
+                        colorParams: { value: uniformColor2 },
+                        size: "uniform",
+                    }, { tag: `superposition-visual` });
+                    spState.refMaps[chainSel.ref] = `${s.pdb_id}_${s.struct_asym_id}`;
+                }
+                // // const addTooltipUpdate = plugin.state.behaviors.build().to(BestDatabaseSequenceMapping.id).update(BestDatabaseSequenceMapping, (old: any) => { old.showTooltip = true; });
+                // // await plugin.runTask(plugin.state.behaviors.updateTree(addTooltipUpdate));
+                // BestDatabaseSequenceMapping
+                // console.log(plugin.state.data.select(modelRef)[0])
+            }
+            let invalidStruct = chainSel ? false : true;
+            if (superpositionParams && superpositionParams.ligandView) {
+                const state = plugin.state.data;
+                const hetInfo = await getLigandNamesFromModelData(plugin, state, modelRef);
+                const hets = hetInfo ? hetInfo.hetNames : [];
+                // const interactingHets = [];
+                if (hets && hets.length > 0) {
+                    for await (const het of hets) {
+                        const ligand = MS.struct.generator.atomGroups({
+                            "chain-test": MS.core.rel.eq([
+                                MS.struct.atomProperty.macromolecular.auth_asym_id(),
+                                s.auth_asym_id,
+                            ]),
+                            "residue-test": MS.core.rel.eq([
+                                MS.struct.atomProperty.macromolecular.label_comp_id(),
+                                het,
+                            ]),
+                            "group-by": MS.core.str.concat([
+                                MS.struct.atomProperty.core.operatorName(),
+                                MS.struct.atomProperty.macromolecular.residueKey(),
+                            ]),
+                        });
+                        const labelTagParams = {
+                            label: `${het}`,
+                            tags: [`superposition-ligand-sel`],
+                        };
+                        let hetColor = Color.fromRgb(253, 3, 253);
+                        if (superpositionParams?.ligandColor) {
+                            const { r, g, b } = superpositionParams.ligandColor;
+                            hetColor = Color.fromRgb(r, g, b);
+                        }
+                        const ligandExp = await plugin.builders.structure.tryCreateComponentFromExpression(strInstance, ligand, `${het}-${segmentIndex}`, labelTagParams);
+                        if (ligandExp) {
+                            await plugin.builders.structure.representation.addRepresentation(ligandExp, {
+                                type: "ball-and-stick",
+                                color: "uniform",
+                                colorParams: { value: hetColor },
+                            }, { tag: `superposition-ligand-visual` });
+                            spState.refMaps[ligandExp.ref] = `${s.pdb_id}_${s.struct_asym_id}`;
+                            invalidStruct = false;
+                            // interactingHets.push(het);
+                        }
+                    }
+                }
+                const carbEntityCount = hetInfo ? hetInfo.carbEntityCount : 0;
+                if (carbEntityCount > 0) {
+                    // Get Carbohydrate Polymers details from PDBe API
+                    const allCarbPolymers = await getCarbPolymerDetailsFromApi(plugin, s.pdb_id);
+                    // Polymer chain + surroundings query
+                    const polymerChainWithSurroundings = MS.struct.modifier.includeSurroundings({
+                        0: MS.struct.generator.atomGroups({
+                            "entity-test": MS.core.rel.eq([
+                                MS.ammp("entityType"),
+                                "polymer",
+                            ]),
+                            "chain-test": MS.core.rel.eq([
+                                MS.struct.atomProperty.macromolecular.auth_asym_id(),
+                                s.auth_asym_id,
+                            ]),
+                            "group-by": MS.core.str.concat([
+                                MS.struct.atomProperty.core.operatorName(),
+                                MS.struct.atomProperty.macromolecular.residueKey(),
+                            ]),
+                        }),
+                        radius: 5,
+                        "as-whole-residues": true,
+                    });
+                    let i = 0;
+                    for (const carbEntityChainId of allCarbPolymers.branchedChains) {
+                        const carbEntityChain = MS.struct.generator.atomGroups({
+                            "entity-test": MS.core.rel.eq([
+                                MS.ammp("entityType"),
+                                "branched",
+                            ]),
+                            "chain-test": MS.core.rel.eq([
+                                MS.struct.atomProperty.macromolecular.auth_asym_id(),
+                                carbEntityChainId,
+                            ]),
+                            "group-by": MS.core.str.concat([
+                                MS.struct.atomProperty.core.operatorName(),
+                                MS.struct.atomProperty.macromolecular.residueKey(),
+                            ]),
+                        });
+                        const carbEntityChainInVicinity = MS.struct.filter.intersectedBy({
+                            0: polymerChainWithSurroundings,
+                            by: carbEntityChain,
+                        });
+                        const data = plugin.state.data.select(strInstance.ref)[0].obj.data;
+                        const carbChainSel = Script.getStructureSelection(carbEntityChainInVicinity, data);
+                        if (carbChainSel && carbChainSel.kind === "sequence") {
+                            // console.log(carbEntityChainId + ' chain present in 5 A radius');
+                            const carbLigands = [];
+                            const carbLigNamesAndCount = {};
+                            const carbLigList = [];
+                            for (const carbLigs of allCarbPolymers
+                                .branchedLigands[i]) {
+                                const ligResDetails = carbLigs.split("-");
+                                carbLigands.push(MS.core.rel.eq([
+                                    MS.struct.atomProperty.macromolecular.auth_seq_id(),
+                                    +ligResDetails[1],
+                                ]));
+                                if (carbLigNamesAndCount[ligResDetails[0]]) {
+                                    carbLigNamesAndCount[ligResDetails[0]]++;
+                                }
+                                else {
+                                    carbLigNamesAndCount[ligResDetails[0]] = 1;
+                                }
+                                carbLigList.push(ligResDetails[0]);
+                            }
+                            const carbVisLabel = createCarbVisLabel(carbLigNamesAndCount);
+                            const branchedEntity = MS.struct.generator.atomGroups({
+                                "entity-test": MS.core.rel.eq([
+                                    MS.ammp("entityType"),
+                                    "branched",
+                                ]),
+                                "group-by": MS.core.str.concat([
+                                    MS.struct.atomProperty.core.operatorName(),
+                                    MS.struct.atomProperty.macromolecular.residueKey(),
+                                ]),
+                                "chain-test": MS.core.rel.eq([
+                                    MS.struct.atomProperty.macromolecular.auth_asym_id(),
+                                    carbEntityChainId,
+                                ]),
+                                "residue-test": MS.core.logic.or(carbLigands),
+                            });
+                            const labelTagParams = {
+                                label: `${carbVisLabel}`,
+                                tags: [`superposition-carb-sel`],
+                            };
+                            const ligandExp = await plugin.builders.structure.tryCreateComponentFromExpression(strInstance, branchedEntity, `${carbLigList.join("-")}-${segmentIndex}`, labelTagParams);
+                            if (ligandExp) {
+                                await plugin.builders.structure.representation.addRepresentation(ligandExp, { type: "carbohydrate" }, { tag: `superposition-carb-visual` });
+                                spState.refMaps[ligandExp.ref] = `${s.pdb_id}_${s.struct_asym_id}`;
+                                invalidStruct = false;
+                            }
+                        }
+                        i++;
+                    }
+                }
+                if (invalidStruct) {
+                    spState.invalidStruct.push(`${s.pdb_id}_${s.struct_asym_id}`);
+                    const loadedStructIndex = spState.loadedStructs[segmentIndex].indexOf(`${s.pdb_id}_${s.struct_asym_id}`);
+                    if (loadedStructIndex > -1)
+                        spState.loadedStructs[segmentIndex].splice(loadedStructIndex, 1);
+                    // remove downloaded data
+                    if (clearOnFail) {
+                        // const m = plugin.state.data.select(modelRef)[0];
+                        // const t = plugin.state.data.select(m.transform.parent)[0];
+                        // const d = plugin.state.data.select(t.transform.parent)[0];
+                        // PluginCommands.State.RemoveObject(plugin, { state: d.parent!, ref: d.transform.parent, removeParentGhosts: true });
+                    }
+                }
+                else {
+                    // if(interactingHets.length > 0) spState.hets[`${s.pdb_id}_${s.struct_asym_id}`] = interactingHets;
+                }
+            }
+        }
+        if (busyFlagOn) {
+            busyFlagOn = false;
+            customState.events?.isBusy.next(false);
+        }
+    });
+}
+async function getLigandNamesFromModelData(plugin, state, modelRef) {
+    const cell = state.select(modelRef)[0];
+    if (!cell || !cell.obj)
+        return void 0;
+    const model = cell.obj.data;
+    if (!model)
+        return;
+    const structures = [];
+    for (const s of plugin.managers.structure.hierarchy.selection.structures) {
+        const structure = s.cell.obj?.data;
+        if (structure)
+            structures.push(structure);
+    }
+    const info = await ModelInfo.get(model, structures);
+    return info;
+}
+async function loadStructure(plugin, url, format, isBinary) {
+    try {
+        const data = await plugin.builders.data.download({
+            url: Asset.Url(url),
+            isBinary: isBinary,
+        });
+        const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
+        const model = await plugin.builders.structure.createModel(trajectory);
+        const modelProperties = await plugin.builders.structure.insertModelProperties(model);
+        const structure = await plugin.builders.structure.createStructure(modelProperties || model, { name: "model", params: {} });
+        await plugin.builders.structure.insertStructureProperties(structure);
+        return { data, trajectory, model, structure };
+    }
+    catch (e) {
+        return { structure: void 0 };
+    }
+}
+function chainSelection(struct_asym_id) {
+    return MS.struct.generator.atomGroups({
+        "chain-test": MS.core.rel.eq([
+            MS.struct.atomProperty.macromolecular.label_asym_id(),
+            struct_asym_id,
+        ]),
+    });
+}
+function transform(plugin, s, matrix) {
+    const b = plugin.state.data
+        .build()
+        .to(s)
+        .insert(StateTransforms.Model.TransformStructureConformation, {
+        transform: {
+            name: "matrix",
+            params: { data: matrix, transpose: false },
+        },
+    });
+    return plugin.runTask(plugin.state.data.updateTree(b));
+}
+async function afTransform(plugin, s, matrix, coordinateSystem) {
+    const r = StateObjectRef.resolveAndCheck(plugin.state.data, s);
+    if (!r)
+        return;
+    const o = plugin.state.data.selectQ((q) => q
+        .byRef(r.transform.ref)
+        .subtree()
+        .withTransformer(StateTransforms.Model.TransformStructureConformation))[0];
+    const transform = coordinateSystem && !Mat4.isIdentity(coordinateSystem.matrix)
+        ? Mat4.mul(Mat4(), coordinateSystem.matrix, matrix)
+        : matrix;
+    const params = {
+        transform: {
+            name: "matrix",
+            params: { data: transform, transpose: false },
+        },
+    };
+    const b = o
+        ? plugin.state.data.build().to(o).update(params)
+        : plugin.state.data
+            .build()
+            .to(s)
+            .insert(StateTransforms.Model.TransformStructureConformation, params, { tags: "SuperpositionTransform" });
+    await plugin.runTask(plugin.state.data.updateTree(b));
+}
+async function getMatrixData(plugin) {
+    const customState = PluginCustomState(plugin);
+    if (!customState.initParams)
+        throw new Error("customState.initParams has not been initialized");
+    if (!customState.superpositionState)
+        throw new Error("customState.superpositionState has not been initialized");
+    const matrixAccession = customState.initParams.superpositionParams?.matrixAccession ??
+        customState.initParams.moleculeId;
+    const clusterRecUrlStr = `${customState.initParams.pdbeUrl}static/superpose/matrices/${matrixAccession}`;
+    const assetManager = plugin.managers.asset;
+    const clusterRecUrl = Asset.getUrlAsset(assetManager, clusterRecUrlStr);
+    try {
+        const clusterRecData = await plugin.runTask(assetManager.resolve(clusterRecUrl, "json", false));
+        if (clusterRecData && clusterRecData.data) {
+            customState.superpositionState.matrixData = clusterRecData.data;
+        }
+    }
+    catch (e) {
+        customState.superpositionError = `Matrix data not available for ${matrixAccession}`;
+        customState.events?.superpositionInit.next(true); // Emit segment API data load event
+    }
+}
+async function getSegmentData(plugin) {
+    const customState = PluginCustomState(plugin);
+    if (!customState.initParams)
+        throw new Error("customState.initParams has not been initialized");
+    if (!customState.superpositionState)
+        throw new Error("customState.superpositionState has not been initialized");
+    // Get Data
+    const segmentsUrl = `${customState.initParams.pdbeUrl}graph-api/uniprot/superposition/${customState.initParams.moleculeId}`;
+    const assetManager = plugin.managers.asset;
+    const url = Asset.getUrlAsset(assetManager, segmentsUrl);
+    try {
+        const result = await plugin.runTask(assetManager.resolve(url, "json", false));
+        if (result?.data) {
+            customState.superpositionState.segmentData =
+                result.data[customState.initParams.moleculeId];
+        }
+    }
+    catch (e) {
+        customState.superpositionError = `Superposition data not available for ${customState.initParams.moleculeId}`;
+        customState.events?.superpositionInit.next(true); // Emit segment API data load event
+    }
+}
+function getChainLigands(carbEntity) {
+    const ligandChain = [];
+    const ligandLabels = [];
+    const ligands = [];
+    const labelValueArr = [];
+    let ligNameStr = "";
+    for (const chemComp of carbEntity.chem_comp_list) {
+        labelValueArr.push(`${chemComp.chem_comp_id} (${chemComp.count})`);
+    }
+    ligNameStr = labelValueArr.join(", ");
+    for (const chain of carbEntity.chains) {
+        ligandChain.push(chain.chain_id);
+        ligandLabels.push(ligNameStr);
+        const chainLigands = [];
+        for (const residue of chain.residues) {
+            chainLigands.push(residue.chem_comp_id + "-" + residue.residue_number);
+        }
+        ligands.push(chainLigands);
+    }
+    return {
+        ligands,
+        ligandChain,
+        ligandLabels,
+    };
+}
+async function getCarbPolymerDetailsFromApi(plugin, pdb_id) {
+    const customState = PluginCustomState(plugin);
+    if (!customState.initParams)
+        throw new Error("customState.initParams has not been initialized");
+    // Get Data
+    const apiUrl = `${customState.initParams.pdbeUrl}api/pdb/entry/carbohydrate_polymer/${pdb_id}`;
+    const assetManager = plugin.managers.asset;
+    const url = Asset.getUrlAsset(assetManager, apiUrl);
+    let branchedLigands = [];
+    let branchedChains = [];
+    let branchedlabels = [];
+    try {
+        const result = await plugin.runTask(assetManager.resolve(url, "json", false));
+        if (result && result.data) {
+            const carbEntities = result.data[pdb_id];
+            for (const carbEntity of carbEntities) {
+                const carbLigData = getChainLigands(carbEntity);
+                branchedLigands = branchedLigands.concat(carbLigData.ligands);
+                branchedChains = branchedChains.concat(carbLigData.ligandChain);
+                branchedlabels = branchedlabels.concat(carbLigData.ligandLabels);
+            }
+        }
+    }
+    catch (e) { }
+    return {
+        branchedChains,
+        branchedLigands,
+        branchedlabels,
+    };
+}
diff --git a/frontend/venome-molstar/lib/ui/alphafold-superposition.d.ts b/frontend/venome-molstar/lib/ui/alphafold-superposition.d.ts
new file mode 100644
index 00000000..b5e60111
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/alphafold-superposition.d.ts
@@ -0,0 +1,56 @@
+import { CollapsableControls, PurePluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
+import { PluginCustomState } from '../plugin-custom-state';
+export declare function InfoIconSvg(): import("react/jsx-runtime").JSX.Element;
+export declare class AlphafoldPaeControls extends CollapsableControls {
+    private axisBoxRef;
+    defaultState(): {
+        isCollapsed: boolean;
+        header: string;
+        brand: {
+            accent: "gray";
+            svg: typeof import("molstar/lib/mol-plugin-ui/controls/icons").FlipToFrontSvg;
+        };
+        isHidden: boolean;
+    };
+    constructor(props: any, context: any);
+    componentDidMount(): void;
+    formatTicks(d: any): any;
+    renderControls(): import("react/jsx-runtime").JSX.Element | null;
+}
+export declare class AlphafoldSuperpositionControls extends CollapsableControls {
+    defaultState(): {
+        isCollapsed: boolean;
+        header: string;
+        brand: {
+            accent: "gray";
+            svg: typeof import("molstar/lib/mol-plugin-ui/controls/icons").FlipToFrontSvg;
+        };
+        isHidden: boolean;
+    };
+    componentDidMount(): void;
+    rmsdTable(): import("react/jsx-runtime").JSX.Element;
+    renderControls(): import("react/jsx-runtime").JSX.Element;
+}
+export declare const AlphafoldSuperpositionParams: {
+    traceOnly: PD.BooleanParam;
+};
+export type AlphafoldSuperpositionOptions = PD.ValuesFor;
+type AfSuperpositionControlsState = {
+    isBusy: boolean;
+    action?: 'byChains' | 'byAtoms' | 'options';
+    canUseDb?: boolean;
+    options: AlphafoldSuperpositionOptions;
+};
+export declare class AfSuperpositionControls extends PurePluginUIComponent<{}, AfSuperpositionControlsState> {
+    state: AfSuperpositionControlsState;
+    componentDidMount(): void;
+    get selection(): import("molstar/lib/mol-plugin-state/manager/structure/selection").StructureSelectionManager;
+    get customState(): PluginCustomState;
+    superposeDb: () => Promise;
+    toggleOptions: () => void;
+    superposeByDbMapping(): import("react/jsx-runtime").JSX.Element;
+    private setOptions;
+    render(): import("react/jsx-runtime").JSX.Element;
+}
+export {};
diff --git a/frontend/venome-molstar/lib/ui/alphafold-superposition.js b/frontend/venome-molstar/lib/ui/alphafold-superposition.js
new file mode 100644
index 00000000..2a78b283
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/alphafold-superposition.js
@@ -0,0 +1,149 @@
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
+import React from 'react';
+import { CollapsableControls, PurePluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { TuneSvg, SuperposeChainsSvg, SuperpositionSvg, Icon } from 'molstar/lib/mol-plugin-ui/controls/icons';
+import { Button, ToggleButton } from 'molstar/lib/mol-plugin-ui/controls/common';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
+import { ParameterControls } from 'molstar/lib/mol-plugin-ui/controls/parameters';
+import { superposeAf } from '../superposition';
+import { scaleLinear as d3ScaleLinear } from 'd3-scale';
+import { axisBottom as d3AxisBotom, axisLeft as d3AxisLeft } from 'd3-axis';
+import { select as d3Select } from 'd3-selection';
+import { PluginCustomState } from '../plugin-custom-state';
+const _InfoIcon = _jsx("svg", { width: '24px', height: '24px', viewBox: '0 0 24 24', strokeWidth: '0.1px', children: _jsx("path", { fill: "currentColor", d: "M11,9H13V7H11M12,20C7.59,20 4,16.41 4,12C4,7.59 7.59,4 12,4C16.41,4 20,7.59 20,12C20,16.41 16.41,20 12,20M12,2A10,10 0 0,0 2,12A10,10 0 0,0 12,22A10,10 0 0,0 22,12A10,10 0 0,0 12,2M11,17H13V11H11V17Z" }) });
+export function InfoIconSvg() { return _InfoIcon; }
+export class AlphafoldPaeControls extends CollapsableControls {
+    axisBoxRef;
+    defaultState() {
+        return {
+            isCollapsed: false,
+            header: 'AlphaFold PAE',
+            brand: { accent: 'gray', svg: SuperpositionSvg },
+            isHidden: true
+        };
+    }
+    constructor(props, context) {
+        super(props, context);
+        this.axisBoxRef = React.createRef();
+    }
+    componentDidMount() {
+        this.subscribe(this.plugin.managers.structure.hierarchy.behaviors.selection, sel => {
+            const superpositionState = PluginCustomState(this.plugin).superpositionState;
+            if (superpositionState && superpositionState.alphafold.ref && superpositionState.alphafold.apiData.pae && superpositionState.alphafold.apiData.pae !== '' && superpositionState.alphafold.apiData.pae !== '') {
+                this.setState({ isHidden: false });
+                const domainMax = superpositionState.alphafold.apiData.length;
+                const x = d3ScaleLinear().domain([0, domainMax]).range([0, 200]);
+                const xAxis = d3AxisBotom(x).ticks(6).tickFormat(this.formatTicks).tickSizeOuter(0);
+                const yAxis = d3AxisLeft(x).ticks(6).tickFormat(this.formatTicks).tickSizeOuter(0);
+                const axisContainer = d3Select(this.axisBoxRef.current);
+                axisContainer.append('svg:svg')
+                    .attr('width', 220)
+                    .attr('height', 30)
+                    .attr('class', 'pae-x-axis')
+                    .style('z-index', '1')
+                    .style('position', 'absolute')
+                    .attr('transform', `translate(-93,202)`)
+                    .append('g')
+                    .attr('transform', `translate(6,0)`)
+                    .call(xAxis);
+                axisContainer.append('svg:svg')
+                    .attr('width', 50)
+                    .attr('height', 220)
+                    .attr('class', 'pae-y-axis')
+                    .style('z-index', '1')
+                    .style('position', 'absolute')
+                    .attr('transform', `translate(-123,0)`)
+                    .append('g')
+                    .attr('transform', `translate(36,4)`)
+                    .call(yAxis);
+            }
+        });
+    }
+    formatTicks(d) {
+        return d > 999 ? d / 1000 + 'k' : d;
+    }
+    renderControls() {
+        const superpositionState = PluginCustomState(this.plugin).superpositionState;
+        if (!superpositionState || !superpositionState.alphafold)
+            return null;
+        const errorScale = [0, 5, 10, 15, 20, 25, 30];
+        return _jsxs("div", { className: 'msp-flex-row', style: { height: 'auto', textAlign: 'center', justifyContent: 'center', padding: '15px 0', position: 'relative', fontSize: '12px' }, children: [_jsx("div", { ref: this.axisBoxRef, className: 'pae-axis-box', style: { position: 'absolute', width: '100%', height: '100%' } }), _jsx("span", { style: { transform: 'rotate(270deg)', position: 'absolute', transformOrigin: '0 0', left: '10px', top: '165px', fontWeight: 500 }, children: "Aligned residue" }), _jsxs("div", { className: 'msp-flex-row', style: { height: 'auto', flexDirection: 'column' }, children: [_jsx("div", { style: { width: '200px', height: '200px', border: '1px solid #6a635a', margin: '2px 0 25px 25px', position: 'relative' }, children: _jsx("img", { style: { width: '100%', height: '100%', position: 'absolute', left: 0, top: 0 }, src: `${superpositionState.alphafold.apiData.pae}`, alt: "PAE" }) }), _jsx("div", { style: { textAlign: 'center', paddingLeft: '30px', marginBottom: '20px', fontWeight: 500 }, children: "Scored residue" }), _jsx("img", { style: { width: '200px', height: '10px', border: '1px solid #6a635a', margin: '2px 0 25px 25px', transform: 'rotate(180deg)' }, src: 'https://alphafold.ebi.ac.uk/assets/img/horizontal_colorbar.png', alt: "PAE Scale" }), _jsx("ul", { style: { listStyleType: 'none', fontWeight: 500, margin: 0, display: 'inline-block', position: 'absolute', top: '292px', marginLeft: '24px' }, children: errorScale.map((errValue) => _jsx("li", { style: { float: 'left', marginRight: '18px' }, children: errValue }, errValue)) }), _jsx("div", { style: { textAlign: 'center', paddingLeft: '20px', fontWeight: 500 }, children: "Expected position error (\u00C5ngstr\u00F6ms)" })] })] });
+    }
+}
+export class AlphafoldSuperpositionControls extends CollapsableControls {
+    defaultState() {
+        return {
+            isCollapsed: false,
+            header: 'AlphaFold Superposition',
+            brand: { accent: 'gray', svg: SuperpositionSvg },
+            isHidden: true
+        };
+    }
+    componentDidMount() {
+        this.subscribe(this.plugin.managers.structure.hierarchy.behaviors.selection, sel => {
+            const superpositionState = PluginCustomState(this.plugin).superpositionState;
+            if (superpositionState && superpositionState.alphafold.apiData.cif && superpositionState.alphafold.apiData.cif !== '') {
+                this.setState({ isHidden: false });
+            }
+        });
+    }
+    rmsdTable() {
+        const spData = PluginCustomState(this.plugin).superpositionState;
+        if (!spData)
+            throw new Error('customState.superpositionState has not been initialized');
+        const { activeSegment } = spData;
+        const { rmsds } = spData.alphafold;
+        return _jsxs("div", { className: 'msp-control-offset', children: [(rmsds.length === 0 || !rmsds[activeSegment - 1]) && _jsx("div", { className: 'msp-flex-row', style: { padding: '5px 0 0 10px' }, children: _jsx("strong", { children: "No overlap found!" }) }), rmsds[activeSegment - 1] && _jsxs("div", { className: 'msp-flex-row', children: [_jsx("div", { style: { width: '40%', borderRight: '1px solid rgb(213 206 196)', padding: '5px 0 0 5px' }, children: _jsx("strong", { children: "Entry" }) }), _jsx("div", { style: { padding: '5px 0 0 5px' }, children: _jsx("strong", { children: "RMSD (\u212B)" }) })] }), rmsds[activeSegment - 1] && rmsds[activeSegment - 1].map((d) => {
+                    const details = d.split(':');
+                    return details[1] !== '-' ? _jsxs("div", { className: 'msp-flex-row', children: [_jsx("div", { className: 'msp-control-row-label', style: { width: '40%', borderRight: '1px solid rgb(213 206 196)', padding: '5px 0 0 5px' }, children: details[0] }), _jsx("div", { style: { padding: '5px 0 0 5px' }, children: details[1] })] }, d) : null;
+                })] });
+    }
+    renderControls() {
+        const superpositionState = PluginCustomState(this.plugin).superpositionState;
+        if (!superpositionState)
+            throw new Error('customState.superpositionState has not been initialized');
+        return _jsxs(_Fragment, { children: [superpositionState.alphafold.ref !== '' && this.rmsdTable(), superpositionState.alphafold.ref === '' && _jsx(AfSuperpositionControls, {})] });
+    }
+}
+export const AlphafoldSuperpositionParams = {
+    // alignSequences: PD.Boolean(true, { isEssential: true, description: 'For Chain-based 3D superposition, perform a sequence alignment and use the aligned residue pairs to guide the 3D superposition.' }),
+    traceOnly: PD.Boolean(true, { description: 'For Chain- and Uniprot-based 3D superposition, base superposition only on CA (and equivalent) atoms.' })
+};
+const DefaultAlphafoldSuperpositionOptions = PD.getDefaultValues(AlphafoldSuperpositionParams);
+export class AfSuperpositionControls extends PurePluginUIComponent {
+    state = {
+        isBusy: false,
+        canUseDb: true,
+        action: undefined,
+        options: DefaultAlphafoldSuperpositionOptions
+    };
+    componentDidMount() {
+        this.subscribe(this.plugin.behaviors.state.isBusy, v => {
+            this.setState({ isBusy: v });
+        });
+    }
+    get selection() {
+        return this.plugin.managers.structure.selection;
+    }
+    get customState() {
+        return PluginCustomState(this.plugin);
+    }
+    superposeDb = async () => {
+        this.setState({ isBusy: true });
+        const spData = this.customState.superpositionState;
+        if (!spData)
+            throw new Error('customState.superpositionState has not been initialized');
+        spData.alphafold.traceOnly = this.state.options.traceOnly;
+        superposeAf(this.plugin, this.state.options.traceOnly);
+    };
+    toggleOptions = () => this.setState({ action: this.state.action === 'options' ? void 0 : 'options' });
+    superposeByDbMapping() {
+        return _jsx(_Fragment, { children: _jsx(Button, { icon: SuperposeChainsSvg, title: 'Superpose AlphaFold structure using intersection of residues from SIFTS UNIPROT mapping.', className: 'msp-btn msp-btn-block', onClick: this.superposeDb, style: { marginTop: '1px', textAlign: 'left' }, disabled: this.state.isBusy, children: "Load AlphaFold structure" }) });
+    }
+    setOptions = (values) => {
+        this.setState({ options: values });
+    };
+    render() {
+        return _jsxs(_Fragment, { children: [_jsx("div", { style: { backgroundColor: '#dce54e', fontWeight: 500, padding: '5px 12px' }, children: "New Feature!" }), _jsx("div", { className: 'msp-help-text', style: { margin: '2px 0' }, children: _jsxs("div", { className: 'msp-help-description', children: [_jsx(Icon, { svg: InfoIconSvg, inline: true }), "Load and superpose AlphaFold structure against representative chains."] }) }), _jsxs("div", { className: 'msp-flex-row', children: [this.state.canUseDb && this.superposeByDbMapping(), _jsx(ToggleButton, { icon: TuneSvg, label: '', title: 'Options', toggle: this.toggleOptions, isSelected: this.state.action === 'options', disabled: this.state.isBusy, style: { flex: '0 0 40px', padding: 0 } })] }), this.state.action === 'options' && _jsx("div", { className: 'msp-control-offset', children: _jsx(ParameterControls, { params: AlphafoldSuperpositionParams, values: this.state.options, onChangeValues: this.setOptions, isDisabled: this.state.isBusy }) })] });
+    }
+}
diff --git a/frontend/venome-molstar/lib/ui/alphafold-tranparency.d.ts b/frontend/venome-molstar/lib/ui/alphafold-tranparency.d.ts
new file mode 100644
index 00000000..cb14b023
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/alphafold-tranparency.d.ts
@@ -0,0 +1,21 @@
+import { CollapsableControls } from 'molstar/lib/mol-plugin-ui/base';
+export declare class AlphafoldTransparencyControls extends CollapsableControls<{}, {
+    transpareny: any;
+}> {
+    defaultState(): {
+        isCollapsed: boolean;
+        header: string;
+        brand: {
+            accent: "gray";
+            svg: typeof import("molstar/lib/mol-plugin-ui/controls/icons").FlipToFrontSvg;
+        };
+        isHidden: boolean;
+        transpareny: {
+            score: number;
+            opacity: number;
+        };
+    };
+    componentDidMount(): void;
+    updateTransparency: (val: any) => Promise;
+    renderControls(): import("react/jsx-runtime").JSX.Element;
+}
diff --git a/frontend/venome-molstar/lib/ui/alphafold-tranparency.js b/frontend/venome-molstar/lib/ui/alphafold-tranparency.js
new file mode 100644
index 00000000..c39892d8
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/alphafold-tranparency.js
@@ -0,0 +1,45 @@
+import { jsx as _jsx, Fragment as _Fragment } from "react/jsx-runtime";
+import { CollapsableControls } from 'molstar/lib/mol-plugin-ui/base';
+import { SuperpositionSvg } from 'molstar/lib/mol-plugin-ui/controls/icons';
+import { ParameterControls } from 'molstar/lib/mol-plugin-ui/controls/parameters';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
+import { applyAFTransparency, clearStructureTransparency } from '../alphafold-transparency';
+import { PluginCustomState } from '../plugin-custom-state';
+const TransparencyParams = {
+    score: PD.Numeric(70, { min: 0, max: 100, step: 1 }, { label: 'pLDDT less than', description: 'pLDDT score value in the range of 0 to 100' }),
+    opacity: PD.Numeric(0.2, { min: 0, max: 1, step: 0.01 }, { description: 'Opacity value in the range 0 to 1' })
+};
+export class AlphafoldTransparencyControls extends CollapsableControls {
+    defaultState() {
+        return {
+            isCollapsed: false,
+            header: 'AlphaFold Structure Opacity',
+            brand: { accent: 'gray', svg: SuperpositionSvg },
+            isHidden: true,
+            transpareny: {
+                score: 70,
+                opacity: 0.2
+            }
+        };
+    }
+    componentDidMount() {
+        this.subscribe(this.plugin.managers.structure.hierarchy.behaviors.selection, sel => {
+            const superpositionState = PluginCustomState(this.plugin).superpositionState;
+            if (superpositionState && superpositionState.alphafold.ref && superpositionState.alphafold.ref !== '') {
+                this.setState({ isHidden: false });
+            }
+        });
+    }
+    updateTransparency = async (val) => {
+        this.setState({ transpareny: val });
+        const superpositionState = PluginCustomState(this.plugin).superpositionState;
+        if (!superpositionState)
+            throw new Error('customState.superpositionState has not been initialized');
+        const afStr = this.plugin.managers.structure.hierarchy.current.refs.get(superpositionState.alphafold.ref);
+        await clearStructureTransparency(this.plugin, afStr.components);
+        await applyAFTransparency(this.plugin, afStr, 1 - val.opacity, val.score);
+    };
+    renderControls() {
+        return _jsx(_Fragment, { children: _jsx(ParameterControls, { params: TransparencyParams, values: this.state.transpareny, onChangeValues: this.updateTransparency }) });
+    }
+}
diff --git a/frontend/venome-molstar/lib/ui/annotation-controls.d.ts b/frontend/venome-molstar/lib/ui/annotation-controls.d.ts
new file mode 100644
index 00000000..d27bc38f
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/annotation-controls.d.ts
@@ -0,0 +1,27 @@
+import { PurePluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+export declare function TextsmsOutlinedSvg(): import("react/jsx-runtime").JSX.Element;
+type AnnotationType = 'validation' | 'domains' | 'symmetry';
+interface AnnotationsComponentControlsState {
+    isCollapsed: boolean;
+    validationApplied: boolean;
+    validationOptions: boolean;
+    validationParams: any;
+    domainsApplied: boolean;
+    domainsOptions: boolean;
+    domainsParams: any;
+    showSymmetryAnnotation: boolean;
+    description?: string;
+}
+export declare class AnnotationsComponentControls extends PurePluginUIComponent<{}, AnnotationsComponentControlsState> {
+    state: AnnotationsComponentControlsState;
+    componentDidMount(): void;
+    initOptionParams: () => void;
+    getStructure: () => import("molstar/lib/mol-state/object").StateObject> | undefined;
+    toggleCollapsed: () => void;
+    applyAnnotation: (type: 'validation' | 'domains', visibleState: boolean, params?: any) => void;
+    toggleAnnotation: (type: AnnotationType) => void;
+    updateValidationParams: (val: any) => void;
+    updateDomainParams: (val: any) => void;
+    render(): import("react/jsx-runtime").JSX.Element;
+}
+export {};
diff --git a/frontend/venome-molstar/lib/ui/annotation-controls.js b/frontend/venome-molstar/lib/ui/annotation-controls.js
new file mode 100644
index 00000000..bd1dfe83
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/annotation-controls.js
@@ -0,0 +1,151 @@
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
+import { PDBeStructureQualityReport } from 'molstar/lib/extensions/pdbe/structure-quality-report/behavior';
+import { StructureQualityReportColorThemeProvider } from 'molstar/lib/extensions/pdbe/structure-quality-report/color';
+import { StructureHierarchyManager } from 'molstar/lib/mol-plugin-state/manager/structure/hierarchy';
+import { PurePluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { Button } from 'molstar/lib/mol-plugin-ui/controls/common';
+import { ArrowDropDownSvg, ArrowRightSvg, Icon } from 'molstar/lib/mol-plugin-ui/controls/icons';
+import { StateSelection, StateTransform } from 'molstar/lib/mol-state';
+import { PDBeDomainAnnotations } from '../domain-annotations/behavior';
+import { DomainAnnotationsColorThemeProvider } from '../domain-annotations/color';
+import { PluginCustomState } from '../plugin-custom-state';
+import { AnnotationRowControls } from './annotation-row-controls';
+import { SymmetryAnnotationControls, isAssemblySymmetryAnnotationApplicable } from './symmetry-annotation-controls';
+const _TextsmsOutlined = _jsxs("svg", { width: '24px', height: '24px', viewBox: '0 0 24 24', children: [_jsx("path", { fill: "none", d: "M0 0h24v24H0V0z" }), _jsxs("g", { children: [_jsx("path", { d: "M20 2H4c-1.1 0-2 .9-2 2v18l4-4h14c1.1 0 2-.9 2-2V4c0-1.1-.9-2-2-2zm0 14H6l-2 2V4h16v12z" }), _jsx("path", { d: "M7 9h2v2H7zM11 9h2v2h-2zM15 9h2v2h-2z" })] })] });
+export function TextsmsOutlinedSvg() { return _TextsmsOutlined; }
+export class AnnotationsComponentControls extends PurePluginUIComponent {
+    state = {
+        isCollapsed: false,
+        validationApplied: false,
+        validationOptions: false,
+        validationParams: undefined,
+        domainsApplied: false,
+        domainsOptions: false,
+        domainsParams: undefined,
+        showSymmetryAnnotation: false,
+    };
+    componentDidMount() {
+        this.subscribe(this.plugin.managers.structure.hierarchy.behaviors.selection, () => {
+            this.initOptionParams();
+            this.forceUpdate();
+        });
+        this.subscribe(this.plugin.managers.structure.hierarchy.behaviors.selection, c => this.setState({
+            description: StructureHierarchyManager.getSelectedStructuresDescription(this.plugin)
+        }));
+    }
+    initOptionParams = () => {
+        const initParams = PluginCustomState(this.plugin).initParams;
+        const validationAnnotationCtrl = !!initParams?.validationAnnotation;
+        const domainAnnotationCtrl = !!initParams?.domainAnnotation;
+        const symmetryAnnotationCtrl = !!initParams?.symmetryAnnotation && isAssemblySymmetryAnnotationApplicable(this.plugin);
+        this.setState({ showSymmetryAnnotation: symmetryAnnotationCtrl });
+        if ((validationAnnotationCtrl && !this.state.validationParams) || (domainAnnotationCtrl && !this.state.domainsParams)) {
+            const structure = this.getStructure()?.data;
+            if (structure) {
+                const themeDataCtx = { structure };
+                if (validationAnnotationCtrl && !this.state.validationParams) {
+                    const validationActionsParams = StructureQualityReportColorThemeProvider.getParams(themeDataCtx);
+                    if (validationActionsParams) {
+                        this.setState({
+                            validationParams: {
+                                params: validationActionsParams,
+                                values: { type: validationActionsParams.type.defaultValue }
+                            }
+                        });
+                    }
+                }
+                if (domainAnnotationCtrl && !this.state.domainsParams) {
+                    const domainActionsParams = DomainAnnotationsColorThemeProvider.getParams(themeDataCtx);
+                    if (domainActionsParams) {
+                        this.setState({
+                            domainsParams: {
+                                params: domainActionsParams,
+                                values: { type: domainActionsParams.type.defaultValue }
+                            }
+                        });
+                    }
+                }
+            }
+        }
+    };
+    getStructure = () => {
+        const groupRef = StateSelection.findTagInSubtree(this.plugin.state.data.tree, StateTransform.RootRef, 'structure-component-static-polymer');
+        return groupRef ? this.plugin.state.data.select(groupRef)[0]?.obj : undefined;
+    };
+    toggleCollapsed = () => {
+        this.setState({ isCollapsed: !this.state.isCollapsed });
+    };
+    applyAnnotation = (type, visibleState, params) => {
+        // Defaults
+        let themeName = 'chain-id';
+        let themePropsToAdd = PDBeStructureQualityReport;
+        let themePropsToRemove = this.state.domainsParams ? PDBeDomainAnnotations : void 0;
+        // Set Theme Params
+        if (type === 'validation') {
+            if (visibleState) {
+                themeName = 'pdbe-structure-quality-report';
+            }
+            this.setState({ validationApplied: visibleState });
+            this.setState({ domainsApplied: false });
+        }
+        else if (type === 'domains') {
+            themePropsToAdd = PDBeDomainAnnotations;
+            themePropsToRemove = this.state.validationParams ? PDBeStructureQualityReport : void 0;
+            if (visibleState)
+                themeName = 'pdbe-domain-annotations';
+            this.setState({ domainsApplied: visibleState });
+            this.setState({ validationApplied: false });
+        }
+        // Update Tooltip
+        if (visibleState && themeName !== 'chain-id') {
+            const addTooltipUpdate = this.plugin.state.behaviors.build().to(themePropsToAdd.id).update(themePropsToAdd, (old) => { old.showTooltip = true; });
+            this.plugin.runTask(this.plugin.state.behaviors.updateTree(addTooltipUpdate));
+            if (themePropsToRemove) {
+                const removeTooltipUpdate = this.plugin.state.behaviors.build().to(themePropsToRemove.id).update(themePropsToRemove, (old) => { old.showTooltip = false; });
+                this.plugin.runTask(this.plugin.state.behaviors.updateTree(removeTooltipUpdate));
+            }
+        }
+        let polymerGroup;
+        const componentGroups = this.plugin.managers.structure.hierarchy.currentComponentGroups;
+        componentGroups.forEach((compGrp) => {
+            if (compGrp[0].key === 'structure-component-static-polymer')
+                polymerGroup = compGrp;
+        });
+        if (polymerGroup) {
+            this.plugin.managers.structure.component.updateRepresentationsTheme(polymerGroup, { color: themeName, colorParams: params ? params : void 0 });
+        }
+    };
+    toggleAnnotation = (type) => {
+        if (type === 'validation')
+            this.applyAnnotation('validation', !this.state.validationApplied, this.state.validationParams.values);
+        if (type === 'domains')
+            this.applyAnnotation('domains', !this.state.domainsApplied, this.state.domainsParams.values);
+    };
+    updateValidationParams = (val) => {
+        const updatedParams = { ...this.state.validationParams };
+        updatedParams.values = val;
+        this.setState({ validationParams: updatedParams });
+        if (this.state.validationApplied)
+            this.applyAnnotation('validation', this.state.validationApplied, val);
+    };
+    updateDomainParams = (val) => {
+        const updatedParams = { ...this.state.domainsParams };
+        updatedParams.values = val;
+        this.setState({ domainsParams: updatedParams });
+        if (this.state.domainsApplied)
+            this.applyAnnotation('domains', this.state.domainsApplied, val);
+    };
+    render() {
+        if (!this.state.validationParams && !this.state.domainsParams && !this.state.showSymmetryAnnotation)
+            return _jsx(_Fragment, {});
+        const brand = {
+            accent: 'green',
+            svg: TextsmsOutlinedSvg
+        };
+        const wrapClass = this.state.isCollapsed
+            ? 'msp-transform-wrapper msp-transform-wrapper-collapsed'
+            : 'msp-transform-wrapper';
+        return _jsxs("div", { className: wrapClass, children: [_jsx("div", { className: 'msp-transform-header', children: _jsxs(Button, { icon: brand ? void 0 : this.state.isCollapsed ? ArrowRightSvg : ArrowDropDownSvg, noOverflow: true, onClick: this.toggleCollapsed, className: brand ? `msp-transform-header-brand msp-transform-header-brand-${brand.accent}` : void 0, title: `Click to ${this.state.isCollapsed ? 'expand' : 'collapse'}`, children: [_jsx(Icon, { svg: brand?.svg, inline: true }), "Annotations", _jsx("small", { style: { margin: '0 6px' }, children: this.state.isCollapsed ? '' : this.state.description })] }) }), !this.state.isCollapsed && _jsxs(_Fragment, { children: [_jsx(AnnotationRowControls, { title: 'Validation', params: this.state.validationParams?.params, values: this.state.validationParams?.values, onChangeValues: this.updateValidationParams, applied: this.state.validationApplied, onChangeApplied: () => this.toggleAnnotation('validation') }), _jsx(AnnotationRowControls, { title: 'Domain Annotations', shortTitle: 'Domains', params: this.state.domainsParams?.params, values: this.state.domainsParams?.values, onChangeValues: this.updateDomainParams, applied: this.state.domainsApplied, onChangeApplied: () => this.toggleAnnotation('domains') }), this.state.showSymmetryAnnotation &&
+                            _jsx(SymmetryAnnotationControls, {})] })] });
+    }
+}
diff --git a/frontend/venome-molstar/lib/ui/annotation-row-controls.d.ts b/frontend/venome-molstar/lib/ui/annotation-row-controls.d.ts
new file mode 100644
index 00000000..5ee97afc
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/annotation-row-controls.d.ts
@@ -0,0 +1,26 @@
+import { ParameterControlsProps } from 'molstar/lib/mol-plugin-ui/controls/parameters';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
+import React from 'react';
+type AnnotationRowControlsProps
 = ParameterControlsProps
 & {
+    shortTitle?: string;
+    title: string;
+    applied?: boolean;
+    onChangeApplied?: (applied: boolean) => void;
+};
+type AnnotationRowControlsState = {
+    applied: boolean;
+    optionsExpanded: boolean;
+};
+/** UI controls for a single annotation source (row) in Annotations section */
+export declare class AnnotationRowControls
 extends React.PureComponent, AnnotationRowControlsState> {
+    state: {
+        applied: boolean;
+        optionsExpanded: boolean;
+    };
+    isApplied(): boolean;
+    toggleApplied(applied?: boolean): void;
+    toggleOptions(): void;
+    render(): import("react/jsx-runtime").JSX.Element | null;
+    renderOptions(): import("react/jsx-runtime").JSX.Element;
+}
+export {};
diff --git a/frontend/venome-molstar/lib/ui/annotation-row-controls.js b/frontend/venome-molstar/lib/ui/annotation-row-controls.js
new file mode 100644
index 00000000..536c54d2
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/annotation-row-controls.js
@@ -0,0 +1,36 @@
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
+import { Button, IconButton } from 'molstar/lib/mol-plugin-ui/controls/common';
+import { MoreHorizSvg, VisibilityOffOutlinedSvg, VisibilityOutlinedSvg } from 'molstar/lib/mol-plugin-ui/controls/icons';
+import { ParameterControls } from 'molstar/lib/mol-plugin-ui/controls/parameters';
+import React from 'react';
+/** UI controls for a single annotation source (row) in Annotations section */
+export class AnnotationRowControls extends React.PureComponent {
+    state = { applied: false, optionsExpanded: false };
+    // componentDidMount() {
+    //     this.subscribe(this.plugin.state.events.cell.stateUpdated, e => {
+    //         if (State.ObjectEvent.isCell(e, this.pivot.cell)) this.forceUpdate();
+    //     });
+    // }
+    isApplied() {
+        return this.props.applied ?? this.state.applied;
+    }
+    toggleApplied(applied) {
+        const newState = applied ?? !this.isApplied();
+        if (this.props.applied === undefined) {
+            this.setState({ applied: newState });
+        }
+        this.props.onChangeApplied?.(newState);
+    }
+    toggleOptions() {
+        this.setState(s => ({ optionsExpanded: !s.optionsExpanded }));
+    }
+    render() {
+        if (!this.props.params)
+            return null;
+        return _jsxs(_Fragment, { children: [_jsxs("div", { className: 'msp-flex-row', children: [_jsx(Button, { noOverflow: true, className: 'msp-control-button-label', title: this.props.title, style: { textAlign: 'left' }, children: this.props.shortTitle ?? this.props.title }), _jsx(IconButton, { onClick: () => this.toggleApplied(), toggleState: false, svg: !this.isApplied() ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, title: `Click to ${this.isApplied() ? 'hide' : 'show'} ${this.props.title}`, small: true, className: 'msp-form-control', flex: true }), _jsx(IconButton, { onClick: () => this.toggleOptions(), svg: MoreHorizSvg, title: 'Options', toggleState: this.state.optionsExpanded, className: 'msp-form-control', flex: true })] }), this.state.optionsExpanded &&
+                    _jsx("div", { style: { marginBottom: '6px' }, children: _jsx("div", { className: "msp-accent-offset", children: _jsx("div", { className: 'msp-representation-entry', children: this.renderOptions() }) }) })] });
+    }
+    renderOptions() {
+        return _jsx(ParameterControls, { params: this.props.params, onChange: this.props.onChange, values: this.props.values, onChangeValues: this.props.onChangeValues, onEnter: this.props.onEnter });
+    }
+}
diff --git a/frontend/venome-molstar/lib/ui/export-superposition.d.ts b/frontend/venome-molstar/lib/ui/export-superposition.d.ts
new file mode 100644
index 00000000..309fb5e9
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/export-superposition.d.ts
@@ -0,0 +1,6 @@
+/// 
+import { CollapsableControls, CollapsableState } from 'molstar/lib/mol-plugin-ui/base';
+export declare class SuperpositionModelExportUI extends CollapsableControls<{}, {}> {
+    protected defaultState(): CollapsableState;
+    protected renderControls(): JSX.Element | null;
+}
diff --git a/frontend/venome-molstar/lib/ui/export-superposition.js b/frontend/venome-molstar/lib/ui/export-superposition.js
new file mode 100644
index 00000000..bc3e1cf4
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/export-superposition.js
@@ -0,0 +1,49 @@
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
+import { CollapsableControls } from 'molstar/lib/mol-plugin-ui/base';
+import { Button } from 'molstar/lib/mol-plugin-ui/controls/common';
+import { GetAppSvg } from 'molstar/lib/mol-plugin-ui/controls/icons';
+import { ParameterControls } from 'molstar/lib/mol-plugin-ui/controls/parameters';
+import { useBehavior } from 'molstar/lib/mol-plugin-ui/hooks/use-behavior';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
+import { superpositionExportHierarchy } from '../superposition-export';
+export class SuperpositionModelExportUI extends CollapsableControls {
+    defaultState() {
+        return {
+            header: 'Export Models',
+            isCollapsed: true,
+            brand: { accent: 'cyan', svg: GetAppSvg }
+        };
+    }
+    renderControls() {
+        return _jsx(SuperpositionExportControls, { plugin: this.plugin });
+    }
+}
+const Params = {
+    format: PD.Select('cif', [['cif', 'mmCIF'], ['bcif', 'Binary mmCIF']])
+};
+const DefaultParams = PD.getDefaultValues(Params);
+function SuperpositionExportControls({ plugin }) {
+    const [params, setParams] = useState(DefaultParams);
+    const [exporting, setExporting] = useState(false);
+    useBehavior(plugin.managers.structure.hierarchy.behaviors.selection); // triggers UI update
+    const isBusy = useBehavior(plugin.behaviors.state.isBusy);
+    const hierarchy = plugin.managers.structure.hierarchy.current;
+    let label = 'Nothing to Export';
+    if (hierarchy.structures.length === 1) {
+        label = 'Export';
+    }
+    if (hierarchy.structures.length > 1) {
+        label = 'Export (as ZIP)';
+    }
+    const onExport = async () => {
+        setExporting(true);
+        try {
+            await superpositionExportHierarchy(plugin, { format: params.format });
+        }
+        finally {
+            setExporting(false);
+        }
+    };
+    return _jsxs(_Fragment, { children: [_jsx(ParameterControls, { params: Params, values: params, onChangeValues: setParams, isDisabled: isBusy || exporting }), _jsx(Button, { onClick: onExport, style: { marginTop: 1 }, disabled: isBusy || hierarchy.structures.length === 0 || exporting, commit: hierarchy.structures.length > 0 ? 'on' : 'off', children: label })] });
+}
diff --git a/frontend/venome-molstar/lib/ui/pdbe-left-panel.d.ts b/frontend/venome-molstar/lib/ui/pdbe-left-panel.d.ts
new file mode 100644
index 00000000..c44cc3bf
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/pdbe-left-panel.d.ts
@@ -0,0 +1,18 @@
+/// 
+import { PluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+export declare function WavesIconSvg(): import("react/jsx-runtime").JSX.Element;
+type LeftPanelTabName = 'none' | 'root' | 'data' | 'states' | 'settings' | 'help' | 'segments';
+export declare class LeftPanelControls extends PluginUIComponent<{}, {
+    tab: LeftPanelTabName;
+}> {
+    state: {
+        tab: LeftPanelTabName;
+    };
+    componentDidMount(): void;
+    set: (tab: LeftPanelTabName) => void;
+    tabs: {
+        [K in LeftPanelTabName]: JSX.Element;
+    };
+    render(): import("react/jsx-runtime").JSX.Element;
+}
+export {};
diff --git a/frontend/venome-molstar/lib/ui/pdbe-left-panel.js b/frontend/venome-molstar/lib/ui/pdbe-left-panel.js
new file mode 100644
index 00000000..c1c55b74
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/pdbe-left-panel.js
@@ -0,0 +1,129 @@
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
+import { Canvas3DParams } from 'molstar/lib/mol-canvas3d/canvas3d';
+import { PluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { IconButton, SectionHeader } from 'molstar/lib/mol-plugin-ui/controls/common';
+import { AccountTreeOutlinedSvg, DeleteOutlinedSvg, HelpOutlineSvg, HomeOutlinedSvg, TuneSvg } from 'molstar/lib/mol-plugin-ui/controls/icons';
+import { ParameterControls } from 'molstar/lib/mol-plugin-ui/controls/parameters';
+import { StateObjectActions } from 'molstar/lib/mol-plugin-ui/state/actions';
+import { RemoteStateSnapshots, StateSnapshots } from 'molstar/lib/mol-plugin-ui/state/snapshots';
+import { StateTree } from 'molstar/lib/mol-plugin-ui/state/tree';
+import { HelpContent, HelpGroup, HelpText } from 'molstar/lib/mol-plugin-ui/viewport/help';
+import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
+import { StateTransform } from 'molstar/lib/mol-state';
+import { PluginCustomState } from '../plugin-custom-state';
+import { SegmentTree } from './segment-tree';
+const _WavesIcon = _jsx("svg", { width: '24px', height: '24px', viewBox: '0 0 24 24', children: _jsx("path", { d: "M17 16.99c-1.35 0-2.2.42-2.95.8-.65.33-1.18.6-2.05.6-.9 0-1.4-.25-2.05-.6-.75-.38-1.57-.8-2.95-.8s-2.2.42-2.95.8c-.65.33-1.17.6-2.05.6v1.95c1.35 0 2.2-.42 2.95-.8.65-.33 1.17-.6 2.05-.6s1.4.25 2.05.6c.75.38 1.57.8 2.95.8s2.2-.42 2.95-.8c.65-.33 1.18-.6 2.05-.6.9 0 1.4.25 2.05.6.75.38 1.58.8 2.95.8v-1.95c-.9 0-1.4-.25-2.05-.6-.75-.38-1.6-.8-2.95-.8zm0-4.45c-1.35 0-2.2.43-2.95.8-.65.32-1.18.6-2.05.6-.9 0-1.4-.25-2.05-.6-.75-.38-1.57-.8-2.95-.8s-2.2.43-2.95.8c-.65.32-1.17.6-2.05.6v1.95c1.35 0 2.2-.43 2.95-.8.65-.35 1.15-.6 2.05-.6s1.4.25 2.05.6c.75.38 1.57.8 2.95.8s2.2-.43 2.95-.8c.65-.35 1.15-.6 2.05-.6s1.4.25 2.05.6c.75.38 1.58.8 2.95.8v-1.95c-.9 0-1.4-.25-2.05-.6-.75-.38-1.6-.8-2.95-.8zm2.95-8.08c-.75-.38-1.58-.8-2.95-.8s-2.2.42-2.95.8c-.65.32-1.18.6-2.05.6-.9 0-1.4-.25-2.05-.6-.75-.37-1.57-.8-2.95-.8s-2.2.42-2.95.8c-.65.33-1.17.6-2.05.6v1.93c1.35 0 2.2-.43 2.95-.8.65-.33 1.17-.6 2.05-.6s1.4.25 2.05.6c.75.38 1.57.8 2.95.8s2.2-.43 2.95-.8c.65-.32 1.18-.6 2.05-.6.9 0 1.4.25 2.05.6.75.38 1.58.8 2.95.8V5.04c-.9 0-1.4-.25-2.05-.58zM17 8.09c-1.35 0-2.2.43-2.95.8-.65.35-1.15.6-2.05.6s-1.4-.25-2.05-.6c-.75-.38-1.57-.8-2.95-.8s-2.2.43-2.95.8c-.65.35-1.15.6-2.05.6v1.95c1.35 0 2.2-.43 2.95-.8.65-.32 1.18-.6 2.05-.6s1.4.25 2.05.6c.75.38 1.57.8 2.95.8s2.2-.43 2.95-.8c.65-.32 1.18-.6 2.05-.6.9 0 1.4.25 2.05.6.75.38 1.58.8 2.95.8V9.49c-.9 0-1.4-.25-2.05-.6-.75-.38-1.6-.8-2.95-.8z" }) });
+export function WavesIconSvg() { return _WavesIcon; }
+export class LeftPanelControls extends PluginUIComponent {
+    state = { tab: this.plugin.behaviors.layout.leftPanelTabName.value };
+    componentDidMount() {
+        this.subscribe(this.plugin.behaviors.layout.leftPanelTabName, tab => {
+            if (this.state.tab !== tab)
+                this.setState({ tab });
+            if (tab === 'none' && this.plugin.layout.state.regionState.left !== 'collapsed') {
+                PluginCommands.Layout.Update(this.plugin, { state: { regionState: { ...this.plugin.layout.state.regionState, left: 'collapsed' } } });
+            }
+        });
+        this.subscribe(this.plugin.state.data.events.changed, ({ state }) => {
+            if (this.state.tab !== 'data')
+                return;
+            if (state.cells.size === 1)
+                this.set('root');
+        });
+    }
+    set = (tab) => {
+        if (this.state.tab === tab) {
+            this.setState({ tab: 'none' }, () => this.plugin.behaviors.layout.leftPanelTabName.next('none'));
+            PluginCommands.Layout.Update(this.plugin, { state: { regionState: { ...this.plugin.layout.state.regionState, left: 'collapsed' } } });
+            return;
+        }
+        this.setState({ tab }, () => this.plugin.behaviors.layout.leftPanelTabName.next(tab));
+        if (this.plugin.layout.state.regionState.left !== 'full') {
+            PluginCommands.Layout.Update(this.plugin, { state: { regionState: { ...this.plugin.layout.state.regionState, left: 'full' } } });
+        }
+    };
+    tabs = {
+        'none': _jsx(_Fragment, {}),
+        'root': _jsxs(_Fragment, { children: [_jsx(SectionHeader, { icon: HomeOutlinedSvg, title: 'Home' }), _jsx(StateObjectActions, { state: this.plugin.state.data, nodeRef: StateTransform.RootRef, hideHeader: true, initiallyCollapsed: true, alwaysExpandFirst: true }), this.plugin.spec.components?.remoteState !== 'none' && _jsx(RemoteStateSnapshots, { listOnly: true })] }),
+        'data': _jsxs(_Fragment, { children: [_jsx(SectionHeader, { icon: AccountTreeOutlinedSvg, title: _jsxs(_Fragment, { children: [_jsx(RemoveAllButton, {}), " State Tree"] }) }), _jsx(StateTree, { state: this.plugin.state.data })] }),
+        'segments': _jsx(_Fragment, { children: _jsx(SegmentTree, {}) }),
+        'states': _jsx(StateSnapshots, {}),
+        'settings': _jsxs(_Fragment, { children: [_jsx(SectionHeader, { icon: TuneSvg, title: 'Plugin Settings' }), _jsx(FullSettings, {})] }),
+        'help': _jsxs(_Fragment, { children: [_jsx(SectionHeader, { icon: HelpOutlineSvg, title: 'Help' }), _jsx(HelpContent, {}), _jsx(SuperpositionHelpContent, {})] })
+    };
+    render() {
+        const tab = this.state.tab;
+        const customState = PluginCustomState(this.plugin);
+        return _jsxs("div", { className: 'msp-left-panel-controls', children: [_jsxs("div", { className: 'msp-left-panel-controls-buttons', children: [_jsx(IconButton, { svg: HelpOutlineSvg, toggleState: tab === 'help', transparent: true, onClick: () => this.set('help'), title: 'Help' }), customState && customState.initParams && customState.initParams.superposition && _jsx(IconButton, { svg: WavesIconSvg, toggleState: tab === 'segments', transparent: true, onClick: () => this.set('segments'), title: 'Superpose segments' }), _jsx("div", { className: 'msp-left-panel-controls-buttons-bottom', children: _jsx(IconButton, { svg: TuneSvg, toggleState: tab === 'settings', transparent: true, onClick: () => this.set('settings'), title: 'Settings' }) })] }), _jsx("div", { className: 'msp-scrollable-container', children: this.tabs[tab] })] });
+    }
+}
+// class DataIcon extends PluginUIComponent<{ set: (tab: LeftPanelTabName) => void }, { changed: boolean }> {
+//     state = { changed: false };
+//     get tab() {
+//         return this.plugin.behaviors.layout.leftPanelTabName.value;
+//     }
+//     componentDidMount() {
+//         this.subscribe(this.plugin.behaviors.layout.leftPanelTabName, tab => {
+//             if (this.tab === 'data') this.setState({ changed: false });
+//             else this.forceUpdate();
+//         });
+//         this.subscribe(this.plugin.state.data.events.changed, state => {
+//             if (this.tab !== 'data') this.setState({ changed: true });
+//         });
+//     }
+//     render() {
+//         return  this.props.set('data')} title='State Tree'
+//             style={{ position: 'relative' }} extraContent={this.state.changed ? 
 : void 0} />;
+//     }
+// }
+class FullSettings extends PluginUIComponent {
+    setSettings = (p) => {
+        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { [p.name]: p.value } });
+    };
+    componentDidMount() {
+        this.subscribe(this.plugin.events.canvas3d.settingsUpdated, () => this.forceUpdate());
+        this.subscribe(this.plugin.layout.events.updated, () => this.forceUpdate());
+        this.subscribe(this.plugin.canvas3d.camera.stateChanged, state => {
+            if (state.radiusMax !== undefined || state.radius !== undefined) {
+                this.forceUpdate();
+            }
+        });
+    }
+    render() {
+        return _jsx(_Fragment, { children: this.plugin.canvas3d && _jsxs(_Fragment, { children: [_jsx(SectionHeader, { title: 'Viewport' }), _jsx(ParameterControls, { params: Canvas3DParams, values: this.plugin.canvas3d.props, onChange: this.setSettings })] }) });
+    }
+}
+class RemoveAllButton extends PluginUIComponent {
+    componentDidMount() {
+        this.subscribe(this.plugin.state.events.cell.created, e => {
+            if (e.cell.transform.parent === StateTransform.RootRef)
+                this.forceUpdate();
+        });
+        this.subscribe(this.plugin.state.events.cell.removed, e => {
+            if (e.parent === StateTransform.RootRef)
+                this.forceUpdate();
+        });
+    }
+    remove = (e) => {
+        e.preventDefault();
+        PluginCommands.State.RemoveObject(this.plugin, { state: this.plugin.state.data, ref: StateTransform.RootRef });
+    };
+    render() {
+        const count = this.plugin.state.data.tree.children.get(StateTransform.RootRef).size;
+        if (count === 0)
+            return null;
+        return _jsx(IconButton, { svg: DeleteOutlinedSvg, onClick: this.remove, title: 'Remove All', style: { display: 'inline-block' }, small: true, className: 'msp-no-hover-outline', transparent: true });
+    }
+}
+function HelpSection(props) {
+    return _jsx("div", { className: 'msp-simple-help-section', children: props.header });
+}
+class SuperpositionHelpContent extends PluginUIComponent {
+    componentDidMount() {
+        this.subscribe(this.plugin.events.canvas3d.settingsUpdated, () => this.forceUpdate());
+    }
+    render() {
+        return _jsxs("div", { children: [_jsx(HelpSection, { header: 'Superposition' }), _jsx(HelpGroup, { header: 'Segment', children: _jsx(HelpText, { children: _jsx("p", { children: "Discrete UniProt sequence range mapped to the structure" }) }) }), _jsx(HelpGroup, { header: 'Cluster', children: _jsx(HelpText, { children: _jsx("p", { children: "Structural chains that possess significantly close superposition Q-score" }) }) }), _jsx(HelpGroup, { header: 'Representative chain', children: _jsx(HelpText, { children: _jsx("p", { children: "The best-ranked chain within a cluster chosen based on the model quality, resolution, observed residues ratio and UniProt sequence coverage" }) }) })] });
+    }
+}
diff --git a/frontend/venome-molstar/lib/ui/pdbe-screenshot-controls.d.ts b/frontend/venome-molstar/lib/ui/pdbe-screenshot-controls.d.ts
new file mode 100644
index 00000000..fb83b23b
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/pdbe-screenshot-controls.d.ts
@@ -0,0 +1,20 @@
+import * as React from 'react';
+import { PluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+interface ImageControlsState {
+    showPreview: boolean;
+    isDisabled: boolean;
+    imageData?: string;
+}
+export declare class DownloadScreenshotControls extends PluginUIComponent<{
+    close: () => void;
+}, ImageControlsState> {
+    state: ImageControlsState;
+    private download;
+    private copy;
+    private copyImg;
+    componentDidMount(): void;
+    componentWillUnmount(): void;
+    open: (e: React.ChangeEvent) => void;
+    render(): import("react/jsx-runtime").JSX.Element;
+}
+export {};
diff --git a/frontend/venome-molstar/lib/ui/pdbe-screenshot-controls.js b/frontend/venome-molstar/lib/ui/pdbe-screenshot-controls.js
new file mode 100644
index 00000000..1a67fc5c
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/pdbe-screenshot-controls.js
@@ -0,0 +1,65 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { ParameterControls } from 'molstar/lib/mol-plugin-ui/controls/parameters';
+import { PluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { ScreenshotPreview } from 'molstar/lib/mol-plugin-ui/controls/screenshot';
+import { Button, ToggleButton } from 'molstar/lib/mol-plugin-ui/controls/common';
+import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
+import { useBehavior } from 'molstar/lib/mol-plugin-ui/hooks/use-behavior';
+import { GetAppSvg, CopySvg, CropOrginalSvg, CropSvg, CropFreeSvg } from 'molstar/lib/mol-plugin-ui/controls/icons';
+export class DownloadScreenshotControls extends PluginUIComponent {
+    state = {
+        showPreview: true,
+        isDisabled: false
+    };
+    download = () => {
+        this.plugin.helpers.viewportScreenshot?.download();
+        this.props.close();
+    };
+    copy = async () => {
+        try {
+            await this.plugin.helpers.viewportScreenshot?.copyToClipboard();
+            PluginCommands.Toast.Show(this.plugin, {
+                message: 'Copied to clipboard.',
+                title: 'Screenshot',
+                timeoutMs: 1500
+            });
+        }
+        catch {
+            return this.copyImg();
+        }
+    };
+    copyImg = async () => {
+        const src = await this.plugin.helpers.viewportScreenshot?.getImageDataUri();
+        this.setState({ imageData: src });
+    };
+    componentDidMount() {
+        this.subscribe(this.plugin.state.data.behaviors.isUpdating, v => {
+            this.setState({ isDisabled: v });
+        });
+    }
+    componentWillUnmount() {
+        this.setState({ imageData: void 0 });
+    }
+    open = (e) => {
+        if (!e.target.files || !e.target.files[0])
+            return;
+        PluginCommands.State.Snapshots.OpenFile(this.plugin, { file: e.target.files[0] });
+    };
+    render() {
+        const hasClipboardApi = !!navigator.clipboard?.write;
+        return _jsxs("div", { children: [this.state.showPreview && _jsxs("div", { className: 'msp-image-preview', children: [_jsx(ScreenshotPreview, { plugin: this.plugin }), _jsx(CropControls, { plugin: this.plugin })] }), _jsxs("div", { className: 'msp-flex-row', children: [!this.state.imageData && _jsx(Button, { icon: CopySvg, onClick: hasClipboardApi ? this.copy : this.copyImg, disabled: this.state.isDisabled, children: "Copy" }), this.state.imageData && _jsx(Button, { onClick: () => this.setState({ imageData: void 0 }), disabled: this.state.isDisabled, children: "Clear" }), _jsx(Button, { icon: GetAppSvg, onClick: this.download, disabled: this.state.isDisabled, children: "Download" })] }), this.state.imageData && _jsxs("div", { className: 'msp-row msp-copy-image-wrapper', children: [_jsx("div", { children: "Right click below + Copy Image" }), _jsx("img", { src: this.state.imageData, style: { width: '100%', height: 32, display: 'block' } })] }), _jsx(ScreenshotParams, { plugin: this.plugin, isDisabled: this.state.isDisabled })] });
+    }
+}
+function ScreenshotParams({ plugin, isDisabled }) {
+    const helper = plugin.helpers.viewportScreenshot;
+    const values = useBehavior(helper.behaviors.values);
+    return _jsx(ParameterControls, { params: helper.params, values: values, onChangeValues: v => helper.behaviors.values.next(v), isDisabled: isDisabled });
+}
+function CropControls({ plugin }) {
+    const helper = plugin.helpers.viewportScreenshot;
+    const cropParams = useBehavior(helper?.behaviors.cropParams);
+    useBehavior(helper?.behaviors.relativeCrop);
+    if (!helper)
+        return null;
+    return _jsxs("div", { style: { width: '100%', height: '24px', marginTop: '8px' }, children: [_jsx(ToggleButton, { icon: CropOrginalSvg, title: 'Auto-crop', inline: true, isSelected: cropParams.auto, style: { background: 'transparent', float: 'left', width: 'auto', height: '24px', lineHeight: '24px' }, toggle: () => helper.toggleAutocrop(), label: 'Auto-crop ' + (cropParams.auto ? 'On' : 'Off') }), !cropParams.auto && _jsx(Button, { icon: CropSvg, title: 'Crop', style: { background: 'transparent', float: 'right', height: '24px', lineHeight: '24px', width: '24px', padding: '0' }, onClick: () => helper.autocrop() }), !cropParams.auto && !helper.isFullFrame && _jsx(Button, { icon: CropFreeSvg, title: 'Reset Crop', style: { background: 'transparent', float: 'right', height: '24px', lineHeight: '24px', width: '24px', padding: '0' }, onClick: () => helper.resetCrop() })] });
+}
diff --git a/frontend/venome-molstar/lib/ui/pdbe-structure-controls.d.ts b/frontend/venome-molstar/lib/ui/pdbe-structure-controls.d.ts
new file mode 100644
index 00000000..d765c0bb
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/pdbe-structure-controls.d.ts
@@ -0,0 +1,18 @@
+import { PluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+export declare class PDBeStructureTools extends PluginUIComponent {
+    render(): import("react/jsx-runtime").JSX.Element;
+}
+export declare class CustomStructureControls extends PluginUIComponent<{
+    initiallyCollapsed?: boolean;
+    takeKeys?: string[];
+    skipKeys?: string[];
+}> {
+    componentDidMount(): void;
+    render(): import("react/jsx-runtime").JSX.Element | null;
+}
+export declare class PDBeLigandViewStructureTools extends PluginUIComponent {
+    render(): import("react/jsx-runtime").JSX.Element;
+}
+export declare class PDBeSuperpositionStructureTools extends PluginUIComponent {
+    render(): import("react/jsx-runtime").JSX.Element;
+}
diff --git a/frontend/venome-molstar/lib/ui/pdbe-structure-controls.js b/frontend/venome-molstar/lib/ui/pdbe-structure-controls.js
new file mode 100644
index 00000000..7a69d90e
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/pdbe-structure-controls.js
@@ -0,0 +1,48 @@
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
+import { PluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { StructureComponentControls } from 'molstar/lib/mol-plugin-ui/structure/components';
+import { StructureMeasurementsControls } from 'molstar/lib/mol-plugin-ui/structure/measurements';
+import { StructureSourceControls } from 'molstar/lib/mol-plugin-ui/structure/source';
+import { VolumeStreamingControls, VolumeSourceControls } from 'molstar/lib/mol-plugin-ui/structure/volume';
+import { AnnotationsComponentControls } from './annotation-controls';
+import { Icon, BuildSvg } from 'molstar/lib/mol-plugin-ui/controls/icons';
+import { SuperpositionComponentControls } from './superposition-components';
+import { StructureQuickStylesControls } from 'molstar/lib/mol-plugin-ui/structure/quick-styles';
+import { AlphafoldPaeControls, AlphafoldSuperpositionControls } from './alphafold-superposition';
+import { SuperpositionModelExportUI } from './export-superposition';
+import { AlphafoldTransparencyControls } from './alphafold-tranparency';
+import { AssemblySymmetry } from 'molstar/lib/extensions/rcsb/assembly-symmetry/prop';
+export class PDBeStructureTools extends PluginUIComponent {
+    render() {
+        const AssemblySymmetryKey = AssemblySymmetry.Tag.Representation;
+        return _jsxs(_Fragment, { children: [_jsxs("div", { className: 'msp-section-header', children: [_jsx(Icon, { svg: BuildSvg }), "Structure Tools"] }), _jsx(StructureSourceControls, {}), _jsx(AnnotationsComponentControls, {}), _jsx(StructureQuickStylesControls, {}), _jsx(StructureComponentControls, {}), _jsx(VolumeStreamingControls, {}), _jsx(VolumeSourceControls, {}), _jsx(StructureMeasurementsControls, {}), _jsx(CustomStructureControls, { skipKeys: [AssemblySymmetryKey] })] });
+    }
+}
+export class CustomStructureControls extends PluginUIComponent {
+    componentDidMount() {
+        this.subscribe(this.plugin.state.behaviors.events.changed, () => this.forceUpdate());
+    }
+    render() {
+        const takeKeys = this.props.takeKeys ?? Array.from(this.plugin.customStructureControls.keys());
+        const result = [];
+        for (const key of takeKeys) {
+            if (this.props.skipKeys?.includes(key))
+                continue;
+            const Controls = this.plugin.customStructureControls.get(key);
+            if (!Controls)
+                continue;
+            result.push(_jsx(Controls, { initiallyCollapsed: this.props.initiallyCollapsed }, key));
+        }
+        return result.length > 0 ? _jsx(_Fragment, { children: result }) : null;
+    }
+}
+export class PDBeLigandViewStructureTools extends PluginUIComponent {
+    render() {
+        return _jsxs(_Fragment, { children: [_jsxs("div", { className: 'msp-section-header', children: [_jsx(Icon, { svg: BuildSvg }), "Structure Tools"] }), _jsx(StructureComponentControls, {}), _jsx(VolumeStreamingControls, {}), _jsx(StructureMeasurementsControls, {}), _jsx(CustomStructureControls, {})] });
+    }
+}
+export class PDBeSuperpositionStructureTools extends PluginUIComponent {
+    render() {
+        return _jsxs(_Fragment, { children: [_jsxs("div", { className: 'msp-section-header', children: [_jsx(Icon, { svg: BuildSvg }), "Structure Tools"] }), _jsx(SuperpositionComponentControls, {}), _jsx(AlphafoldTransparencyControls, {}), _jsx(AlphafoldPaeControls, {}), _jsx(AlphafoldSuperpositionControls, {}), _jsx(StructureMeasurementsControls, {}), _jsx(SuperpositionModelExportUI, {}), _jsx(CustomStructureControls, {})] });
+    }
+}
diff --git a/frontend/venome-molstar/lib/ui/pdbe-viewport-controls.d.ts b/frontend/venome-molstar/lib/ui/pdbe-viewport-controls.d.ts
new file mode 100644
index 00000000..36b5ed19
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/pdbe-viewport-controls.d.ts
@@ -0,0 +1,5 @@
+import { ViewportControls } from 'molstar/lib/mol-plugin-ui/viewport';
+export declare class PDBeViewportControls extends ViewportControls {
+    private isBlack;
+    render(): import("react/jsx-runtime").JSX.Element;
+}
diff --git a/frontend/venome-molstar/lib/ui/pdbe-viewport-controls.js b/frontend/venome-molstar/lib/ui/pdbe-viewport-controls.js
new file mode 100644
index 00000000..a4d5e05d
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/pdbe-viewport-controls.js
@@ -0,0 +1,26 @@
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
+import { ViewportControls } from 'molstar/lib/mol-plugin-ui/viewport';
+import { PluginCustomState } from '../plugin-custom-state';
+export class PDBeViewportControls extends ViewportControls {
+    isBlack() {
+        const bgColor = PluginCustomState(this.plugin).initParams?.bgColor;
+        return bgColor !== undefined && bgColor.r === 0 && bgColor.g === 0 && bgColor.b === 0;
+    }
+    render() {
+        const initParams = PluginCustomState(this.plugin).initParams;
+        const showPDBeLink = initParams?.moleculeId && initParams?.pdbeLink && !initParams?.superposition;
+        const pdbeLinkColor = this.isBlack() ? '#fff' : '#555';
+        const pdbeLink = {
+            parentStyle: { width: 'auto' },
+            bgStyle: { position: 'absolute', height: '27px', width: '54px', marginLeft: '-33px' },
+            containerStyle: { position: 'absolute', right: '10px', top: '10px', padding: '3px 3px 3px 18px' },
+            style: { display: 'inline-block', fontSize: '14px', color: pdbeLinkColor, borderBottom: 'none', cursor: 'pointer', textDecoration: 'none', position: 'absolute', right: '5px' },
+            pdbeImg: {
+                src: 'https://www.ebi.ac.uk/pdbe/entry/static/images/logos/PDBe/logo_T_64.png',
+                alt: 'PDBe logo',
+                style: { height: '12px', width: '12px', border: 0, position: 'absolute', margin: '4px 0 0 -13px' }
+            }
+        };
+        return _jsxs(_Fragment, { children: [showPDBeLink && _jsxs("div", { className: 'msp-viewport-controls-buttons', style: pdbeLink.containerStyle, children: [_jsx("div", { className: 'msp-semi-transparent-background', style: pdbeLink.bgStyle }), _jsxs("a", { className: 'msp-pdbe-link', style: pdbeLink.style, target: "_blank", href: `https://pdbe.org/${initParams.moleculeId}`, children: [_jsx("img", { src: pdbeLink.pdbeImg.src, alt: pdbeLink.pdbeImg.alt, style: pdbeLink.pdbeImg.style }), initParams.moleculeId] })] }), _jsx("div", { style: { position: 'absolute', top: showPDBeLink ? (27 + 4) : 0, right: 0 }, children: super.render() })] });
+    }
+}
diff --git a/frontend/venome-molstar/lib/ui/segment-tree.d.ts b/frontend/venome-molstar/lib/ui/segment-tree.d.ts
new file mode 100644
index 00000000..c4bfed66
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/segment-tree.d.ts
@@ -0,0 +1,18 @@
+import { Mat4 } from 'molstar/lib/mol-math/linear-algebra';
+import { PluginStateObject } from 'molstar/lib/mol-plugin-state/objects';
+import { PurePluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { StateObjectRef } from 'molstar/lib/mol-state';
+import { PluginCustomState } from '../plugin-custom-state';
+export declare class SegmentTree extends PurePluginUIComponent<{}, {
+    segment?: any;
+    isBusy: boolean;
+}> {
+    componentDidMount(): void;
+    get customState(): PluginCustomState;
+    getSegmentParams: () => void;
+    updateSegment: (val: any) => Promise;
+    hideStructures: (segmentIndex: number) => void;
+    displayStructures: (segmentIndex: number) => Promise;
+    transform(s: StateObjectRef, matrix: Mat4): Promise;
+    render(): import("react/jsx-runtime").JSX.Element;
+}
diff --git a/frontend/venome-molstar/lib/ui/segment-tree.js b/frontend/venome-molstar/lib/ui/segment-tree.js
new file mode 100644
index 00000000..c094ed56
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/segment-tree.js
@@ -0,0 +1,652 @@
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
+import { StateTransforms } from 'molstar/lib/mol-plugin-state/transforms';
+import { PluginUIComponent, PurePluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { Button, ExpandGroup, IconButton, SectionHeader } from 'molstar/lib/mol-plugin-ui/controls/common';
+import { ArrowDropDownSvg, ArrowRightSvg, CheckSvg, CloseSvg, VisibilityOffOutlinedSvg, VisibilityOutlinedSvg } from 'molstar/lib/mol-plugin-ui/controls/icons';
+import { ParameterControls } from 'molstar/lib/mol-plugin-ui/controls/parameters';
+import { UpdateTransformControl } from 'molstar/lib/mol-plugin-ui/state/update-transform';
+import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
+import { MolScriptBuilder as MS } from 'molstar/lib/mol-script/language/builder';
+import { State, StateObjectRef, StateSelection } from 'molstar/lib/mol-state';
+import { Color } from 'molstar/lib/mol-util/color';
+import { ColorLists } from 'molstar/lib/mol-util/color/lists';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
+import { Subject } from 'rxjs';
+import { debounceTime, filter } from 'rxjs/operators';
+import { PluginCustomState } from '../plugin-custom-state';
+import { renderSuperposition, superposeAf } from '../superposition';
+const SuperpositionTag = 'SuperpositionTransform';
+export class SegmentTree extends PurePluginUIComponent {
+    componentDidMount() {
+        this.subscribe(PluginCustomState(this.plugin).events.superpositionInit, () => {
+            const customState = this.customState;
+            if (customState && !customState.superpositionError) {
+                this.getSegmentParams();
+            }
+            this.forceUpdate();
+        });
+        this.subscribe(PluginCustomState(this.plugin).events.isBusy, (e) => {
+            this.setState({ isBusy: e });
+            if (e) {
+                PluginCommands.Toast.Show(this.plugin, {
+                    title: 'Process',
+                    message: 'Loading / computing large dataset!',
+                    key: 'is-busy-toast'
+                });
+            }
+            else {
+                PluginCommands.Toast.Hide(this.plugin, { key: 'is-busy-toast' });
+            }
+        });
+        this.subscribe(this.plugin.behaviors.layout.leftPanelTabName, (e) => {
+            if (e !== 'segments')
+                return;
+            this.getSegmentParams();
+            this.forceUpdate();
+        });
+    }
+    get customState() {
+        return PluginCustomState(this.plugin);
+    }
+    getSegmentParams = () => {
+        const customState = this.customState;
+        if (!customState.superpositionState || !customState.superpositionState.segmentData)
+            return;
+        const segmentData = customState.superpositionState.segmentData;
+        const segmentArr = segmentData.map((segment, i) => {
+            const segmentLabel = `${i + 1} ( ${segment.segment_start} - ${segment.segment_end} )`;
+            return [segmentLabel, segmentLabel];
+        });
+        const segmentOptions = {
+            segment: PD.Select('', segmentArr, { label: 'Select Segment', description: 'Select segment to view its clusters below' })
+        };
+        const segmentIndex = customState.superpositionState.activeSegment - 1;
+        this.setState({
+            segment: {
+                params: segmentOptions,
+                value: { segment: segmentArr[segmentIndex][0] }
+            }
+        });
+        this.setState({ isBusy: false });
+    };
+    updateSegment = async (val) => {
+        if (!this.state.segment)
+            return;
+        if (!this.state.segment)
+            return;
+        const customState = this.customState;
+        if (!customState.superpositionState)
+            throw new Error('customState.superpositionState has not been initialized');
+        customState.events?.isBusy.next(true);
+        // Hide pervious segement structures
+        this.hideStructures(customState.superpositionState.activeSegment - 1);
+        // Set current segment params
+        const updatedParams = { ...this.state.segment };
+        updatedParams.value = val;
+        this.setState({ segment: updatedParams });
+        setTimeout(async () => {
+            const updatedSegmentIndex = parseInt(val.segment.split(' ')[0]);
+            customState.superpositionState.activeSegment = updatedSegmentIndex;
+            // Display current segment visible structures
+            await this.displayStructures(customState.superpositionState.activeSegment - 1);
+            customState.events?.isBusy.next(false);
+            customState.events?.segmentUpdate.next(true);
+        }, 100);
+        return false;
+    };
+    hideStructures = (segmentIndex) => {
+        // clear selections
+        this.plugin.managers.interactivity.lociSelects.deselectAll();
+        // clear Focus
+        this.plugin.managers.structure.focus.clear();
+        // remove measurements
+        const measurements = this.plugin.managers.structure.measurement.state;
+        const measureTypes = ['labels', 'distances', 'angles', 'dihedrals'];
+        let measurementCell = void 0;
+        measureTypes.forEach((type) => {
+            if (measurementCell)
+                return;
+            if (measurements[type][0]) {
+                measurementCell = this.plugin.state.data.cells.get(measurements[type][0].transform.parent);
+            }
+        });
+        if (measurementCell) {
+            PluginCommands.State.RemoveObject(this.plugin, { state: measurementCell.parent, ref: measurementCell.transform.parent, removeParentGhosts: true });
+        }
+        // hide structures
+        const customState = this.customState;
+        if (!customState.superpositionState)
+            throw new Error('customState.superpositionState has not been initialized');
+        customState.superpositionState.visibleRefs[segmentIndex] = [];
+        for (const struct of customState.superpositionState.loadedStructs[segmentIndex]) {
+            const structRef = customState.superpositionState.models[struct];
+            if (structRef) {
+                const structHierarchy = this.plugin.managers.structure.hierarchy.current.refs.get(structRef);
+                if (structHierarchy && structHierarchy.components) {
+                    for (const c of structHierarchy.components) {
+                        if (c && c.cell && !c.cell.state.isHidden) {
+                            customState.superpositionState.visibleRefs[segmentIndex].push(c.cell.transform.ref);
+                            PluginCommands.State.ToggleVisibility(this.plugin, { state: c.cell.parent, ref: c.cell.transform.ref });
+                        }
+                    }
+                }
+            }
+        }
+        if (customState.superpositionState.alphafold.ref) {
+            const afStr = this.plugin.managers.structure.hierarchy.current.refs.get(customState.superpositionState.alphafold.ref);
+            if (afStr && afStr.components) {
+                for (const c of afStr.components) {
+                    if (c && c.cell && !c.cell.state.isHidden) {
+                        PluginCommands.State.ToggleVisibility(this.plugin, { state: c.cell.parent, ref: c.cell.transform.ref });
+                    }
+                }
+            }
+        }
+    };
+    displayStructures = async (segmentIndex) => {
+        const customState = this.customState;
+        const spState = customState.superpositionState;
+        if (!spState)
+            throw new Error('customState.superpositionState has not been initialized');
+        if (spState.visibleRefs[segmentIndex].length === 0) {
+            const loadStrs = [];
+            spState.segmentData?.[segmentIndex].clusters.forEach(cluster => {
+                let entryList = [cluster[0]];
+                if (customState.initParams?.superpositionParams?.superposeAll) {
+                    entryList = cluster;
+                }
+                entryList.forEach((str) => {
+                    const structStateId = `${str.pdb_id}_${str.struct_asym_id}`;
+                    const structRef = spState.models[structStateId];
+                    if (structRef) {
+                        const cell = this.plugin.state.data.cells.get(structRef);
+                        const isHidden = cell.state.isHidden ? true : false;
+                        if (isHidden) {
+                            PluginCommands.State.ToggleVisibility(this.plugin, { state: cell.parent, ref: structRef });
+                            // PluginCommands.State.ToggleVisibility(this.plugin, { state: cell.parent!, ref: cell.transform.parent });
+                        }
+                    }
+                    else {
+                        loadStrs.push(str);
+                    }
+                });
+            });
+            PluginCommands.Camera.Reset(this.plugin);
+            if (loadStrs.length > 0) {
+                await renderSuperposition(this.plugin, segmentIndex, loadStrs);
+                PluginCommands.Camera.Reset(this.plugin);
+            }
+        }
+        else {
+            for (const ref of spState.visibleRefs[segmentIndex]) {
+                const cell = this.plugin.state.data.cells.get(ref);
+                if (cell && cell.state.isHidden) {
+                    PluginCommands.State.ToggleVisibility(this.plugin, { state: cell.parent, ref });
+                }
+            }
+            PluginCommands.Camera.Reset(this.plugin);
+        }
+        if (spState.alphafold.ref) {
+            superposeAf(this.plugin, spState.alphafold.traceOnly);
+            PluginCommands.Camera.Reset(this.plugin);
+        }
+        if (spState.alphafold.ref && spState.alphafold.visibility[segmentIndex]) {
+            const afStr = this.plugin.managers.structure.hierarchy.current.refs.get(spState.alphafold.ref);
+            if (afStr && afStr.components) {
+                for (const c of afStr.components) {
+                    if (c && c.cell && c.cell.state.isHidden) {
+                        PluginCommands.State.ToggleVisibility(this.plugin, { state: c.cell.parent, ref: c.cell.transform.ref });
+                    }
+                }
+            }
+        }
+    };
+    async transform(s, matrix) {
+        const r = StateObjectRef.resolveAndCheck(this.plugin.state.data, s);
+        if (!r)
+            return;
+        // TODO should find any TransformStructureConformation decorator instance
+        const o = StateSelection.findTagInSubtree(this.plugin.state.data.tree, r.transform.ref, SuperpositionTag);
+        const params = {
+            transform: {
+                name: 'matrix',
+                params: { data: matrix, transpose: false }
+            }
+        };
+        // TODO add .insertOrUpdate to StateBuilder?
+        const b = o
+            ? this.plugin.state.data.build().to(o).update(params)
+            : this.plugin.state.data.build().to(s)
+                .insert(StateTransforms.Model.TransformStructureConformation, params, { tags: SuperpositionTag });
+        await this.plugin.runTask(this.plugin.state.data.updateTree(b));
+    }
+    render() {
+        let sectionHeader = _jsx(SectionHeader, { title: `Structure clusters` });
+        const customState = this.customState;
+        if (customState && customState.initParams && !customState.initParams.superposition) {
+            return _jsxs(_Fragment, { children: [sectionHeader, _jsx("div", { children: "Functionality unavailable!" })] });
+        }
+        else {
+            if (customState && customState.initParams && customState.initParams.superposition) {
+                sectionHeader = _jsx(SectionHeader, { title: `Structure clusters - ${customState.initParams.moleculeId}` });
+                if (customState.superpositionError) {
+                    return _jsxs(_Fragment, { children: [sectionHeader, _jsx("div", { style: { textAlign: 'center' }, children: customState.superpositionError })] });
+                }
+                else if (!customState.superpositionState || !customState.superpositionState.segmentData) {
+                    return _jsxs(_Fragment, { children: [sectionHeader, _jsx("div", { style: { textAlign: 'center' }, children: "Loading Segment Data!" })] });
+                }
+            }
+        }
+        if (this.state) {
+            const segmentIndex = parseInt(this.state.segment.value.segment.split(' ')[0]) - 1;
+            if (!customState.superpositionState?.segmentData)
+                throw new Error('customState.superpositionState.segmentData has not been initialized');
+            const segmentData = customState.superpositionState.segmentData;
+            const fullSegmentRange = `( ${segmentData[0].segment_start} - ${segmentData[segmentData.length - 1].segment_end} )`;
+            sectionHeader = _jsx(SectionHeader, { title: `Structure clusters ${customState.initParams.moleculeId}`, desc: fullSegmentRange });
+            return _jsxs(_Fragment, { children: [sectionHeader, _jsx(ParameterControls, { params: this.state.segment.params, values: this.state.segment.value, onChangeValues: this.updateSegment, isDisabled: this.state.isBusy }), segmentData[segmentIndex].clusters.map((c, i) => _jsx(ClusterNode, { cluster: c, totalClusters: segmentData[segmentIndex].clusters.length, segmentIndex: segmentIndex, clusterIndex: i }, `cluster-${segmentIndex}-${i}`))] });
+        }
+        return _jsx(_Fragment, {});
+    }
+}
+class ClusterNode extends PluginUIComponent {
+    state = {
+        isCollapsed: false,
+        showAll: false,
+        showNone: false,
+        showSearch: false,
+        isBusy: false,
+        cluster: this.props.cluster,
+        searchText: ''
+    };
+    inputStream = new Subject();
+    handleInputStream = (inputStr) => {
+        this.setState({ searchText: inputStr });
+        const filteredRes = this.props.cluster.filter((item) => {
+            return item.pdb_id.toLowerCase().indexOf(inputStr.toLowerCase()) >= 0;
+        });
+        this.setState({ cluster: filteredRes });
+    };
+    componentDidMount() {
+        this.subscribe(PluginCustomState(this.plugin).events.isBusy, (e) => {
+            this.setState({ isBusy: e, showAll: false, showNone: false });
+        });
+        this.subscribe(this.inputStream.pipe(debounceTime(1000 / 24)), (e) => this.handleInputStream(e));
+    }
+    get customState() {
+        return PluginCustomState(this.plugin);
+    }
+    toggleExpanded = (e) => {
+        e.preventDefault();
+        this.setState({ isCollapsed: !this.state.isCollapsed });
+        e.currentTarget.blur();
+    };
+    selectAll = (e) => {
+        e.preventDefault();
+        this.setState({ showAll: !this.state.showAll, showNone: false });
+        e.currentTarget.blur();
+    };
+    selectNone = (e) => {
+        e.preventDefault();
+        this.setState({ showAll: false, showNone: !this.state.showNone });
+        e.currentTarget.blur();
+    };
+    applyAction = async (e) => {
+        e.preventDefault();
+        e.currentTarget.blur();
+        const customState = this.customState;
+        customState.events?.isBusy.next(true);
+        const currentState = { ...this.state };
+        this.setState({ showAll: false, showNone: false });
+        setTimeout(async () => {
+            const loadStrs = [];
+            for await (const str of this.state.cluster) {
+                const structStateId = `${str.pdb_id}_${str.struct_asym_id}`;
+                let structRef = undefined;
+                if (customState && customState.superpositionState && customState.superpositionState.models[structStateId]) {
+                    structRef = customState.superpositionState.models[structStateId];
+                }
+                if (structRef) {
+                    const cell = this.plugin.state.data.cells.get(structRef);
+                    if (cell) {
+                        const isHidden = cell.state.isHidden ? true : false;
+                        if ((isHidden && currentState.showAll) || (!isHidden && currentState.showNone)) {
+                            await PluginCommands.State.ToggleVisibility(this.plugin, { state: cell.parent, ref: structRef });
+                            // await PluginCommands.State.ToggleVisibility(this.plugin, { state: cell.parent!, ref: cell.transform.parent });
+                        }
+                    }
+                }
+                else {
+                    if (currentState.showAll)
+                        loadStrs.push(str);
+                }
+            }
+            ;
+            PluginCommands.Camera.Reset(this.plugin);
+            if (loadStrs.length > 0) {
+                await renderSuperposition(this.plugin, this.props.segmentIndex, loadStrs);
+            }
+            customState.events?.isBusy.next(false);
+        });
+    };
+    cancelAction = (e) => {
+        e.preventDefault();
+        this.setState({ showAll: false, showNone: false });
+        e.currentTarget.blur();
+    };
+    clearSearch = (e) => {
+        e.preventDefault();
+        this.setState({ searchText: '' });
+        this.inputStream.next('');
+        e.currentTarget.blur();
+    };
+    render() {
+        const customState = this.customState;
+        if (!customState.superpositionState || !customState.superpositionState.segmentData)
+            return _jsx(_Fragment, {});
+        const expand = _jsx(IconButton, { svg: this.state.isCollapsed ? ArrowRightSvg : ArrowDropDownSvg, flex: '20px', onClick: this.toggleExpanded, transparent: true, disabled: this.state.isBusy, className: 'msp-no-hover-outline' });
+        const title = `Segment ${customState.superpositionState.activeSegment} Cluster ${this.props.clusterIndex + 1}`;
+        const label = _jsxs(Button, { className: `msp-btn-tree-label`, noOverflow: true, title: title, disabled: this.state.isBusy, children: [_jsxs("span", { children: ["Cluster ", this.props.clusterIndex + 1] }), " ", _jsxs("small", { children: [this.state.cluster.length < this.props.cluster.length ? `${this.state.cluster.length} / ` : '', this.props.cluster.length, " chain", this.props.cluster.length > 1 ? 's' : ''] })] });
+        const selectionControls = _jsxs(_Fragment, { children: [_jsx(Button, { icon: CheckSvg, flex: true, onClick: this.selectAll, style: { flex: '0 0 50px', textAlign: 'center', fontSize: '80%', color: '#9cacc3', padding: 0 }, disabled: this.state.isBusy, title: `Show all chains`, children: "All" }), _jsx(Button, { icon: CloseSvg, flex: true, onClick: this.selectNone, style: { flex: '0 0 50px', textAlign: 'center', fontSize: '80%', color: '#9cacc3', padding: 0 }, disabled: this.state.isBusy, title: `Hide all chains`, children: "None" })] });
+        const mainRow = _jsxs("div", { className: `msp-flex-row msp-tree-row`, style: { marginTop: '10px' }, children: [expand, label, this.props.cluster.length > 1 && selectionControls] });
+        const searchControls = _jsxs("div", { className: 'msp-mapped-parameter-group', style: { fontSize: '90%' }, children: [_jsxs("div", { className: 'msp-control-row msp-transform-header-brand-gray', style: { height: '33px', marginLeft: '30px' }, children: [_jsx("span", { className: 'msp-control-row-label', children: "Search PDB ID" }), _jsx("div", { className: 'msp-control-row-ctrl', children: _jsx("input", { type: 'text', placeholder: 'Enter PDB ID..', disabled: this.state.isBusy, onChange: e => this.inputStream.next(e.target.value), value: this.state.searchText, maxLength: 4 }) })] }), _jsx(IconButton, { svg: CloseSvg, flex: true, onClick: this.clearSearch, style: { flex: '0 0 24px', padding: 0 }, disabled: this.state.isBusy || this.state.searchText === '', toggleState: this.state.searchText !== '', title: 'Clear search input' })] });
+        return _jsxs(_Fragment, { children: [mainRow, (this.state.showAll || this.state.showNone) && _jsx("div", { children: _jsxs("div", { className: `msp-control-row msp-transform-header-brand-${this.state.showAll ? 'green' : 'red'}`, style: { display: 'flex', marginLeft: '20px', height: '35px' }, children: [_jsxs("span", { className: 'msp-control-row-label', style: { flex: '1 1 auto', textAlign: 'left', fontSize: '85%' }, children: [this.state.showAll ? 'Display' : 'Hide', " ", this.state.cluster.length < this.props.cluster.length ? `${this.state.cluster.length} / ` : 'all ', this.props.cluster.length, " chains"] }), _jsx(Button, { icon: CheckSvg, flex: true, onClick: this.applyAction, style: { flex: '0 0 60px', textAlign: 'center', fontSize: '78%', color: '#9cacc3', padding: 0, margin: '0 1px' }, title: `Apply action`, children: "Apply" }), _jsx(Button, { icon: CloseSvg, flex: true, onClick: this.cancelAction, style: { flex: '0 0 60px', textAlign: 'center', fontSize: '78%', color: '#9cacc3', padding: 0, margin: '0 1px' }, title: `Cancel action`, children: "Cancel" })] }) }), (!this.state.isCollapsed && this.props.cluster.length > 5) && searchControls, !this.state.isCollapsed && _jsx("div", { className: 'msp-tree-updates-wrapper', style: { maxHeight: (this.props.totalClusters > 1) ? '330px' : '87%', overflowY: 'auto' }, children: this.state.cluster.map((s, i) => _jsx(StructureNode, { segmentIndex: this.props.segmentIndex, structure: s, isRep: i === 0 ? true : false }, `str-${s.pdb_id}${s.struct_asym_id}${i}`)) })] });
+    }
+}
+class StructureNode extends PluginUIComponent {
+    state = {
+        showControls: false,
+        isBusy: false,
+        isProcessing: false,
+        isHidden: true,
+    };
+    get customState() {
+        return PluginCustomState(this.plugin);
+    }
+    get ref() {
+        if (this.customState && this.customState.superpositionState && this.customState.superpositionState.models[`${this.props.structure.pdb_id}_${this.props.structure.struct_asym_id}`]) {
+            return this.customState.superpositionState.models[`${this.props.structure.pdb_id}_${this.props.structure.struct_asym_id}`];
+        }
+        else {
+            return undefined;
+        }
+    }
+    get modelCell() {
+        if (this.ref) {
+            return this.plugin.state.data.cells.get(this.ref);
+        }
+        else {
+            return undefined;
+        }
+    }
+    get isAllHidden() {
+        let isHidden = true;
+        if (this.ref) {
+            const structHierarchy = this.plugin.managers.structure.hierarchy.current.refs.get(this.ref);
+            if (structHierarchy && structHierarchy.components) {
+                for (const c of structHierarchy.components) {
+                    if (c && c.cell && !c.cell.state.isHidden) {
+                        isHidden = false;
+                        break;
+                    }
+                }
+            }
+            else {
+                isHidden = false;
+            }
+        }
+        return isHidden;
+    }
+    checkRelation(ref) {
+        let isRelated = false;
+        const cell = this.plugin.state.data.cells.get(ref);
+        if (cell && cell.transform.parent) {
+            if (cell && cell.transform.parent === this.ref) {
+                isRelated = true;
+            }
+            else {
+                const pcell = this.plugin.state.data.cells.get(cell.transform.parent);
+                if (pcell && pcell.transform.parent === this.ref)
+                    isRelated = true;
+            }
+        }
+        else {
+            const currentNodeCell = this.plugin.state.data.cells.get(this.ref);
+            if (currentNodeCell && currentNodeCell.transform.parent === cell.transform.parent) {
+                isRelated = true;
+            }
+        }
+        return isRelated;
+    }
+    is(e) {
+        if (!this.ref)
+            return false;
+        let isRelated = false;
+        if (this.ref && e.ref !== this.ref) {
+            isRelated = this.checkRelation(e.ref);
+        }
+        if (e.ref === this.ref || isRelated) {
+            return true;
+        }
+        else {
+            const id = `${this.props.structure.pdb_id}_${this.props.structure.struct_asym_id}`;
+            const invalidStruct = this.customState.superpositionState?.invalidStruct.includes(id) ?? false;
+            return invalidStruct;
+        }
+    }
+    componentDidMount() {
+        this.setState({ isHidden: this.isAllHidden });
+        this.subscribe(PluginCustomState(this.plugin).events.isBusy, (e) => {
+            this.setState({ isBusy: e, showControls: false });
+        });
+        this.subscribe(this.plugin.state.events.cell.stateUpdated.pipe(filter(e => this.is(e)), debounceTime(33)), e => {
+            this.setState({ isHidden: this.isAllHidden });
+            // this.forceUpdate();
+        });
+    }
+    toggleVisible = async (e) => {
+        e.preventDefault();
+        e.currentTarget.blur();
+        this.setState({ isProcessing: true, showControls: false });
+        if (this.ref) {
+            const structHierarchy = this.plugin.managers.structure.hierarchy.current.refs.get(this.ref);
+            if (structHierarchy && structHierarchy.components) {
+                for (const c of structHierarchy.components) {
+                    const currentHiddenState = c.cell.state.isHidden ? true : false;
+                    if (currentHiddenState === this.state.isHidden) {
+                        PluginCommands.State.ToggleVisibility(this.plugin, { state: c.cell.parent, ref: c.cell.transform.ref });
+                    }
+                }
+                this.setState({ isHidden: !this.state.isHidden });
+            }
+        }
+        else {
+            await renderSuperposition(this.plugin, this.props.segmentIndex, [this.props.structure]);
+        }
+        this.setState({ isProcessing: false });
+        PluginCommands.Camera.Reset(this.plugin);
+    };
+    selectAction = item => {
+        if (!item)
+            return;
+        this.setState({ showControls: false });
+        (item?.value)();
+    };
+    getTagRefs(tags) {
+        const TagSet = new Set(tags);
+        const tree = this.plugin.state.data.tree;
+        return StateSelection.findUniqueTagsInSubtree(tree, this.modelCell.transform.ref, TagSet);
+    }
+    ;
+    getRandomColor() {
+        const clList = ColorLists;
+        const spState = PluginCustomState(this.plugin).superpositionState;
+        if (!spState)
+            throw new Error('customState.superpositionState has not been initialized');
+        let palleteIndex = spState.colorState[this.props.segmentIndex].palleteIndex;
+        let colorIndex = spState.colorState[this.props.segmentIndex].colorIndex;
+        if (clList[spState.colorPalette[palleteIndex]].list[colorIndex + 1]) {
+            colorIndex += 1;
+        }
+        else {
+            colorIndex = 0;
+            palleteIndex = spState.colorPalette[palleteIndex + 1] ? palleteIndex + 1 : 0;
+        }
+        const palleteName = spState.colorPalette[palleteIndex];
+        spState.colorState[this.props.segmentIndex].palleteIndex = palleteIndex;
+        spState.colorState[this.props.segmentIndex].colorIndex = colorIndex;
+        return clList[palleteName].list[colorIndex];
+    }
+    async addChainRepr() {
+        const uniformColor1 = this.getRandomColor();
+        const strInstance = this.plugin.state.data.select(this.ref)[0];
+        const query = MS.struct.generator.atomGroups({
+            'chain-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.label_asym_id(), this.props.structure.struct_asym_id])
+        });
+        const chainSel = await this.plugin.builders.structure.tryCreateComponentFromExpression(strInstance, query, `Chain-${this.props.segmentIndex}`, { label: `Chain`, tags: [`superposition-sel`] });
+        if (chainSel) {
+            await this.plugin.builders.structure.representation.addRepresentation(chainSel, { type: 'cartoon', color: 'uniform', colorParams: { value: uniformColor1 } }, { tag: `superposition-visual` });
+        }
+    }
+    updates() {
+        const structHierarchy = this.plugin.managers.structure.hierarchy.current.refs.get(this.ref);
+        if (structHierarchy && structHierarchy.components) {
+            const representations = [];
+            let showAddChainBtn = true;
+            structHierarchy.components.forEach((comps) => {
+                const gKeys = comps.key.split(',');
+                const cId1Arr = gKeys[0].split('-');
+                if (cId1Arr[2] === 'Chain')
+                    showAddChainBtn = false;
+                if (comps.representations) {
+                    comps.representations.forEach((repr) => {
+                        representations.push(repr);
+                    });
+                }
+            });
+            const customState = PluginCustomState(this.plugin);
+            if (customState.initParams?.superpositionParams && !customState.initParams.superpositionParams.ligandView) {
+                showAddChainBtn = false;
+            }
+            if (representations.length > 0) {
+                return _jsxs("div", { className: 'msp-accent-offset', style: { marginLeft: '40px' }, children: [representations.length > 0 && representations.map((r, i) => _jsx(StructureRepresentationEntry, { group: [structHierarchy], representation: r }, `${r.cell.transform.ref}-${i}`)), showAddChainBtn && _jsx("div", { className: 'msp-control-group-header', style: { marginTop: '1px' }, children: _jsxs(Button, { noOverflow: true, className: 'msp-control-button-label', title: `Click to add chain representaion`, onClick: () => this.addChainRepr(), children: ["\u00A0\u00A0Add Chain ", this.props.structure.struct_asym_id, " Representation"] }) })] });
+            }
+        }
+        return _jsx(_Fragment, {});
+    }
+    highlight = (e) => {
+        e.preventDefault();
+        if (this.ref) {
+            const cell = this.plugin.state.data.cells.get(this.ref);
+            PluginCommands.Interactivity.Object.Highlight(this.plugin, { state: cell.parent, ref: this.ref });
+        }
+        e.currentTarget.blur();
+    };
+    clearHighlight = (e) => {
+        e.preventDefault();
+        PluginCommands.Interactivity.ClearHighlights(this.plugin);
+        e.currentTarget.blur();
+    };
+    toggleControls = (e) => {
+        e.preventDefault();
+        this.setState({ showControls: !this.state.showControls });
+        e.currentTarget.blur();
+    };
+    getSubtitle() {
+        if (!this.customState.superpositionState)
+            throw new Error('customState.superpositionState has not been initialized');
+        const hetList = this.customState.superpositionState.hets[`${this.props.structure.pdb_id}_${this.props.structure.struct_asym_id}`];
+        let subtitle;
+        if (hetList) {
+            const hetLimit = this.props.structure.is_representative ? 1 : 4;
+            const totalHets = hetList.length;
+            let hetStr = hetList.join(', ');
+            if (totalHets > hetLimit) {
+                hetStr = hetList.slice(0, hetLimit).join(', ');
+                hetStr += ` + ${totalHets - hetLimit}`;
+            }
+            subtitle = ` ( ${hetStr} )`;
+            if (this.props.structure.is_representative)
+                subtitle = ` ${subtitle} ( Representative )`;
+        }
+        else if (this.props.structure.is_representative) {
+            subtitle = ' ( Representative )';
+        }
+        return subtitle;
+    }
+    get panelColor() {
+        let panelColor = '#808080';
+        if (!this.state.isHidden) {
+            if (this.modelCell) {
+                const refs = this.getTagRefs([`superposition-visual`, `superposition-ligand-visual`]);
+                const visualRef = refs[`superposition-ligand-visual`] ? refs[`superposition-ligand-visual`] : refs[`superposition-visual`] ? refs[`superposition-visual`] : undefined;
+                if (visualRef) {
+                    const visualCell = this.plugin.state.data.cells.get(visualRef);
+                    if (visualCell.params && visualCell.params.values && visualCell.params.values.colorTheme) {
+                        const colorTheme = visualCell.params.values.colorTheme;
+                        if (colorTheme.params && colorTheme.params.value) {
+                            panelColor = `${Color.toStyle(colorTheme.params.value)}`;
+                        }
+                        else if (colorTheme.params && colorTheme.params.palette) {
+                            const colorList1 = colorTheme.params.palette.params.list.colors;
+                            panelColor = `${Color.toStyle(colorList1[0])}`;
+                        }
+                        else if (colorTheme.params && colorTheme.params.list) {
+                            const colorList2 = colorTheme.params.list.colors;
+                            panelColor = `${Color.toStyle(colorList2[0])}`;
+                        }
+                    }
+                }
+            }
+        }
+        return panelColor;
+    }
+    render() {
+        const superpositionParams = this.customState.initParams.superpositionParams;
+        const strutStateId = `${this.props.structure.pdb_id}_${this.props.structure.struct_asym_id}`;
+        const invalidStruct = this.customState.superpositionState?.invalidStruct.includes(strutStateId);
+        const noMatrixStruct = this.customState.superpositionState?.noMatrixStruct.includes(strutStateId);
+        const subTitle = invalidStruct ? noMatrixStruct ? ` Matrix not available!` : ` No Ligand found!` : this.getSubtitle();
+        let strTitle = `${this.props.structure.pdb_id} chain ${this.props.structure.auth_asym_id}`;
+        if (superpositionParams && superpositionParams.ligandView) {
+            strTitle = `${this.props.structure.pdb_id} ${this.props.structure.struct_asym_id}`;
+        }
+        const label = _jsxs(Button, { className: `msp-btn-tree-label`, style: { borderLeftColor: this.panelColor }, noOverflow: true, title: strTitle, disabled: (invalidStruct || this.state.isBusy || this.state.isProcessing) ? true : false, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, children: [_jsx("span", { children: strTitle }), subTitle && _jsx("small", { children: subTitle })] });
+        const expand = _jsx(IconButton, { svg: !this.state.showControls ? ArrowRightSvg : ArrowDropDownSvg, flex: '20px', onClick: this.toggleControls, transparent: true, className: 'msp-no-hover-outline', disabled: (invalidStruct || this.state.isBusy || this.state.isProcessing) ? true : false });
+        const visibility = _jsx(IconButton, { svg: this.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, small: true, onClick: this.toggleVisible, disabled: (invalidStruct || this.state.isBusy || this.state.isProcessing) ? true : false, title: this.state.isHidden ? `Show chain` : `Hide chain` });
+        const row = _jsxs("div", { className: `msp-flex-row msp-tree-row`, style: { marginLeft: !this.state.isHidden ? '10px' : '31px' }, children: [!this.state.isHidden && expand, label, visibility] });
+        return _jsxs("div", { style: { marginBottom: '1px' }, children: [row, this.state.showControls && this.updates()] });
+    }
+}
+class StructureRepresentationEntry extends PurePluginUIComponent {
+    componentDidMount() {
+        this.subscribe(this.plugin.state.events.cell.stateUpdated, e => {
+            if (State.ObjectEvent.isCell(e, this.props.representation.cell))
+                this.forceUpdate();
+        });
+    }
+    toggleVisible = (e) => {
+        e.preventDefault();
+        e.currentTarget.blur();
+        const cell = this.props.representation.cell;
+        PluginCommands.State.ToggleVisibility(this.plugin, { state: cell.parent, ref: cell.transform.parent });
+    };
+    render() {
+        const repr = this.props.representation.cell;
+        let label = repr.obj?.label;
+        if (repr.obj?.data.repr && repr.obj?.data.repr.label) {
+            let sourceLabel = (repr.obj?.data.repr.label.indexOf('[Focus]') >= 0) ? '[Focus]' : repr.obj?.data.repr.label;
+            const isLargeLabel = sourceLabel.length > 10 ? true : false;
+            sourceLabel = `${isLargeLabel ? `${sourceLabel.substring(0, 28)}...` : sourceLabel}`;
+            if (isLargeLabel) {
+                label = sourceLabel;
+            }
+            else {
+                label = `${sourceLabel} ${(label && label.length < 21) ? ' - ' + label : ''}`;
+            }
+        }
+        if (repr.obj?.data.repr && repr.obj?.data.repr.label === 'Custom Selection')
+            label = 'Custom Selection';
+        return _jsxs("div", { className: 'msp-representation-entry', children: [repr.parent && _jsx(ExpandGroup, { header: `${label || 'Representation'}`, noOffset: true, headerStyle: { overflow: 'hidden' }, children: _jsx(UpdateTransformControl, { state: repr.parent, transform: repr.transform, customHeader: 'none', noMargin: true }) }), _jsx(IconButton, { svg: this.props.representation.cell.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, onClick: this.toggleVisible, title: this.props.representation.cell.state.isHidden ? `Show representation` : `Hide representation`, small: true, className: 'msp-default-bg', style: { position: 'absolute', top: 0, right: 0, lineHeight: '24px', height: '24px', textAlign: 'right', width: '32px', paddingRight: '6px', background: 'none' } })] });
+    }
+}
diff --git a/frontend/venome-molstar/lib/ui/superposition-components.d.ts b/frontend/venome-molstar/lib/ui/superposition-components.d.ts
new file mode 100644
index 00000000..6a43f431
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/superposition-components.d.ts
@@ -0,0 +1,9 @@
+import { CollapsableControls, CollapsableState } from 'molstar/lib/mol-plugin-ui/base';
+interface StructureComponentControlState extends CollapsableState {
+    isDisabled: boolean;
+}
+export declare class SuperpositionComponentControls extends CollapsableControls<{}, StructureComponentControlState> {
+    protected defaultState(): StructureComponentControlState;
+    renderControls(): import("react/jsx-runtime").JSX.Element;
+}
+export {};
diff --git a/frontend/venome-molstar/lib/ui/superposition-components.js b/frontend/venome-molstar/lib/ui/superposition-components.js
new file mode 100644
index 00000000..53d16d8e
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/superposition-components.js
@@ -0,0 +1,364 @@
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
+import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
+import { State } from 'molstar/lib/mol-state';
+import { ParamDefinition } from 'molstar/lib/mol-util/param-definition';
+import { CollapsableControls, PurePluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { Button, IconButton } from 'molstar/lib/mol-plugin-ui/controls/common';
+import { CubeOutlineSvg, VisibilityOffOutlinedSvg, VisibilityOutlinedSvg, MoreHorizSvg, CheckSvg, CloseSvg } from 'molstar/lib/mol-plugin-ui/controls/icons';
+import { ParameterControls } from 'molstar/lib/mol-plugin-ui/controls/parameters';
+import { debounceTime } from 'rxjs/operators';
+import { Subject } from 'rxjs';
+import { PluginCustomState } from '../plugin-custom-state';
+export class SuperpositionComponentControls extends CollapsableControls {
+    defaultState() {
+        return {
+            header: 'Components',
+            isCollapsed: false,
+            isDisabled: false,
+            brand: { accent: 'blue', svg: CubeOutlineSvg }
+        };
+    }
+    renderControls() {
+        return _jsx(_Fragment, { children: _jsx(ComponentListControls, {}) });
+    }
+}
+;
+class ComponentListControls extends PurePluginUIComponent {
+    state = {
+        segmentWatch: false,
+        ligSearchText: '',
+        carbSearchText: '',
+        componentGroups: { nonLigGroups: [], ligGroups: [], carbGroups: [], alphafold: [] },
+        ligGroups: [],
+        isLigCollapsed: false,
+        carbGroups: [],
+        isCarbCollapsed: false,
+        isBusy: false
+    };
+    ligInputStream = new Subject();
+    handleLigInputStream = (inputStr) => {
+        this.setState({ ligSearchText: inputStr });
+        const filteredRes = this.state.componentGroups.ligGroups.filter((g) => {
+            const gKeys = g[0].key.split(',');
+            const cId1Arr = gKeys[0].split('-');
+            return cId1Arr[2].toLowerCase().indexOf(inputStr.toLowerCase()) >= 0;
+        });
+        this.setState({ ligGroups: filteredRes });
+    };
+    carbInputStream = new Subject();
+    handleCarbInputStream = (inputStr) => {
+        this.setState({ carbSearchText: inputStr });
+        const filteredRes = this.state.componentGroups.carbGroups.filter((g) => {
+            const gKeys = g[0].key.split(',');
+            const cId1Arr = gKeys[0].split('-');
+            cId1Arr.splice(0, 2);
+            cId1Arr.pop();
+            return cId1Arr.join('-').toLowerCase().indexOf(inputStr.toLowerCase()) >= 0;
+        });
+        this.setState({ carbGroups: filteredRes });
+    };
+    componentDidMount() {
+        this.subscribe(this.plugin.managers.structure.hierarchy.behaviors.selection, () => {
+            this.categoriseGroups();
+            this.forceUpdate();
+        });
+        this.subscribe(this.plugin.behaviors.state.isBusy, v => {
+            this.setState({ isBusy: v });
+        });
+    }
+    componentDidUpdate() {
+        const customState = PluginCustomState(this.plugin);
+        if (customState.events && !this.state.segmentWatch) {
+            this.setState({ segmentWatch: true });
+            this.subscribe(customState.events.segmentUpdate, () => {
+                this.categoriseGroups();
+                this.forceUpdate();
+            });
+        }
+        this.subscribe(this.ligInputStream.pipe(debounceTime(1000 / 24)), e => this.handleLigInputStream(e));
+        this.subscribe(this.carbInputStream.pipe(debounceTime(1000 / 24)), e => this.handleCarbInputStream(e));
+    }
+    categoriseGroups() {
+        const componentGroupsVal = { nonLigGroups: [], ligGroups: [], carbGroups: [], alphafold: [] };
+        const componentGroups = this.plugin.managers.structure.hierarchy.currentComponentGroups;
+        const customState = PluginCustomState(this.plugin);
+        componentGroups.forEach((g) => {
+            const superpositionState = customState.superpositionState;
+            if (!superpositionState)
+                throw new Error('customState.superpositionState has not been initialized');
+            let isLigandView = false;
+            if (customState.initParams && customState.initParams.superpositionParams && customState.initParams.superpositionParams.ligandView) {
+                isLigandView = true;
+            }
+            if (isLigandView) {
+                const gKeys = g[0].key.split(',');
+                const cId1Arr = gKeys[0].split('-');
+                if (gKeys.indexOf('superposition-focus-surr-sel') === -1) {
+                    if (cId1Arr[cId1Arr.length - 1] !== (superpositionState.activeSegment - 1) + '')
+                        return;
+                    if (gKeys.indexOf('superposition-ligand-sel') >= 0) {
+                        componentGroupsVal.ligGroups.push(g);
+                    }
+                    else if (gKeys.indexOf('superposition-carb-sel') >= 0) {
+                        componentGroupsVal.carbGroups.push(g);
+                    }
+                    else if (gKeys.indexOf('alphafold-chain') >= 0) {
+                        componentGroupsVal.alphafold.push(g);
+                    }
+                    else {
+                        componentGroupsVal.nonLigGroups.push(g);
+                    }
+                }
+                else {
+                    componentGroupsVal.nonLigGroups.push(g);
+                }
+            }
+            else {
+                const gKeys = g[0].key.split(',');
+                if (gKeys.indexOf('superposition-focus-surr-sel') >= 0 || gKeys.indexOf(`Chain-${superpositionState.activeSegment - 1}`) >= 0) {
+                    componentGroupsVal.nonLigGroups.push(g);
+                }
+                else if (gKeys.indexOf('alphafold-chain') >= 0) {
+                    componentGroupsVal.alphafold.push(g);
+                }
+            }
+        });
+        this.setState({ componentGroups: componentGroupsVal, ligGroups: componentGroupsVal.ligGroups, carbGroups: componentGroupsVal.carbGroups, ligSearchText: '', carbSearchText: '' });
+    }
+    toggleVisible = (e, action, type) => {
+        e.preventDefault();
+        e.currentTarget.blur();
+        const customState = PluginCustomState(this.plugin);
+        customState.events?.isBusy.next(true);
+        const visualEntites = (type === 'ligands') ? this.state.ligGroups : this.state.carbGroups;
+        setTimeout(async () => {
+            for await (const visualEntity of visualEntites) {
+                this.plugin.managers.structure.hierarchy.toggleVisibility(visualEntity, action);
+            }
+            ;
+            customState.events?.isBusy.next(false);
+        });
+    };
+    showHideAllControls = (type) => {
+        return _jsxs(_Fragment, { children: [_jsx(Button, { icon: CheckSvg, flex: true, onClick: (e) => this.toggleVisible(e, 'show', type), style: { flex: '0 0 50px', textAlign: 'center', fontSize: '80%', color: '#9cacc3', padding: 0 }, title: `Show all ${type}`, disabled: false, children: "All" }), _jsx(Button, { icon: CloseSvg, flex: true, onClick: (e) => this.toggleVisible(e, 'hide', type), style: { flex: '0 0 50px', textAlign: 'center', fontSize: '80%', color: '#9cacc3', padding: 0 }, title: `Hide all ${type}`, disabled: false, children: "None" })] });
+    };
+    clearLigSearch = (e) => {
+        e.preventDefault();
+        this.setState({ ligSearchText: '' });
+        this.ligInputStream.next('');
+        e.currentTarget.blur();
+    };
+    clearCarbSearch = (e) => {
+        e.preventDefault();
+        this.setState({ carbSearchText: '' });
+        this.carbInputStream.next('');
+        e.currentTarget.blur();
+    };
+    collapseSection = (e, type) => {
+        e.preventDefault();
+        e.currentTarget.blur();
+        if (type === 'ligands') {
+            this.setState({ isLigCollapsed: !this.state.isLigCollapsed });
+        }
+        else {
+            this.setState({ isCarbCollapsed: !this.state.isCarbCollapsed });
+        }
+    };
+    sectionHeader = (type) => {
+        const showHideAllControls = (type === 'ligands') ? this.showHideAllControls('ligands') : this.showHideAllControls('carbohydrates');
+        const title = (type === 'ligands') ? 'Ligand' : 'Carbohydrates';
+        const visibleVisuals = (type === 'ligands') ? this.state.ligGroups.length : this.state.carbGroups.length;
+        const totalVisuals = (type === 'ligands') ? this.state.componentGroups.ligGroups.length : this.state.componentGroups.carbGroups.length;
+        return _jsxs("div", { className: 'msp-flex-row', style: { marginTop: '6px' }, children: [_jsxs("button", { className: 'msp-form-control msp-control-button-label msp-transform-header-brand-gray', style: { textAlign: 'left' }, onClick: (e) => this.collapseSection(e, type), children: [_jsx("span", { children: _jsx("strong", { children: title }) }), _jsxs("small", { style: { color: '#7d91b0' }, children: [" ( ", visibleVisuals, visibleVisuals < totalVisuals ? ` / ${totalVisuals}` : '', " )"] })] }), visibleVisuals > 1 && showHideAllControls] });
+    };
+    render() {
+        const ligSearchControls = _jsxs("div", { className: 'msp-mapped-parameter-group', style: { fontSize: '90%' }, children: [_jsxs("div", { className: 'msp-control-row msp-transform-header-brand-gray', style: { height: '33px' }, children: [_jsx("span", { className: 'msp-control-row-label', children: "Search Ligand" }), _jsx("div", { className: 'msp-control-row-ctrl', children: _jsx("input", { type: 'text', placeholder: 'Enter HET code', disabled: this.state.isBusy, onChange: e => this.ligInputStream.next(e.target.value), value: this.state.ligSearchText, maxLength: 3 }) })] }), _jsx(IconButton, { svg: CloseSvg, flex: true, onClick: this.clearLigSearch, style: { flex: '0 0 24px', padding: 0 }, disabled: this.state.ligSearchText === '' || this.state.isBusy, toggleState: this.state.ligSearchText !== '', title: 'Clear search input' })] });
+        const carbSearchControls = _jsxs("div", { className: 'msp-mapped-parameter-group', style: { fontSize: '90%' }, children: [_jsxs("div", { className: 'msp-control-row msp-transform-header-brand-gray', style: { height: '33px' }, children: [_jsx("span", { className: 'msp-control-row-label', children: "Search Carbohydrate" }), _jsx("div", { className: 'msp-control-row-ctrl', children: _jsx("input", { type: 'text', placeholder: 'Enter HET code', disabled: this.state.isBusy, onChange: e => this.carbInputStream.next(e.target.value), value: this.state.carbSearchText, maxLength: 3 }) })] }), _jsx(IconButton, { svg: CloseSvg, flex: true, onClick: this.clearCarbSearch, style: { flex: '0 0 24px', padding: 0 }, disabled: this.state.carbSearchText === '' || this.state.isBusy, toggleState: this.state.carbSearchText !== '', title: 'Clear search input' })] });
+        const ligSectionHeader = this.sectionHeader('ligands');
+        const carbSectionHeader = this.sectionHeader('carbohydrates');
+        return _jsxs(_Fragment, { children: [(this.state.componentGroups.nonLigGroups.length > 0) && _jsx("div", { children: this.state.componentGroups.nonLigGroups.map((g) => _jsx(StructureComponentGroup, { group: g, boldHeader: true }, g[0].cell.transform.ref)) }), (this.state.componentGroups.alphafold.length > 0) && _jsx("div", { children: this.state.componentGroups.alphafold.map((g) => _jsx(StructureComponentGroup, { group: g, boldHeader: true, type: 'alphafold' }, g[0].cell.transform.ref)) }), (this.state.componentGroups.ligGroups.length > 0) && ligSectionHeader, (!this.state.isLigCollapsed && this.state.componentGroups.ligGroups.length > 5) && ligSearchControls, (this.state.componentGroups.ligGroups.length > 0) && _jsx("div", { className: 'msp-control-offset', style: { maxHeight: '800px', overflowY: 'auto' }, children: !this.state.isLigCollapsed && this.state.ligGroups.map((g) => _jsx(StructureComponentGroup, { group: g, boldHeader: false }, g[0].cell.transform.ref)) }), (this.state.componentGroups.carbGroups.length > 0) && carbSectionHeader, (!this.state.isCarbCollapsed && this.state.componentGroups.carbGroups.length > 5) && carbSearchControls, (this.state.componentGroups.carbGroups.length > 0) && _jsx("div", { className: 'msp-control-offset', style: { maxHeight: '800px', overflowY: 'auto' }, children: !this.state.isCarbCollapsed && this.state.carbGroups.map((g) => _jsx(StructureComponentGroup, { group: g, boldHeader: false }, g[0].cell.transform.ref)) })] });
+    }
+}
+class StructureComponentGroup extends PurePluginUIComponent {
+    state = {
+        action: void 0,
+        isHidden: false,
+        isBusy: false
+    };
+    get pivot() {
+        return this.props.group[0];
+    }
+    checkAllHidden = async () => {
+        let allHidden = true;
+        for (const c of this.props.group) {
+            if (!c.cell.state.isHidden) {
+                allHidden = false;
+                break;
+            }
+        }
+        if (allHidden)
+            this.setState({ isHidden: true });
+    };
+    componentDidMount() {
+        this.checkAllHidden();
+        this.subscribe(this.plugin.state.events.cell.stateUpdated, e => {
+            // if (State.ObjectEvent.isCell(e, this.pivot.cell)) this.forceUpdate();
+            if (this.pivot.cell.obj?.label === e.cell.obj?.label) {
+                if (!e.cell.state.isHidden) {
+                    this.setState({ isHidden: false });
+                }
+                else {
+                    this.checkAllHidden();
+                }
+            }
+        });
+        this.subscribe(this.plugin.behaviors.state.isBusy, v => {
+            this.setState({ isBusy: v });
+        });
+        this.subscribe(PluginCustomState(this.plugin).events.isBusy, (e) => {
+            this.setState({ isBusy: e });
+        });
+    }
+    toggleVisible = (e) => {
+        e.preventDefault();
+        e.currentTarget.blur();
+        this.plugin.managers.structure.component.toggleVisibility(this.props.group);
+        this.setState({ isHidden: !this.state.isHidden });
+        if (this.props.type === 'alphafold') {
+            const spState = PluginCustomState(this.plugin).superpositionState;
+            if (!spState)
+                throw new Error('customState.superpositionState has not been initialized');
+            spState.alphafold.visibility[spState.activeSegment - 1] = this.state.isHidden;
+        }
+    };
+    toggleAction = () => this.setState({ action: this.state.action === 'action' ? void 0 : 'action' });
+    highlight = (e) => {
+        e.preventDefault();
+        if (!this.props.group[0].cell.parent)
+            return;
+        PluginCommands.Interactivity.Object.Highlight(this.plugin, { state: this.props.group[0].cell.parent, ref: this.props.group.map(c => c.cell.transform.ref) });
+    };
+    clearHighlight = (e) => {
+        e.preventDefault();
+        PluginCommands.Interactivity.ClearHighlights(this.plugin);
+    };
+    focus = () => {
+        let allHidden = true;
+        for (const c of this.props.group) {
+            if (!c.cell.state.isHidden) {
+                allHidden = false;
+                break;
+            }
+        }
+        if (allHidden) {
+            this.plugin.managers.structure.hierarchy.toggleVisibility(this.props.group, 'show');
+        }
+        this.plugin.managers.camera.focusSpheres(this.props.group, e => {
+            if (e.cell.state.isHidden)
+                return;
+            return e.cell.obj?.data.boundary.sphere;
+        });
+    };
+    render() {
+        const component = this.pivot;
+        const cell = component.cell;
+        const label = cell.obj?.label;
+        const labelEle = this.props.boldHeader ? _jsx("strong", { children: label }) : label;
+        return _jsxs(_Fragment, { children: [_jsxs("div", { className: 'msp-flex-row', children: [_jsx(Button, { noOverflow: true, className: 'msp-control-button-label', title: `${label} - Click to focus.`, onClick: this.focus, style: { textAlign: 'left' }, disabled: this.state.isBusy, children: labelEle }), _jsx(IconButton, { disabled: this.state.isBusy, svg: this.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, onClick: this.toggleVisible, title: `${this.state.isHidden ? 'Show' : 'Hide'} component`, small: true, className: 'msp-form-control', flex: true }), _jsx(IconButton, { disabled: this.state.isBusy, svg: MoreHorizSvg, onClick: this.toggleAction, title: 'Actions', toggleState: this.state.action === 'action', className: 'msp-form-control', flex: true })] }), this.state.action === 'action' && _jsx("div", { className: 'msp-accent-offset', children: _jsx("div", { style: { marginBottom: '6px' }, children: component.representations.map(r => _jsx(StructureRepresentationEntry, { group: this.props.group, representation: r }, r.cell.transform.ref)) }) })] });
+    }
+}
+class StructureRepresentationEntry extends PurePluginUIComponent {
+    state = {
+        isBusy: false,
+        clusterVal: { cluster: 'All' }
+    };
+    remove = () => this.plugin.managers.structure.component.removeRepresentations(this.props.group, this.props.representation);
+    toggleVisible = (e) => {
+        e.preventDefault();
+        e.currentTarget.blur();
+        this.plugin.managers.structure.component.toggleVisibility(this.props.group, this.props.representation);
+    };
+    componentDidMount() {
+        this.subscribe(this.plugin.state.events.cell.stateUpdated, e => {
+            if (State.ObjectEvent.isCell(e, this.props.representation.cell))
+                this.forceUpdate();
+        });
+        this.subscribe(this.plugin.behaviors.state.isBusy, v => {
+            this.setState({ isBusy: v });
+        });
+        this.subscribe(PluginCustomState(this.plugin).events.isBusy, (e) => {
+            this.setState({ isBusy: e });
+        });
+    }
+    updateRepresentations(components, pivot, params) {
+        if (components.length === 0)
+            return Promise.resolve();
+        const index = components[0].representations.indexOf(pivot);
+        if (index < 0)
+            return Promise.resolve();
+        const superpositionState = PluginCustomState(this.plugin).superpositionState;
+        if (!superpositionState)
+            throw new Error('customState.superpositionState has not been initialized');
+        let filteredComps = [];
+        if (this.state.clusterVal.cluster !== 'All') {
+            if (!superpositionState.segmentData)
+                throw new Error('customState.superpositionState.segmentData has not been initialized');
+            const clusterData = superpositionState.segmentData[superpositionState.activeSegment - 1].clusters[parseInt(this.state.clusterVal.cluster) - 1];
+            filteredComps = clusterData.map((s) => {
+                return `${s.pdb_id}_${s.struct_asym_id}`;
+            });
+            if (filteredComps.length === 0)
+                return;
+        }
+        const update = this.plugin.state.data.build();
+        for (const c of components) {
+            // TODO: is it ok to use just the index here? Could possible lead to ugly edge cases, but perhaps not worth the trouble to "fix".
+            const repr = c.representations[index];
+            if (!repr)
+                continue;
+            if (repr.cell.transform.transformer !== pivot.cell.transform.transformer)
+                continue;
+            if (this.state.clusterVal.cluster !== 'All') {
+                const rmIndex = filteredComps.indexOf(superpositionState.refMaps[repr.cell.transform.parent]);
+                if (rmIndex === -1)
+                    continue;
+            }
+            const updatedParams = {
+                type: params.type ? params.type : repr.cell.params?.values.type,
+                colorTheme: params.colorTheme ? params.colorTheme : repr.cell.params?.values.colorTheme,
+                sizeTheme: params.sizeTheme ? params.sizeTheme : repr.cell.params?.values.sizeTheme
+            };
+            update.to(repr.cell).update(updatedParams);
+        }
+        return update.commit({ canUndo: 'Update Representation' });
+    }
+    update = (params) => {
+        return this.updateRepresentations(this.props.group, this.props.representation, params);
+    };
+    selectCluster = (params) => {
+        this.setState({ clusterVal: { cluster: params.cluster } });
+    };
+    render() {
+        const repr = this.props.representation.cell;
+        const superpositionState = PluginCustomState(this.plugin).superpositionState;
+        const clusterSelectArr = [['All', 'All']];
+        if (!superpositionState?.segmentData)
+            throw new Error('customState.superpositionState.segmentData has not been initialized');
+        superpositionState.segmentData[superpositionState.activeSegment - 1].clusters.forEach((c, i) => {
+            clusterSelectArr.push([(i + 1) + '', (i + 1) + '']);
+        });
+        const clusterOptions = {
+            cluster: ParamDefinition.Select('All', clusterSelectArr, { label: 'Select Cluster' })
+        };
+        let isSurrVisual = false;
+        let isAlphafold = false;
+        if (repr && repr.obj) {
+            const reprObj = repr.obj;
+            if (reprObj.tags && reprObj.tags.indexOf('superposition-focus-surr-repr') >= 0)
+                isSurrVisual = true;
+            if (reprObj.tags && reprObj.tags.indexOf('af-superposition-visual') >= 0)
+                isAlphafold = true;
+        }
+        return _jsx("div", { className: 'msp-representation-entry', children: repr.parent && _jsxs("div", { children: [(clusterSelectArr.length > 2 && !isSurrVisual && !isAlphafold) && _jsx("div", { className: 'msp-representation-entry', children: _jsx(ParameterControls, { params: clusterOptions, values: this.state.clusterVal, onChangeValues: this.selectCluster, isDisabled: this.state.isBusy }) }), _jsx("div", { className: 'msp-representation-entry', children: _jsx(ParameterControls, { params: { type: repr.params?.definition.type }, values: { type: repr.params?.values.type }, onChangeValues: this.update, isDisabled: this.state.isBusy }) }), _jsx("div", { className: 'msp-representation-entry', children: _jsx(ParameterControls, { params: { colorTheme: repr.params?.definition.colorTheme }, values: { colorTheme: repr.params?.values.colorTheme }, onChangeValues: this.update, isDisabled: this.state.isBusy }) }), _jsx("div", { className: 'msp-representation-entry', children: _jsx(ParameterControls, { params: { sizeTheme: repr.params?.definition.sizeTheme }, values: { sizeTheme: repr.params?.values.sizeTheme }, onChangeValues: this.update, isDisabled: this.state.isBusy }) })] }) });
+    }
+}
diff --git a/frontend/venome-molstar/lib/ui/superposition-viewport.d.ts b/frontend/venome-molstar/lib/ui/superposition-viewport.d.ts
new file mode 100644
index 00000000..44faa1bf
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/superposition-viewport.d.ts
@@ -0,0 +1,4 @@
+import { PluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+export declare class SuperpostionViewport extends PluginUIComponent {
+    render(): import("react/jsx-runtime").JSX.Element;
+}
diff --git a/frontend/venome-molstar/lib/ui/superposition-viewport.js b/frontend/venome-molstar/lib/ui/superposition-viewport.js
new file mode 100644
index 00000000..d5e761da
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/superposition-viewport.js
@@ -0,0 +1,12 @@
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
+import { PluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { LociLabels, StateSnapshotViewportControls, SelectionViewportControls } from 'molstar/lib/mol-plugin-ui/controls';
+import { BackgroundTaskProgress } from 'molstar/lib/mol-plugin-ui/task';
+import { Toasts } from 'molstar/lib/mol-plugin-ui/toast';
+import { Viewport, ViewportControls } from 'molstar/lib/mol-plugin-ui/viewport';
+export class SuperpostionViewport extends PluginUIComponent {
+    render() {
+        const VPControls = this.plugin.spec.components?.viewport?.controls || ViewportControls;
+        return _jsxs(_Fragment, { children: [_jsx(Viewport, {}), _jsx("div", { className: 'msp-viewport-top-left-controls', children: _jsx(StateSnapshotViewportControls, {}) }), _jsx(SelectionViewportControls, {}), _jsx(VPControls, {}), _jsx(BackgroundTaskProgress, {}), _jsxs("div", { className: 'msp-highlight-toast-wrapper', children: [_jsx(LociLabels, {}), _jsx(Toasts, {})] })] });
+    }
+}
diff --git a/frontend/venome-molstar/lib/ui/symmetry-annotation-controls.d.ts b/frontend/venome-molstar/lib/ui/symmetry-annotation-controls.d.ts
new file mode 100644
index 00000000..e934934a
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/symmetry-annotation-controls.d.ts
@@ -0,0 +1,46 @@
+import { AssemblySymmetryParams, AssemblySymmetryProps } from 'molstar/lib/extensions/rcsb/assembly-symmetry/prop';
+import { StructureRef } from 'molstar/lib/mol-plugin-state/manager/structure/hierarchy-state';
+import { PurePluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { PluginContext } from 'molstar/lib/mol-plugin/context';
+import { UUID } from 'molstar/lib/mol-util';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
+type SymmetryParams = {
+    /** State of the visibility button */
+    on: PD.BooleanParam;
+    /** Index of the currently selected symmetry (in case there a more symmetries for an assembly), regardless of whether visibility is on of off */
+    symmetryIndex: PD.Select;
+    /** `true` if symmetry data have been retrieved but do not contain any non-trivial symmetry */
+    noSymmetries: PD.BooleanParam;
+};
+type SymmetryParamValues = PD.ValuesFor;
+interface SymmetryControlsState {
+    params: SymmetryParams;
+    values: SymmetryParamValues;
+}
+/** UI controls for showing Assembly Symmetry annotations (a row within Annotations section) */
+export declare class SymmetryAnnotationControls extends PurePluginUIComponent<{}, SymmetryControlsState> {
+    state: SymmetryControlsState;
+    currentStructureId: UUID | undefined;
+    componentDidMount(): void;
+    /** Synchronize parameters and values in UI with real parameters currently applied in `AssemblySymmetryProvider` */
+    syncParams(): void;
+    /** Return `true` if symmetry data have been retrieved and do not contain any non-trivial symmetry. */
+    noSymmetriesAvailable(): boolean;
+    /** Get the first loaded structure, if any. */
+    getPivotStructure(): StructureRef | undefined;
+    /** Get parameters currently applied in `AssemblySymmetryProvider` */
+    getRealParams(): AssemblySymmetryParams;
+    /** Get parameter values currently applied in `AssemblySymmetryProvider` */
+    getRealValues(): AssemblySymmetryProps;
+    /** Return `true` if an `AssemblySymmetry3D` node existing in the   */
+    hasAssemblySymmetry3D(): boolean;
+    /** Run changes needed to set visibility on or off, and set UI accordingly */
+    apply(applied: boolean): Promise;
+    /** Run changes needed to change parameter values, and set UI accordingly*/
+    changeParamValues(values: SymmetryParamValues): Promise;
+    /** Try to retrieve symmetry data and create `AssemblySymmetry3D` representation */
+    initSymmetry(initialSymmetryIndex?: number): Promise;
+    render(): import("react/jsx-runtime").JSX.Element;
+}
+export declare function isAssemblySymmetryAnnotationApplicable(plugin: PluginContext): boolean;
+export {};
diff --git a/frontend/venome-molstar/lib/ui/symmetry-annotation-controls.js b/frontend/venome-molstar/lib/ui/symmetry-annotation-controls.js
new file mode 100644
index 00000000..3ec66757
--- /dev/null
+++ b/frontend/venome-molstar/lib/ui/symmetry-annotation-controls.js
@@ -0,0 +1,213 @@
+import { jsx as _jsx, Fragment as _Fragment } from "react/jsx-runtime";
+import { AssemblySymmetry3D, getRCSBAssemblySymmetryConfig, tryCreateAssemblySymmetry } from 'molstar/lib/extensions/rcsb/assembly-symmetry/behavior';
+import { AssemblySymmetry, AssemblySymmetryDataProvider, AssemblySymmetryProvider } from 'molstar/lib/extensions/rcsb/assembly-symmetry/prop';
+import { PurePluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { StateSelection } from 'molstar/lib/mol-state';
+import { Task } from 'molstar/lib/mol-task';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
+import { AnnotationRowControls } from './annotation-row-controls';
+const DefaultSymmetryControlsState = {
+    params: {
+        on: PD.Boolean(false, { isHidden: true }),
+        symmetryIndex: PD.Select(0, [[0, 'Auto']]),
+        noSymmetries: PD.Boolean(false, { isHidden: true }),
+    },
+    values: {
+        on: false,
+        symmetryIndex: 0,
+        noSymmetries: false,
+    },
+};
+/** UI controls for showing Assembly Symmetry annotations (a row within Annotations section) */
+export class SymmetryAnnotationControls extends PurePluginUIComponent {
+    state = DefaultSymmetryControlsState;
+    currentStructureId = undefined;
+    componentDidMount() {
+        // Reset state when the pivot structure changes
+        this.subscribe(this.plugin.managers.structure.hierarchy.behaviors.selection, c => {
+            const structureObj = c.structures[0]?.cell.obj;
+            const structureId = structureObj?.id;
+            if (structureId !== this.currentStructureId) {
+                this.currentStructureId = structureId;
+                this.syncParams();
+            }
+        });
+        // Synchronize params when AssemblySymmetry3D changes
+        this.subscribe(this.plugin.state.events.cell.stateUpdated, e => {
+            if (e.cell.transform.transformer === AssemblySymmetry3D) {
+                this.syncParams();
+            }
+        });
+        // Synchronize params when AssemblySymmetry3D is removed
+        this.subscribe(this.plugin.state.events.cell.removed, e => {
+            this.syncParams();
+        });
+    }
+    /** Synchronize parameters and values in UI with real parameters currently applied in `AssemblySymmetryProvider` */
+    syncParams() {
+        if (this.hasAssemblySymmetry3D()) {
+            const noSymmetries = this.noSymmetriesAvailable();
+            const realParams = this.getRealParams();
+            const realValues = this.getRealValues();
+            const options = noSymmetries ?
+                [[0, 'None']]
+                : realParams.symmetryIndex.options.filter(([index, label]) => index >= 0); // Removing the 'off' option (having index -1)
+            const params = {
+                ...this.state.params,
+                symmetryIndex: PD.Select(0, options),
+            };
+            const values = (realValues.symmetryIndex >= 0) ? {
+                on: true,
+                symmetryIndex: realValues.symmetryIndex,
+                noSymmetries: noSymmetries,
+            } : {
+                on: false,
+                symmetryIndex: this.state.values.symmetryIndex,
+                noSymmetries: noSymmetries,
+            };
+            this.setState({ params, values });
+        }
+        else {
+            this.setState({
+                params: DefaultSymmetryControlsState.params,
+                values: DefaultSymmetryControlsState.values,
+            });
+        }
+    }
+    /** Return `true` if symmetry data have been retrieved and do not contain any non-trivial symmetry. */
+    noSymmetriesAvailable() {
+        const structure = this.getPivotStructure()?.cell.obj?.data;
+        const symmetryData = structure && AssemblySymmetryDataProvider.get(structure).value;
+        return symmetryData !== undefined && symmetryData.filter(sym => sym.symbol !== 'C1').length === 0;
+    }
+    /** Get the first loaded structure, if any. */
+    getPivotStructure() {
+        return getPivotStructure(this.plugin);
+    }
+    /** Get parameters currently applied in `AssemblySymmetryProvider` */
+    getRealParams() {
+        const structure = this.getPivotStructure()?.cell.obj?.data;
+        let params;
+        if (structure) {
+            params = AssemblySymmetryProvider.getParams(structure);
+        }
+        else {
+            params = AssemblySymmetryProvider.defaultParams;
+        }
+        return params;
+    }
+    /** Get parameter values currently applied in `AssemblySymmetryProvider` */
+    getRealValues() {
+        const structure = this.getPivotStructure()?.cell.obj?.data;
+        if (structure) {
+            return AssemblySymmetryProvider.props(structure);
+        }
+        else {
+            return { ...PD.getDefaultValues(AssemblySymmetryProvider.defaultParams), symmetryIndex: -1 };
+        }
+    }
+    /** Return `true` if an `AssemblySymmetry3D` node existing in the   */
+    hasAssemblySymmetry3D() {
+        const struct = this.getPivotStructure();
+        const state = struct?.cell.parent;
+        return state !== undefined && !!StateSelection.findTagInSubtree(state.tree, struct.cell.transform.ref, AssemblySymmetry.Tag.Representation);
+    }
+    /** Run changes needed to set visibility on or off, and set UI accordingly */
+    async apply(applied) {
+        if (applied) {
+            if (this.hasAssemblySymmetry3D()) {
+                await this.changeParamValues({ ...this.state.values, on: true });
+            }
+            else {
+                await this.initSymmetry();
+            }
+            this.setState(old => ({ values: { ...old.values, on: true } }));
+        }
+        else {
+            if (this.hasAssemblySymmetry3D()) {
+                await this.changeParamValues({ ...this.state.values, on: false });
+            }
+            else {
+                // no action needed
+            }
+            this.setState(old => ({ values: { ...old.values, on: false } }));
+        }
+    }
+    /** Run changes needed to change parameter values, and set UI accordingly*/
+    async changeParamValues(values) {
+        const struct = this.getPivotStructure();
+        if (!struct)
+            return;
+        const currValues = this.getRealValues();
+        const newValues = { ...currValues, symmetryIndex: values.on ? values.symmetryIndex : -1 };
+        if (struct.properties) {
+            const b = this.plugin.state.data.build();
+            b.to(struct.properties.cell).update(old => {
+                old.properties[AssemblySymmetryProvider.descriptor.name] = newValues;
+            });
+            await b.commit();
+        }
+        else {
+            const pd = this.plugin.customStructureProperties.getParams(struct.cell.obj?.data);
+            const params = PD.getDefaultValues(pd);
+            params.properties[AssemblySymmetryProvider.descriptor.name] = newValues;
+            await this.plugin.builders.structure.insertStructureProperties(struct.cell, params);
+        }
+        if (!values.on) { // if values.on, parameters will be updated via subscription
+            this.setState({ values });
+        }
+    }
+    /** Try to retrieve symmetry data and create `AssemblySymmetry3D` representation */
+    async initSymmetry(initialSymmetryIndex) {
+        await Task.create('Initialize Assembly Symmetry', async (ctx) => {
+            const struct = this.getPivotStructure();
+            const data = struct?.cell.obj?.data;
+            if (!data)
+                return;
+            try {
+                const propCtx = { runtime: ctx, assetManager: this.plugin.managers.asset };
+                const config = getRCSBAssemblySymmetryConfig(this.plugin);
+                const symmetryDataProps = {
+                    serverType: config.DefaultServerType,
+                    serverUrl: config.DefaultServerUrl,
+                };
+                await AssemblySymmetryDataProvider.attach(propCtx, data, symmetryDataProps);
+                const assemblySymmetryData = AssemblySymmetryDataProvider.get(data).value;
+                const symmetryIndex = initialSymmetryIndex ?? (assemblySymmetryData ? AssemblySymmetry.firstNonC1(assemblySymmetryData) : -1);
+                const symmetryProps = { ...symmetryDataProps, symmetryIndex };
+                await AssemblySymmetryProvider.attach(propCtx, data, symmetryProps);
+            }
+            catch (e) {
+                this.plugin.log.error(`Assembly Symmetry: ${e}`);
+                return;
+            }
+            await tryCreateAssemblySymmetry(this.plugin, struct.cell);
+        }).run();
+    }
+    render() {
+        const shortTitle = 'Assembly Symmetry' + (this.state.values.noSymmetries ? ' [Not Available]' : '');
+        const title = 'Assembly Symmetry' + (this.state.values.noSymmetries ? ' [Not Available]\nSymmetry information for this assembly is not available' : '');
+        return _jsx(_Fragment, { children: _jsx(SymmetryAnnotationRowControls, { shortTitle: shortTitle, title: title, applied: this.state.values.on, onChangeApplied: applied => this.apply(applied), params: this.state.params, values: this.state.values, onChangeValues: v => this.changeParamValues(v) }) });
+    }
+}
+class SymmetryAnnotationRowControls extends AnnotationRowControls {
+    renderOptions() {
+        if (this.props.values.noSymmetries) {
+            return _jsx("div", { className: 'msp-row-text', children: _jsx("div", { title: 'Symmetry information for this assembly is not available', children: "Symmetry information not available" }) });
+        }
+        return super.renderOptions();
+    }
+}
+/** Get the first loaded structure, if any. */
+function getPivotStructure(plugin) {
+    return plugin.managers.structure.hierarchy.selection.structures[0];
+}
+export function isAssemblySymmetryAnnotationApplicable(plugin) {
+    const struct = getPivotStructure(plugin);
+    const isAssembly = struct?.cell.obj?.data?.units[0].conformation.operator.assembly !== undefined;
+    return isAssembly && AssemblySymmetry.isApplicable(struct?.cell.obj?.data);
+    // It would be nice to disable the default `AssemblySymmetry.isApplicable` behavior
+    // (i.e. hiding Assembly Symmetry controls for non-biological assemblies, e.g. 1smv assembly 3)
+    // by `AssemblySymmetry.isApplicable = struct => struct?.units[0].conformation.operator.assembly !== undefined;`
+    // But we cannot easily override the `fetch` function which calls the original `isApplicable`.
+}
diff --git a/frontend/venome-molstar/package-lock.json b/frontend/venome-molstar/package-lock.json
new file mode 100644
index 00000000..de37a0df
--- /dev/null
+++ b/frontend/venome-molstar/package-lock.json
@@ -0,0 +1,11725 @@
+{
+	"name": "venome-molstar",
+	"version": "3.1.3",
+	"lockfileVersion": 3,
+	"requires": true,
+	"packages": {
+		"": {
+			"name": "venome-molstar",
+			"version": "3.1.3",
+			"license": "Apache-2.0",
+			"dependencies": {
+				"crypto-browserify": "^3.12.0",
+				"d3-axis": "^3.0.0",
+				"d3-brush": "^3.0.0",
+				"d3-scale": "^4.0.2",
+				"d3-selection": "^3.0.0",
+				"lit": "^3.1.1",
+				"molstar": "3.44.0",
+				"path-browserify": "^1.0.1",
+				"stream-browserify": "^3.0.0"
+			},
+			"devDependencies": {
+				"@babel/core": "^7.17.10",
+				"@babel/plugin-transform-runtime": "^7.17.10",
+				"@babel/preset-env": "^7.17.10",
+				"@babel/runtime": "^7.17.9",
+				"@types/d3": "^7.4.0",
+				"@types/react": "^18.0.17",
+				"@types/react-dom": "^18.0.6",
+				"@typescript-eslint/eslint-plugin": "^6.10.0",
+				"@typescript-eslint/parser": "^6.10.0",
+				"babel-loader": "^8.2.5",
+				"concurrently": "^7.3.0",
+				"cpx2": "^4.2.0",
+				"css-loader": "^6.7.1",
+				"eslint": "^8.53.0",
+				"extra-watch-webpack-plugin": "^1.0.3",
+				"file-loader": "^6.2.0",
+				"http-server": "^14.1.0",
+				"mini-css-extract-plugin": "^2.6.1",
+				"react": "^18.2.0",
+				"react-dom": "^18.2.0",
+				"sass": "^1.51.0",
+				"sass-loader": "^12.6.0",
+				"style-loader": "^3.3.1",
+				"typescript": "^4.6.4",
+				"webpack": "^5.89.0",
+				"webpack-cli": "^5.1.4"
+			}
+		},
+		"node_modules/@aashutoshrathi/word-wrap": {
+			"version": "1.2.6",
+			"resolved": "https://registry.npmjs.org/@aashutoshrathi/word-wrap/-/word-wrap-1.2.6.tgz",
+			"integrity": "sha512-1Yjs2SvM8TflER/OD3cOjhWWOZb58A2t7wpE2S9XfBYTiIl+XFhQG2bjy4Pu1I+EAlCNUzRDYDdFwFYUKvXcIA==",
+			"dev": true,
+			"engines": {
+				"node": ">=0.10.0"
+			}
+		},
+		"node_modules/@ampproject/remapping": {
+			"version": "2.2.1",
+			"resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.2.1.tgz",
+			"integrity": "sha512-lFMjJTrFL3j7L9yBxwYfCq2k6qqwHyzuUl/XBnif78PWTJYyL/dfowQHWE3sp6U6ZzqWiiIZnpTMO96zhkjwtg==",
+			"dev": true,
+			"dependencies": {
+				"@jridgewell/gen-mapping": "^0.3.0",
+				"@jridgewell/trace-mapping": "^0.3.9"
+			},
+			"engines": {
+				"node": ">=6.0.0"
+			}
+		},
+		"node_modules/@babel/code-frame": {
+			"version": "7.23.5",
+			"resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.23.5.tgz",
+			"integrity": "sha512-CgH3s1a96LipHCmSUmYFPwY7MNx8C3avkq7i4Wl3cfa662ldtUe4VM1TPXX70pfmrlWTb6jLqTYrZyT2ZTJBgA==",
+			"dev": true,
+			"dependencies": {
+				"@babel/highlight": "^7.23.4",
+				"chalk": "^2.4.2"
+			},
+			"engines": {
+				"node": ">=6.9.0"
+			}
+		},
+		"node_modules/@babel/compat-data": {
+			"version": "7.23.5",
+			"resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.23.5.tgz",
+			"integrity": "sha512-uU27kfDRlhfKl+w1U6vp16IuvSLtjAxdArVXPa9BvLkrr7CYIsxH5adpHObeAGY/41+syctUWOZ140a2Rvkgjw==",
+			"dev": true,
+			"engines": {
+				"node": ">=6.9.0"
+			}
+		},
+		"node_modules/@babel/core": {
+			"version": "7.23.7",
+			"resolved": "https://registry.npmjs.org/@babel/core/-/core-7.23.7.tgz",
+			"integrity": "sha512-+UpDgowcmqe36d4NwqvKsyPMlOLNGMsfMmQ5WGCu+siCe3t3dfe9njrzGfdN4qq+bcNUt0+Vw6haRxBOycs4dw==",
+			"dev": true,
+			"dependencies": {
+				"@ampproject/remapping": "^2.2.0",
+				"@babel/code-frame": "^7.23.5",
+				"@babel/generator": "^7.23.6",
+				"@babel/helper-compilation-targets": "^7.23.6",
+				"@babel/helper-module-transforms": "^7.23.3",
+				"@babel/helpers": "^7.23.7",
+				"@babel/parser": "^7.23.6",
+				"@babel/template": "^7.22.15",
+				"@babel/traverse": "^7.23.7",
+				"@babel/types": "^7.23.6",
+				"convert-source-map": "^2.0.0",
+				"debug": "^4.1.0",
+				"gensync": "^1.0.0-beta.2",
+				"json5": "^2.2.3",
+				"semver": "^6.3.1"
+			},
+			"engines": {
+				"node": ">=6.9.0"
+			},
+			"funding": {
+				"type": "opencollective",
+				"url": "https://opencollective.com/babel"
+			}
+		},
+		"node_modules/@babel/generator": {
+			"version": "7.23.6",
+			"resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.23.6.tgz",
+			"integrity": "sha512-qrSfCYxYQB5owCmGLbl8XRpX1ytXlpueOb0N0UmQwA073KZxejgQTzAmJezxvpwQD9uGtK2shHdi55QT+MbjIw==",
+			"dev": true,
+			"dependencies": {
+				"@babel/types": "^7.23.6",
+				"@jridgewell/gen-mapping": "^0.3.2",
+				"@jridgewell/trace-mapping": "^0.3.17",
+				"jsesc": "^2.5.1"
+			},
+			"engines": {
+				"node": ">=6.9.0"
+			}
+		},
+		"node_modules/@babel/helper-annotate-as-pure": {
+			"version": "7.22.5",
+			"resolved": "https://registry.npmjs.org/@babel/helper-annotate-as-pure/-/helper-annotate-as-pure-7.22.5.tgz",
+			"integrity": "sha512-LvBTxu8bQSQkcyKOU+a1btnNFQ1dMAd0R6PyW3arXes06F6QLWLIrd681bxRPIXlrMGR3XYnW9JyML7dP3qgxg==",
+			"dev": true,
+			"dependencies": {
+				"@babel/types": "^7.22.5"
+			},
+			"engines": {
+				"node": ">=6.9.0"
+			}
+		},
+		"node_modules/@babel/helper-builder-binary-assignment-operator-visitor": {
+			"version": "7.22.15",
+			"resolved": "https://registry.npmjs.org/@babel/helper-builder-binary-assignment-operator-visitor/-/helper-builder-binary-assignment-operator-visitor-7.22.15.tgz",
+			"integrity": "sha512-QkBXwGgaoC2GtGZRoma6kv7Szfv06khvhFav67ZExau2RaXzy8MpHSMO2PNoP2XtmQphJQRHFfg77Bq731Yizw==",
+			"dev": true,
+			"dependencies": {
+				"@babel/types": "^7.22.15"
+			},
+			"engines": {
+				"node": ">=6.9.0"
+			}
+		},
+		"node_modules/@babel/helper-compilation-targets": {
+			"version": "7.23.6",
+			"resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.23.6.tgz",
+			"integrity": "sha512-9JB548GZoQVmzrFgp8o7KxdgkTGm6xs9DW0o/Pim72UDjzr5ObUQ6ZzYPqA+g9OTS2bBQoctLJrky0RDCAWRgQ==",
+			"dev": true,
+			"dependencies": {
+				"@babel/compat-data": "^7.23.5",
+				"@babel/helper-validator-option": "^7.23.5",
+				"browserslist": "^4.22.2",
+				"lru-cache": "^5.1.1",
+				"semver": "^6.3.1"
+			},
+			"engines": {
+				"node": ">=6.9.0"
+			}
+		},
+		"node_modules/@babel/helper-create-class-features-plugin": {
+			"version": "7.23.7",
+			"resolved": "https://registry.npmjs.org/@babel/helper-create-class-features-plugin/-/helper-create-class-features-plugin-7.23.7.tgz",
+			"integrity": "sha512-xCoqR/8+BoNnXOY7RVSgv6X+o7pmT5q1d+gGcRlXYkI+9B31glE4jeejhKVpA04O1AtzOt7OSQ6VYKP5FcRl9g==",
+			"dev": true,
+			"dependencies": {
+				"@babel/helper-annotate-as-pure": "^7.22.5",
+				"@babel/helper-environment-visitor": "^7.22.20",
+				"@babel/helper-function-name": "^7.23.0",
+				"@babel/helper-member-expression-to-functions": "^7.23.0",
+				"@babel/helper-optimise-call-expression": "^7.22.5",
+				"@babel/helper-replace-supers": "^7.22.20",
+				"@babel/helper-skip-transparent-expression-wrappers": "^7.22.5",
+				"@babel/helper-split-export-declaration": "^7.22.6",
+				"semver": "^6.3.1"
+			},
+			"engines": {
+				"node": ">=6.9.0"
+			},
+			"peerDependencies": {
+				"@babel/core": "^7.0.0"
+			}
+		},
+		"node_modules/@babel/helper-create-regexp-features-plugin": {
+			"version": "7.22.15",
+			"resolved": "https://registry.npmjs.org/@babel/helper-create-regexp-features-plugin/-/helper-create-regexp-features-plugin-7.22.15.tgz",
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+			"dev": true,
+			"dependencies": {
+				"@babel/helper-annotate-as-pure": "^7.22.5",
+				"regexpu-core": "^5.3.1",
+				"semver": "^6.3.1"
+			},
+			"engines": {
+				"node": ">=6.9.0"
+			},
+			"peerDependencies": {
+				"@babel/core": "^7.0.0"
+			}
+		},
+		"node_modules/@babel/helper-define-polyfill-provider": {
+			"version": "0.5.0",
+			"resolved": "https://registry.npmjs.org/@babel/helper-define-polyfill-provider/-/helper-define-polyfill-provider-0.5.0.tgz",
+			"integrity": "sha512-NovQquuQLAQ5HuyjCz7WQP9MjRj7dx++yspwiyUiGl9ZyadHRSql1HZh5ogRd8W8w6YM6EQ/NTB8rgjLt5W65Q==",
+			"dev": true,
+			"dependencies": {
+				"@babel/helper-compilation-targets": "^7.22.6",
+				"@babel/helper-plugin-utils": "^7.22.5",
+				"debug": "^4.1.1",
+				"lodash.debounce": "^4.0.8",
+				"resolve": "^1.14.2"
+			},
+			"peerDependencies": {
+				"@babel/core": "^7.4.0 || ^8.0.0-0 <8.0.0"
+			}
+		},
+		"node_modules/@babel/helper-environment-visitor": {
+			"version": "7.22.20",
+			"resolved": "https://registry.npmjs.org/@babel/helper-environment-visitor/-/helper-environment-visitor-7.22.20.tgz",
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+			"dev": true,
+			"engines": {
+				"node": ">=6.9.0"
+			}
+		},
+		"node_modules/@babel/helper-function-name": {
+			"version": "7.23.0",
+			"resolved": "https://registry.npmjs.org/@babel/helper-function-name/-/helper-function-name-7.23.0.tgz",
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+			"dependencies": {
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+				"@babel/types": "^7.23.0"
+			},
+			"engines": {
+				"node": ">=6.9.0"
+			}
+		},
+		"node_modules/@babel/helper-hoist-variables": {
+			"version": "7.22.5",
+			"resolved": "https://registry.npmjs.org/@babel/helper-hoist-variables/-/helper-hoist-variables-7.22.5.tgz",
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+			"dependencies": {
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+			},
+			"engines": {
+				"node": ">=6.9.0"
+			}
+		},
+		"node_modules/@babel/helper-member-expression-to-functions": {
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+			}
+		},
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+			},
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+				"@babel/core": "^7.0.0"
+			}
+		},
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+			"version": "7.22.5",
+			"resolved": "https://registry.npmjs.org/@babel/helper-optimise-call-expression/-/helper-optimise-call-expression-7.22.5.tgz",
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+			"engines": {
+				"node": ">=6.9.0"
+			}
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+		"node_modules/@babel/helper-plugin-utils": {
+			"version": "7.22.5",
+			"resolved": "https://registry.npmjs.org/@babel/helper-plugin-utils/-/helper-plugin-utils-7.22.5.tgz",
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+		"node_modules/@babel/helper-remap-async-to-generator": {
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+				"node": ">=6.9.0"
+			},
+			"peerDependencies": {
+				"@babel/core": "^7.0.0"
+			}
+		},
+		"node_modules/@babel/helper-replace-supers": {
+			"version": "7.22.20",
+			"resolved": "https://registry.npmjs.org/@babel/helper-replace-supers/-/helper-replace-supers-7.22.20.tgz",
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+			"integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==",
+			"dev": true,
+			"engines": {
+				"node": ">=10"
+			},
+			"funding": {
+				"url": "https://github.com/sponsors/sindresorhus"
+			}
+		},
+		"node_modules/zwitch": {
+			"version": "2.0.4",
+			"resolved": "https://registry.npmjs.org/zwitch/-/zwitch-2.0.4.tgz",
+			"integrity": "sha512-bXE4cR/kVZhKZX/RjPEflHaKVhUVl85noU3v6b8apfQEc1x4A+zBxjZ4lN8LqGd6WZ3dl98pY4o717VFmoPp+A==",
+			"funding": {
+				"type": "github",
+				"url": "https://github.com/sponsors/wooorm"
+			}
+		}
+	}
+}
diff --git a/frontend/venome-molstar/package.json b/frontend/venome-molstar/package.json
new file mode 100644
index 00000000..32c341a6
--- /dev/null
+++ b/frontend/venome-molstar/package.json
@@ -0,0 +1,82 @@
+{
+	"name": "venome-molstar",
+	"version": "3.1.3",
+	"description": "Molstar implementation for venome forked from PDBe Molstar",
+	"main": "lib/",
+	"scripts": {
+		"test": "echo \"Error: no test specified\"",
+		"lint": "eslint src",
+		"build": "npm run build-tsc && npm run build-extra && node scripts.js light-skin && npm run build-webpack && node scripts.js clean-rubbish && npm run bundle-webcomponent",
+		"rebuild": "npm run clean && npm run build",
+		"clean": "node scripts.js clean-all",
+		"build-tsc": "tsc --incremental",
+		"build-extra": "cpx 'src/**/*.{scss,html,ico}' lib/",
+		"build-webpack": "webpack --mode production --config ./webpack.config.production.js",
+		"watch": "concurrently -c 'green,gray,blue' --names 'tsc,ext,wpc' --kill-others 'npm:watch-tsc' 'npm:watch-extra' 'npm:watch-webpack'",
+		"watch-tsc": "tsc --watch --incremental",
+		"watch-extra": "cpx 'src/**/*.{scss,html,ico}' lib/ --watch",
+		"watch-webpack": "webpack -w --mode development --stats minimal --config ./webpack.config.development.js",
+		"serve": "http-server -p 1338 -g",
+		"bundle-webcomponent": "node scripts.js bundle-webcomponent",
+		"ts:build": "tsc && cp src/*.scss lib/"
+	},
+	"files": [
+		"lib/",
+		"build/"
+	],
+	"repository": {
+		"type": "git",
+		"url": "git+https://github.com/PDBeurope/pdbe-molstar.git"
+	},
+	"keywords": [
+		"Molstar",
+		"3D viewer",
+		"PDBe",
+		"biojs"
+	],
+	"author": "Mandar Deshpande ",
+	"license": "Apache-2.0",
+	"bugs": {
+		"url": "https://github.com/PDBeurope/pdbe-molstar/lib/issues"
+	},
+	"homepage": "https://github.com/PDBeurope/pdbe-molstar#readme",
+	"devDependencies": {
+		"@babel/core": "^7.17.10",
+		"@babel/plugin-transform-runtime": "^7.17.10",
+		"@babel/preset-env": "^7.17.10",
+		"@babel/runtime": "^7.17.9",
+		"@types/d3": "^7.4.0",
+		"@types/react": "^18.0.17",
+		"@types/react-dom": "^18.0.6",
+		"@typescript-eslint/eslint-plugin": "^6.10.0",
+		"@typescript-eslint/parser": "^6.10.0",
+		"babel-loader": "^8.2.5",
+		"concurrently": "^7.3.0",
+		"cpx2": "^4.2.0",
+		"css-loader": "^6.7.1",
+		"eslint": "^8.53.0",
+		"extra-watch-webpack-plugin": "^1.0.3",
+		"file-loader": "^6.2.0",
+		"http-server": "^14.1.0",
+		"mini-css-extract-plugin": "^2.6.1",
+		"react": "^18.2.0",
+		"react-dom": "^18.2.0",
+		"sass": "^1.51.0",
+		"sass-loader": "^12.6.0",
+		"style-loader": "^3.3.1",
+		"typescript": "^4.6.4",
+		"webpack": "^5.89.0",
+		"webpack-cli": "^5.1.4"
+	},
+	"dependencies": {
+		"crypto-browserify": "^3.12.0",
+		"d3-axis": "^3.0.0",
+		"d3-brush": "^3.0.0",
+		"d3-scale": "^4.0.2",
+		"d3-selection": "^3.0.0",
+		"lit": "^3.1.1",
+		"molstar": "3.44.0",
+		"path-browserify": "^1.0.1",
+		"stream-browserify": "^3.0.0"
+	}
+}
diff --git a/frontend/venome-molstar/portfolio.html b/frontend/venome-molstar/portfolio.html
new file mode 100644
index 00000000..da91a49c
--- /dev/null
+++ b/frontend/venome-molstar/portfolio.html
@@ -0,0 +1,415 @@
+
+
+
+
+  
+  
+  PDBe Molstar
+  
+
+
+
+
+  

+    

+      

+      

+        
+        

+          Frame URL:
+          
+        

+      

+    

+  

+
+  
+
+  
+
+
+
\ No newline at end of file
diff --git a/frontend/venome-molstar/scripts.js b/frontend/venome-molstar/scripts.js
new file mode 100644
index 00000000..43b1b4c4
--- /dev/null
+++ b/frontend/venome-molstar/scripts.js
@@ -0,0 +1,91 @@
+const fs = require('fs');
+const path = require('path');
+var argparse = require('argparse');
+
+const PACKAGE_ROOT_PATH = process.cwd();
+const PACKAGE = require(path.join(PACKAGE_ROOT_PATH, 'package.json'));
+
+const banner = [
+    '/**',
+    ` * ${PACKAGE.name}`,
+    ` * @version ${PACKAGE.version}`,
+    ' * @link https://github.com/PDBeurope/pdbe-molstar',
+    ' * @license Apache 2.0',
+    ' */',
+].join('\n');
+
+const license = [
+    '/**',
+    ' * Copyright 2019-2023 Mandar Deshpande , Adam Midlik ',
+    ' * European Bioinformatics Institute (EBI, http://www.ebi.ac.uk/)',
+    ' * European Molecular Biology Laboratory (EMBL, http://www.embl.de/)',
+    ' * Licensed under the Apache License, Version 2.0 (the "License");',
+    ' * you may not use this file except in compliance with the License.',
+    ' * You may obtain a copy of the License at ',
+    ' * http://www.apache.org/licenses/LICENSE-2.0',
+    ' * ',
+    ' * Unless required by applicable law or agreed to in writing, software',
+    ' * distributed under the License is distributed on an "AS IS" BASIS, ',
+    ' * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.',
+    ' * See the License for the specific language governing permissions and ',
+    ' * limitations under the License.',
+    ' */',
+].join('\n');
+
+function removeFiles(...paths) {
+    for (const path of paths) {
+        fs.rmSync(path, { recursive: true, force: true });
+    }
+}
+
+function replaceSkin(srcFile, skin, destFile) {
+    let text = fs.readFileSync(srcFile, { encoding: 'utf8' });
+    text = text.replaceAll('mol-plugin-ui/skin/dark.scss', `mol-plugin-ui/skin/${skin}.scss`);
+    fs.writeFileSync(destFile, text, { encoding: 'utf8' });
+}
+
+const scripts = {
+    /** Remove any files produced by the build process */
+    'clean-all': () => {
+        removeFiles('lib', 'build', 'tsconfig.tsbuildinfo');
+    },
+
+    /** Build web component */
+    'bundle-webcomponent': () => {
+        const outputFile = `build/${PACKAGE.name}-component-${PACKAGE.version}.js`;
+        removeFiles(outputFile);
+        const contents = [
+            banner,
+            license,
+            fs.readFileSync(`build/${PACKAGE.name}-plugin-${PACKAGE.version}.js`),
+            fs.readFileSync(`lib/${PACKAGE.name}-component-build-${PACKAGE.version}.js`),
+        ];
+        fs.writeFileSync(outputFile, contents.join('\n\n'), { encoding: 'utf8' });
+    },
+
+    /** Prepare module files for light skin */
+    'light-skin': () => {
+        replaceSkin('lib/index.js', 'light', 'lib/index(light).js');
+        replaceSkin('lib/index.d.ts', 'light', 'lib/index(light).d.ts');
+    },
+
+    /** Remove unnecessary files produced by the build process */
+    'clean-rubbish': () => {
+        removeFiles(
+            `build/${PACKAGE.name}-light-plugin-${PACKAGE.version}.js`,
+            `build/${PACKAGE.name}-light-plugin-${PACKAGE.version}.js.LICENSE.txt`
+        );
+    },
+};
+
+// scripts['clean-rubbish']();
+
+// console.log(process.argv)
+
+const parser = new argparse.ArgumentParser({ description: '' });
+parser.add_argument('script_name', { choices: Object.keys(scripts) });
+const args = parser.parse_args();
+
+console.log('Running script', args.script_name);
+
+scripts[args.script_name]();
diff --git a/frontend/venome-molstar/src/app/alphafold-transparency.ts b/frontend/venome-molstar/src/app/alphafold-transparency.ts
new file mode 100644
index 00000000..fe41a809
--- /dev/null
+++ b/frontend/venome-molstar/src/app/alphafold-transparency.ts
@@ -0,0 +1,191 @@
+import { Structure, StructureElement } from "molstar/lib/mol-model/structure";
+import { PluginStateObject } from "molstar/lib/mol-plugin-state/objects";
+import { StateTransforms } from "molstar/lib/mol-plugin-state/transforms";
+import { PluginContext } from "molstar/lib/mol-plugin/context";
+import {
+	StateBuilder,
+	StateObjectCell,
+	StateSelection,
+	StateTransform,
+} from "molstar/lib/mol-state";
+import {
+	StructureComponentRef,
+	StructureRef,
+} from "molstar/lib/mol-plugin-state/manager/structure/hierarchy-state";
+import { isEmptyLoci, Loci } from "molstar/lib/mol-model/loci";
+import { Transparency } from "molstar/lib/mol-theme/transparency";
+import { MolScriptBuilder as MS } from "molstar/lib/mol-script/language/builder";
+import { QualityAssessment } from "molstar/lib/extensions/model-archive/quality-assessment/prop";
+import { compile } from "molstar/lib/mol-script/runtime/query/compiler";
+import {
+	StructureSelection,
+	QueryContext,
+} from "molstar/lib/mol-model/structure";
+
+type TransparencyEachReprCallback = (
+	update: StateBuilder.Root,
+	repr: StateObjectCell<
+		PluginStateObject.Molecule.Structure.Representation3D,
+		StateTransform<
+			typeof StateTransforms.Representation.StructureRepresentation3D
+		>
+	>,
+	transparency?: StateObjectCell<
+		any,
+		StateTransform<
+			typeof StateTransforms.Representation.TransparencyStructureRepresentation3DFromBundle
+		>
+	>
+) => Promise;
+const TransparencyManagerTag = "transparency-controls";
+
+function getLociByPLDDT(score: number, contextData: Structure) {
+	const queryExp = MS.struct.modifier.union([
+		MS.struct.modifier.wholeResidues([
+			MS.struct.modifier.union([
+				MS.struct.generator.atomGroups({
+					"chain-test": MS.core.rel.eq([
+						MS.ammp("objectPrimitive"),
+						"atomistic",
+					]),
+					"residue-test": MS.core.rel.lte([
+						QualityAssessment.symbols.pLDDT.symbol(),
+						score,
+					]),
+				}),
+			]),
+		]),
+	]);
+
+	const query = compile(queryExp);
+	const sel = query(new QueryContext(contextData));
+	return StructureSelection.toLociWithSourceUnits(sel);
+}
+
+export async function applyAFTransparency(
+	plugin: PluginContext,
+	structure: Readonly,
+	transparency: number,
+	pLDDT = 70
+) {
+	return plugin.dataTransaction(
+		async (ctx) => {
+			const loci = getLociByPLDDT(pLDDT, structure.cell.obj!.data);
+			await setStructureTransparency(
+				plugin,
+				structure.components,
+				transparency,
+				loci
+			);
+		},
+		{ canUndo: "Apply Transparency" }
+	);
+}
+
+export async function setStructureTransparency(
+	plugin: PluginContext,
+	components: StructureComponentRef[],
+	value: number,
+	loci: StructureElement.Loci,
+	types?: string[]
+) {
+	await eachRepr(
+		plugin,
+		components,
+		async (update, repr, transparencyCell) => {
+			if (
+				types &&
+				types.length > 0 &&
+				!types.includes(repr.params!.values.type.name)
+			)
+				return;
+
+			const structure = repr.obj!.data.sourceData;
+			if (Loci.isEmpty(loci) || isEmptyLoci(loci)) return;
+
+			const layer = {
+				bundle: StructureElement.Bundle.fromLoci(loci),
+				value,
+			};
+
+			if (transparencyCell) {
+				const bundleLayers = [
+					...transparencyCell.params!.values.layers,
+					layer,
+				];
+				const filtered = getFilteredBundle(bundleLayers, structure);
+				update
+					.to(transparencyCell)
+					.update(Transparency.toBundle(filtered));
+			} else {
+				const filtered = getFilteredBundle([layer], structure);
+				update
+					.to(repr.transform.ref)
+					.apply(
+						StateTransforms.Representation
+							.TransparencyStructureRepresentation3DFromBundle,
+						Transparency.toBundle(filtered),
+						{ tags: TransparencyManagerTag }
+					);
+			}
+		}
+	);
+}
+
+export async function clearStructureTransparency(
+	plugin: PluginContext,
+	components: StructureComponentRef[],
+	types?: string[]
+) {
+	await eachRepr(
+		plugin,
+		components,
+		async (update, repr, transparencyCell) => {
+			if (
+				types &&
+				types.length > 0 &&
+				!types.includes(repr.params!.values.type.name)
+			)
+				return;
+			if (transparencyCell) {
+				update.delete(transparencyCell.transform.ref);
+			}
+		}
+	);
+}
+
+async function eachRepr(
+	plugin: PluginContext,
+	components: StructureComponentRef[],
+	callback: TransparencyEachReprCallback
+) {
+	const state = plugin.state.data;
+	const update = state.build();
+	for (const c of components) {
+		for (const r of c.representations) {
+			const transparency = state.select(
+				StateSelection.Generators.ofTransformer(
+					StateTransforms.Representation
+						.TransparencyStructureRepresentation3DFromBundle,
+					r.cell.transform.ref
+				).withTag(TransparencyManagerTag)
+			);
+			await callback(update, r.cell, transparency[0]);
+		}
+	}
+
+	return update.commit({ doNotUpdateCurrent: true });
+}
+
+/** filter transparency layers for given structure */
+function getFilteredBundle(
+	layers: Transparency.BundleLayer[],
+	structure: Structure
+) {
+	const transparency = Transparency.ofBundle(layers, structure.root);
+	const merged = Transparency.merge(transparency);
+	return Transparency.filter(
+		merged,
+		structure
+	) as Transparency;
+}
diff --git a/frontend/venome-molstar/src/app/custom-events.ts b/frontend/venome-molstar/src/app/custom-events.ts
new file mode 100644
index 00000000..82cdaa34
--- /dev/null
+++ b/frontend/venome-molstar/src/app/custom-events.ts
@@ -0,0 +1,99 @@
+import { PluginContext } from "molstar/lib/mol-plugin/context";
+import { lociDetails, EventDetail } from "./loci-details";
+import { InteractivityManager } from "molstar/lib/mol-plugin-state/manager/interactivity";
+import { debounceTime } from "rxjs/operators";
+
+export namespace CustomEvents {
+	function create(eventTypeArr: string[]) {
+		const eventObj = {} as any;
+		for (let ei = 0, el = eventTypeArr.length; ei < el; ei++) {
+			const eventType = eventTypeArr[ei];
+			let event;
+			if (typeof MouseEvent == "function") {
+				// current standard
+				event = new MouseEvent(eventType, {
+					view: window,
+					bubbles: true,
+					cancelable: true,
+				});
+			} else if (typeof document.createEvent == "function") {
+				// older standard
+				event = document.createEvent("MouseEvents");
+				event.initEvent(
+					eventType,
+					true /* bubbles */,
+					true /* cancelable */
+				);
+			}
+			eventObj[eventType] = event;
+		}
+		return eventObj;
+	}
+
+	function dispatchCustomEvent(
+		event: any,
+		eventData: EventDetail,
+		targetElement: HTMLElement
+	) {
+		if (typeof eventData !== "undefined") {
+			(eventData as any)["residueNumber"] = eventData.seq_id;
+			event["eventData"] = eventData;
+			event.eventData.residueNumber = eventData.seq_id;
+			targetElement.dispatchEvent(event);
+		}
+	}
+
+	export function add(plugin: PluginContext, targetElement: HTMLElement) {
+		const pdbevents = create([
+			"PDB.molstar.click",
+			"PDB.molstar.mouseover",
+			"PDB.molstar.mouseout",
+		]);
+		plugin.behaviors.interaction.click.subscribe(
+			(e: InteractivityManager.ClickEvent) => {
+				if (
+					e.button === 1 &&
+					e.current &&
+					e.current.loci.kind !== "empty-loci"
+				) {
+					const evData = lociDetails(e.current.loci);
+					if (evData)
+						dispatchCustomEvent(
+							pdbevents["PDB.molstar.click"],
+							evData,
+							targetElement
+						);
+				}
+			}
+		);
+		plugin.behaviors.interaction.hover
+			.pipe(debounceTime(100))
+			.subscribe((e: InteractivityManager.HoverEvent) => {
+				if (
+					e.current &&
+					e.current.loci &&
+					e.current.loci.kind !== "empty-loci"
+				) {
+					const evData = lociDetails(e.current.loci);
+					if (evData)
+						dispatchCustomEvent(
+							pdbevents["PDB.molstar.mouseover"],
+							evData,
+							targetElement
+						);
+				}
+
+				if (
+					e.current &&
+					e.current.loci &&
+					e.current.loci.kind === "empty-loci"
+				) {
+					dispatchCustomEvent(
+						pdbevents["PDB.molstar.mouseout"],
+						{},
+						targetElement
+					);
+				}
+			});
+	}
+}
diff --git a/frontend/venome-molstar/src/app/domain-annotations/behavior.ts b/frontend/venome-molstar/src/app/domain-annotations/behavior.ts
new file mode 100644
index 00000000..c9cdb7e8
--- /dev/null
+++ b/frontend/venome-molstar/src/app/domain-annotations/behavior.ts
@@ -0,0 +1,68 @@
+import { DomainAnnotationsProvider } from "./prop";
+import { DomainAnnotationsColorThemeProvider } from "./color";
+import { Loci } from "molstar/lib/mol-model/loci";
+import { ParamDefinition as PD } from "molstar/lib/mol-util/param-definition";
+import { PluginBehavior } from "molstar/lib/mol-plugin/behavior";
+
+export const PDBeDomainAnnotations = PluginBehavior.create<{
+	autoAttach: boolean;
+	showTooltip: boolean;
+}>({
+	name: "pdbe-domain-annotations-prop",
+	category: "custom-props",
+	display: {
+		name: "Domain annotations",
+		description: "Data for domain annotations, obtained via PDBe.",
+	},
+	ctor: class extends PluginBehavior.Handler<{
+		autoAttach: boolean;
+		showTooltip: boolean;
+	}> {
+		private provider = DomainAnnotationsProvider;
+
+		private labelDomainAnnotations = {
+			label: (loci: Loci): string | undefined => void 0,
+		};
+
+		register(): void {
+			this.ctx.customModelProperties.register(
+				this.provider,
+				this.params.autoAttach
+			);
+			this.ctx.managers.lociLabels.addProvider(
+				this.labelDomainAnnotations
+			);
+
+			this.ctx.representation.structure.themes.colorThemeRegistry.add(
+				DomainAnnotationsColorThemeProvider
+			);
+		}
+
+		update(p: { autoAttach: boolean; showTooltip: boolean }) {
+			const updated = this.params.autoAttach !== p.autoAttach;
+			this.params.autoAttach = p.autoAttach;
+			this.params.showTooltip = p.showTooltip;
+			this.ctx.customModelProperties.setDefaultAutoAttach(
+				this.provider.descriptor.name,
+				this.params.autoAttach
+			);
+			return updated;
+		}
+
+		unregister() {
+			this.ctx.customModelProperties.unregister(
+				DomainAnnotationsProvider.descriptor.name
+			);
+			this.ctx.managers.lociLabels.removeProvider(
+				this.labelDomainAnnotations
+			);
+			this.ctx.representation.structure.themes.colorThemeRegistry.remove(
+				DomainAnnotationsColorThemeProvider
+			);
+		}
+	},
+	params: () => ({
+		autoAttach: PD.Boolean(false),
+		showTooltip: PD.Boolean(true),
+	}),
+});
diff --git a/frontend/venome-molstar/src/app/domain-annotations/color.ts b/frontend/venome-molstar/src/app/domain-annotations/color.ts
new file mode 100644
index 00000000..c2d3ff55
--- /dev/null
+++ b/frontend/venome-molstar/src/app/domain-annotations/color.ts
@@ -0,0 +1,122 @@
+import { DomainAnnotations, DomainAnnotationsProvider } from "./prop";
+import { Location } from "molstar/lib/mol-model/location";
+import { StructureElement } from "molstar/lib/mol-model/structure";
+import { ColorTheme, LocationColor } from "molstar/lib/mol-theme/color";
+import { ThemeDataContext } from "molstar/lib/mol-theme/theme";
+import { Color } from "molstar/lib/mol-util/color";
+import { ParamDefinition as PD } from "molstar/lib/mol-util/param-definition";
+import { CustomProperty } from "molstar/lib/mol-model-props/common/custom-property";
+
+const DomainColors = [
+	Color.fromRgb(170, 170, 170), // not applicable
+	Color.fromRgb(255, 112, 3),
+];
+
+export const DomainAnnotationsColorThemeParams = {
+	type: PD.MappedStatic("", {
+		"": PD.EmptyGroup(),
+	}),
+};
+
+type Params = any; // typeof DomainAnnotationsColorThemeParams
+
+export function DomainAnnotationsColorTheme(
+	ctx: ThemeDataContext,
+	props: PD.Values
+): ColorTheme {
+	let color: LocationColor;
+
+	if (
+		ctx.structure &&
+		!ctx.structure.isEmpty &&
+		ctx.structure.models[0].customProperties.has(
+			DomainAnnotationsProvider.descriptor
+		)
+	) {
+		const getDomains = DomainAnnotations.getDomains;
+
+		const issue = props.type.params.kind;
+		color = (location: Location) => {
+			if (
+				StructureElement.Location.is(location) &&
+				getDomains(location).indexOf(issue) >= 0
+			) {
+				return DomainColors[1];
+			}
+			return DomainColors[0];
+		};
+	} else {
+		color = () => DomainColors[0];
+	}
+
+	return {
+		factory: DomainAnnotationsColorTheme,
+		granularity: "group",
+		color: color,
+		props: props,
+		description:
+			"Highlights Sequnece and Structure Domain Annotations. Data obtained via PDBe.",
+	};
+}
+
+export const DomainAnnotationsColorThemeProvider: ColorTheme.Provider<
+	Params,
+	"pdbe-domain-annotations"
+> = {
+	name: "pdbe-domain-annotations",
+	label: "Domain annotations",
+	category: ColorTheme.Category.Misc,
+	factory: DomainAnnotationsColorTheme,
+	getParams: (ctx) => {
+		const domainNames = DomainAnnotations.getDomainNames(ctx.structure);
+		const domainTypes = DomainAnnotations.getDomainTypes(ctx.structure);
+
+		const optionObj: any = {};
+		domainTypes.forEach((tp, index) => {
+			if (domainNames[index].length > 0) {
+				optionObj[tp as string] = PD.Group(
+					{
+						kind: PD.Select(
+							domainNames[index][0] as string,
+							PD.arrayToOptions(domainNames[index] as string[])
+						),
+					},
+					{ isFlat: true }
+				);
+			}
+		});
+
+		if (Object.keys(optionObj).length > 0) {
+			return {
+				type: PD.MappedStatic(optionObj[0], optionObj),
+			};
+		} else {
+			return {
+				type: PD.MappedStatic("", {
+					"": PD.EmptyGroup(),
+				}),
+			};
+		}
+	},
+	defaultValues: PD.getDefaultValues(DomainAnnotationsColorThemeParams),
+	isApplicable: (ctx: ThemeDataContext) =>
+		DomainAnnotations.isApplicable(ctx.structure?.models[0]),
+	ensureCustomProperties: {
+		attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => {
+			return data.structure
+				? DomainAnnotationsProvider.attach(
+						ctx,
+						data.structure.models[0],
+						void 0,
+						true
+				  )
+				: Promise.resolve();
+		},
+		detach: (data) =>
+			data.structure &&
+			data.structure.models[0].customProperties.reference(
+				DomainAnnotationsProvider.descriptor,
+				false
+			),
+	},
+};
diff --git a/frontend/venome-molstar/src/app/domain-annotations/prop.ts b/frontend/venome-molstar/src/app/domain-annotations/prop.ts
new file mode 100644
index 00000000..05eed54e
--- /dev/null
+++ b/frontend/venome-molstar/src/app/domain-annotations/prop.ts
@@ -0,0 +1,198 @@
+import {
+	Model,
+	ResidueIndex,
+	Unit,
+	IndexedCustomProperty,
+} from "molstar/lib/mol-model/structure";
+import {
+	StructureElement,
+	Structure,
+} from "molstar/lib/mol-model/structure/structure";
+import { PropertyWrapper } from "molstar/lib/mol-model-props/common/wrapper";
+import { CustomModelProperty } from "molstar/lib/mol-model-props/common/custom-model-property";
+import { ParamDefinition as PD } from "molstar/lib/mol-util/param-definition";
+import { CustomProperty } from "molstar/lib/mol-model-props/common/custom-property";
+import { arraySetAdd } from "molstar/lib/mol-util/array";
+import { Asset } from "molstar/lib/mol-util/assets";
+import { CustomPropertyDescriptor } from "molstar/lib/mol-model/custom-property";
+import { ChainIndex } from "molstar/lib/mol-model/structure/model/indexing";
+
+export { DomainAnnotations };
+type DomainAnnotations = PropertyWrapper<
+	| {
+			domains: IndexedCustomProperty.Residue;
+			domainNames: string[][];
+			domainTypes: string[];
+	  }
+	| undefined
+>;
+
+namespace DomainAnnotations {
+	export const DefaultServerUrl = "https://www.ebi.ac.uk/pdbe/api/mappings";
+	export function getEntryUrl(pdbId: string, serverUrl: string) {
+		return `${serverUrl}/${pdbId.toLowerCase()}`;
+	}
+
+	export function isApplicable(model?: Model): boolean {
+		return !!model && Model.hasPdbId(model);
+	}
+
+	export function fromJson(model: Model, data: any) {
+		const info = PropertyWrapper.createInfo();
+		const domainMap = createdomainMapFromJson(model, data);
+		return { info, data: domainMap };
+	}
+
+	export async function fromServer(
+		ctx: CustomProperty.Context,
+		model: Model,
+		props: DomainAnnotationsProps
+	): Promise> {
+		const url = Asset.getUrlAsset(
+			ctx.assetManager,
+			getEntryUrl(model.entryId, props.serverUrl)
+		);
+		const json = await ctx.assetManager
+			.resolve(url, "json")
+			.runInContext(ctx.runtime);
+		const data = json.data[model.entryId.toLowerCase()];
+		if (!data) throw new Error("missing data");
+		return { value: fromJson(model, data), assets: [json] };
+	}
+
+	const _emptyArray: string[] = [];
+	export function getDomains(e: StructureElement.Location) {
+		if (!Unit.isAtomic(e.unit)) return _emptyArray;
+		const prop = DomainAnnotationsProvider.get(e.unit.model).value;
+		if (!prop || !prop.data) return _emptyArray;
+		const rI = e.unit.residueIndex[e.element];
+		return prop.data.domains.has(rI)
+			? prop.data.domains.get(rI)!
+			: _emptyArray;
+	}
+
+	export function getDomainTypes(structure?: Structure) {
+		if (!structure) return _emptyArray;
+		const prop = DomainAnnotationsProvider.get(structure.models[0]).value;
+		if (!prop || !prop.data) return _emptyArray;
+		return prop.data.domainTypes;
+	}
+
+	export function getDomainNames(structure?: Structure) {
+		if (!structure) return _emptyArray;
+		const prop = DomainAnnotationsProvider.get(structure.models[0]).value;
+		if (!prop || !prop.data) return _emptyArray;
+		return prop.data.domainNames;
+	}
+}
+
+export const DomainAnnotationsParams = {
+	serverUrl: PD.Text(DomainAnnotations.DefaultServerUrl, {
+		description: "JSON API Server URL",
+	}),
+};
+export type DomainAnnotationsParams = typeof DomainAnnotationsParams;
+export type DomainAnnotationsProps = PD.Values;
+
+export const DomainAnnotationsProvider: CustomModelProperty.Provider<
+	DomainAnnotationsParams,
+	DomainAnnotations
+> = CustomModelProperty.createProvider({
+	label: "Domain annotations",
+	descriptor: CustomPropertyDescriptor({
+		name: "domain_annotations",
+	}),
+	type: "static",
+	defaultParams: DomainAnnotationsParams,
+	getParams: (data: Model) => DomainAnnotationsParams,
+	isApplicable: (data: Model) => DomainAnnotations.isApplicable(data),
+	obtain: async (
+		ctx: CustomProperty.Context,
+		data: Model,
+		props: Partial
+	) => {
+		const p = { ...PD.getDefaultValues(DomainAnnotationsParams), ...props };
+		return await DomainAnnotations.fromServer(ctx, data, p);
+	},
+});
+
+function findChainLabel(
+	map: any,
+	label_entity_id: string,
+	label_asym_id: string
+): ChainIndex {
+	const entityIndex = map.entities.getEntityIndex;
+	const eI = entityIndex(label_entity_id);
+	if (eI < 0 || !map.entity_index_label_asym_id.has(eI))
+		return -1 as ChainIndex;
+	const cm = map.entity_index_label_asym_id.get(eI);
+	if (!cm) return -1 as ChainIndex;
+	return cm.has(label_asym_id) ? cm.get(label_asym_id)! : (-1 as ChainIndex);
+}
+
+function findResidue(
+	modelData: Model,
+	map: any,
+	label_entity_id: string,
+	label_asym_id: string,
+	label_seq_id: number
+) {
+	const cI = findChainLabel(map, label_entity_id, label_asym_id);
+	if (cI < 0) return -1 as ResidueIndex;
+	const rm = map.chain_index_auth_seq_id.get(cI)!;
+	return rm.has(label_seq_id) ? rm.get(label_seq_id)! : (-1 as ResidueIndex);
+}
+
+function createdomainMapFromJson(
+	modelData: Model,
+	data: any
+): DomainAnnotations["data"] | undefined {
+	const domainTypes: string[] = [];
+	const domainNames: string[][] = [];
+	const ret = new Map();
+	const defaultDomains = ["Pfam", "InterPro", "CATH", "SCOP"];
+
+	for (const db_name of Object.keys(data)) {
+		if (defaultDomains.indexOf(db_name) === -1) continue;
+		const tempDomains: string[] = [];
+		domainTypes.push(db_name);
+		const db = data[db_name];
+		for (const db_code of Object.keys(db)) {
+			const domain = db[db_code];
+			for (const map of domain.mappings) {
+				arraySetAdd(tempDomains, domain.identifier);
+
+				const indexData = modelData.atomicHierarchy.index as any;
+				const indexMap = indexData.map;
+				for (
+					let i = map.start.residue_number;
+					i <= map.end.residue_number;
+					i++
+				) {
+					const seq_id = i;
+					const idx = findResidue(
+						modelData,
+						indexMap,
+						map.entity_id + "",
+						map.chain_id,
+						seq_id
+					);
+					let addVal: string[] = [domain.identifier];
+					const prevVal = ret.get(idx);
+					if (prevVal) {
+						prevVal.push(domain.identifier);
+						addVal = prevVal;
+					}
+					ret.set(idx, addVal);
+				}
+			}
+		}
+		domainNames.push(tempDomains);
+	}
+
+	return {
+		domains: IndexedCustomProperty.fromResidueMap(ret),
+		domainNames,
+		domainTypes,
+	};
+}
diff --git a/frontend/venome-molstar/src/app/helpers.ts b/frontend/venome-molstar/src/app/helpers.ts
new file mode 100644
index 00000000..b05790ca
--- /dev/null
+++ b/frontend/venome-molstar/src/app/helpers.ts
@@ -0,0 +1,588 @@
+import { QualityAssessment } from "molstar/lib/extensions/model-archive/quality-assessment/prop";
+import {
+	Model,
+	Queries,
+	QueryContext,
+	ResidueIndex,
+	Structure,
+	StructureProperties,
+	StructureSelection,
+} from "molstar/lib/mol-model/structure";
+import { AtomsQueryParams } from "molstar/lib/mol-model/structure/query/queries/generators";
+import { StructureQuery } from "molstar/lib/mol-model/structure/query/query";
+import { BuiltInTrajectoryFormat } from "molstar/lib/mol-plugin-state/formats/trajectory";
+import { CreateVolumeStreamingInfo } from "molstar/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers";
+import { PluginCommands } from "molstar/lib/mol-plugin/commands";
+import { PluginContext } from "molstar/lib/mol-plugin/context";
+import { MolScriptBuilder as MS } from "molstar/lib/mol-script/language/builder";
+import Expression from "molstar/lib/mol-script/language/expression";
+import { compile } from "molstar/lib/mol-script/runtime/query/compiler";
+import { StateSelection } from "molstar/lib/mol-state";
+import { Task } from "molstar/lib/mol-task";
+import { SIFTSMapping, SIFTSMappingMapping } from "./sifts-mapping";
+import { InitParams } from "./spec";
+
+export type SupportedFormats = "mmcif" | "bcif" | "cif" | "pdb" | "sdf";
+export type LoadParams = {
+	url: string;
+	format?: BuiltInTrajectoryFormat;
+	assemblyId?: string;
+	isHetView?: boolean;
+	isBinary?: boolean;
+	progressMessage?: string;
+};
+
+export type MapParams = {
+	em?: MapStyle;
+	"2fo-fc"?: MapStyle;
+	"fo-fc(+ve)"?: MapStyle;
+	"fo-fc(-ve)"?: MapStyle;
+};
+interface MapStyle {
+	opacity?: number;
+	wireframe?: boolean;
+}
+
+export namespace PDBeVolumes {
+	export function mapParams(
+		defaultParams: any,
+		mapParams?: MapParams,
+		ref?: string | number
+	) {
+		const pdbeParams = { ...defaultParams };
+		pdbeParams.options.behaviorRef =
+			"volume-streaming" +
+			"" +
+			Math.floor(Math.random() * Math.floor(100));
+		pdbeParams.options.emContourProvider = "pdbe";
+		pdbeParams.options.serverUrl =
+			"https://www.ebi.ac.uk/pdbe/volume-server";
+		const MAIN_MAP_DEFAULTS: MapStyle = { opacity: 0.49, wireframe: false };
+		const DIFF_MAP_DEFAULTS: MapStyle = { opacity: 0.3, wireframe: true };
+		pdbeParams.options.channelParams["em"] = addDefaults(
+			mapParams?.["em"],
+			MAIN_MAP_DEFAULTS
+		);
+		pdbeParams.options.channelParams["2fo-fc"] = addDefaults(
+			mapParams?.["2fo-fc"],
+			MAIN_MAP_DEFAULTS
+		);
+		pdbeParams.options.channelParams["fo-fc(+ve)"] = addDefaults(
+			mapParams?.["fo-fc(+ve)"],
+			DIFF_MAP_DEFAULTS
+		);
+		pdbeParams.options.channelParams["fo-fc(-ve)"] = addDefaults(
+			mapParams?.["fo-fc(-ve)"],
+			DIFF_MAP_DEFAULTS
+		);
+		return pdbeParams;
+	}
+
+	export function displayUsibilityMessage(plugin: PluginContext) {
+		PluginCommands.Toast.Show(plugin, {
+			title: "Volume",
+			message:
+				"Streaming enabled, click on a residue or an atom to view the data.",
+			key: "toast-1",
+			timeoutMs: 7000,
+		});
+	}
+
+	export function toggle(plugin: PluginContext) {
+		const state = plugin.state.data;
+		const streamingState = state.select(
+			StateSelection.Generators.ofTransformer(CreateVolumeStreamingInfo)
+		)[0];
+
+		if (streamingState) {
+			PluginCommands.State.ToggleVisibility(plugin, {
+				state: state,
+				ref: streamingState.transform.ref,
+			});
+			return;
+		}
+	}
+}
+
+export namespace AlphafoldView {
+	export function getLociByPLDDT(score: number, contextData: Structure) {
+		const queryExp = MS.struct.modifier.union([
+			MS.struct.modifier.wholeResidues([
+				MS.struct.modifier.union([
+					MS.struct.generator.atomGroups({
+						"chain-test": MS.core.rel.eq([
+							MS.ammp("objectPrimitive"),
+							"atomistic",
+						]),
+						"residue-test": MS.core.rel.gr([
+							QualityAssessment.symbols.pLDDT.symbol(),
+							score,
+						]),
+					}),
+				]),
+			]),
+		]);
+
+		const query = compile(queryExp);
+		const sel = query(new QueryContext(contextData));
+		return StructureSelection.toLociWithSourceUnits(sel);
+	}
+}
+
+export type LigandQueryParam = {
+	label_comp_id_list?: any;
+	auth_asym_id?: string;
+	struct_asym_id?: string;
+	label_comp_id?: string;
+	auth_seq_id?: number;
+	show_all?: boolean;
+};
+
+export namespace LigandView {
+	export function query(ligandViewParams: LigandQueryParam): {
+		core: Expression.Expression;
+		surroundings: Expression.Expression;
+	} {
+		const atomGroupsParams: any = {
+			"group-by": MS.core.str.concat([
+				MS.struct.atomProperty.core.operatorName(),
+				MS.struct.atomProperty.macromolecular.residueKey(),
+			]),
+		};
+
+		// Residue Param
+		let residueParam: any;
+		if (ligandViewParams.auth_seq_id !== undefined) {
+			residueParam = MS.core.rel.eq([
+				MS.struct.atomProperty.macromolecular.auth_seq_id(),
+				ligandViewParams.auth_seq_id,
+			]);
+		} else if (ligandViewParams.label_comp_id) {
+			residueParam = MS.core.rel.eq([
+				MS.struct.atomProperty.macromolecular.label_comp_id(),
+				ligandViewParams.label_comp_id,
+			]);
+		}
+		if (residueParam) atomGroupsParams["residue-test"] = residueParam;
+
+		// Chain Param
+		if (ligandViewParams.auth_asym_id) {
+			atomGroupsParams["chain-test"] = MS.core.rel.eq([
+				MS.struct.atomProperty.macromolecular.auth_asym_id(),
+				ligandViewParams.auth_asym_id,
+			]);
+		} else if (ligandViewParams.struct_asym_id) {
+			atomGroupsParams["chain-test"] = MS.core.rel.eq([
+				MS.struct.atomProperty.macromolecular.label_asym_id(),
+				ligandViewParams.struct_asym_id,
+			]);
+		}
+
+		// Construct core query
+		const core = ligandViewParams.show_all
+			? MS.struct.generator.atomGroups(atomGroupsParams)
+			: MS.struct.filter.first([
+					MS.struct.generator.atomGroups(atomGroupsParams),
+			  ]);
+
+		// Construct surroundings query
+		const surroundings = MS.struct.modifier.includeSurroundings({
+			0: core,
+			radius: 5,
+			"as-whole-residues": true,
+		});
+
+		return {
+			core,
+			surroundings,
+		};
+	}
+
+	export function branchedQuery(params: any): {
+		core: Expression.Expression;
+		surroundings: Expression.Expression;
+	} {
+		const entityObjArray: any[] = [];
+
+		params.atom_site.forEach((param: any) => {
+			const qEntities = {
+				"group-by": MS.core.str.concat([
+					MS.struct.atomProperty.core.operatorName(),
+					MS.struct.atomProperty.macromolecular.residueKey(),
+				]),
+				"residue-test": MS.core.rel.eq([
+					MS.struct.atomProperty.macromolecular.auth_seq_id(),
+					param.auth_seq_id,
+				]),
+			};
+			entityObjArray.push(qEntities);
+		});
+
+		const atmGroupsQueries: Expression.Expression[] = [];
+
+		entityObjArray.forEach((entityObj: any) => {
+			atmGroupsQueries.push(MS.struct.generator.atomGroups(entityObj));
+		});
+
+		const core = MS.struct.modifier.union([
+			atmGroupsQueries.length === 1
+				? atmGroupsQueries[0]
+				: // Need to union before merge for fast performance
+				  MS.struct.combinator.merge(
+						atmGroupsQueries.map((q) =>
+							MS.struct.modifier.union([q])
+						)
+				  ),
+		]);
+
+		// Construct surroundings query
+		const surroundings = MS.struct.modifier.includeSurroundings({
+			0: core,
+			radius: 5,
+			"as-whole-residues": true,
+		});
+
+		return {
+			core,
+			surroundings,
+		};
+	}
+}
+
+export type QueryParam = {
+	auth_seq_id?: number;
+	entity_id?: string;
+	auth_asym_id?: string;
+	struct_asym_id?: string;
+	residue_number?: number;
+	start_residue_number?: number;
+	end_residue_number?: number;
+	auth_residue_number?: number;
+	auth_ins_code_id?: string;
+	start_auth_residue_number?: number;
+	start_auth_ins_code_id?: string;
+	end_auth_residue_number?: number;
+	end_auth_ins_code_id?: string;
+	atoms?: string[];
+	label_comp_id?: string;
+	color?: any;
+	sideChain?: boolean;
+	representation?: string;
+	representationColor?: any;
+	focus?: boolean;
+	tooltip?: string;
+	start?: any;
+	end?: any;
+	atom_id?: number[];
+	uniprot_accession?: string;
+	uniprot_residue_number?: number;
+	start_uniprot_residue_number?: number;
+	end_uniprot_residue_number?: number;
+};
+
+export namespace QueryHelper {
+	export function getQueryObject(
+		params: QueryParam[],
+		contextData: any
+	): Expression.Expression {
+		const selections: Partial[] = [];
+		let siftMappings: SIFTSMappingMapping | undefined;
+		let currentAccession: string;
+
+		params.forEach((param) => {
+			const selection: Partial = {};
+
+			// entity
+			if (param.entity_id)
+				selection["entityTest"] = (l) =>
+					StructureProperties.entity.id(l.element) ===
+					param.entity_id;
+
+			// chain
+			if (param.struct_asym_id) {
+				selection["chainTest"] = (l) =>
+					StructureProperties.chain.label_asym_id(l.element) ===
+					param.struct_asym_id;
+			} else if (param.auth_asym_id) {
+				selection["chainTest"] = (l) =>
+					StructureProperties.chain.auth_asym_id(l.element) ===
+					param.auth_asym_id;
+			}
+
+			// residues
+			if (param.label_comp_id) {
+				selection["residueTest"] = (l) =>
+					StructureProperties.atom.label_comp_id(l.element) ===
+					param.label_comp_id;
+			} else if (
+				param.uniprot_accession &&
+				param.uniprot_residue_number !== undefined
+			) {
+				selection["residueTest"] = (l) => {
+					if (
+						!siftMappings ||
+						currentAccession !== param.uniprot_accession
+					) {
+						siftMappings = SIFTSMapping.Provider.get(
+							contextData.models[0]
+						).value;
+						currentAccession = param.uniprot_accession!;
+					}
+					const rI = StructureProperties.residue.key(l.element);
+					return (
+						!!siftMappings &&
+						param.uniprot_accession ===
+							siftMappings.accession[rI] &&
+						param.uniprot_residue_number === +siftMappings.num[rI]
+					);
+				};
+			} else if (
+				param.uniprot_accession &&
+				param.start_uniprot_residue_number !== undefined &&
+				param.end_uniprot_residue_number !== undefined
+			) {
+				selection["residueTest"] = (l) => {
+					if (
+						!siftMappings ||
+						currentAccession !== param.uniprot_accession
+					) {
+						siftMappings = SIFTSMapping.Provider.get(
+							contextData.models[0]
+						).value;
+						currentAccession = param.uniprot_accession!;
+					}
+					const rI = StructureProperties.residue.key(l.element);
+					return (
+						!!siftMappings &&
+						param.uniprot_accession ===
+							siftMappings.accession[rI] &&
+						param.start_uniprot_residue_number! <=
+							+siftMappings.num[rI] &&
+						param.end_uniprot_residue_number! >=
+							+siftMappings.num[rI]
+					);
+				};
+			} else if (param.residue_number !== undefined) {
+				selection["residueTest"] = (l) =>
+					StructureProperties.residue.label_seq_id(l.element) ===
+					param.residue_number;
+			} else if (
+				param.start_residue_number !== undefined &&
+				param.end_residue_number !== undefined &&
+				param.end_residue_number > param.start_residue_number
+			) {
+				selection["residueTest"] = (l) => {
+					const labelSeqId = StructureProperties.residue.label_seq_id(
+						l.element
+					);
+					return (
+						labelSeqId >= param.start_residue_number! &&
+						labelSeqId <= param.end_residue_number!
+					);
+				};
+			} else if (
+				param.start_residue_number !== undefined &&
+				param.end_residue_number !== undefined &&
+				param.end_residue_number === param.start_residue_number
+			) {
+				selection["residueTest"] = (l) =>
+					StructureProperties.residue.label_seq_id(l.element) ===
+					param.start_residue_number;
+			} else if (param.auth_seq_id !== undefined) {
+				selection["residueTest"] = (l) =>
+					StructureProperties.residue.auth_seq_id(l.element) ===
+					param.auth_seq_id;
+			} else if (
+				param.auth_residue_number !== undefined &&
+				!param.auth_ins_code_id
+			) {
+				selection["residueTest"] = (l) =>
+					StructureProperties.residue.auth_seq_id(l.element) ===
+					param.auth_residue_number;
+			} else if (
+				param.auth_residue_number !== undefined &&
+				param.auth_ins_code_id
+			) {
+				selection["residueTest"] = (l) =>
+					StructureProperties.residue.auth_seq_id(l.element) ===
+					param.auth_residue_number;
+			} else if (
+				param.start_auth_residue_number !== undefined &&
+				param.end_auth_residue_number !== undefined &&
+				param.end_auth_residue_number > param.start_auth_residue_number
+			) {
+				selection["residueTest"] = (l) => {
+					const authSeqId = StructureProperties.residue.auth_seq_id(
+						l.element
+					);
+					return (
+						authSeqId >= param.start_auth_residue_number! &&
+						authSeqId <= param.end_auth_residue_number!
+					);
+				};
+			} else if (
+				param.start_auth_residue_number !== undefined &&
+				param.end_auth_residue_number !== undefined &&
+				param.end_auth_residue_number ===
+					param.start_auth_residue_number
+			) {
+				selection["residueTest"] = (l) =>
+					StructureProperties.residue.auth_seq_id(l.element) ===
+					param.start_auth_residue_number;
+			}
+
+			// atoms
+			if (param.atoms) {
+				selection["atomTest"] = (l) =>
+					param.atoms!.includes(
+						StructureProperties.atom.label_atom_id(l.element)
+					);
+			}
+
+			if (param.atom_id) {
+				selection["atomTest"] = (l) =>
+					param.atom_id!.includes(
+						StructureProperties.atom.id(l.element)
+					);
+			}
+
+			selections.push(selection);
+		});
+
+		const atmGroupsQueries: StructureQuery[] = [];
+		selections.forEach((selection) => {
+			atmGroupsQueries.push(Queries.generators.atoms(selection));
+		});
+
+		return Queries.combinators.merge(atmGroupsQueries);
+	}
+
+	export function getInteractivityLoci(params: any, contextData: any) {
+		const sel = StructureQuery.run(
+			QueryHelper.getQueryObject(params, contextData) as any,
+			contextData
+		);
+		return StructureSelection.toLociWithSourceUnits(sel);
+	}
+
+	export function getHetLoci(
+		queryExp: Expression.Expression,
+		contextData: any
+	) {
+		const query = compile(queryExp);
+		const sel = query(new QueryContext(contextData));
+		return StructureSelection.toLociWithSourceUnits(sel);
+	}
+}
+
+export interface ModelInfo {
+	hetNames: string[];
+	carbEntityCount: number;
+}
+
+export namespace ModelInfo {
+	export async function get(
+		model: Model,
+		structures: any
+	): Promise {
+		const { _rowCount: residueCount } = model.atomicHierarchy.residues;
+		const { offsets: residueOffsets } =
+			model.atomicHierarchy.residueAtomSegments;
+		const chainIndex = model.atomicHierarchy.chainAtomSegments.index;
+
+		const hetNames: ModelInfo["hetNames"] = [];
+		let carbEntityCount: ModelInfo["carbEntityCount"] = 0;
+		for (let rI = 0 as ResidueIndex; rI < residueCount; rI++) {
+			const cI = chainIndex[residueOffsets[rI]];
+			const eI = model.atomicHierarchy.index.getEntityFromChain(cI);
+			const entityType = model.entities.data.type.value(eI);
+
+			if (entityType !== "non-polymer" && entityType !== "branched")
+				continue;
+
+			// const comp_id = model.atomicHierarchy.atoms.label_comp_id.value(rI);
+			const comp_id = model.atomicHierarchy.atoms.label_comp_id.value(
+				residueOffsets[rI]
+			);
+			if (entityType === "branched") {
+				carbEntityCount++;
+			} else {
+				if (hetNames.indexOf(comp_id) === -1) hetNames.push(comp_id);
+			}
+		}
+
+		return {
+			hetNames,
+			carbEntityCount,
+		};
+	}
+}
+
+/** Run `action` with showing a message in the bottom-left corner of the plugin UI */
+export async function runWithProgressMessage(
+	plugin: PluginContext,
+	progressMessage: string | undefined,
+	action: () => any
+) {
+	const task = Task.create(progressMessage ?? "Task", async (ctx) => {
+		let done = false;
+		try {
+			if (progressMessage) {
+				setTimeout(() => {
+					if (!done) ctx.update(progressMessage);
+				}, 1000); // Delay the first update to force showing message in UI
+			}
+			await action();
+		} finally {
+			done = true;
+		}
+	});
+	await plugin.runTask(task);
+}
+
+/** Parameters for a request to ModelServer */
+export interface ModelServerRequest {
+	pdbId: string;
+	queryType: "full" | "residueSurroundings" | "atoms"; // add more when needed
+	queryParams?: Record;
+}
+
+/** Return URL for a ModelServer request.
+ * If `queryType` is 'full' and `lowPrecisionCoords` is false, return URL of the static file instead (updated mmCIF or bCIF). */
+export function getStructureUrl(
+	initParams: InitParams,
+	request: ModelServerRequest
+) {
+	const pdbeUrl = initParams.pdbeUrl.replace(/\/$/, ""); // without trailing slash
+	const useStaticFile =
+		request.queryType === "full" && !initParams.lowPrecisionCoords;
+	if (useStaticFile) {
+		const suffix =
+			initParams.encoding === "bcif" ? ".bcif" : "_updated.cif";
+		return `${pdbeUrl}/entry-files/download/${request.pdbId}${suffix}`;
+	} else {
+		const queryParams = {
+			...request.queryParams,
+			encoding: initParams.encoding,
+			lowPrecisionCoords: initParams.lowPrecisionCoords ? 1 : undefined,
+		};
+		const queryString = Object.entries(queryParams)
+			.filter(([key, value]) => value !== undefined)
+			.map(([key, value]) => `${key}=${value}`)
+			.join("&");
+		const url = `${pdbeUrl}/model-server/v1/${request.pdbId}/${request.queryType}`;
+		return queryString !== "" ? `${url}?${queryString}` : url;
+	}
+}
+
+/** Create a copy of object `object`, fill in missing/undefined keys using `defaults` */
+export function addDefaults(
+	object: Partial | undefined,
+	defaults: T
+): T {
+	const result: Partial = { ...object };
+	for (const key in defaults) {
+		result[key] ??= defaults[key];
+	}
+	return result as T;
+}
diff --git a/frontend/venome-molstar/src/app/index.ts b/frontend/venome-molstar/src/app/index.ts
new file mode 100644
index 00000000..4720a281
--- /dev/null
+++ b/frontend/venome-molstar/src/app/index.ts
@@ -0,0 +1,1255 @@
+import { GeometryExport } from "molstar/lib/extensions/geo-export";
+import { MAQualityAssessment } from "molstar/lib/extensions/model-archive/quality-assessment/behavior";
+import { Mp4Export } from "molstar/lib/extensions/mp4-export";
+import { PDBeStructureQualityReport } from "molstar/lib/extensions/pdbe";
+import {
+	RCSBAssemblySymmetry,
+	RCSBAssemblySymmetryConfig,
+} from "molstar/lib/extensions/rcsb/assembly-symmetry/behavior";
+import { Canvas3DProps } from "molstar/lib/mol-canvas3d/canvas3d";
+import { EmptyLoci, Loci } from "molstar/lib/mol-model/loci";
+import { AnimateAssemblyUnwind } from "molstar/lib/mol-plugin-state/animation/built-in/assembly-unwind";
+import { AnimateCameraRock } from "molstar/lib/mol-plugin-state/animation/built-in/camera-rock";
+import { AnimateCameraSpin } from "molstar/lib/mol-plugin-state/animation/built-in/camera-spin";
+import { AnimateModelIndex } from "molstar/lib/mol-plugin-state/animation/built-in/model-index";
+import { AnimateStructureSpin } from "molstar/lib/mol-plugin-state/animation/built-in/spin-structure";
+import { AnimateStateInterpolation } from "molstar/lib/mol-plugin-state/animation/built-in/state-interpolation";
+import { AnimateStateSnapshots } from "molstar/lib/mol-plugin-state/animation/built-in/state-snapshots";
+import { BuiltInTrajectoryFormat } from "molstar/lib/mol-plugin-state/formats/trajectory";
+import { clearStructureOverpaint } from "molstar/lib/mol-plugin-state/helpers/structure-overpaint";
+import { createStructureRepresentationParams } from "molstar/lib/mol-plugin-state/helpers/structure-representation-params";
+import { StructureComponentManager } from "molstar/lib/mol-plugin-state/manager/structure/component";
+import { PluginStateObject } from "molstar/lib/mol-plugin-state/objects";
+import { createPluginUI } from "molstar/lib/mol-plugin-ui/react18";
+import { PluginUISpec } from "molstar/lib/mol-plugin-ui/spec";
+import { FocusLoci } from "molstar/lib/mol-plugin/behavior/dynamic/camera";
+import { SelectLoci } from "molstar/lib/mol-plugin/behavior/dynamic/representation";
+import { StructureFocusRepresentation } from "molstar/lib/mol-plugin/behavior/dynamic/selection/structure-focus-representation";
+import { InitVolumeStreaming } from "molstar/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers";
+import { PluginCommands } from "molstar/lib/mol-plugin/commands";
+import { PluginConfig } from "molstar/lib/mol-plugin/config";
+import { PluginContext } from "molstar/lib/mol-plugin/context";
+import { PluginLayoutStateParams } from "molstar/lib/mol-plugin/layout";
+import { PluginSpec } from "molstar/lib/mol-plugin/spec";
+import { Representation } from "molstar/lib/mol-repr/representation";
+import { StateSelection, StateTransform } from "molstar/lib/mol-state";
+import { ElementSymbolColorThemeParams } from "molstar/lib/mol-theme/color/element-symbol";
+import { Asset } from "molstar/lib/mol-util/assets";
+import { Color } from "molstar/lib/mol-util/color/color";
+import { ParamDefinition } from "molstar/lib/mol-util/param-definition";
+import { RxEventHelper } from "molstar/lib/mol-util/rx-event-helper";
+import { CustomEvents } from "./custom-events";
+import { PDBeDomainAnnotations } from "./domain-annotations/behavior";
+import {
+	AlphafoldView,
+	LigandView,
+	LoadParams,
+	ModelServerRequest,
+	PDBeVolumes,
+	QueryHelper,
+	QueryParam,
+	addDefaults,
+	getStructureUrl,
+	runWithProgressMessage,
+} from "./helpers";
+import { LoadingOverlay } from "./overlay";
+import { PluginCustomState } from "./plugin-custom-state";
+import {
+	ColorParams,
+	DefaultParams,
+	DefaultPluginUISpec,
+	InitParams,
+	validateInitParams,
+} from "./spec";
+import { initParamsFromHtmlAttributes } from "./spec-from-html";
+import { subscribeToComponentEvents } from "./subscribe-events";
+import { initSuperposition } from "./superposition";
+import { SuperpositionFocusRepresentation } from "./superposition-focus-representation";
+import { LeftPanelControls } from "./ui/pdbe-left-panel";
+import {
+	PDBeLigandViewStructureTools,
+	PDBeStructureTools,
+	PDBeSuperpositionStructureTools,
+} from "./ui/pdbe-structure-controls";
+import { PDBeViewportControls } from "./ui/pdbe-viewport-controls";
+import { SuperpostionViewport } from "./ui/superposition-viewport";
+
+import "molstar/lib/mol-plugin-ui/skin/dark.scss";
+import "./overlay.scss";
+
+export class PDBeMolstarPlugin {
+	private _ev = RxEventHelper.create();
+
+	readonly events = {
+		loadComplete: this._ev(),
+	};
+
+	plugin: PluginContext;
+	initParams: InitParams;
+	targetElement: HTMLElement;
+	assemblyRef = "";
+	selectedParams: any;
+	defaultRendererProps: Canvas3DProps["renderer"];
+	defaultMarkingProps: Canvas3DProps["marking"];
+	isHighlightColorUpdated = false;
+	isSelectedColorUpdated = false;
+
+	/** Extract InitParams from attributes of an HTML element */
+	static initParamsFromHtmlAttributes(
+		element: HTMLElement
+	): Partial {
+		return initParamsFromHtmlAttributes(element);
+	}
+
+	async render(target: string | HTMLElement, options: Partial) {
+		console.debug(
+			"Rendering PDBeMolstarPlugin instance with options:",
+			options
+		);
+		// Validate options
+		if (!options) {
+			console.error(
+				"Missing `options` argument to `PDBeMolstarPlugin.render"
+			);
+			return;
+		}
+		const validationIssues = validateInitParams(options);
+		if (validationIssues) {
+			console.error("Invalid PDBeMolstarPlugin options:", options);
+			return;
+		}
+		this.initParams = addDefaults(options, DefaultParams);
+
+		// Set PDBe Plugin Spec
+		const pdbePluginSpec: PluginUISpec = DefaultPluginUISpec();
+		pdbePluginSpec.config ??= [];
+
+		if (
+			!this.initParams.ligandView &&
+			!this.initParams.superposition &&
+			this.initParams.selectInteraction
+		) {
+			pdbePluginSpec.behaviors.push(
+				PluginSpec.Behavior(StructureFocusRepresentation)
+			);
+		}
+
+		if (this.initParams.superposition) {
+			pdbePluginSpec.behaviors.push(
+				PluginSpec.Behavior(SuperpositionFocusRepresentation),
+				PluginSpec.Behavior(MAQualityAssessment, {
+					autoAttach: true,
+					showTooltip: true,
+				})
+			);
+		}
+
+		// Add custom properties
+		if (this.initParams.domainAnnotation) {
+			pdbePluginSpec.behaviors.push(
+				PluginSpec.Behavior(PDBeDomainAnnotations, {
+					autoAttach: true,
+					showTooltip: false,
+				})
+			);
+		}
+		if (this.initParams.validationAnnotation) {
+			pdbePluginSpec.behaviors.push(
+				PluginSpec.Behavior(PDBeStructureQualityReport, {
+					autoAttach: true,
+					showTooltip: false,
+				})
+			);
+		}
+		if (this.initParams.symmetryAnnotation) {
+			pdbePluginSpec.behaviors.push(
+				PluginSpec.Behavior(RCSBAssemblySymmetry)
+			);
+			pdbePluginSpec.config.push(
+				[RCSBAssemblySymmetryConfig.DefaultServerType, "pdbe"],
+				[
+					RCSBAssemblySymmetryConfig.DefaultServerUrl,
+					"https://www.ebi.ac.uk/pdbe/aggregated-api/pdb/symmetry",
+				],
+				[RCSBAssemblySymmetryConfig.ApplyColors, false]
+			);
+		}
+
+		pdbePluginSpec.layout = {
+			initial: {
+				isExpanded: this.initParams.expanded,
+				showControls: !this.initParams.hideControls,
+				regionState: {
+					left: "full",
+					right: "full",
+					top: this.initParams.sequencePanel ? "full" : "hidden",
+					bottom: "full",
+				},
+				controlsDisplay: this.initParams.reactive
+					? "reactive"
+					: this.initParams.landscape
+					? "landscape"
+					: PluginLayoutStateParams.controlsDisplay.defaultValue,
+			},
+		};
+
+		pdbePluginSpec.components = {
+			controls: {
+				left: LeftPanelControls,
+				// right: DefaultStructureTools,
+				// top: 'none',
+				bottom: "none",
+			},
+			viewport: {
+				controls: PDBeViewportControls,
+				view: this.initParams.superposition
+					? SuperpostionViewport
+					: void 0,
+			},
+			remoteState: "none",
+			structureTools: this.initParams.superposition
+				? PDBeSuperpositionStructureTools
+				: this.initParams.ligandView
+				? PDBeLigandViewStructureTools
+				: PDBeStructureTools,
+		};
+
+		if (this.initParams.alphafoldView) {
+			pdbePluginSpec.behaviors.push(
+				PluginSpec.Behavior(MAQualityAssessment, {
+					autoAttach: true,
+					showTooltip: true,
+				})
+			);
+		}
+
+		pdbePluginSpec.config.push([
+			PluginConfig.Structure.DefaultRepresentationPresetParams,
+			{
+				theme: {
+					globalName: this.initParams.alphafoldView
+						? "plddt-confidence"
+						: undefined,
+					carbonColor: { name: "element-symbol", params: {} },
+					focus: {
+						name: "element-symbol",
+						params: {
+							carbonColor: { name: "element-symbol", params: {} },
+						},
+					},
+				},
+			},
+		]);
+
+		ElementSymbolColorThemeParams.carbonColor.defaultValue = {
+			name: "element-symbol",
+			params: {},
+		};
+
+		// Add animation props
+		if (!this.initParams.ligandView && !this.initParams.superposition) {
+			pdbePluginSpec.animations = [
+				AnimateModelIndex,
+				AnimateCameraSpin,
+				AnimateCameraRock,
+				AnimateStateSnapshots,
+				AnimateAssemblyUnwind,
+				AnimateStructureSpin,
+				AnimateStateInterpolation,
+			];
+			pdbePluginSpec.behaviors.push(PluginSpec.Behavior(Mp4Export));
+			pdbePluginSpec.behaviors.push(PluginSpec.Behavior(GeometryExport));
+		}
+
+		if (this.initParams.hideCanvasControls.includes("expand"))
+			pdbePluginSpec.config.push([
+				PluginConfig.Viewport.ShowExpand,
+				false,
+			]);
+		if (this.initParams.hideCanvasControls.includes("selection"))
+			pdbePluginSpec.config.push([
+				PluginConfig.Viewport.ShowSelectionMode,
+				false,
+			]);
+		if (this.initParams.hideCanvasControls.includes("animation"))
+			pdbePluginSpec.config.push([
+				PluginConfig.Viewport.ShowAnimation,
+				false,
+			]);
+		if (this.initParams.hideCanvasControls.includes("controlToggle"))
+			pdbePluginSpec.config.push([
+				PluginConfig.Viewport.ShowControls,
+				false,
+			]);
+		if (this.initParams.hideCanvasControls.includes("controlInfo"))
+			pdbePluginSpec.config.push([
+				PluginConfig.Viewport.ShowSettings,
+				false,
+			]);
+
+		// override default event bindings
+		if (this.initParams.selectBindings) {
+			pdbePluginSpec.behaviors.push(
+				PluginSpec.Behavior(SelectLoci, {
+					bindings: this.initParams.selectBindings,
+				})
+			);
+		}
+
+		if (this.initParams.focusBindings) {
+			pdbePluginSpec.behaviors.push(
+				PluginSpec.Behavior(FocusLoci, {
+					bindings: this.initParams.focusBindings,
+				})
+			);
+		}
+
+		this.targetElement =
+			typeof target === "string"
+				? document.getElementById(target)!
+				: target;
+		(this.targetElement as any).viewerInstance = this;
+
+		// Create/ Initialise Plugin
+		this.plugin = await createPluginUI(this.targetElement, pdbePluginSpec);
+		PluginCustomState(this.plugin).initParams = { ...this.initParams };
+		PluginCustomState(this.plugin).events = {
+			segmentUpdate: this._ev(),
+			superpositionInit: this._ev(),
+			isBusy: this._ev(),
+		};
+
+		// Set background colour
+		if (this.initParams.bgColor || this.initParams.lighting) {
+			this.canvas.applySettings({
+				color: this.initParams.bgColor,
+				lighting: this.initParams.lighting,
+			});
+		}
+
+		// Set selection granularity
+		if (this.initParams.granularity) {
+			this.plugin.managers.interactivity.setProps({
+				granularity: this.initParams.granularity,
+			});
+		}
+
+		// Set default highlight and selection colors
+		if (this.initParams.highlightColor || this.initParams.selectColor) {
+			this.visual.setColor({
+				highlight: this.initParams.highlightColor,
+				select: this.initParams.selectColor,
+			});
+		}
+
+		// Save renderer defaults
+		this.defaultRendererProps = { ...this.plugin.canvas3d!.props.renderer };
+		this.defaultMarkingProps = { ...this.plugin.canvas3d!.props.marking };
+
+		if (this.initParams.superposition) {
+			// Set left panel tab
+			this.plugin.behaviors.layout.leftPanelTabName.next(
+				"segments" as any
+			);
+
+			// Initialise superposition
+			if (this.initParams.loadingOverlay) {
+				new LoadingOverlay(this.targetElement, {
+					resize: this.plugin?.canvas3d?.resized,
+					hide: this.events.loadComplete,
+				}).show();
+			}
+			initSuperposition(this.plugin, this.events.loadComplete);
+		} else {
+			// Collapse left panel and set left panel tab to none
+			PluginCommands.Layout.Update(this.plugin, {
+				state: {
+					regionState: {
+						...this.plugin.layout.state.regionState,
+						left: "collapsed",
+					},
+				},
+			});
+			this.plugin.behaviors.layout.leftPanelTabName.next("none");
+
+			// Load Molecule CIF or coordQuery and Parse
+			const dataSource = this.getMoleculeSrcUrl();
+			if (dataSource) {
+				if (this.initParams.loadingOverlay) {
+					new LoadingOverlay(this.targetElement, {
+						resize: this.plugin?.canvas3d?.resized,
+						hide: this.events.loadComplete,
+					}).show();
+				}
+				this.load({
+					url: dataSource.url,
+					format: dataSource.format as BuiltInTrajectoryFormat,
+					assemblyId: this.initParams.assemblyId,
+					isBinary: dataSource.isBinary,
+					progressMessage: `Loading ${
+						this.initParams.moleculeId ?? ""
+					} ...`,
+				});
+			}
+
+			// Binding to other PDB Component events
+			if (this.initParams.subscribeEvents) {
+				subscribeToComponentEvents(this);
+			}
+
+			// Event handling
+			CustomEvents.add(this.plugin, this.targetElement);
+		}
+	}
+
+	getMoleculeSrcUrl() {
+		if (this.initParams.customData) {
+			let { url, format, binary } = this.initParams.customData;
+			if (!url || !format) {
+				throw new Error(`Provide all custom data parameters`);
+			}
+			if (format === "cif" || format === "bcif") format = "mmcif";
+			// Validate supported format
+			const supportedFormats = ["mmcif", "pdb", "sdf"];
+			if (!supportedFormats.includes(format)) {
+				throw new Error(`${format} not supported.`);
+			}
+			return {
+				url: url,
+				format: format,
+				isBinary: binary,
+			};
+		}
+
+		if (this.initParams.moleculeId) {
+			const request: Required = {
+				pdbId: this.initParams.moleculeId,
+				queryType: "full",
+				queryParams: {},
+			};
+			if (this.initParams.ligandView) {
+				request.queryType = "residueSurroundings";
+				request.queryParams["data_source"] = "pdb-h";
+				if (!this.initParams.ligandView.label_comp_id_list) {
+					request.queryParams["label_comp_id"] =
+						this.initParams.ligandView.label_comp_id;
+					request.queryParams["auth_seq_id"] =
+						this.initParams.ligandView.auth_seq_id;
+					request.queryParams["auth_asym_id"] =
+						this.initParams.ligandView.auth_asym_id;
+				}
+			}
+			return {
+				url: getStructureUrl(this.initParams, request),
+				format: "mmcif",
+				isBinary: this.initParams.encoding === "bcif",
+			};
+		}
+
+		throw new Error(
+			`Mandatory parameters missing! (customData or moleculeId must be defined)`
+		);
+	}
+
+	screenshotData() {
+		return this.plugin.helpers.viewportScreenshot?.getImageDataUri();
+	}
+
+	get state() {
+		return this.plugin.state.data;
+	}
+
+	async createLigandStructure(isBranched: boolean) {
+		if (this.assemblyRef === "") return;
+		for await (const comp of this.plugin.managers.structure.hierarchy
+			.currentComponentGroups) {
+			await PluginCommands.State.RemoveObject(this.plugin, {
+				state: comp[0].cell.parent!,
+				ref: comp[0].cell.transform.ref,
+				removeParentGhosts: true,
+			});
+		}
+
+		const structure = this.state.select(this.assemblyRef)[0];
+
+		let ligandQuery;
+		if (isBranched) {
+			ligandQuery = LigandView.branchedQuery(
+				this.initParams.ligandView?.label_comp_id_list!
+			);
+		} else {
+			ligandQuery = LigandView.query(this.initParams.ligandView!);
+		}
+
+		const ligandVis =
+			await this.plugin.builders.structure.tryCreateComponentFromExpression(
+				structure,
+				ligandQuery.core,
+				"pivot",
+				{ label: "Ligand" }
+			);
+		if (ligandVis)
+			await this.plugin.builders.structure.representation.addRepresentation(
+				ligandVis,
+				{
+					type: "ball-and-stick",
+					color: "element-symbol",
+					colorParams: {
+						carbonColor: { name: "element-symbol", params: {} },
+					},
+					size: "uniform",
+					sizeParams: { value: 2.5 },
+				},
+				{ tag: "ligand-vis" }
+			);
+
+		const ligandSurr =
+			await this.plugin.builders.structure.tryCreateComponentFromExpression(
+				structure,
+				ligandQuery.surroundings,
+				"rest",
+				{ label: "Surroundings" }
+			);
+		if (ligandSurr)
+			await this.plugin.builders.structure.representation.addRepresentation(
+				ligandSurr,
+				{
+					type: "ball-and-stick",
+					color: "element-symbol",
+					colorParams: {
+						carbonColor: { name: "element-symbol", params: {} },
+					},
+					size: "uniform",
+					sizeParams: { value: 0.8 },
+				}
+			);
+
+		// Focus ligand
+		const ligRef = StateSelection.findTagInSubtree(
+			this.plugin.state.data.tree,
+			StateTransform.RootRef,
+			"ligand-vis"
+		);
+		if (!ligRef) return;
+		const cell = this.plugin.state.data.cells.get(ligRef)!;
+		if (cell?.obj) {
+			const repr = cell.obj.data.repr as Representation;
+			const ligLoci = repr.getAllLoci()[0]; // getAllLoci returns multiple copies of the same loci (one per representation visual)
+			this.plugin.managers.structure.focus.setFromLoci(ligLoci);
+			// focus-add is not handled in camera behavior, doing it here
+			const current = this.plugin.managers.structure.focus.current?.loci;
+			if (current) this.plugin.managers.camera.focusLoci(current);
+		}
+	}
+
+	async load(
+		{
+			url,
+			format = "mmcif",
+			isBinary = false,
+			assemblyId = "",
+			progressMessage,
+		}: LoadParams,
+		fullLoad = true
+	) {
+		await runWithProgressMessage(this.plugin, progressMessage, async () => {
+			let success = false;
+			try {
+				if (fullLoad) await this.clear();
+				const isHetView = this.initParams.ligandView ? true : false;
+				let downloadOptions: any = void 0;
+				let isBranchedView = false;
+				if (
+					this.initParams.ligandView &&
+					this.initParams.ligandView.label_comp_id_list
+				) {
+					isBranchedView = true;
+					downloadOptions = {
+						body: JSON.stringify(
+							this.initParams.ligandView.label_comp_id_list
+						),
+						headers: [["Content-type", "application/json"]],
+					};
+				}
+
+				const data = await this.plugin.builders.data.download(
+					{ url: Asset.Url(url, downloadOptions), isBinary },
+					{ state: { isGhost: true } }
+				);
+				const trajectory =
+					await this.plugin.builders.structure.parseTrajectory(
+						data,
+						format
+					);
+
+				if (!isHetView) {
+					await this.plugin.builders.structure.hierarchy.applyPreset(
+						trajectory,
+						this.initParams.defaultPreset as any,
+						{
+							structure: assemblyId
+								? assemblyId === "preferred"
+									? void 0
+									: {
+											name: "assembly",
+											params: { id: assemblyId },
+									  }
+								: { name: "model", params: {} },
+							showUnitcell: false,
+							representationPreset: "auto",
+						}
+					);
+
+					if (
+						this.initParams.hideStructure.length > 0 ||
+						this.initParams.visualStyle
+					) {
+						this.applyVisualParams();
+					}
+				} else {
+					const model =
+						await this.plugin.builders.structure.createModel(
+							trajectory
+						);
+					await this.plugin.builders.structure.createStructure(
+						model,
+						{ name: "model", params: {} }
+					);
+				}
+
+				// show selection if param is set
+				if (this.initParams.selection) {
+					this.visual.select(this.initParams.selection);
+				}
+
+				// Store assembly ref
+				const pivotIndex =
+					this.plugin.managers.structure.hierarchy.selection
+						.structures.length - 1;
+				const pivot =
+					this.plugin.managers.structure.hierarchy.selection
+						.structures[pivotIndex];
+				if (pivot && pivot.cell.parent)
+					this.assemblyRef = pivot.cell.transform.ref;
+
+				// Load Volume
+				if (this.initParams.loadMaps) {
+					if (this.assemblyRef === "") return;
+					const asm = this.state.select(this.assemblyRef)[0].obj!;
+					const defaultMapParams =
+						InitVolumeStreaming.createDefaultParams(
+							asm,
+							this.plugin
+						);
+					const pdbeMapParams = PDBeVolumes.mapParams(
+						defaultMapParams,
+						this.initParams.mapSettings,
+						""
+					);
+					if (pdbeMapParams) {
+						await this.plugin.runTask(
+							this.state.applyAction(
+								InitVolumeStreaming,
+								pdbeMapParams,
+								this.assemblyRef
+							)
+						);
+						if (
+							pdbeMapParams.method !== "em" &&
+							!this.initParams.ligandView
+						)
+							PDBeVolumes.displayUsibilityMessage(this.plugin);
+					}
+				}
+
+				// Create Ligand Representation
+				if (isHetView) {
+					await this.createLigandStructure(isBranchedView);
+				}
+				success = true;
+			} finally {
+				this.events.loadComplete.next(success);
+			}
+		});
+	}
+
+	applyVisualParams = () => {
+		const componentGroups =
+			this.plugin.managers.structure.hierarchy.currentComponentGroups;
+		for (const compGroup of componentGroups) {
+			const compRef = compGroup[compGroup.length - 1];
+			const tag = compRef.key ?? "";
+			const remove = this.initParams.hideStructure.some((type) =>
+				StructureComponentTags[type]?.includes(tag)
+			);
+			if (remove) {
+				this.plugin.managers.structure.hierarchy.remove([compRef]);
+			}
+			if (!remove && this.initParams.visualStyle) {
+				if (compRef && compRef.representations) {
+					compRef.representations.forEach((rep) => {
+						const currentParams =
+							createStructureRepresentationParams(
+								this.plugin,
+								void 0,
+								{ type: this.initParams.visualStyle }
+							);
+						this.plugin.managers.structure.component.updateRepresentations(
+							[compRef],
+							rep,
+							currentParams
+						);
+					});
+				}
+			}
+		}
+	};
+
+	canvas = {
+		toggleControls: (isVisible?: boolean) => {
+			if (typeof isVisible === "undefined")
+				isVisible = !this.plugin.layout.state.showControls;
+			PluginCommands.Layout.Update(this.plugin, {
+				state: { showControls: isVisible },
+			});
+		},
+
+		toggleExpanded: (isExpanded?: boolean) => {
+			if (typeof isExpanded === "undefined")
+				isExpanded = !this.plugin.layout.state.isExpanded;
+			PluginCommands.Layout.Update(this.plugin, {
+				state: { isExpanded: isExpanded },
+			});
+		},
+
+		setBgColor: async (color?: { r: number; g: number; b: number }) => {
+			if (!color) return;
+			await this.canvas.applySettings({ color });
+		},
+
+		applySettings: async (settings?: {
+			color?: { r: number; g: number; b: number };
+			lighting?: string;
+		}) => {
+			if (!settings) return;
+			if (!this.plugin.canvas3d) return;
+			const renderer = { ...this.plugin.canvas3d.props.renderer };
+			if (settings.color) {
+				renderer.backgroundColor = Color.fromRgb(
+					settings.color.r,
+					settings.color.g,
+					settings.color.b
+				);
+			}
+			if (settings.lighting) {
+				(renderer as any).style = { name: settings.lighting }; // I don't think this does anything and I don't see how it could ever have worked
+			}
+			await PluginCommands.Canvas3D.SetSettings(this.plugin, {
+				settings: { renderer },
+			});
+		},
+	};
+
+	getLociForParams(params: QueryParam[], structureNumber?: number) {
+		let assemblyRef = this.assemblyRef;
+		if (structureNumber) {
+			assemblyRef =
+				this.plugin.managers.structure.hierarchy.current.structures[
+					structureNumber - 1
+				].cell.transform.ref;
+		}
+
+		if (assemblyRef === "") return EmptyLoci;
+		const data = (
+			this.plugin.state.data.select(assemblyRef)[0]
+				.obj as PluginStateObject.Molecule.Structure
+		).data;
+		if (!data) return EmptyLoci;
+		return QueryHelper.getInteractivityLoci(params, data);
+	}
+
+	getLociByPLDDT(score: number, structureNumber?: number) {
+		let assemblyRef = this.assemblyRef;
+		if (structureNumber) {
+			assemblyRef =
+				this.plugin.managers.structure.hierarchy.current.structures[
+					structureNumber - 1
+				].cell.transform.ref;
+		}
+
+		if (assemblyRef === "") return EmptyLoci;
+		const data = (
+			this.plugin.state.data.select(assemblyRef)[0]
+				.obj as PluginStateObject.Molecule.Structure
+		).data;
+		if (!data) return EmptyLoci;
+		return AlphafoldView.getLociByPLDDT(score, data);
+	}
+
+	normalizeColor(colorVal: any, defaultColor?: Color) {
+		let color = Color.fromRgb(170, 170, 170);
+		try {
+			if (typeof colorVal.r !== "undefined") {
+				color = Color.fromRgb(colorVal.r, colorVal.g, colorVal.b);
+			} else if (colorVal[0] === "#") {
+				color = Color(Number(`0x${colorVal.substr(1)}`));
+			} else {
+				color = Color(colorVal);
+			}
+		} catch (e) {
+			if (defaultColor) color = defaultColor;
+		}
+		return color;
+	}
+
+	visual = {
+		highlight: (params: {
+			data: QueryParam[];
+			color?: any;
+			focus?: boolean;
+			structureNumber?: number;
+		}) => {
+			const loci = this.getLociForParams(
+				params.data,
+				params.structureNumber
+			);
+			if (Loci.isEmpty(loci)) return;
+			if (params.color) {
+				this.visual.setColor({ highlight: params.color });
+			}
+			this.plugin.managers.interactivity.lociHighlights.highlightOnly({
+				loci,
+			});
+			if (params.focus) this.plugin.managers.camera.focusLoci(loci);
+		},
+		clearHighlight: async () => {
+			this.plugin.managers.interactivity.lociHighlights.highlightOnly({
+				loci: EmptyLoci,
+			});
+			if (this.isHighlightColorUpdated)
+				this.visual.reset({ highlightColor: true });
+		},
+		select: async (params: {
+			data: QueryParam[];
+			nonSelectedColor?: any;
+			addedRepr?: boolean;
+			structureNumber?: number;
+		}) => {
+			// clear prvious selection
+			if (this.selectedParams) {
+				await this.visual.clearSelection(params.structureNumber);
+			}
+
+			// Structure list to apply selection
+			let structureData =
+				this.plugin.managers.structure.hierarchy.current.structures;
+			if (params.structureNumber) {
+				structureData = [
+					this.plugin.managers.structure.hierarchy.current.structures[
+						params.structureNumber - 1
+					],
+				];
+			}
+
+			// set non selected theme color
+			if (params.nonSelectedColor) {
+				for await (const s of structureData) {
+					await this.plugin.managers.structure.component.updateRepresentationsTheme(
+						s.components,
+						{
+							color: "uniform",
+							colorParams: {
+								value: this.normalizeColor(
+									params.nonSelectedColor
+								),
+							},
+						}
+					);
+				}
+			}
+
+			// apply individual selections
+			for await (const param of params.data) {
+				// get loci from param
+				const loci = this.getLociForParams(
+					[param],
+					params.structureNumber
+				);
+				if (Loci.isEmpty(loci)) return;
+				// set default selection color to minimise change display
+				this.visual.setColor({
+					select: param.color
+						? param.color
+						: { r: 255, g: 112, b: 3 },
+				});
+				// apply selection
+				this.plugin.managers.interactivity.lociSelects.selectOnly({
+					loci,
+				});
+				// create theme param values and apply them to create overpaint
+				const themeParams = StructureComponentManager.getThemeParams(
+					this.plugin,
+					this.plugin.managers.structure.component.pivotStructure
+				);
+				const colorValue =
+					ParamDefinition.getDefaultValues(themeParams);
+				colorValue.action.params = {
+					color: param.color
+						? this.normalizeColor(param.color)
+						: Color.fromRgb(255, 112, 3),
+					opacity: 1,
+				};
+				await this.plugin.managers.structure.component.applyTheme(
+					colorValue,
+					structureData
+				);
+				// add new representations
+				if (param.sideChain || param.representation) {
+					let repr = "ball-and-stick";
+					if (param.representation) repr = param.representation;
+					const defaultParams =
+						StructureComponentManager.getAddParams(this.plugin, {
+							allowNone: false,
+							hideSelection: true,
+							checkExisting: true,
+						});
+					const defaultValues =
+						ParamDefinition.getDefaultValues(defaultParams);
+					defaultValues.options = {
+						label: "selection-by-script",
+						checkExisting: params.structureNumber ? false : true,
+					};
+					const values = {
+						...defaultValues,
+						...{ representation: repr },
+					};
+					const structures =
+						this.plugin.managers.structure.hierarchy.getStructuresWithSelection();
+					await this.plugin.managers.structure.component.add(
+						values,
+						structures
+					);
+
+					// Apply uniform theme
+					if (param.representationColor) {
+						let updatedStructureData =
+							this.plugin.managers.structure.hierarchy.current
+								.structures;
+						if (params.structureNumber) {
+							updatedStructureData = [
+								this.plugin.managers.structure.hierarchy.current
+									.structures[params.structureNumber - 1],
+							];
+						}
+						const comps = updatedStructureData[0].components;
+						const lastCompsIndex = comps.length - 1;
+						const recentRepComp = [comps[lastCompsIndex]];
+						const uniformColor = param.representationColor
+							? this.normalizeColor(param.representationColor)
+							: Color.fromRgb(255, 112, 3);
+						this.plugin.managers.structure.component.updateRepresentationsTheme(
+							recentRepComp,
+							{
+								color: "uniform",
+								colorParams: { value: uniformColor },
+							}
+						);
+					}
+
+					params.addedRepr = true;
+				}
+				// focus loci
+				if (param.focus) this.plugin.managers.camera.focusLoci(loci);
+				// remove selection
+				this.plugin.managers.interactivity.lociSelects.deselect({
+					loci,
+				});
+			}
+
+			// reset selection color
+			this.visual.reset({ selectColor: true });
+			// save selection params to optimise clear
+			this.selectedParams = params;
+		},
+		clearSelection: async (structureNumber?: number) => {
+			const structIndex = structureNumber ? structureNumber - 1 : 0;
+			this.plugin.managers.interactivity.lociSelects.deselectAll();
+			// reset theme to default
+			if (this.selectedParams && this.selectedParams.nonSelectedColor) {
+				this.visual.reset({ theme: true });
+			}
+			// remove overpaints
+			await clearStructureOverpaint(
+				this.plugin,
+				this.plugin.managers.structure.hierarchy.current.structures[
+					structIndex
+				].components
+			);
+			// remove selection representations
+			if (this.selectedParams && this.selectedParams.addedRepr) {
+				const selReprCells = [];
+				for (const c of this.plugin.managers.structure.hierarchy.current
+					.structures[structIndex].components) {
+					if (
+						c.cell &&
+						c.cell.params &&
+						c.cell.params.values &&
+						c.cell.params.values.label === "selection-by-script"
+					)
+						selReprCells.push(c.cell);
+				}
+				if (selReprCells.length > 0) {
+					for await (const selReprCell of selReprCells) {
+						await PluginCommands.State.RemoveObject(this.plugin, {
+							state: selReprCell.parent!,
+							ref: selReprCell.transform.ref,
+						});
+					}
+				}
+			}
+			this.selectedParams = undefined;
+		},
+		update: async (options: Partial, fullLoad?: boolean) => {
+			console.debug(
+				"Updating PDBeMolstarPlugin instance with options:",
+				options
+			);
+			// Validate options
+			if (!options) {
+				console.error(
+					"Missing `options` argument to `PDBeMolstarPlugin.visual.update"
+				);
+				return;
+			}
+			const validationIssues = validateInitParams(options);
+			if (validationIssues) {
+				console.error("Invalid PDBeMolstarPlugin options:", options);
+				return;
+			}
+
+			this.initParams = addDefaults(options, DefaultParams);
+
+			if (!this.initParams.moleculeId && !this.initParams.customData)
+				return false;
+			if (
+				this.initParams.customData &&
+				this.initParams.customData.url &&
+				!this.initParams.customData.format
+			)
+				return false;
+			PluginCustomState(this.plugin).initParams = this.initParams;
+
+			// Show/hide buttons in the viewport control panel
+			this.plugin.config.set(
+				PluginConfig.Viewport.ShowExpand,
+				!this.initParams.hideCanvasControls.includes("expand")
+			);
+			this.plugin.config.set(
+				PluginConfig.Viewport.ShowSelectionMode,
+				!this.initParams.hideCanvasControls.includes("selection")
+			);
+			this.plugin.config.set(
+				PluginConfig.Viewport.ShowAnimation,
+				!this.initParams.hideCanvasControls.includes("animation")
+			);
+			this.plugin.config.set(
+				PluginConfig.Viewport.ShowControls,
+				!this.initParams.hideCanvasControls.includes("controlToggle")
+			);
+			this.plugin.config.set(
+				PluginConfig.Viewport.ShowSettings,
+				!this.initParams.hideCanvasControls.includes("controlInfo")
+			);
+
+			// Set background colour
+			if (this.initParams.bgColor || this.initParams.lighting) {
+				await this.canvas.applySettings({
+					color: this.initParams.bgColor,
+					lighting: this.initParams.lighting,
+				});
+			}
+
+			// Load Molecule CIF or coordQuery and Parse
+			const dataSource = this.getMoleculeSrcUrl();
+			if (dataSource) {
+				await this.load(
+					{
+						url: dataSource.url,
+						format: dataSource.format as BuiltInTrajectoryFormat,
+						assemblyId: this.initParams.assemblyId,
+						isBinary: dataSource.isBinary,
+					},
+					fullLoad
+				);
+			}
+		},
+		visibility: async (data: {
+			polymer?: boolean;
+			het?: boolean;
+			water?: boolean;
+			carbs?: boolean;
+			nonStandard?: boolean;
+			maps?: boolean;
+			[key: string]: any;
+		}) => {
+			if (!data) return;
+
+			for (const visual in data) {
+				const tags =
+					StructureComponentTags[
+						visual as keyof typeof StructureComponentTags
+					] ?? [];
+				for (const tag of tags) {
+					const componentRef = StateSelection.findTagInSubtree(
+						this.plugin.state.data.tree,
+						StateTransform.RootRef,
+						tag
+					);
+					if (componentRef) {
+						const compVisual =
+							this.plugin.state.data.select(componentRef)[0];
+						if (compVisual && compVisual.obj) {
+							const currentlyVisible =
+								compVisual.state && compVisual.state.isHidden
+									? false
+									: true;
+							if (data[visual] !== currentlyVisible) {
+								await PluginCommands.State.ToggleVisibility(
+									this.plugin,
+									{ state: this.state, ref: componentRef }
+								);
+							}
+						}
+					}
+				}
+			}
+		},
+		toggleSpin: async (isSpinning?: boolean, resetCamera?: boolean) => {
+			if (!this.plugin.canvas3d) return;
+			const trackball = this.plugin.canvas3d.props.trackball;
+
+			let toggleSpinParam: any =
+				trackball.animate.name === "spin"
+					? { name: "off", params: {} }
+					: { name: "spin", params: { speed: 1 } };
+
+			if (typeof isSpinning !== "undefined") {
+				toggleSpinParam = { name: "off", params: {} };
+				if (isSpinning)
+					toggleSpinParam = { name: "spin", params: { speed: 1 } };
+			}
+			await PluginCommands.Canvas3D.SetSettings(this.plugin, {
+				settings: {
+					trackball: { ...trackball, animate: toggleSpinParam },
+				},
+			});
+			if (resetCamera) await PluginCommands.Camera.Reset(this.plugin, {});
+		},
+		focus: async (params: QueryParam[], structureNumber?: number) => {
+			const loci = this.getLociForParams(params, structureNumber);
+			this.plugin.managers.camera.focusLoci(loci);
+		},
+		setColor: async (param: {
+			highlight?: ColorParams;
+			select?: ColorParams;
+		}) => {
+			if (!this.plugin.canvas3d) return;
+			if (!param.highlight && !param.select) return;
+			const renderer = { ...this.plugin.canvas3d.props.renderer };
+			const marking = { ...this.plugin.canvas3d.props.marking };
+			if (param.highlight) {
+				renderer.highlightColor = this.normalizeColor(param.highlight);
+				marking.highlightEdgeColor = Color.darken(
+					this.normalizeColor(param.highlight),
+					1
+				);
+				this.isHighlightColorUpdated = true;
+			}
+			if (param.select) {
+				renderer.selectColor = this.normalizeColor(param.select);
+				marking.selectEdgeColor = Color.darken(
+					this.normalizeColor(param.select),
+					1
+				);
+				this.isSelectedColorUpdated = true;
+			}
+			await PluginCommands.Canvas3D.SetSettings(this.plugin, {
+				settings: { renderer, marking },
+			});
+		},
+		reset: async (params: {
+			camera?: boolean;
+			theme?: boolean;
+			highlightColor?: boolean;
+			selectColor?: boolean;
+		}) => {
+			if (params.camera)
+				await PluginCommands.Camera.Reset(this.plugin, {
+					durationMs: 250,
+				});
+
+			if (params.theme) {
+				const defaultTheme: any = {
+					color: this.initParams.alphafoldView
+						? "plddt-confidence"
+						: "default",
+				};
+				const componentGroups =
+					this.plugin.managers.structure.hierarchy
+						.currentComponentGroups;
+				for (const compGrp of componentGroups) {
+					await this.plugin.managers.structure.component.updateRepresentationsTheme(
+						compGrp,
+						defaultTheme
+					);
+				}
+			}
+
+			if (params.highlightColor || params.selectColor) {
+				if (!this.plugin.canvas3d) return;
+				const renderer = { ...this.plugin.canvas3d.props.renderer };
+				const marking = { ...this.plugin.canvas3d.props.marking };
+				if (params.highlightColor) {
+					renderer.highlightColor =
+						this.defaultRendererProps.highlightColor;
+					marking.highlightEdgeColor =
+						this.defaultMarkingProps.highlightEdgeColor;
+					this.isHighlightColorUpdated = false;
+				}
+				if (params.selectColor) {
+					renderer.selectColor =
+						this.defaultRendererProps.selectColor;
+					marking.selectEdgeColor =
+						this.defaultMarkingProps.selectEdgeColor;
+					this.isSelectedColorUpdated = false;
+				}
+				await PluginCommands.Canvas3D.SetSettings(this.plugin, {
+					settings: { renderer, marking },
+				});
+			}
+		},
+	};
+
+	async clear() {
+		await this.plugin.clear();
+		this.assemblyRef = "";
+		this.selectedParams = void 0;
+		this.isHighlightColorUpdated = false;
+		this.isSelectedColorUpdated = false;
+	}
+}
+
+const StructureComponentTags = {
+	polymer: ["structure-component-static-polymer"],
+	het: [
+		"structure-component-static-ligand",
+		"structure-component-static-ion",
+	],
+	water: ["structure-component-static-water"],
+	carbs: ["structure-component-static-branched"],
+	nonStandard: ["structure-component-static-non-standard"],
+	coarse: ["structure-component-static-coarse"],
+	maps: ["volume-streaming-info"],
+};
+
+(window as any).PDBeMolstarPlugin = PDBeMolstarPlugin;
diff --git a/frontend/venome-molstar/src/app/labels.ts b/frontend/venome-molstar/src/app/labels.ts
new file mode 100644
index 00000000..99f86d4d
--- /dev/null
+++ b/frontend/venome-molstar/src/app/labels.ts
@@ -0,0 +1,58 @@
+import { PluginContext } from "molstar/lib/mol-plugin/context";
+import { PluginBehavior } from "molstar/lib/mol-plugin/behavior";
+import { Loci } from "molstar/lib/mol-model/loci";
+import {
+	StructureElement,
+	StructureProperties,
+} from "molstar/lib/mol-model/structure";
+import { lociLabel } from "molstar/lib/mol-theme/label";
+import { LociLabel } from "molstar/lib/mol-plugin-state/manager/loci-label";
+import { PluginCustomState } from "./plugin-custom-state";
+
+export const PDBeLociLabelProvider = PluginBehavior.create({
+	name: "pdbe-loci-label-provider",
+	category: "interaction",
+	ctor: class implements PluginBehavior {
+		private f = {
+			label: (loci: Loci) => {
+				const superpositionView = PluginCustomState(this.ctx)
+					.initParams!.superposition;
+
+				const label: string[] = [];
+				if (
+					!superpositionView &&
+					StructureElement.Loci.is(loci) &&
+					loci.elements.length === 1
+				) {
+					const entityNames = new Set();
+					for (const { unit: u } of loci.elements) {
+						const l = StructureElement.Location.create(
+							loci.structure,
+							u,
+							u.elements[0]
+						);
+						const name = StructureProperties.entity
+							.pdbx_description(l)
+							.join(", ");
+						entityNames.add(name);
+					}
+					if (entityNames.size === 1)
+						entityNames.forEach((name) => label.push(name));
+				}
+				label.push(lociLabel(loci));
+				return label.filter((l) => !!l).join("
");
+			},
+			group: (label: LociLabel) =>
+				label.toString().replace(/Model [0-9]+/g, "Models"),
+			priority: 100,
+		};
+		register() {
+			this.ctx.managers.lociLabels.addProvider(this.f);
+		}
+		unregister() {
+			this.ctx.managers.lociLabels.removeProvider(this.f);
+		}
+		constructor(protected ctx: PluginContext) {}
+	},
+	display: { name: "Provide PDBe Loci Label" },
+});
diff --git a/frontend/venome-molstar/src/app/loci-details.ts b/frontend/venome-molstar/src/app/loci-details.ts
new file mode 100644
index 00000000..1d577850
--- /dev/null
+++ b/frontend/venome-molstar/src/app/loci-details.ts
@@ -0,0 +1,227 @@
+import {
+	Unit,
+	StructureElement,
+	StructureProperties as Props,
+	Bond,
+} from "molstar/lib/mol-model/structure";
+import { Loci } from "molstar/lib/mol-model/loci";
+import { OrderedSet } from "molstar/lib/mol-data/int";
+import { SIFTSMapping as BestDatabaseSequenceMappingProp } from "molstar/lib/mol-model-props/sequence/sifts-mapping";
+
+export type EventDetail = {
+	models?: string[];
+	entity_id?: string;
+	label_asym_id?: string;
+	asym_id?: string;
+	auth_asym_id?: string;
+	unp_accession?: string;
+	unp_seq_id?: number;
+	seq_id?: number;
+	auth_seq_id?: number;
+	ins_code?: string;
+	comp_id?: string;
+	atom_id?: string[];
+	alt_id?: string;
+	micro_het_comp_ids?: string[];
+	seq_id_begin?: number;
+	seq_id_end?: number;
+	button?: number;
+	modifiers?: any;
+};
+
+type LabelGranularity =
+	| "element"
+	| "conformation"
+	| "residue"
+	| "chain"
+	| "structure";
+
+export function lociDetails(loci: Loci): EventDetail | undefined {
+	switch (loci.kind) {
+		case "structure-loci":
+			return {
+				models: loci.structure.models
+					.map((m) => m.entry)
+					.filter((l) => !!l),
+			};
+		case "element-loci":
+			return structureElementStatsDetail(
+				StructureElement.Stats.ofLoci(loci)
+			);
+		case "bond-loci":
+			const bond = loci.bonds[0];
+			return bond ? bondLabel(bond, "element") : "";
+		default:
+			return void 0;
+	}
+}
+
+function structureElementStatsDetail(
+	stats: StructureElement.Stats
+): EventDetail | undefined {
+	const { chainCount, residueCount, elementCount } = stats;
+
+	if (elementCount === 1 && residueCount === 0 && chainCount === 0) {
+		return getElementDetails(stats.firstElementLoc, "element");
+	} else if (elementCount === 0 && residueCount === 1 && chainCount === 0) {
+		return getElementDetails(stats.firstResidueLoc, "residue");
+	} else {
+		return void 0;
+	}
+}
+
+function getElementDetails(
+	location: StructureElement.Location,
+	granularity: LabelGranularity = "element"
+): EventDetail {
+	const basicDetails: any = {};
+
+	let entry = location.unit.model.entry;
+	if (entry.length > 30) entry = entry.substr(0, 27) + "\u2026"; // ellipsis
+	basicDetails["entry_id"] = entry; // entry
+	if (granularity !== "structure") {
+		basicDetails["model"] = location.unit.model.modelNum; // model
+		basicDetails["instance"] = location.unit.conformation.operator.name; // instance
+	}
+
+	let elementDetails: any;
+	if (Unit.isAtomic(location.unit)) {
+		elementDetails = atomicElementDetails(
+			location as StructureElement.Location,
+			granularity
+		);
+	} else if (Unit.isCoarse(location.unit)) {
+		elementDetails = coarseElementDetails(
+			location as StructureElement.Location<
+				Unit.Spheres | Unit.Gaussians
+			>,
+			granularity
+		);
+	}
+
+	return { ...basicDetails, ...elementDetails };
+}
+
+function atomicElementDetails(
+	location: StructureElement.Location,
+	granularity: LabelGranularity
+): EventDetail {
+	const elementDetails: EventDetail = {
+		entity_id: Props.chain.label_entity_id(location),
+		label_asym_id: Props.chain.label_asym_id(location),
+		auth_asym_id: Props.chain.auth_asym_id(location),
+		unp_accession: undefined,
+		unp_seq_id: undefined,
+		seq_id: Props.residue.label_seq_id(location),
+		auth_seq_id: Props.residue.auth_seq_id(location),
+		ins_code: Props.residue.pdbx_PDB_ins_code(location),
+		comp_id: Props.atom.label_comp_id(location),
+		atom_id: [Props.atom.label_atom_id(location)],
+		alt_id: Props.atom.label_alt_id(location),
+	};
+
+	const unpLabel = BestDatabaseSequenceMappingProp.getLabel(location);
+
+	if (unpLabel) {
+		const unpLabelDetails = unpLabel.split(" ");
+		if (unpLabelDetails[0] === "UNP") {
+			elementDetails.unp_accession = unpLabelDetails[1];
+			elementDetails.unp_seq_id = +unpLabelDetails[2];
+		}
+	}
+
+	const microHetCompIds = Props.residue.microheterogeneityCompIds(location);
+	elementDetails["micro_het_comp_ids"] =
+		granularity === "residue" && microHetCompIds.length > 1
+			? microHetCompIds
+			: ([elementDetails["comp_id"]] as any);
+
+	return elementDetails;
+}
+
+function coarseElementDetails(
+	location: StructureElement.Location,
+	granularity: LabelGranularity
+): EventDetail {
+	const elementDetails: EventDetail = {
+		asym_id: Props.coarse.asym_id(location),
+		seq_id_begin: Props.coarse.seq_id_begin(location),
+		seq_id_end: Props.coarse.seq_id_end(location),
+	};
+
+	if (granularity === "residue") {
+		if (elementDetails.seq_id_begin === elementDetails.seq_id_end) {
+			const entityIndex = Props.coarse.entityKey(location);
+			const seq = location.unit.model.sequence.byEntityKey[entityIndex];
+			elementDetails["comp_id"] = seq.sequence.compId.value(
+				elementDetails.seq_id_begin! - 1
+			); // 1-indexed
+		}
+	}
+
+	return elementDetails;
+}
+
+export function bondLabel(
+	bond: Bond.Location,
+	granularity: LabelGranularity
+): any {
+	return _bundleLabel(
+		{
+			loci: [
+				StructureElement.Loci(bond.aStructure, [
+					{
+						unit: bond.aUnit,
+						indices: OrderedSet.ofSingleton(bond.aIndex),
+					},
+				]),
+				StructureElement.Loci(bond.bStructure, [
+					{
+						unit: bond.bUnit,
+						indices: OrderedSet.ofSingleton(bond.bIndex),
+					},
+				]),
+			],
+		},
+		granularity
+	);
+}
+
+export function _bundleLabel(
+	bundle: Loci.Bundle,
+	granularity: LabelGranularity
+) {
+	let isSingleElements = true;
+	for (const l of bundle.loci) {
+		if (
+			!StructureElement.Loci.is(l) ||
+			StructureElement.Loci.size(l) !== 1
+		) {
+			isSingleElements = false;
+			break;
+		}
+	}
+	if (isSingleElements) {
+		const locations = (bundle.loci as StructureElement.Loci[]).map((l) => {
+			const { unit, indices } = l.elements[0];
+			return StructureElement.Location.create(
+				l.structure,
+				unit,
+				unit.elements[OrderedSet.start(indices)]
+			);
+		});
+		const elementDetailsArr: EventDetail[] = locations.map((l) =>
+			getElementDetails(l, granularity)
+		);
+		const atomIds: any = [
+			elementDetailsArr[0].atom_id![0],
+			elementDetailsArr[1].atom_id![0],
+		];
+		const elementDetails: EventDetail = elementDetailsArr[0];
+		elementDetails["atom_id"] = atomIds;
+		return elementDetails;
+	} else {
+		const elementDetails = bundle.loci.map((l) => lociDetails(l));
+		return elementDetails;
+	}
+}
diff --git a/frontend/venome-molstar/src/app/overlay.ts b/frontend/venome-molstar/src/app/overlay.ts
new file mode 100644
index 00000000..d71f6a49
--- /dev/null
+++ b/frontend/venome-molstar/src/app/overlay.ts
@@ -0,0 +1,59 @@
+import { Subject, Subscription } from 'rxjs';
+
+
+const PdbeAnimatedLogoSvg = '';
+const OverlayBox = `
${PdbeAnimatedLogoSvg}
`;
+
+type OverlayEvents = 'resize' | 'hide';
+
+/** Shows overlay layer with animated PDBe logo */
+export class LoadingOverlay {
+    private readonly subscriptions: { [key in OverlayEvents]?: Subscription } = {};
+
+    constructor(
+        private readonly target: HTMLElement,
+        private readonly subjects: { readonly [key in OverlayEvents]?: Subject } = {},
+        private readonly overlayHtml: string = OverlayBox,
+    ) { }
+
+    private getOverlayParent() {
+        return this.target.parentElement ?? document.body;
+    }
+
+    show() {
+        this.hide();
+
+        const overlayParent = this.getOverlayParent();
+        const divOverlay = document.createElement('div');
+        divOverlay.classList.add('pdbemolstar-overlay');
+        // divOverlay.setAttribute('title', 'Loading...');
+        divOverlay.innerHTML = this.overlayHtml;
+        overlayParent.appendChild(divOverlay);
+
+        const resize = () => {
+            const viewerRect = this.target.getElementsByClassName('msp-layout-main').item(0)?.getBoundingClientRect();
+            if (viewerRect) {
+                const { left, top, width, height } = viewerRect;
+                const origin = this.target.offsetParent?.getBoundingClientRect() ?? { left: 0, top: 0 };
+                divOverlay.setAttribute('style', `position: absolute; left: ${left - origin?.left}px; top: ${top - origin.top}px; width: ${width}px; height: ${height}px;`);
+            } else {
+                divOverlay.setAttribute('style', `position: fixed; top: 0px; bottom: 0px; left: 0px; right: 0px;`);
+            }
+        };
+
+        resize();
+        this.subscriptions.resize = this.subjects.resize?.subscribe(() => resize());
+        this.subscriptions.hide = this.subjects.hide?.subscribe(() => this.hide());
+    }
+
+    hide() {
+        const existingOverlays = this.getOverlayParent().getElementsByClassName('pdbemolstar-overlay');
+        for (let i = 0; i < existingOverlays.length; i++) {
+            existingOverlays.item(i)?.remove();
+        }
+        this.subscriptions.resize?.unsubscribe();
+        this.subscriptions.resize = undefined;
+        this.subscriptions.hide?.unsubscribe();
+        this.subscriptions.hide = undefined;
+    }
+}
diff --git a/frontend/venome-molstar/src/app/plugin-custom-state.ts b/frontend/venome-molstar/src/app/plugin-custom-state.ts
new file mode 100644
index 00000000..f2a43721
--- /dev/null
+++ b/frontend/venome-molstar/src/app/plugin-custom-state.ts
@@ -0,0 +1,74 @@
+import { SymmetryOperator } from "molstar/lib/mol-math/geometry";
+import { Mat4 } from "molstar/lib/mol-math/linear-algebra";
+import { PluginContext } from "molstar/lib/mol-plugin/context";
+import { StateSelection, StateTransform } from "molstar/lib/mol-state";
+import { Subject } from "rxjs";
+import { InitParams } from "./spec";
+
+export interface PluginCustomState {
+	initParams?: InitParams;
+	events?: {
+		segmentUpdate: Subject;
+		superpositionInit: Subject;
+		isBusy: Subject;
+	};
+	superpositionState?: {
+		models: { [molId: string]: string };
+		entries: { [pdbId: string]: StateSelection.Selector };
+		refMaps: { [ref: string]: string };
+		segmentData: Segment[] | undefined;
+		matrixData: { [key: string]: { matrix: number[][] } };
+		activeSegment: number;
+		loadedStructs: string[][];
+		visibleRefs: StateTransform.Ref[][];
+		invalidStruct: string[];
+		noMatrixStruct: string[];
+		hets: { [key: string]: unknown[] };
+		colorPalette: [
+			"dark-2",
+			"red-yellow-green",
+			"paired",
+			"set-1",
+			"accent",
+			"set-2",
+			"rainbow"
+		];
+		colorState: { palleteIndex: number; colorIndex: number }[];
+		alphafold: {
+			apiData: {
+				cif: string;
+				pae: string;
+				length: number;
+			};
+			length: number;
+			ref: string;
+			traceOnly: boolean;
+			visibility: boolean[];
+			transforms: Mat4[];
+			rmsds: string[][];
+			coordinateSystems: (SymmetryOperator | undefined)[];
+		};
+	};
+	superpositionError?: string;
+}
+
+export interface ClusterMember {
+	pdb_id: string;
+	auth_asym_id: string;
+	struct_asym_id: string;
+	entity_id: number;
+	is_representative: boolean;
+}
+export interface Segment {
+	segment_start: number;
+	segment_end: number;
+	clusters: ClusterMember[][];
+	isHetView?: boolean;
+	isBinary?: boolean;
+}
+
+/** Access `plugin.customState` only through this function to get proper typing.
+ * Supports getting and setting properties. */
+export function PluginCustomState(plugin: PluginContext): PluginCustomState {
+	return ((plugin.customState as any) ??= {});
+}
diff --git a/frontend/venome-molstar/src/app/sifts-mapping.ts b/frontend/venome-molstar/src/app/sifts-mapping.ts
new file mode 100644
index 00000000..177fbeac
--- /dev/null
+++ b/frontend/venome-molstar/src/app/sifts-mapping.ts
@@ -0,0 +1,116 @@
+import { Column } from "molstar/lib/mol-data/db";
+import { MmcifFormat } from "molstar/lib/mol-model-formats/structure/mmcif";
+import { CustomPropertyDescriptor } from "molstar/lib/mol-model/custom-property";
+import { Model } from "molstar/lib/mol-model/structure";
+import { StructureElement } from "molstar/lib/mol-model/structure/structure";
+import { CustomModelProperty } from "molstar/lib/mol-model-props/common/custom-model-property";
+
+export { SIFTSMapping as SIFTSMapping };
+
+export interface SIFTSMappingMapping {
+	readonly dbName: string[];
+	readonly accession: string[];
+	readonly num: string[];
+	readonly residue: string[];
+}
+
+namespace SIFTSMapping {
+	export const Provider: CustomModelProperty.Provider<
+		{},
+		SIFTSMappingMapping
+	> = CustomModelProperty.createProvider({
+		label: "SIFTS Mapping",
+		descriptor: CustomPropertyDescriptor({
+			name: "sifts_sequence_mapping",
+		}),
+		type: "static",
+		defaultParams: {},
+		getParams: () => ({}),
+		isApplicable: (data: Model) => isAvailable(data),
+		obtain: async (ctx, data) => {
+			return { value: fromCif(data) };
+		},
+	});
+
+	export function isAvailable(model: Model) {
+		if (!MmcifFormat.is(model.sourceData)) return false;
+
+		const {
+			pdbx_sifts_xref_db_name: db_name,
+			pdbx_sifts_xref_db_acc: db_acc,
+			pdbx_sifts_xref_db_num: db_num,
+			pdbx_sifts_xref_db_res: db_res,
+		} = model.sourceData.data.db.atom_site;
+
+		return (
+			db_name.isDefined &&
+			db_acc.isDefined &&
+			db_num.isDefined &&
+			db_res.isDefined
+		);
+	}
+
+	export function getKey(loc: StructureElement.Location) {
+		const model = loc.unit.model;
+		const data = Provider.get(model).value;
+		if (!data) return "";
+		const rI = model.atomicHierarchy.residueAtomSegments.index[loc.element];
+		return data.accession[rI];
+	}
+
+	export function getLabel(loc: StructureElement.Location) {
+		const model = loc.unit.model;
+		const data = Provider.get(model).value;
+		if (!data) return;
+		const rI = model.atomicHierarchy.residueAtomSegments.index[loc.element];
+		const dbName = data.dbName[rI];
+		if (!dbName) return;
+		return `${dbName} ${data.accession[rI]} ${data.num[rI]} ${data.residue[rI]}`;
+	}
+
+	function fromCif(model: Model): SIFTSMappingMapping | undefined {
+		if (!MmcifFormat.is(model.sourceData)) return;
+
+		const {
+			pdbx_sifts_xref_db_name: db_name,
+			pdbx_sifts_xref_db_acc: db_acc,
+			pdbx_sifts_xref_db_num: db_num,
+			pdbx_sifts_xref_db_res: db_res,
+		} = model.sourceData.data.db.atom_site;
+
+		if (
+			!db_name.isDefined ||
+			!db_acc.isDefined ||
+			!db_num.isDefined ||
+			!db_res.isDefined
+		)
+			return;
+
+		const { atomSourceIndex } = model.atomicHierarchy;
+		const { count, offsets: residueOffsets } =
+			model.atomicHierarchy.residueAtomSegments;
+		const dbName = new Array(count);
+		const accession = new Array(count);
+		const num = new Array(count);
+		const residue = new Array(count);
+
+		for (let i = 0; i < count; i++) {
+			const row = atomSourceIndex.value(residueOffsets[i]);
+
+			if (db_name.valueKind(row) !== Column.ValueKind.Present) {
+				dbName[i] = "";
+				accession[i] = "";
+				num[i] = "";
+				residue[i] = "";
+				continue;
+			}
+
+			dbName[i] = db_name.value(row);
+			accession[i] = db_acc.value(row);
+			num[i] = db_num.value(row);
+			residue[i] = db_res.value(row);
+		}
+
+		return { dbName, accession, num, residue };
+	}
+}
diff --git a/frontend/venome-molstar/src/app/sifts-mappings-behaviour.ts b/frontend/venome-molstar/src/app/sifts-mappings-behaviour.ts
new file mode 100644
index 00000000..08c7a93f
--- /dev/null
+++ b/frontend/venome-molstar/src/app/sifts-mappings-behaviour.ts
@@ -0,0 +1,84 @@
+import { OrderedSet } from "molstar/lib/mol-data/int";
+import { SIFTSMapping as BestDatabaseSequenceMappingProp } from "./sifts-mapping";
+import { SIFTSMappingColorThemeProvider } from "molstar/lib/mol-model-props/sequence/themes/sifts-mapping";
+import { Loci } from "molstar/lib/mol-model/loci";
+import { StructureElement } from "molstar/lib/mol-model/structure";
+import { ParamDefinition as PD } from "molstar/lib/mol-util/param-definition";
+import { PluginBehavior } from "molstar/lib/mol-plugin/behavior";
+
+export const PDBeSIFTSMapping = PluginBehavior.create<{
+	autoAttach: boolean;
+	showTooltip: boolean;
+}>({
+	name: "pdbe-sifts-mapping-prop",
+	category: "custom-props",
+	display: { name: "PDBe SIFTS Mapping" },
+	ctor: class extends PluginBehavior.Handler<{
+		autoAttach: boolean;
+		showTooltip: boolean;
+	}> {
+		private provider = BestDatabaseSequenceMappingProp.Provider;
+
+		private labelProvider = {
+			label: (loci: Loci): string | undefined => {
+				if (!this.params.showTooltip) return;
+				return PDBeBestDatabaseSequenceMappingLabel(loci);
+			},
+		};
+
+		update(p: { autoAttach: boolean; showTooltip: boolean }) {
+			const updated =
+				this.params.autoAttach !== p.autoAttach ||
+				this.params.showTooltip !== p.showTooltip;
+			this.params.autoAttach = p.autoAttach;
+			this.params.showTooltip = p.showTooltip;
+			this.ctx.customStructureProperties.setDefaultAutoAttach(
+				this.provider.descriptor.name,
+				this.params.autoAttach
+			);
+			return updated;
+		}
+
+		register(): void {
+			this.ctx.customModelProperties.register(
+				this.provider,
+				this.params.autoAttach
+			);
+			this.ctx.representation.structure.themes.colorThemeRegistry.add(
+				SIFTSMappingColorThemeProvider
+			);
+			this.ctx.managers.lociLabels.addProvider(this.labelProvider);
+		}
+
+		unregister() {
+			this.ctx.customModelProperties.unregister(
+				this.provider.descriptor.name
+			);
+			this.ctx.representation.structure.themes.colorThemeRegistry.remove(
+				SIFTSMappingColorThemeProvider
+			);
+			this.ctx.managers.lociLabels.removeProvider(this.labelProvider);
+		}
+	},
+	params: () => ({
+		autoAttach: PD.Boolean(true),
+		showTooltip: PD.Boolean(true),
+	}),
+});
+
+//
+
+function PDBeBestDatabaseSequenceMappingLabel(loci: Loci): string | undefined {
+	if (loci.kind === "element-loci") {
+		if (loci.elements.length === 0) return;
+
+		const e = loci.elements[0];
+		const u = e.unit;
+		const se = StructureElement.Location.create(
+			loci.structure,
+			u,
+			u.elements[OrderedSet.getAt(e.indices, 0)]
+		);
+		return BestDatabaseSequenceMappingProp.getLabel(se);
+	}
+}
diff --git a/frontend/venome-molstar/src/app/spec-from-html.ts b/frontend/venome-molstar/src/app/spec-from-html.ts
new file mode 100644
index 00000000..bd1da2d5
--- /dev/null
+++ b/frontend/venome-molstar/src/app/spec-from-html.ts
@@ -0,0 +1,125 @@
+import { ColorParams, Encoding, InitParams, Lighting, Preset, VisualStyle, validateInitParams } from './spec';
+
+
+/** Extract InitParams from attributes of an HTML element */
+export function initParamsFromHtmlAttributes(element: HTMLElement): Partial {
+    const params = loadHtmlAttributes(element, InitParamsLoadingActions, {});
+    const validationIssues = validateInitParams(params);
+    if (validationIssues) console.error('Invalid PDBeMolstarPlugin options:', params);
+    return params;
+}
+
+
+/** Actions for loading individual HTML attributes into InitParams object */
+const InitParamsLoadingActions: AttributeLoadingActions> = {
+    'molecule-id': setString('moleculeId'),
+    'custom-data-url': (value, params) => { (params.customData ??= defaultCustomData()).url = value; },
+    'custom-data-format': (value, params) => { (params.customData ??= defaultCustomData()).format = value; },
+    'custom-data-binary': (value, params) => { (params.customData ??= defaultCustomData()).binary = parseBool(value); },
+    'assembly-id': setString('assemblyId'),
+    'default-preset': setLiteral(Preset, 'defaultPreset'),
+    'ligand-label-comp-id': (value, params) => { (params.ligandView ??= {}).label_comp_id = value; },
+    'ligand-auth-asym-id': (value, params) => { (params.ligandView ??= {}).auth_asym_id = value; },
+    'ligand-struct-asym-id': (value, params) => { (params.ligandView ??= {}).struct_asym_id = value; },
+    'ligand-auth-seq-id': (value, params) => { (params.ligandView ??= {}).auth_seq_id = Number(value); },
+    'ligand-show-all': (value, params) => { (params.ligandView ??= {}).show_all = parseBool(value); },
+    'alphafold-view': setBool('alphafoldView'),
+
+    'visual-style': setLiteral(VisualStyle, 'visualStyle'),
+    'hide-polymer': pushItem('hideStructure', 'polymer'),
+    'hide-water': pushItem('hideStructure', 'water'),
+    'hide-het': pushItem('hideStructure', 'het'),
+    'hide-carbs': pushItem('hideStructure', 'carbs'),
+    'hide-non-standard': pushItem('hideStructure', 'nonStandard'),
+    'hide-coarse': pushItem('hideStructure', 'coarse'),
+    'load-maps': setBool('loadMaps'),
+    'bg-color-r': setColorComponent('bgColor', 'r'),
+    'bg-color-g': setColorComponent('bgColor', 'g'),
+    'bg-color-b': setColorComponent('bgColor', 'b'),
+    'highlight-color-r': setColorComponent('highlightColor', 'r'),
+    'highlight-color-g': setColorComponent('highlightColor', 'g'),
+    'highlight-color-b': setColorComponent('highlightColor', 'b'),
+    'select-color-r': setColorComponent('selectColor', 'r'),
+    'select-color-g': setColorComponent('selectColor', 'g'),
+    'select-color-b': setColorComponent('selectColor', 'b'),
+    'lighting': setLiteral(Lighting, 'lighting'),
+
+    'validation-annotation': setBool('validationAnnotation'),
+    'domain-annotation': setBool('domainAnnotation'),
+    'symmetry-annotation': setBool('symmetryAnnotation'),
+    'pdbe-url': setString('pdbeUrl'),
+    'encoding': setLiteral(Encoding, 'encoding'),
+    'low-precision': setBool('lowPrecisionCoords'),
+    'select-interaction': setBool('selectInteraction'),
+    'subscribe-events': setBool('subscribeEvents'),
+
+    'hide-controls': setBool('hideControls'),
+    'hide-expand-icon': pushItem('hideCanvasControls', 'expand'),
+    'hide-selection-icon': pushItem('hideCanvasControls', 'selection'),
+    'hide-animation-icon': pushItem('hideCanvasControls', 'animation'),
+    'hide-control-toggle-icon': pushItem('hideCanvasControls', 'controlToggle'),
+    'hide-control-info-icon': pushItem('hideCanvasControls', 'controlInfo'),
+    'sequence-panel': setBool('sequencePanel'),
+    'pdbe-link': setBool('pdbeLink'),
+    'loading-overlay': setBool('loadingOverlay'),
+    'expanded': setBool('expanded'),
+    'landscape': setBool('landscape'),
+    'reactive': setBool('reactive'),
+};
+
+
+/** Actions for loading individual HTML attributes into a context */
+type AttributeLoadingActions = { [attribute: string]: (value: string, context: TContext) => any }
+
+/** Load attributes of an HTML element into a context */
+function loadHtmlAttributes(element: HTMLElement, actions: AttributeLoadingActions, context: TContext): TContext {
+    for (const attribute in actions) {
+        const value = element.getAttribute(attribute);
+        if (typeof value === 'string') {
+            actions[attribute](value, context);
+        }
+    }
+    return context;
+}
+
+
+/** Select keys of an object type `T` which except type `V` as value */
+type KeyWith = Exclude<{ [key in keyof T]: V extends T[key] ? key : never }[keyof T], undefined>
+
+function setString(key: KeyWith) {
+    return (value: string, obj: T) => { obj[key] = value as any; };
+}
+function setLiteral(allowedValues: readonly E[], key: KeyWith) {
+    return (value: string, ctx: T) => {
+        if (!allowedValues.includes(value as E)) console.error(`Value "${value}" is not valid for type ${allowedValues.map(s => `"${s}"`).join(' | ')}`);
+        ctx[key] = value as any;
+    };
+}
+function setBool(key: KeyWith) {
+    return (value: string, obj: T) => { obj[key] = parseBool(value) as any; };
+}
+function setColorComponent(key: KeyWith, component: 'r' | 'g' | 'b') {
+    return (value: string, obj: T) => {
+        const color = obj[key] ??= { r: 0, g: 0, b: 0 } as any;
+        color[component] = Number(value);
+    };
+}
+function pushItem(key: KeyWith, item: any) {
+    return (value: string, obj: T) => {
+        if (parseBool(value)) {
+            const array = obj[key] ??= [] as any;
+            array.push(item);
+        }
+    };
+}
+
+/** Parse a string into a boolean.
+ * Consider strings like 'false', 'OFF', '0' as false; others as true.
+ * Empty string is parsed as true, because HTML attribute without value must be treated as truthy. */
+function parseBool(value: string): boolean {
+    const FalseyStrings = ['false', 'off', '0'];
+    return !FalseyStrings.includes(value.toLowerCase());
+}
+function defaultCustomData(): Exclude {
+    return { url: '', format: '', binary: false };
+}
diff --git a/frontend/venome-molstar/src/app/spec.ts b/frontend/venome-molstar/src/app/spec.ts
new file mode 100644
index 00000000..38df4c52
--- /dev/null
+++ b/frontend/venome-molstar/src/app/spec.ts
@@ -0,0 +1,267 @@
+import { Loci } from "molstar/lib/mol-model/loci";
+import { StateActions } from "molstar/lib/mol-plugin-state/actions";
+import { VolumeStreamingCustomControls } from "molstar/lib/mol-plugin-ui/custom/volume";
+import { PluginUISpec } from "molstar/lib/mol-plugin-ui/spec";
+import { PluginBehaviors } from "molstar/lib/mol-plugin/behavior";
+import { DefaultFocusLociBindings } from "molstar/lib/mol-plugin/behavior/dynamic/camera";
+import { DefaultSelectLociBindings } from "molstar/lib/mol-plugin/behavior/dynamic/representation";
+import { CreateVolumeStreamingBehavior } from "molstar/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers";
+import { PluginConfig } from "molstar/lib/mol-plugin/config";
+import { PluginSpec } from "molstar/lib/mol-plugin/spec";
+import { LigandQueryParam, MapParams, QueryParam } from "./helpers";
+import { PDBeLociLabelProvider } from "./labels";
+import { PDBeSIFTSMapping } from "./sifts-mappings-behaviour";
+
+export const DefaultPluginSpec = (): PluginSpec => ({
+	actions: [
+		PluginSpec.Action(StateActions.Structure.EnableStructureCustomProps),
+	],
+	behaviors: [
+		PluginSpec.Behavior(PluginBehaviors.Representation.HighlightLoci),
+		PluginSpec.Behavior(PluginBehaviors.Representation.SelectLoci),
+		PluginSpec.Behavior(PDBeLociLabelProvider),
+		PluginSpec.Behavior(PluginBehaviors.Representation.FocusLoci),
+		PluginSpec.Behavior(PluginBehaviors.Camera.FocusLoci),
+		PluginSpec.Behavior(PluginBehaviors.Camera.CameraAxisHelper),
+
+		PluginSpec.Behavior(PluginBehaviors.CustomProps.StructureInfo),
+		PluginSpec.Behavior(PluginBehaviors.CustomProps.AccessibleSurfaceArea),
+		PluginSpec.Behavior(PDBeSIFTSMapping, {
+			autoAttach: true,
+			showTooltip: true,
+		}),
+		PluginSpec.Behavior(PluginBehaviors.CustomProps.Interactions),
+		PluginSpec.Behavior(PluginBehaviors.CustomProps.SecondaryStructure),
+		PluginSpec.Behavior(PluginBehaviors.CustomProps.ValenceModel),
+		PluginSpec.Behavior(PluginBehaviors.CustomProps.CrossLinkRestraint),
+	],
+	// animations: [],
+	config: [
+		[
+			PluginConfig.VolumeStreaming.DefaultServer,
+			"https://www.ebi.ac.uk/pdbe/volume-server",
+		],
+		[
+			PluginConfig.VolumeStreaming.EmdbHeaderServer,
+			"https://files.wwpdb.org/pub/emdb/structures",
+		],
+	],
+});
+
+export const DefaultPluginUISpec = (): PluginUISpec => ({
+	...DefaultPluginSpec(),
+	customParamEditors: [
+		[CreateVolumeStreamingBehavior, VolumeStreamingCustomControls],
+	],
+});
+
+/** RGB color (r, g, b values 0-255) */
+export interface ColorParams {
+	r: number;
+	g: number;
+	b: number;
+}
+
+export const Preset = [
+	"default",
+	"unitcell",
+	"all-models",
+	"supercell",
+] as const;
+export type Preset = (typeof Preset)[number];
+
+export const Lighting = [
+	"flat",
+	"matte",
+	"glossy",
+	"metallic",
+	"plastic",
+] as const;
+export type Lighting = (typeof Lighting)[number];
+
+export const VisualStyle = [
+	"cartoon",
+	"ball-and-stick",
+	"carbohydrate",
+	"ellipsoid",
+	"gaussian-surface",
+	"molecular-surface",
+	"point",
+	"putty",
+	"spacefill",
+] as const;
+export type VisualStyle = (typeof VisualStyle)[number];
+
+export const Encoding = ["cif", "bcif"] as const;
+export type Encoding = (typeof Encoding)[number];
+
+/** Options for initializing `PDBeMolstarPlugin` */
+export interface InitParams {
+	// DATA
+	/** PDB ID (example: '1cbs'), or UniProt ID if `superposition` is `true`. Leave `undefined` only when setting `customData` */
+	moleculeId?: string;
+	/** Load data from a specific data source.
+	 * Example: `{ url: 'https://www.ebi.ac.uk/pdbe/model-server/v1/1cbs/atoms?label_entity_id=1&auth_asym_id=A&encoding=bcif', format: 'cif', binary: true }` */
+	customData?: { url: string; format: string; binary: boolean };
+	/** Leave `undefined` to load deposited model structure. Use assembly identifier to load assembly structure. or 'preferred' to load default assembly (i.e. the first assembly). */
+	assemblyId?: string;
+	/** Specify type of structure to be loaded */
+	defaultPreset: Preset;
+	/** Use to display the PDBe ligand page 3D view like here (https://www.ebi.ac.uk/pdbe/entry/pdb/1cbs/bound/REA).
+	 * Example: `{ label_comp_id: 'REA' }`. At least one is required of `label_comp_id` and `auth_seq_id` */
+	ligandView?: LigandQueryParam;
+	/** This applies AlphaFold confidence score colouring theme for AlphaFold model */
+	alphafoldView: boolean;
+	/** Display the superposed structures view like the one on the PDBe-KB pages. */
+	superposition: boolean;
+	/** Customize the superposed structures view. Example: `{ matrixAccession: 'P08684', segment: 1, ligandView: true, ligandColor: { r: 255, g: 255, b: 50} }`. */
+	superpositionParams?: {
+		matrixAccession?: string;
+		segment?: number;
+		cluster?: number[];
+		superposeCompleteCluster?: boolean;
+		ligandView?: boolean;
+		superposeAll?: boolean;
+		ligandColor?: ColorParams;
+	};
+	/** Specify parts of the structure to highlight with different colors */
+	selection?: {
+		data: QueryParam[];
+		nonSelectedColor?: ColorParams;
+		clearPrevious?: boolean;
+	};
+
+	// APPEARANCE
+	/** Leave `undefined` to keep both cartoon and ball-and-sticks based on component type */
+	visualStyle?: VisualStyle;
+	/** Molstar renders multiple visuals (polymer, ligand, water...) visuals by default. This option is to exclude any of these default visuals */
+	hideStructure: (
+		| "polymer"
+		| "het"
+		| "water"
+		| "carbs"
+		| "nonStandard"
+		| "coarse"
+	)[];
+	/** Load electron density (or EM) maps from Volume Server if value is set to true */
+	loadMaps: boolean;
+	/** Customize map style (opacity and solid/wireframe) */
+	mapSettings?: MapParams;
+	/** Canvas background color */
+	bgColor: ColorParams;
+	/** Color appearing on mouse-over */
+	highlightColor?: ColorParams;
+	/** Color for marking the selected part of structure (when Selection Mode is active) */
+	selectColor?: ColorParams;
+	/** Default lighting (I don't think it really works) */
+	lighting?: Lighting;
+
+	// BEHAVIOR
+	/** Load Validation Report Annotations. Adds 'Annotations' control in the menu */
+	validationAnnotation: boolean;
+	/** Load Domain Annotations. Adds 'Annotations' control in the menu */
+	domainAnnotation: boolean;
+	/** Load Assembly Symmetry Annotations. Adds 'Annotations' control in the menu */
+	symmetryAnnotation: boolean;
+	/** This option is to set the default base URL for the data source. Mostly used internally to test the plugin on different environments */
+	pdbeUrl: string;
+	/** Preferred encoding of input structural data */
+	encoding: Encoding;
+	/** Load low precision coordinates from Model Server */
+	lowPrecisionCoords: boolean;
+	/** Controls the action performed when clicking a residue. `true` (default) will zoom the residue
+	 * and show ball-and-stick visual for its surroundings, `false` will only zoom the residue.
+	 * If `ligandView` or `superposition` option is set, `selectInteraction` behaves as if `false`. */
+	selectInteraction: boolean;
+	/** Override mouse selection behavior */
+	selectBindings?: typeof DefaultSelectLociBindings;
+	/** Override mouse click focus behaviour */
+	focusBindings?: typeof DefaultFocusLociBindings;
+	/** Structure granularity level for interactions like highlight, focus, select.
+	 * (Granularity levels ending with `Instances` treat multiple copies of the same element/residue/chain in an assembly as one object). */
+	granularity?: Loci.Granularity;
+	/** Subscribe to other PDB Web-components custom events */
+	subscribeEvents: boolean;
+
+	// INTERFACE
+	/** Hide all control panels by default (can be shown by the Toggle Controls Panel button (wrench icon)) */
+	hideControls: boolean;
+	/** Hide individual icon buttons in the top-right corner of the canvas */
+	hideCanvasControls: (
+		| "expand"
+		| "selection"
+		| "animation"
+		| "controlToggle"
+		| "controlInfo"
+	)[];
+	/** Display Sequence panel */
+	sequencePanel: boolean;
+	/** Display PDBe entry link in top right corner of the canvas */
+	pdbeLink: boolean;
+	/** Show overlay with PDBe logo while the initial structure is being loaded */
+	loadingOverlay: boolean;
+	/** Display full-screen by default on load */
+	expanded: boolean;
+	/** Set landscape layout (control panels on the sides instead of above and under the canvas) */
+	landscape: boolean;
+	/** Set reactive layout (switching between landscape and portrait based on the browser window size). Overrides `landscape`. */
+	reactive: boolean;
+}
+
+/** Default values for `InitParams` */
+export const DefaultParams: InitParams = {
+	moleculeId: undefined,
+	customData: undefined,
+	assemblyId: undefined,
+	defaultPreset: "default",
+	ligandView: undefined,
+	alphafoldView: false,
+	superposition: false,
+	superpositionParams: undefined,
+	selection: undefined,
+
+	visualStyle: undefined,
+	hideStructure: [],
+	loadMaps: false,
+	mapSettings: undefined,
+	bgColor: { r: 0, g: 0, b: 0 },
+	highlightColor: undefined,
+	selectColor: undefined,
+	lighting: undefined,
+
+	validationAnnotation: false,
+	domainAnnotation: false,
+	symmetryAnnotation: false,
+	pdbeUrl: "https://www.ebi.ac.uk/pdbe/",
+	encoding: "bcif",
+	lowPrecisionCoords: false,
+	selectInteraction: true,
+	selectBindings: undefined,
+	focusBindings: undefined,
+	granularity: undefined,
+	subscribeEvents: false,
+
+	hideControls: false,
+	hideCanvasControls: [],
+	sequencePanel: false,
+	pdbeLink: true,
+	loadingOverlay: false,
+	expanded: false,
+	landscape: false,
+	reactive: false,
+};
+
+/** Return `undefined` if `params` are valid, an error message otherwise. */
+export function validateInitParams(
+	params: Partial
+): string | undefined {
+	if (!params.moleculeId && !params.customData?.url)
+		return "Option `moleculeId` or `customData` must be defined";
+	if (params.customData) {
+		if (!params.customData.url)
+			return "Option `customData.url` must be a non-empty string";
+		if (!params.customData.format)
+			return "Option `customData.format` must be a non-empty string";
+	}
+	return undefined;
+}
diff --git a/frontend/venome-molstar/src/app/subscribe-events.ts b/frontend/venome-molstar/src/app/subscribe-events.ts
new file mode 100644
index 00000000..db23096d
--- /dev/null
+++ b/frontend/venome-molstar/src/app/subscribe-events.ts
@@ -0,0 +1,209 @@
+export function subscribeToComponentEvents(wrapperCtx: any) {
+    document.addEventListener('PDB.interactions.click', function (e: any) {
+        if (typeof e.detail !== 'undefined') {
+            const data = e.detail.interacting_nodes ? { data: e.detail.interacting_nodes } : { data: [e.detail.selected_node] };
+            data.data[0]['focus'] = true;
+            wrapperCtx.visual.select(data);
+        }
+    });
+
+    document.addEventListener('PDB.interactions.mouseover', function (e: any) {
+        if (typeof e.detail !== 'undefined') {
+            const data = e.detail.interacting_nodes ? { data: e.detail.interacting_nodes } : { data: [e.detail.selected_node] };
+            wrapperCtx.visual.highlight(data);
+        }
+    });
+
+    document.addEventListener('PDB.interactions.mouseout', function (e: any) {
+        wrapperCtx.visual.clearHighlight();
+    });
+
+    document.addEventListener('PDB.topologyViewer.click', function (e: any) {
+        if (typeof e.eventData !== 'undefined') {
+            // Create query object from event data
+            const highlightQuery = {
+                entity_id: e.eventData.entityId,
+                struct_asym_id: e.eventData.structAsymId,
+                start_residue_number: e.eventData.residueNumber,
+                end_residue_number: e.eventData.residueNumber,
+                sideChain: true,
+                focus: true
+            };
+            // Call highlightAnnotation
+            wrapperCtx.visual.select({ data: [highlightQuery] });
+        }
+    });
+
+    document.addEventListener('PDB.topologyViewer.mouseover', function (e: any) {
+        if (typeof e.eventData !== 'undefined') {
+            // Abort if entryid do not match or viewer type is unipdb
+            // if(e.eventData.entryId != scope.pdbId) return;
+
+            // Create query object from event data
+            const highlightQuery = {
+                entity_id: e.eventData.entityId,
+                struct_asym_id: e.eventData.structAsymId,
+                start_residue_number: e.eventData.residueNumber,
+                end_residue_number: e.eventData.residueNumber
+            };
+            // Call highlightAnnotation
+            wrapperCtx.visual.highlight({ data: [highlightQuery] });
+        }
+    });
+
+    document.addEventListener('PDB.topologyViewer.mouseout', function (e: any) {
+        wrapperCtx.visual.clearHighlight();
+    });
+
+    document.addEventListener('protvista-mouseover', function (e: any) {
+        if (typeof e.detail !== 'undefined') {
+
+            let highlightQuery: any = undefined;
+
+            // Create query object from event data
+            if (e.detail.start && e.detail.end) {
+                highlightQuery = {
+                    start_residue_number: parseInt(e.detail.start),
+                    end_residue_number: parseInt(e.detail.end)
+                };
+            }
+
+            if (e.detail.feature && e.detail.feature.entityId) highlightQuery['entity_id'] = e.detail.feature.entityId + '';
+            if (e.detail.feature && e.detail.feature.bestChainId) highlightQuery['struct_asym_id'] = e.detail.feature.bestChainId;
+            if (e.detail.feature && e.detail.feature.chainId) highlightQuery['struct_asym_id'] = e.detail.feature.chainId;
+
+            if (highlightQuery) wrapperCtx.visual.highlight({ data: [highlightQuery] });
+        }
+    });
+
+    document.addEventListener('protvista-mouseout', function (e: any) {
+        wrapperCtx.visual.clearHighlight();
+    });
+
+    document.addEventListener('protvista-click', function (e: any) {
+        if (typeof e.detail !== 'undefined') {
+
+            let showInteraction = false;
+            let highlightQuery: any = undefined;
+
+            // Create query object from event data
+            if (e.detail.start && e.detail.end) {
+                highlightQuery = {
+                    start_residue_number: parseInt(e.detail.start),
+                    end_residue_number: parseInt(e.detail.end)
+                };
+            }
+
+            if (e.detail.feature && e.detail.feature.entityId) highlightQuery['entity_id'] = e.detail.feature.entityId + '';
+            if (e.detail.feature && e.detail.feature.bestChainId) highlightQuery['struct_asym_id'] = e.detail.feature.bestChainId;
+            if (e.detail.feature && e.detail.feature.chainId) highlightQuery['struct_asym_id'] = e.detail.feature.chainId;
+
+            if (e.detail.feature && e.detail.feature.accession && e.detail.feature.accession.split(' ')[0] === 'Chain' || e.detail.feature.tooltipContent === 'Ligand binding site') {
+                showInteraction = true;
+            }
+
+            if (e.detail.start === e.detail.end) showInteraction = true;
+
+            if (highlightQuery) {
+
+                if (showInteraction) {
+                    highlightQuery['sideChain'] = true;
+                } else {
+                    let selColor = undefined;
+                    if (e.detail.trackIndex > -1 && e.detail.feature.locations && e.detail.feature.locations[0].fragments[e.detail.trackIndex].color) selColor = e.detail.feature.locations[0].fragments[e.detail.trackIndex].color;
+                    if (typeof selColor == 'undefined' && e.detail.feature.color) selColor = e.detail.feature.color;
+                    if (typeof selColor == 'undefined' && e.detail.color) selColor = e.detail.color;
+
+                    if (typeof selColor == 'undefined') {
+                        selColor = { r: 65, g: 96, b: 91 };
+                    } else {
+                        const isRgb = /rgb/g;
+                        if (isRgb.test(selColor)) {
+                            const rgbArr = selColor.substring(4, selColor.length - 1).split(',');
+                            selColor = { r: rgbArr[0], g: rgbArr[1], b: rgbArr[2] };
+                        }
+                    }
+
+                    highlightQuery['color'] = selColor;
+                }
+                highlightQuery['focus'] = true;
+                wrapperCtx.visual.select({ data: [highlightQuery] });
+            }
+        }
+    });
+
+    const elementTypeArrForRange = ['uniprot', 'pfam', 'cath', 'scop', 'strand', 'helice'];
+    const elementTypeArrForSingle = ['chain', 'quality', 'quality_outlier', 'binding site', 'alternate conformer'];
+    document.addEventListener('PDB.seqViewer.click', function (e: any) {
+        if (typeof e.eventData !== 'undefined') {
+            // Abort if entryid and entityid do not match or viewer type is unipdb
+            // if(e.eventData.entryId != scope.pdbId) return;
+
+            if (typeof e.eventData.elementData !== 'undefined' && elementTypeArrForSingle.indexOf(e.eventData.elementData.elementType) > -1) {
+                // Create query object from event data
+                const highlightQuery = {
+                    entity_id: e.eventData.entityId,
+                    struct_asym_id: e.eventData.elementData.pathData.struct_asym_id,
+                    start_residue_number: e.eventData.residueNumber,
+                    end_residue_number: e.eventData.residueNumber,
+                    sideChain: true,
+                    focus: true
+                };
+
+                // Call highlightAnnotation
+                wrapperCtx.visual.select({ data: [highlightQuery] });
+
+            } else if (typeof e.eventData.elementData !== 'undefined' && elementTypeArrForRange.indexOf(e.eventData.elementData.elementType) > -1) {
+
+                const seqColorArray = e.eventData.elementData.color;
+
+                // Create query object from event data
+                const highlightQuery = {
+                    entity_id: e.eventData.entityId,
+                    struct_asym_id: e.eventData.elementData.pathData.struct_asym_id,
+                    start_residue_number: e.eventData.elementData.pathData.start.residue_number,
+                    end_residue_number: e.eventData.elementData.pathData.end.residue_number,
+                    color: { r: seqColorArray[0], g: seqColorArray[1], b: seqColorArray[2] },
+                    focus: true
+                };
+                wrapperCtx.visual.select({ data: [highlightQuery] });
+            }
+
+        }
+    });
+
+    document.addEventListener('PDB.seqViewer.mouseover', function (e: any) {
+        if (typeof e.eventData !== 'undefined') {
+            // Abort if entryid and entityid do not match or viewer type is unipdb
+            // if(e.eventData.entryId != scope.pdbId) return;
+
+            if (typeof e.eventData.elementData !== 'undefined' && elementTypeArrForSingle.indexOf(e.eventData.elementData.elementType) > -1) {
+                // Create query object from event data
+                const highlightQuery = {
+                    entity_id: e.eventData.entityId,
+                    struct_asym_id: e.eventData.elementData.pathData.struct_asym_id,
+                    start_residue_number: e.eventData.residueNumber,
+                    end_residue_number: e.eventData.residueNumber,
+                    focus: true
+                };
+                wrapperCtx.visual.select({ data: [highlightQuery] });
+
+            } else if (typeof e.eventData.elementData !== 'undefined' && elementTypeArrForRange.indexOf(e.eventData.elementData.elementType) > -1) {
+
+                // Create query object from event data
+                const highlightQuery = {
+                    entity_id: e.eventData.entityId,
+                    struct_asym_id: e.eventData.elementData.pathData.struct_asym_id,
+                    start_residue_number: e.eventData.elementData.pathData.start.residue_number,
+                    end_residue_number: e.eventData.elementData.pathData.end.residue_number
+                };
+                // Call highlightAnnotation
+                wrapperCtx.visual.highlight({ data: [highlightQuery] });
+            }
+        }
+    });
+
+    document.addEventListener('PDB.seqViewer.mouseout', function (e) {
+        wrapperCtx.visual.clearHighlight();
+    });
+}
\ No newline at end of file
diff --git a/frontend/venome-molstar/src/app/superposition-export.ts b/frontend/venome-molstar/src/app/superposition-export.ts
new file mode 100644
index 00000000..31311f57
--- /dev/null
+++ b/frontend/venome-molstar/src/app/superposition-export.ts
@@ -0,0 +1,157 @@
+import { utf8ByteCount, utf8Write } from "molstar/lib/mol-io/common/utf8";
+import { to_mmCIF, Unit } from "molstar/lib/mol-model/structure";
+import { PluginContext } from "molstar/lib/mol-plugin/context";
+import { Task } from "molstar/lib/mol-task";
+import { getFormattedTime } from "molstar/lib/mol-util/date";
+import { download } from "molstar/lib/mol-util/download";
+import { zip } from "molstar/lib/mol-util/zip/zip";
+import { PluginCommands } from "molstar/lib/mol-plugin/commands";
+import { PluginCustomState } from "./plugin-custom-state";
+
+export async function superpositionExportHierarchy(
+	plugin: PluginContext,
+	options?: { format?: "cif" | "bcif" }
+) {
+	try {
+		await plugin.runTask(_superpositionExportHierarchy(plugin, options), {
+			useOverlay: true,
+		});
+	} catch (e) {
+		console.error(e);
+		plugin.log.error(`Model export failed. See console for details.`);
+	}
+}
+
+function _superpositionExportHierarchy(
+	plugin: PluginContext,
+	options?: { format?: "cif" | "bcif" }
+) {
+	return Task.create("Export", async (ctx) => {
+		await ctx.update({
+			message: "Exporting...",
+			isIndeterminate: true,
+			canAbort: false,
+		});
+
+		const format = options?.format ?? "cif";
+		//  const { structures } = plugin.managers.structure.hierarchy.current;
+		const customState = PluginCustomState(plugin);
+		if (!customState.initParams)
+			throw new Error("customState.initParams has not been initialized");
+		if (!customState.superpositionState)
+			throw new Error(
+				"customState.superpositionState has not been initialized"
+			);
+		const superpositionState = customState.superpositionState;
+
+		const segmentIndex = superpositionState.activeSegment - 1;
+		const files: [name: string, data: string | Uint8Array][] = [];
+		const entryMap = new Map();
+		const structures =
+			superpositionState.loadedStructs[segmentIndex].slice();
+		if (!customState.initParams.moleculeId)
+			throw new Error("initParams.moleculeId is not defined");
+		if (superpositionState.alphafold.ref)
+			structures.push(`AF-${customState.initParams.moleculeId}`);
+		for (const molId of structures) {
+			const modelRef = superpositionState.models[molId];
+			if (!modelRef) continue;
+			let isStrHidden = false;
+			const _s: any =
+				plugin.managers.structure.hierarchy.current.refs.get(modelRef!);
+			if (_s.cell.state.isHidden) isStrHidden = true;
+			for (const strComp of _s.components) {
+				if (strComp.cell.state.isHidden) isStrHidden = true;
+			}
+			if (isStrHidden) continue;
+
+			const s = _s.transform?.cell.obj?.data ?? _s.cell.obj?.data;
+			if (!s) continue;
+			if (s.models.length > 1) {
+				plugin.log.warn(
+					`[Export] Skipping ${_s.cell.obj?.label}: Multimodel exports not supported.`
+				);
+				continue;
+			}
+			if (s.units.some((u: any) => !Unit.isAtomic(u))) {
+				plugin.log.warn(
+					`[Export] Skipping ${_s.cell.obj?.label}: Non-atomic model exports not supported.`
+				);
+				continue;
+			}
+
+			const name = entryMap.has(s.model.entryId)
+				? `${s.model.entryId}_${
+						entryMap.get(s.model.entryId)! + 1
+				  }.${format}`
+				: `${s.model.entryId}.${format}`;
+			entryMap.set(
+				s.model.entryId,
+				(entryMap.get(s.model.entryId) ?? 0) + 1
+			);
+
+			await ctx.update({
+				message: `Exporting ${s.model.entryId}...`,
+				isIndeterminate: true,
+				canAbort: false,
+			});
+			if (s.elementCount > 100000) {
+				// Give UI chance to update, only needed for larger structures.
+				await new Promise((res) => setTimeout(res, 50));
+			}
+
+			try {
+				files.push([
+					name,
+					to_mmCIF(s.model.entryId, s, format === "bcif", {
+						copyAllCategories: true,
+					}),
+				]);
+			} catch (e) {
+				if (format === "cif" && s.elementCount > 2000000) {
+					plugin.log.warn(
+						`[Export] The structure might be too big to be exported as Text CIF, consider using the BinaryCIF format instead.`
+					);
+				}
+				throw e;
+			}
+		}
+
+		if (files.length === 0) {
+			PluginCommands.Toast.Show(plugin, {
+				title: "Export Models",
+				message: "No visible structure in the 3D view to export!",
+				key: "superposition-toast-1",
+				timeoutMs: 7000,
+			});
+			return;
+		}
+
+		if (files.length === 1) {
+			download(new Blob([files[0][1]]), files[0][0]);
+		} else if (files.length > 1) {
+			const zipData: Record = {};
+			for (const [fn, data] of files) {
+				if (data instanceof Uint8Array) {
+					zipData[fn] = data;
+				} else {
+					const bytes = new Uint8Array(utf8ByteCount(data));
+					utf8Write(bytes, 0, data);
+					zipData[fn] = bytes;
+				}
+			}
+			await ctx.update({
+				message: `Compressing Data...`,
+				isIndeterminate: true,
+				canAbort: false,
+			});
+			const buffer = await zip(ctx, zipData);
+			download(
+				new Blob([new Uint8Array(buffer, 0, buffer.byteLength)]),
+				`structures_${getFormattedTime()}.zip`
+			);
+		}
+
+		plugin.log.info(`[Export] Done.`);
+	});
+}
diff --git a/frontend/venome-molstar/src/app/superposition-focus-representation.ts b/frontend/venome-molstar/src/app/superposition-focus-representation.ts
new file mode 100644
index 00000000..3f506c95
--- /dev/null
+++ b/frontend/venome-molstar/src/app/superposition-focus-representation.ts
@@ -0,0 +1,213 @@
+import { StructureElement } from "molstar/lib/mol-model/structure";
+import { createStructureRepresentationParams } from "molstar/lib/mol-plugin-state/helpers/structure-representation-params";
+import { PluginStateObject } from "molstar/lib/mol-plugin-state/objects";
+import { StateTransforms } from "molstar/lib/mol-plugin-state/transforms";
+import { PluginBehavior } from "molstar/lib/mol-plugin/behavior";
+import { MolScriptBuilder as MS } from "molstar/lib/mol-script/language/builder";
+import {
+	StateObjectCell,
+	StateSelection,
+	StateTransform,
+} from "molstar/lib/mol-state";
+import { ParamDefinition as PD } from "molstar/lib/mol-util/param-definition";
+import { PluginCommands } from "molstar/lib/mol-plugin/commands";
+import { PluginContext } from "molstar/lib/mol-plugin/context";
+import { lociDetails } from "./loci-details";
+
+const SuperpositionFocusRepresentationParams = (plugin: PluginContext) => {
+	const reprParams = StateTransforms.Representation.StructureRepresentation3D
+		.definition.params!(void 0, plugin) as PD.Params;
+	return {
+		expandRadius: PD.Numeric(5, { min: 1, max: 10, step: 1 }),
+		surroundingsParams: PD.Group(reprParams, {
+			label: "Surroundings",
+			customDefault: createStructureRepresentationParams(plugin, void 0, {
+				type: "ball-and-stick",
+				size: "physical",
+				typeParams: { sizeFactor: 0.16 },
+				sizeParams: { scale: 0.3 },
+			}),
+		}),
+	};
+};
+
+type SuperpositionFocusRepresentationProps = PD.ValuesFor<
+	ReturnType
+>;
+
+export enum SuperpositionFocusRepresentationTags {
+	SurrSel = "superposition-focus-surr-sel",
+	SurrRepr = "superposition-focus-surr-repr",
+}
+
+const TagSet: Set = new Set([
+	SuperpositionFocusRepresentationTags.SurrSel,
+	SuperpositionFocusRepresentationTags.SurrRepr,
+]);
+
+class SuperpositionFocusRepresentationBehavior extends PluginBehavior.WithSubscribers {
+	private get surrLabel() {
+		return `[Focus] Surroundings (${this.params.expandRadius} Å)`;
+	}
+
+	private ensureShape(
+		cell: StateObjectCell
+	) {
+		const state = this.plugin.state.data,
+			tree = state.tree;
+		const builder = state.build();
+		const refs = StateSelection.findUniqueTagsInSubtree(
+			tree,
+			cell.transform.ref,
+			TagSet
+		);
+
+		// Selections
+		if (!refs[SuperpositionFocusRepresentationTags.SurrSel]) {
+			refs[SuperpositionFocusRepresentationTags.SurrSel] = builder
+				.to(cell)
+				.apply(
+					StateTransforms.Model.StructureSelectionFromExpression,
+					{
+						expression: MS.struct.generator.empty(),
+						label: this.surrLabel,
+					},
+					{ tags: SuperpositionFocusRepresentationTags.SurrSel }
+				).ref;
+		}
+
+		// Representations
+		if (!refs[SuperpositionFocusRepresentationTags.SurrRepr]) {
+			refs[SuperpositionFocusRepresentationTags.SurrRepr] = builder
+				.to(refs[SuperpositionFocusRepresentationTags.SurrSel]!)
+				.apply(
+					StateTransforms.Representation.StructureRepresentation3D,
+					this.params.surroundingsParams,
+					{ tags: SuperpositionFocusRepresentationTags.SurrRepr }
+				).ref;
+		}
+
+		return { state, builder, refs };
+	}
+
+	private clear(root: StateTransform.Ref) {
+		const state = this.plugin.state.data;
+
+		const surrs = state.select(
+			StateSelection.Generators.byRef(root)
+				.subtree()
+				.withTag(SuperpositionFocusRepresentationTags.SurrSel)
+		);
+		if (surrs.length === 0) return;
+
+		const update = state.build();
+		const expression = MS.struct.generator.empty();
+		for (const s of surrs) {
+			update
+				.to(s)
+				.update(
+					StateTransforms.Model.StructureSelectionFromExpression,
+					(old) => ({ ...old, expression })
+				);
+		}
+
+		return PluginCommands.State.Update(this.plugin, {
+			state,
+			tree: update,
+			options: { doNotLogTiming: true, doNotUpdateCurrent: true },
+		});
+	}
+
+	private async focus(sourceLoci: StructureElement.Loci) {
+		const parent = this.plugin.helpers.substructureParent.get(
+			sourceLoci.structure
+		);
+		if (!parent || !parent.obj) return;
+
+		const loci = StructureElement.Loci.remap(sourceLoci, parent.obj!.data);
+
+		const residueLoci = StructureElement.Loci.extendToWholeResidues(loci);
+		const residueBundle = StructureElement.Bundle.fromLoci(residueLoci);
+		const target = StructureElement.Bundle.toExpression(residueBundle);
+
+		let surroundings = MS.struct.modifier.includeSurroundings({
+			0: target,
+			radius: this.params.expandRadius,
+			"as-whole-residues": true,
+		});
+
+		const lociDeatils = lociDetails(sourceLoci);
+		if (!lociDeatils) {
+			surroundings = MS.struct.modifier.exceptBy({
+				0: surroundings,
+				by: target,
+			});
+		}
+
+		const { state, builder, refs } = this.ensureShape(parent);
+
+		builder
+			.to(refs[SuperpositionFocusRepresentationTags.SurrSel]!)
+			.update(
+				StateTransforms.Model.StructureSelectionFromExpression,
+				(old) => ({
+					...old,
+					expression: surroundings,
+					label: this.surrLabel,
+				})
+			);
+
+		await PluginCommands.State.Update(this.plugin, {
+			state,
+			tree: builder,
+			options: { doNotLogTiming: true, doNotUpdateCurrent: true },
+		});
+	}
+
+	register(ref: string): void {
+		this.subscribeObservable(
+			this.plugin.managers.structure.focus.behaviors.current,
+			(entry) => {
+				// if (entry) this.focus(entry.loci);
+				// else this.clear(StateTransform.RootRef);
+				this.clear(StateTransform.RootRef);
+				if (entry) this.focus(entry.loci);
+			}
+		);
+	}
+
+	async update(params: SuperpositionFocusRepresentationProps) {
+		const old = this.params;
+		this.params = params;
+
+		const state = this.plugin.state.data;
+		const builder = state.build();
+
+		const all = StateSelection.Generators.root.subtree();
+
+		for (const repr of state.select(
+			all.withTag(SuperpositionFocusRepresentationTags.SurrRepr)
+		)) {
+			builder.to(repr).update(this.params.surroundingsParams);
+		}
+
+		await PluginCommands.State.Update(this.plugin, {
+			state,
+			tree: builder,
+			options: { doNotLogTiming: true, doNotUpdateCurrent: true },
+		});
+
+		if (params.expandRadius !== old.expandRadius)
+			await this.clear(StateTransform.RootRef);
+
+		return true;
+	}
+}
+
+export const SuperpositionFocusRepresentation = PluginBehavior.create({
+	name: "create-superposition-focus-representation",
+	display: { name: "Superposition Focus Representation" },
+	category: "interaction",
+	ctor: SuperpositionFocusRepresentationBehavior,
+	params: (_, plugin) => SuperpositionFocusRepresentationParams(plugin),
+});
diff --git a/frontend/venome-molstar/src/app/superposition-sifts-mapping.ts b/frontend/venome-molstar/src/app/superposition-sifts-mapping.ts
new file mode 100644
index 00000000..01c8b807
--- /dev/null
+++ b/frontend/venome-molstar/src/app/superposition-sifts-mapping.ts
@@ -0,0 +1,250 @@
+import { Segmentation } from "molstar/lib/mol-data/int";
+import { MinimizeRmsd } from "molstar/lib/mol-math/linear-algebra/3d/minimize-rmsd";
+import { SIFTSMapping } from "./sifts-mapping";
+import {
+	ElementIndex,
+	ResidueIndex,
+} from "molstar/lib/mol-model/structure/model/indexing";
+import { StructureElement } from "molstar/lib/mol-model/structure/structure/element";
+import { Structure } from "molstar/lib/mol-model/structure";
+import { Unit } from "molstar/lib/mol-model/structure/structure/unit";
+
+export interface AlignmentResultEntry {
+	transform: MinimizeRmsd.Result;
+	pivot: number;
+	other: number;
+}
+
+export interface AlignmentResult {
+	entries: AlignmentResultEntry[];
+	zeroOverlapPairs: [number, number][];
+	failedPairs: [number, number][];
+}
+
+type IncludeResidueTest = (
+	traceElementOrFirstAtom: StructureElement.Location,
+	residueIndex: ResidueIndex,
+	startIndex: ElementIndex,
+	endIndex: ElementIndex
+) => boolean;
+
+export function alignAndSuperposeWithSIFTSMapping(
+	structures: Structure[],
+	options?: {
+		traceOnly?: boolean;
+		includeResidueTest?: IncludeResidueTest;
+		applyTestIndex?: number[];
+	}
+): AlignmentResult {
+	const indexMap = new Map();
+
+	for (let i = 0; i < structures.length; i++) {
+		let includeResidueTest =
+			options?.includeResidueTest ?? _includeAllResidues;
+		if (options?.applyTestIndex && !options.applyTestIndex.includes(i))
+			includeResidueTest = _includeAllResidues;
+		buildIndex(
+			structures[i],
+			indexMap,
+			i,
+			options?.traceOnly ?? true,
+			includeResidueTest
+		);
+	}
+
+	const index = Array.from(indexMap.values());
+
+	// TODO: support non-first structure pivots
+	const pairs = findPairs(structures.length, index);
+
+	const zeroOverlapPairs: AlignmentResult["zeroOverlapPairs"] = [];
+	const failedPairs: AlignmentResult["failedPairs"] = [];
+
+	const entries: AlignmentResultEntry[] = [];
+	for (const p of pairs) {
+		if (p.count === 0) {
+			zeroOverlapPairs.push([p.i, p.j]);
+		} else {
+			const [a, b] = getPositionTables(index, p.i, p.j, p.count);
+			const transform = MinimizeRmsd.compute({ a, b });
+			if (Number.isNaN(transform.rmsd)) {
+				failedPairs.push([p.i, p.j]);
+			} else {
+				entries.push({ transform, pivot: p.i, other: p.j });
+			}
+		}
+	}
+
+	return { entries, zeroOverlapPairs, failedPairs };
+}
+
+function getPositionTables(
+	index: IndexEntry[],
+	pivot: number,
+	other: number,
+	N: number
+) {
+	const xs = MinimizeRmsd.Positions.empty(N);
+	const ys = MinimizeRmsd.Positions.empty(N);
+
+	let o = 0;
+	for (const { pivots } of index) {
+		const a = pivots[pivot];
+		const b = pivots[other];
+		if (!a || !b) continue;
+
+		const l = Math.min(a[2] - a[1], b[2] - b[1]);
+
+		// TODO: check if residue types match?
+		for (let i = 0; i < l; i++) {
+			let eI = (a[1] + i) as ElementIndex;
+			xs.x[o] = a[0].conformation.x(eI);
+			xs.y[o] = a[0].conformation.y(eI);
+			xs.z[o] = a[0].conformation.z(eI);
+
+			eI = (b[1] + i) as ElementIndex;
+			ys.x[o] = b[0].conformation.x(eI);
+			ys.y[o] = b[0].conformation.y(eI);
+			ys.z[o] = b[0].conformation.z(eI);
+			o++;
+		}
+	}
+
+	return [xs, ys];
+}
+
+function findPairs(N: number, index: IndexEntry[]) {
+	const pairwiseCounts: number[][] = [];
+	for (let i = 0; i < N; i++) {
+		pairwiseCounts[i] = [];
+		for (let j = 0; j < N; j++) pairwiseCounts[i][j] = 0;
+	}
+
+	for (const { pivots } of index) {
+		for (let i = 0; i < N; i++) {
+			if (!pivots[i]) continue;
+
+			const lI = pivots[i]![2] - pivots[i]![1];
+
+			for (let j = i + 1; j < N; j++) {
+				if (!pivots[j]) continue;
+
+				const lJ = pivots[j]![2] - pivots[j]![1];
+				pairwiseCounts[i][j] = pairwiseCounts[i][j] + Math.min(lI, lJ);
+			}
+		}
+	}
+
+	const ret: { i: number; j: number; count: number }[] = [];
+
+	for (let j = 1; j < N; j++) {
+		ret[j - 1] = { i: 0, j, count: pairwiseCounts[0][j] };
+	}
+
+	// TODO: support non-first structure pivots
+	// for (let i = 0; i < N - 1; i++) {
+	//     let max = 0, maxJ = i;
+	//     for (let j = i + 1; j < N; j++) {
+	//         if (pairwiseCounts[i][j] > max) {
+	//             maxJ = j;
+	//             max = pairwiseCounts[i][j];
+	//         }
+	//     }
+
+	//     ret[i] = { i, j: maxJ, count: max };
+	// }
+
+	return ret;
+}
+
+interface IndexEntry {
+	key: string;
+	pivots: {
+		[i: number]:
+			| [unit: Unit.Atomic, start: ElementIndex, end: ElementIndex]
+			| undefined;
+	};
+}
+
+function _includeAllResidues() {
+	return true;
+}
+
+function buildIndex(
+	structure: Structure,
+	index: Map,
+	sI: number,
+	traceOnly: boolean,
+	includeTest: IncludeResidueTest
+) {
+	const loc = StructureElement.Location.create(structure);
+
+	for (const unit of structure.units) {
+		if (unit.kind !== Unit.Kind.Atomic) continue;
+
+		const { elements, model } = unit;
+		loc.unit = unit;
+
+		const map = SIFTSMapping.Provider.get(model).value;
+		if (!map) return;
+
+		const { dbName, accession, num } = map;
+
+		const chainsIt = Segmentation.transientSegments(
+			unit.model.atomicHierarchy.chainAtomSegments,
+			elements
+		);
+		const residuesIt = Segmentation.transientSegments(
+			unit.model.atomicHierarchy.residueAtomSegments,
+			elements
+		);
+		const traceElementIndex =
+			unit.model.atomicHierarchy.derived.residue.traceElementIndex;
+
+		while (chainsIt.hasNext) {
+			const chainSegment = chainsIt.move();
+			residuesIt.setSegment(chainSegment);
+			while (residuesIt.hasNext) {
+				const residueSegment = residuesIt.move();
+				const rI = residueSegment.index;
+
+				if (!dbName[rI]) continue;
+
+				const traceElement = traceElementIndex[rI];
+
+				let start, end;
+				if (traceOnly) {
+					start = traceElement;
+					if (start === -1) continue;
+					end = (start + 1) as ElementIndex;
+				} else {
+					start = elements[residueSegment.start];
+					end = (elements[residueSegment.end - 1] +
+						1) as ElementIndex;
+				}
+
+				loc.element = (
+					traceElement >= 0 ? traceElement : start
+				) as ElementIndex;
+				if (!includeTest(loc, rI, start, end)) continue;
+
+				const key = `${dbName[rI]}-${accession[rI].split("-")[0]}-${
+					num[rI]
+				}`;
+
+				if (!index.has(key)) {
+					index.set(key, {
+						key,
+						pivots: { [sI]: [unit, start, end] },
+					});
+				} else {
+					const entry = index.get(key)!;
+
+					if (!entry.pivots[sI]) {
+						entry.pivots[sI] = [unit, start, end];
+					}
+				}
+			}
+		}
+	}
+}
diff --git a/frontend/venome-molstar/src/app/superposition.ts b/frontend/venome-molstar/src/app/superposition.ts
new file mode 100644
index 00000000..4fb4f1b2
--- /dev/null
+++ b/frontend/venome-molstar/src/app/superposition.ts
@@ -0,0 +1,1006 @@
+import { SymmetryOperator } from "molstar/lib/mol-math/geometry";
+import { Mat4 } from "molstar/lib/mol-math/linear-algebra";
+import { StructureProperties } from "molstar/lib/mol-model/structure";
+import { BuiltInTrajectoryFormat } from "molstar/lib/mol-plugin-state/formats/trajectory";
+import {
+	PluginStateObject as PSO,
+	PluginStateObject,
+} from "molstar/lib/mol-plugin-state/objects";
+import { StateTransforms } from "molstar/lib/mol-plugin-state/transforms";
+import { PluginContext } from "molstar/lib/mol-plugin/context";
+import { MolScriptBuilder as MS } from "molstar/lib/mol-script/language/builder";
+import { Script } from "molstar/lib/mol-script/script";
+import {
+	State,
+	StateObjectRef,
+	StateObjectSelector,
+} from "molstar/lib/mol-state";
+import { Task } from "molstar/lib/mol-task";
+import { Asset } from "molstar/lib/mol-util/assets";
+import { Color } from "molstar/lib/mol-util/color/color";
+import { ColorLists } from "molstar/lib/mol-util/color/lists";
+import { Subject } from "rxjs";
+import { applyAFTransparency } from "./alphafold-transparency";
+import { ModelInfo, ModelServerRequest, getStructureUrl } from "./helpers";
+import { ClusterMember, PluginCustomState } from "./plugin-custom-state";
+import { alignAndSuperposeWithSIFTSMapping } from "./superposition-sifts-mapping";
+
+function getRandomColor(plugin: PluginContext, segmentIndex: number) {
+	const clList: any = ColorLists;
+	const spState = PluginCustomState(plugin).superpositionState;
+	if (!spState)
+		throw new Error(
+			"customState.superpositionState has not been initialized"
+		);
+	let palleteIndex = spState.colorState[segmentIndex].palleteIndex;
+	let colorIndex = spState.colorState[segmentIndex].colorIndex;
+	if (clList[spState.colorPalette[palleteIndex]].list[colorIndex + 1]) {
+		colorIndex += 1;
+	} else {
+		colorIndex = 0;
+		palleteIndex = spState.colorPalette[palleteIndex + 1]
+			? palleteIndex + 1
+			: 0;
+	}
+	const palleteName = spState.colorPalette[palleteIndex];
+	spState.colorState[segmentIndex].palleteIndex = palleteIndex;
+	spState.colorState[segmentIndex].colorIndex = colorIndex;
+	return clList[palleteName].list[colorIndex];
+}
+
+export async function initSuperposition(
+	plugin: PluginContext,
+	completeSubject?: Subject
+) {
+	let success = false;
+	try {
+		await plugin.clear();
+
+		const customState = PluginCustomState(plugin);
+		customState.superpositionState = {
+			models: {},
+			entries: {},
+			refMaps: {},
+			segmentData: void 0,
+			matrixData: {},
+			activeSegment: 0,
+			loadedStructs: [],
+			visibleRefs: [],
+			invalidStruct: [],
+			noMatrixStruct: [],
+			hets: {},
+			colorPalette: [
+				"dark-2",
+				"red-yellow-green",
+				"paired",
+				"set-1",
+				"accent",
+				"set-2",
+				"rainbow",
+			],
+			colorState: [],
+			alphafold: {
+				apiData: {
+					cif: "",
+					pae: "",
+					length: 0,
+				},
+				length: 0,
+				ref: "",
+				traceOnly: true,
+				visibility: [],
+				transforms: [],
+				rmsds: [],
+				coordinateSystems: [],
+			},
+		};
+
+		// Get segment and cluster information for the given uniprot accession
+		await getSegmentData(plugin);
+		const segmentData = customState.superpositionState.segmentData;
+		if (!segmentData) return;
+
+		// Load Matrix Data
+		await getMatrixData(plugin);
+		if (!customState.superpositionState.segmentData) return;
+
+		if (!customState.initParams!.moleculeId)
+			throw new Error("initParams.moleculeId is not defined");
+		const afStrUrls = await getAfUrl(
+			plugin,
+			customState.initParams!.moleculeId
+		);
+		if (afStrUrls)
+			customState.superpositionState.alphafold.apiData = afStrUrls;
+
+		segmentData.forEach(() => {
+			customState.superpositionState!.loadedStructs.push([]);
+			customState.superpositionState!.visibleRefs.push([]);
+			customState.superpositionState!.colorState.push({
+				palleteIndex: 0,
+				colorIndex: -1,
+			});
+		});
+
+		// Set segment and cluster details from superPositionParams
+		const superpositionParams = customState.initParams!.superpositionParams;
+		const segmentIndex = superpositionParams?.segment
+			? superpositionParams.segment - 1
+			: 0;
+		customState.superpositionState.activeSegment = segmentIndex + 1;
+		const clusterIndexs = superpositionParams?.cluster
+			? superpositionParams.cluster
+			: void 0;
+
+		// Emit segment API data load event
+		customState.events?.superpositionInit.next(true);
+
+		// Get entry list to load matrix data
+		let entryList: ClusterMember[] = [];
+		const clusters = segmentData[segmentIndex].clusters;
+		clusters.forEach((cluster: ClusterMember[], clusterIndex: number) => {
+			// Validate for cluster index if provided in superPositionParams
+			if (clusterIndexs && clusterIndexs.indexOf(clusterIndex) === -1)
+				return;
+
+			// Add respresentative structure to the list
+			if (superpositionParams?.superposeAll) {
+				entryList = entryList.concat(cluster);
+			} else {
+				entryList.push(cluster[0]);
+			}
+		});
+
+		await renderSuperposition(plugin, segmentIndex, entryList);
+		success = true;
+	} finally {
+		completeSubject?.next(success);
+	}
+}
+
+function createCarbVisLabel(carbLigNamesAndCount: any) {
+	const compList = [];
+	for (const carbCompId in carbLigNamesAndCount) {
+		compList.push(`${carbCompId} (${carbLigNamesAndCount[carbCompId]})`);
+	}
+
+	return compList.join(", ");
+}
+
+async function getAfUrl(plugin: PluginContext, accession: string) {
+	let apiResponse: any;
+	let apiData: any;
+	await plugin.runTask(
+		Task.create("Get AlphaFold URL", async (ctx) => {
+			try {
+				apiResponse = await plugin
+					.fetch({
+						url: `https://alphafold.ebi.ac.uk/api/prediction/${accession}`,
+						type: "json",
+					})
+					.runInContext(ctx);
+				if (apiResponse && apiResponse?.[0].bcifUrl) {
+					apiData = {
+						cif: apiResponse?.[0].cifUrl,
+						pae: apiResponse?.[0].paeImageUrl,
+						length: apiResponse?.[0].uniprotEnd,
+					};
+				}
+			} catch (e) {
+				// console.warn(e);
+			}
+		})
+	);
+
+	return apiData;
+}
+
+export async function loadAfStructure(plugin: PluginContext) {
+	const customState = PluginCustomState(plugin);
+	if (!customState.superpositionState)
+		throw new Error(
+			"customState.superpositionState has not been initialized"
+		);
+	const { structure } = await loadStructure(
+		plugin,
+		customState.superpositionState.alphafold.apiData.cif,
+		"mmcif",
+		false
+	);
+	const strInstance = structure;
+	if (!strInstance) return false;
+
+	// Store Refs in state
+	const spState = customState.superpositionState;
+	spState.alphafold.ref = strInstance?.ref;
+	if (!customState.initParams?.moleculeId)
+		throw new Error("initParams.moleculeId is not defined");
+	spState.models[`AF-${customState.initParams.moleculeId}`] =
+		strInstance?.ref;
+
+	const chainSel = await plugin.builders.structure.tryCreateComponentStatic(
+		strInstance,
+		"polymer",
+		{
+			label: `AlphaFold Structure`,
+			tags: [`alphafold-chain`, `superposition-sel`],
+		}
+	);
+
+	if (chainSel) {
+		await plugin.builders.structure.representation.addRepresentation(
+			chainSel,
+			{
+				type: "putty",
+				color: "plddt-confidence" as any,
+				size: "uniform",
+				sizeParams: { value: 1.5 },
+			},
+			{ tag: `af-superposition-visual` }
+		);
+		return strInstance?.ref;
+	}
+
+	return false;
+}
+
+export async function superposeAf(
+	plugin: PluginContext,
+	traceOnly: boolean,
+	segmentIndex?: number
+) {
+	const customState = PluginCustomState(plugin);
+	const spState = customState.superpositionState;
+	if (!spState?.segmentData) return;
+
+	// Load AF structure
+	const afStrRef = spState.alphafold.ref || (await loadAfStructure(plugin));
+	if (!afStrRef) return;
+	const afStr: any = plugin.managers.structure.hierarchy.current.refs.get(
+		afStrRef!
+	);
+
+	const segmentNum = segmentIndex ? segmentIndex : spState.activeSegment - 1;
+	if (!spState.alphafold.transforms[segmentNum]) {
+		// Create representative list
+		const mappingResult: any = [];
+		const coordinateSystems: any = [];
+		const failedPairsResult: any = [];
+		const zeroOverlapPairsResult: any = [];
+
+		let minRmsd = 0;
+		let minIndex = 0;
+		const rmsdList: string[] = [];
+		const segmentClusters = spState.segmentData[segmentNum].clusters;
+		segmentClusters.forEach((cluster: any) => {
+			const modelRef =
+				spState.models[
+					`${cluster[0].pdb_id}_${cluster[0].struct_asym_id}`
+				];
+			if (modelRef) {
+				const structHierarchy: any =
+					plugin.managers.structure.hierarchy.current.refs.get(
+						modelRef!
+					);
+				if (structHierarchy) {
+					const input = [structHierarchy.components[0], afStr];
+					const structures = input.map((s) => s.cell.obj?.data!);
+					let { entries, failedPairs, zeroOverlapPairs } =
+						alignAndSuperposeWithSIFTSMapping(structures, {
+							traceOnly,
+							includeResidueTest: (loc) =>
+								StructureProperties.atom.B_iso_or_equiv(loc) >
+								70,
+							applyTestIndex: [1],
+						});
+
+					if (
+						entries.length === 0 ||
+						(entries &&
+							entries[0] &&
+							entries[0].transform.rmsd.toFixed(1) === "0.0")
+					) {
+						const alignWithoutPlddt =
+							alignAndSuperposeWithSIFTSMapping(structures, {
+								traceOnly,
+							});
+						entries = alignWithoutPlddt.entries;
+					}
+
+					if (entries && entries[0]) {
+						mappingResult.push(entries[0]);
+						coordinateSystems.push(
+							input[0]?.transform?.cell.obj?.data.coordinateSystem
+						);
+						const totalMappings = mappingResult.length;
+						if (
+							totalMappings === 1 ||
+							entries[0].transform.rmsd < minRmsd
+						) {
+							minRmsd = entries[0].transform.rmsd;
+							minIndex =
+								totalMappings === 1
+									? 0
+									: mappingResult.length - 1;
+						}
+
+						rmsdList.push(
+							`${cluster[0].pdb_id} chain ${
+								cluster[0].struct_asym_id
+							}:${entries[0].transform.rmsd.toFixed(2)}`
+						);
+					} else {
+						if (failedPairs.length > 0)
+							failedPairsResult.push(failedPairs);
+						if (zeroOverlapPairs.length > 0)
+							zeroOverlapPairsResult.push(zeroOverlapPairs);
+						// rmsdList.push(`${cluster[0].pdb_id} ${cluster[0].struct_asym_id}:-`)
+					}
+				}
+			}
+		});
+
+		// console.log(failedPairsResult);
+		// console.log(zeroOverlapPairsResult);
+		if (mappingResult.length > 0) {
+			spState.alphafold.visibility[segmentNum] = true;
+			spState.alphafold.transforms[segmentNum] =
+				mappingResult[minIndex].transform.bTransform;
+			spState.alphafold.coordinateSystems[segmentNum] =
+				coordinateSystems[minIndex];
+			spState.alphafold.rmsds[segmentNum] = rmsdList.sort(
+				(a: string, b: string) =>
+					parseFloat(a.split(":")[1]) - parseFloat(b.split(":")[1])
+			);
+		}
+	}
+
+	await afTransform(
+		plugin,
+		afStr.cell,
+		spState.alphafold.transforms[segmentNum],
+		spState.alphafold.coordinateSystems[segmentNum]
+	);
+	applyAFTransparency(plugin, afStr, 0.8, 70);
+
+	return true;
+}
+
+export async function renderSuperposition(
+	plugin: PluginContext,
+	segmentIndex: number,
+	entryList: ClusterMember[]
+) {
+	const customState = PluginCustomState(plugin);
+	const superpositionParams = customState.initParams!.superpositionParams;
+	let busyFlagOn = false;
+	if (entryList.length > 1) {
+		busyFlagOn = true;
+		customState.events?.isBusy.next(true);
+	}
+
+	// Load Coordinates and render respresentations
+	return plugin.dataTransaction(async () => {
+		if (!customState.initParams)
+			throw new Error("customState.initParams has not been initialized");
+		if (!customState.superpositionState)
+			throw new Error(
+				"customState.superpositionState has not been initialized"
+			);
+		const spState = customState.superpositionState;
+
+		for await (const s of entryList) {
+			// validate matrix availability
+			if (!spState.matrixData[`${s.pdb_id}_${s.auth_asym_id}`]) {
+				spState.noMatrixStruct.push(`${s.pdb_id}_${s.struct_asym_id}`);
+				spState.invalidStruct.push(`${s.pdb_id}_${s.struct_asym_id}`);
+				continue;
+			}
+			spState.loadedStructs[segmentIndex].push(
+				`${s.pdb_id}_${s.struct_asym_id}`
+			);
+
+			// Set Coordinate server url
+			const request: ModelServerRequest =
+				superpositionParams && superpositionParams.ligandView
+					? { pdbId: s.pdb_id, queryType: "full" }
+					: {
+							pdbId: s.pdb_id,
+							queryType: "atoms",
+							queryParams: { auth_asym_id: s.auth_asym_id },
+					  };
+			const strUrl = getStructureUrl(customState.initParams, request);
+
+			// Load Data
+			let strInstance: any;
+			let modelRef: any;
+			let clearOnFail = true;
+			if (
+				superpositionParams &&
+				superpositionParams.ligandView &&
+				spState.entries[s.pdb_id]
+			) {
+				const polymerInstance = plugin.state.data.select(
+					spState.entries[s.pdb_id]
+				)[0];
+				modelRef = polymerInstance.transform.parent;
+				const modelInstance = plugin.state.data.select(modelRef)[0];
+				strInstance = await plugin.builders.structure.createStructure(
+					modelInstance,
+					{ name: "model", params: {} }
+				);
+				clearOnFail = false;
+			} else {
+				const isBinary =
+					customState.initParams.encoding === "bcif" ? true : false;
+				const { model, structure } = await loadStructure(
+					plugin,
+					strUrl,
+					"mmcif",
+					isBinary
+				);
+				strInstance = structure;
+				modelRef = model!.ref;
+			}
+
+			if (!strInstance) continue;
+
+			// Store Refs in state
+			if (!spState.models[`${s.pdb_id}_${s.struct_asym_id}`])
+				spState.models[`${s.pdb_id}_${s.struct_asym_id}`] =
+					strInstance?.ref;
+			if (
+				superpositionParams &&
+				superpositionParams.ligandView &&
+				!spState.entries[s.pdb_id]
+			)
+				spState.entries[s.pdb_id] = strInstance?.ref;
+
+			// Apply tranform matrix
+			const matrix = Mat4.ofRows(
+				customState.superpositionState.matrixData[
+					`${s.pdb_id}_${s.auth_asym_id}`
+				].matrix
+			);
+			await transform(plugin, strInstance, matrix);
+
+			// Create representations
+			let chainSel: StateObjectSelector | undefined;
+			if (
+				superpositionParams &&
+				superpositionParams.ligandView &&
+				s.is_representative
+			) {
+				const uniformColor1 = getRandomColor(plugin, segmentIndex); // random color
+				chainSel =
+					await plugin.builders.structure.tryCreateComponentFromExpression(
+						strInstance,
+						chainSelection(s.struct_asym_id),
+						`Chain-${segmentIndex}`,
+						{ label: `Chain`, tags: [`superposition-sel`] }
+					);
+				if (chainSel) {
+					await plugin.builders.structure.representation.addRepresentation(
+						chainSel,
+						{
+							type: "putty",
+							color: "uniform",
+							colorParams: { value: uniformColor1 },
+							size: "uniform",
+						},
+						{ tag: `superposition-visual` }
+					);
+					spState.refMaps[
+						chainSel.ref
+					] = `${s.pdb_id}_${s.struct_asym_id}`;
+				}
+			} else if (
+				superpositionParams &&
+				superpositionParams.ligandView &&
+				!s.is_representative
+			) {
+				// Do nothing
+			} else {
+				const uniformColor2 = getRandomColor(plugin, segmentIndex); // random color
+				chainSel =
+					await plugin.builders.structure.tryCreateComponentStatic(
+						strInstance,
+						"polymer",
+						{
+							label: `Chain`,
+							tags: [
+								`Chain-${segmentIndex}`,
+								`superposition-sel`,
+							],
+						}
+					);
+				if (chainSel) {
+					await plugin.builders.structure.representation.addRepresentation(
+						chainSel,
+						{
+							type: "putty",
+							color: "uniform",
+							colorParams: { value: uniformColor2 },
+							size: "uniform",
+						},
+						{ tag: `superposition-visual` }
+					);
+					spState.refMaps[
+						chainSel.ref
+					] = `${s.pdb_id}_${s.struct_asym_id}`;
+				}
+
+				// // const addTooltipUpdate = plugin.state.behaviors.build().to(BestDatabaseSequenceMapping.id).update(BestDatabaseSequenceMapping, (old: any) => { old.showTooltip = true; });
+				// // await plugin.runTask(plugin.state.behaviors.updateTree(addTooltipUpdate));
+				// BestDatabaseSequenceMapping
+				// console.log(plugin.state.data.select(modelRef)[0])
+			}
+
+			let invalidStruct = chainSel ? false : true;
+			if (superpositionParams && superpositionParams.ligandView) {
+				const state = plugin.state.data;
+				const hetInfo = await getLigandNamesFromModelData(
+					plugin,
+					state,
+					modelRef
+				);
+				const hets = hetInfo ? hetInfo.hetNames : [];
+				// const interactingHets = [];
+				if (hets && hets.length > 0) {
+					for await (const het of hets) {
+						const ligand = MS.struct.generator.atomGroups({
+							"chain-test": MS.core.rel.eq([
+								MS.struct.atomProperty.macromolecular.auth_asym_id(),
+								s.auth_asym_id,
+							]),
+							"residue-test": MS.core.rel.eq([
+								MS.struct.atomProperty.macromolecular.label_comp_id(),
+								het,
+							]),
+							"group-by": MS.core.str.concat([
+								MS.struct.atomProperty.core.operatorName(),
+								MS.struct.atomProperty.macromolecular.residueKey(),
+							]),
+						});
+
+						const labelTagParams = {
+							label: `${het}`,
+							tags: [`superposition-ligand-sel`],
+						};
+						let hetColor = Color.fromRgb(253, 3, 253);
+						if (superpositionParams?.ligandColor) {
+							const { r, g, b } = superpositionParams.ligandColor;
+							hetColor = Color.fromRgb(r, g, b);
+						}
+						const ligandExp =
+							await plugin.builders.structure.tryCreateComponentFromExpression(
+								strInstance,
+								ligand,
+								`${het}-${segmentIndex}`,
+								labelTagParams
+							);
+						if (ligandExp) {
+							await plugin.builders.structure.representation.addRepresentation(
+								ligandExp,
+								{
+									type: "ball-and-stick",
+									color: "uniform",
+									colorParams: { value: hetColor },
+								},
+								{ tag: `superposition-ligand-visual` }
+							);
+							spState.refMaps[
+								ligandExp.ref
+							] = `${s.pdb_id}_${s.struct_asym_id}`;
+							invalidStruct = false;
+							// interactingHets.push(het);
+						}
+					}
+				}
+
+				const carbEntityCount = hetInfo ? hetInfo.carbEntityCount : 0;
+				if (carbEntityCount > 0) {
+					// Get Carbohydrate Polymers details from PDBe API
+					const allCarbPolymers = await getCarbPolymerDetailsFromApi(
+						plugin,
+						s.pdb_id
+					);
+
+					// Polymer chain + surroundings query
+					const polymerChainWithSurroundings =
+						MS.struct.modifier.includeSurroundings({
+							0: MS.struct.generator.atomGroups({
+								"entity-test": MS.core.rel.eq([
+									MS.ammp("entityType"),
+									"polymer",
+								]),
+								"chain-test": MS.core.rel.eq([
+									MS.struct.atomProperty.macromolecular.auth_asym_id(),
+									s.auth_asym_id,
+								]),
+								"group-by": MS.core.str.concat([
+									MS.struct.atomProperty.core.operatorName(),
+									MS.struct.atomProperty.macromolecular.residueKey(),
+								]),
+							}),
+							radius: 5,
+							"as-whole-residues": true,
+						});
+
+					let i = 0;
+					for (const carbEntityChainId of allCarbPolymers.branchedChains) {
+						const carbEntityChain = MS.struct.generator.atomGroups({
+							"entity-test": MS.core.rel.eq([
+								MS.ammp("entityType"),
+								"branched",
+							]),
+							"chain-test": MS.core.rel.eq([
+								MS.struct.atomProperty.macromolecular.auth_asym_id(),
+								carbEntityChainId,
+							]),
+							"group-by": MS.core.str.concat([
+								MS.struct.atomProperty.core.operatorName(),
+								MS.struct.atomProperty.macromolecular.residueKey(),
+							]),
+						});
+
+						const carbEntityChainInVicinity =
+							MS.struct.filter.intersectedBy({
+								0: polymerChainWithSurroundings,
+								by: carbEntityChain,
+							});
+
+						const data = plugin.state.data.select(
+							strInstance.ref
+						)[0].obj.data;
+						const carbChainSel = Script.getStructureSelection(
+							carbEntityChainInVicinity,
+							data
+						);
+						if (carbChainSel && carbChainSel.kind === "sequence") {
+							// console.log(carbEntityChainId + ' chain present in 5 A radius');
+							const carbLigands = [];
+							const carbLigNamesAndCount: any = {};
+							const carbLigList = [];
+
+							for (const carbLigs of allCarbPolymers
+								.branchedLigands[i]) {
+								const ligResDetails = carbLigs.split("-");
+								carbLigands.push(
+									MS.core.rel.eq([
+										MS.struct.atomProperty.macromolecular.auth_seq_id(),
+										+ligResDetails[1],
+									])
+								);
+
+								if (carbLigNamesAndCount[ligResDetails[0]]) {
+									carbLigNamesAndCount[ligResDetails[0]]++;
+								} else {
+									carbLigNamesAndCount[ligResDetails[0]] = 1;
+								}
+
+								carbLigList.push(ligResDetails[0]);
+							}
+
+							const carbVisLabel =
+								createCarbVisLabel(carbLigNamesAndCount);
+
+							const branchedEntity =
+								MS.struct.generator.atomGroups({
+									"entity-test": MS.core.rel.eq([
+										MS.ammp("entityType"),
+										"branched",
+									]),
+									"group-by": MS.core.str.concat([
+										MS.struct.atomProperty.core.operatorName(),
+										MS.struct.atomProperty.macromolecular.residueKey(),
+									]),
+									"chain-test": MS.core.rel.eq([
+										MS.struct.atomProperty.macromolecular.auth_asym_id(),
+										carbEntityChainId,
+									]),
+									"residue-test":
+										MS.core.logic.or(carbLigands),
+								});
+
+							const labelTagParams = {
+								label: `${carbVisLabel}`,
+								tags: [`superposition-carb-sel`],
+							};
+							const ligandExp =
+								await plugin.builders.structure.tryCreateComponentFromExpression(
+									strInstance,
+									branchedEntity,
+									`${carbLigList.join("-")}-${segmentIndex}`,
+									labelTagParams
+								);
+							if (ligandExp) {
+								await plugin.builders.structure.representation.addRepresentation(
+									ligandExp,
+									{ type: "carbohydrate" },
+									{ tag: `superposition-carb-visual` }
+								);
+								spState.refMaps[
+									ligandExp.ref
+								] = `${s.pdb_id}_${s.struct_asym_id}`;
+								invalidStruct = false;
+							}
+						}
+
+						i++;
+					}
+				}
+
+				if (invalidStruct) {
+					spState.invalidStruct.push(
+						`${s.pdb_id}_${s.struct_asym_id}`
+					);
+					const loadedStructIndex = spState.loadedStructs[
+						segmentIndex
+					].indexOf(`${s.pdb_id}_${s.struct_asym_id}`);
+					if (loadedStructIndex > -1)
+						spState.loadedStructs[segmentIndex].splice(
+							loadedStructIndex,
+							1
+						);
+
+					// remove downloaded data
+					if (clearOnFail) {
+						// const m = plugin.state.data.select(modelRef)[0];
+						// const t = plugin.state.data.select(m.transform.parent)[0];
+						// const d = plugin.state.data.select(t.transform.parent)[0];
+						// PluginCommands.State.RemoveObject(plugin, { state: d.parent!, ref: d.transform.parent, removeParentGhosts: true });
+					}
+				} else {
+					// if(interactingHets.length > 0) spState.hets[`${s.pdb_id}_${s.struct_asym_id}`] = interactingHets;
+				}
+			}
+		}
+		if (busyFlagOn) {
+			busyFlagOn = false;
+			customState.events?.isBusy.next(false);
+		}
+	});
+}
+
+async function getLigandNamesFromModelData(
+	plugin: PluginContext,
+	state: State,
+	modelRef: string
+) {
+	const cell = state.select(modelRef)[0];
+	if (!cell || !cell.obj) return void 0;
+	const model = cell.obj.data;
+	if (!model) return;
+
+	const structures: any[] = [];
+	for (const s of plugin.managers.structure.hierarchy.selection.structures) {
+		const structure = s.cell.obj?.data;
+		if (structure) structures.push(structure);
+	}
+
+	const info = await ModelInfo.get(model, structures);
+	return info;
+}
+
+async function loadStructure(
+	plugin: PluginContext,
+	url: string,
+	format: BuiltInTrajectoryFormat,
+	isBinary?: boolean
+) {
+	try {
+		const data = await plugin.builders.data.download({
+			url: Asset.Url(url),
+			isBinary: isBinary,
+		});
+		const trajectory = await plugin.builders.structure.parseTrajectory(
+			data,
+			format
+		);
+		const model = await plugin.builders.structure.createModel(trajectory);
+		const modelProperties =
+			await plugin.builders.structure.insertModelProperties(model);
+		const structure = await plugin.builders.structure.createStructure(
+			modelProperties || model,
+			{ name: "model", params: {} }
+		);
+		await plugin.builders.structure.insertStructureProperties(structure);
+
+		return { data, trajectory, model, structure };
+	} catch (e) {
+		return { structure: void 0 };
+	}
+}
+
+function chainSelection(struct_asym_id: string) {
+	return MS.struct.generator.atomGroups({
+		"chain-test": MS.core.rel.eq([
+			MS.struct.atomProperty.macromolecular.label_asym_id(),
+			struct_asym_id,
+		]),
+	});
+}
+
+function transform(
+	plugin: PluginContext,
+	s: StateObjectRef,
+	matrix: Mat4
+) {
+	const b = plugin.state.data
+		.build()
+		.to(s)
+		.insert(StateTransforms.Model.TransformStructureConformation, {
+			transform: {
+				name: "matrix",
+				params: { data: matrix, transpose: false },
+			},
+		});
+	return plugin.runTask(plugin.state.data.updateTree(b));
+}
+
+async function afTransform(
+	plugin: PluginContext,
+	s: StateObjectRef,
+	matrix: Mat4,
+	coordinateSystem?: SymmetryOperator
+) {
+	const r = StateObjectRef.resolveAndCheck(plugin.state.data, s);
+	if (!r) return;
+	const o = plugin.state.data.selectQ((q) =>
+		q
+			.byRef(r.transform.ref)
+			.subtree()
+			.withTransformer(
+				StateTransforms.Model.TransformStructureConformation
+			)
+	)[0];
+
+	const transform =
+		coordinateSystem && !Mat4.isIdentity(coordinateSystem.matrix)
+			? Mat4.mul(Mat4(), coordinateSystem.matrix, matrix)
+			: matrix;
+
+	const params = {
+		transform: {
+			name: "matrix" as const,
+			params: { data: transform, transpose: false },
+		},
+	};
+	const b = o
+		? plugin.state.data.build().to(o).update(params)
+		: plugin.state.data
+				.build()
+				.to(s)
+				.insert(
+					StateTransforms.Model.TransformStructureConformation,
+					params,
+					{ tags: "SuperpositionTransform" }
+				);
+	await plugin.runTask(plugin.state.data.updateTree(b));
+}
+
+async function getMatrixData(plugin: PluginContext) {
+	const customState = PluginCustomState(plugin);
+	if (!customState.initParams)
+		throw new Error("customState.initParams has not been initialized");
+	if (!customState.superpositionState)
+		throw new Error(
+			"customState.superpositionState has not been initialized"
+		);
+
+	const matrixAccession =
+		customState.initParams.superpositionParams?.matrixAccession ??
+		customState.initParams.moleculeId;
+	const clusterRecUrlStr = `${customState.initParams.pdbeUrl}static/superpose/matrices/${matrixAccession}`;
+	const assetManager = plugin.managers.asset;
+	const clusterRecUrl = Asset.getUrlAsset(assetManager, clusterRecUrlStr);
+	try {
+		const clusterRecData = await plugin.runTask(
+			assetManager.resolve(clusterRecUrl, "json", false)
+		);
+		if (clusterRecData && clusterRecData.data) {
+			customState.superpositionState.matrixData = clusterRecData.data;
+		}
+	} catch (e) {
+		customState.superpositionError = `Matrix data not available for ${matrixAccession}`;
+		customState.events?.superpositionInit.next(true); // Emit segment API data load event
+	}
+}
+
+async function getSegmentData(plugin: PluginContext) {
+	const customState = PluginCustomState(plugin);
+	if (!customState.initParams)
+		throw new Error("customState.initParams has not been initialized");
+	if (!customState.superpositionState)
+		throw new Error(
+			"customState.superpositionState has not been initialized"
+		);
+
+	// Get Data
+	const segmentsUrl = `${customState.initParams.pdbeUrl}graph-api/uniprot/superposition/${customState.initParams.moleculeId}`;
+	const assetManager = plugin.managers.asset;
+	const url = Asset.getUrlAsset(assetManager, segmentsUrl);
+	try {
+		const result = await plugin.runTask(
+			assetManager.resolve(url, "json", false)
+		);
+		if (result?.data) {
+			customState.superpositionState.segmentData =
+				result.data[customState.initParams.moleculeId!];
+		}
+	} catch (e) {
+		customState.superpositionError = `Superposition data not available for ${customState.initParams.moleculeId}`;
+		customState.events?.superpositionInit.next(true); // Emit segment API data load event
+	}
+}
+
+function getChainLigands(carbEntity: any) {
+	const ligandChain: string[] = [];
+	const ligandLabels: string[] = [];
+	const ligands: string[][] = [];
+
+	const labelValueArr = [];
+	let ligNameStr = "";
+	for (const chemComp of carbEntity.chem_comp_list) {
+		labelValueArr.push(`${chemComp.chem_comp_id} (${chemComp.count})`);
+	}
+	ligNameStr = labelValueArr.join(", ");
+
+	for (const chain of carbEntity.chains) {
+		ligandChain.push(chain.chain_id);
+		ligandLabels.push(ligNameStr);
+		const chainLigands = [];
+		for (const residue of chain.residues) {
+			chainLigands.push(
+				residue.chem_comp_id + "-" + residue.residue_number
+			);
+		}
+		ligands.push(chainLigands);
+	}
+
+	return {
+		ligands,
+		ligandChain,
+		ligandLabels,
+	};
+}
+
+async function getCarbPolymerDetailsFromApi(
+	plugin: PluginContext,
+	pdb_id: string
+) {
+	const customState = PluginCustomState(plugin);
+	if (!customState.initParams)
+		throw new Error("customState.initParams has not been initialized");
+
+	// Get Data
+	const apiUrl = `${customState.initParams.pdbeUrl}api/pdb/entry/carbohydrate_polymer/${pdb_id}`;
+	const assetManager = plugin.managers.asset;
+	const url = Asset.getUrlAsset(assetManager, apiUrl);
+	let branchedLigands: string[][] = [];
+	let branchedChains: string[] = [];
+	let branchedlabels: string[] = [];
+	try {
+		const result = await plugin.runTask(
+			assetManager.resolve(url, "json", false)
+		);
+		if (result && result.data) {
+			const carbEntities = result.data[pdb_id];
+			for (const carbEntity of carbEntities) {
+				const carbLigData = getChainLigands(carbEntity);
+				branchedLigands = branchedLigands.concat(carbLigData.ligands);
+				branchedChains = branchedChains.concat(carbLigData.ligandChain);
+				branchedlabels = branchedlabels.concat(
+					carbLigData.ligandLabels
+				);
+			}
+		}
+	} catch (e) {}
+
+	return {
+		branchedChains,
+		branchedLigands,
+		branchedlabels,
+	};
+}
diff --git a/frontend/venome-molstar/src/app/ui/alphafold-superposition.tsx b/frontend/venome-molstar/src/app/ui/alphafold-superposition.tsx
new file mode 100644
index 00000000..9b6509de
--- /dev/null
+++ b/frontend/venome-molstar/src/app/ui/alphafold-superposition.tsx
@@ -0,0 +1,236 @@
+import React from 'react';
+import { CollapsableControls, PurePluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { TuneSvg, SuperposeChainsSvg, SuperpositionSvg, Icon } from 'molstar/lib/mol-plugin-ui/controls/icons';
+import { Button, ToggleButton } from 'molstar/lib/mol-plugin-ui/controls/common';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
+import { ParameterControls } from 'molstar/lib/mol-plugin-ui/controls/parameters';
+import { superposeAf } from '../superposition';
+import { scaleLinear as d3ScaleLinear } from 'd3-scale';
+import { axisBottom as d3AxisBotom, axisLeft as d3AxisLeft } from 'd3-axis';
+import { select as d3Select } from 'd3-selection';
+import { PluginCustomState } from '../plugin-custom-state';
+
+const _InfoIcon = ;
+export function InfoIconSvg() { return _InfoIcon; }
+
+export class AlphafoldPaeControls extends CollapsableControls {
+    private axisBoxRef: any;
+    defaultState() {
+        return {
+            isCollapsed: false,
+            header: 'AlphaFold PAE',
+            brand: { accent: 'gray' as const, svg: SuperpositionSvg },
+            isHidden: true
+        };
+    }
+
+    constructor(props: any, context: any) {
+        super(props, context);
+        this.axisBoxRef = React.createRef();
+    }
+
+    componentDidMount() {
+        this.subscribe(this.plugin.managers.structure.hierarchy.behaviors.selection, sel => {
+            const superpositionState = PluginCustomState(this.plugin).superpositionState;
+            if (superpositionState && superpositionState.alphafold.ref && superpositionState.alphafold.apiData.pae && superpositionState.alphafold.apiData.pae !== '' && superpositionState.alphafold.apiData.pae !== '') {
+                this.setState({ isHidden: false });
+
+                const domainMax = superpositionState.alphafold.apiData.length;
+
+                const x = d3ScaleLinear().domain([0, domainMax]).range([0, 200]);
+                const xAxis = d3AxisBotom(x).ticks(6).tickFormat(this.formatTicks).tickSizeOuter(0);
+                const yAxis = d3AxisLeft(x).ticks(6).tickFormat(this.formatTicks).tickSizeOuter(0);
+                const axisContainer = d3Select(this.axisBoxRef.current);
+
+                axisContainer.append('svg:svg')
+                    .attr('width', 220)
+                    .attr('height', 30)
+                    .attr('class', 'pae-x-axis')
+                    .style('z-index', '1')
+                    .style('position', 'absolute')
+                    .attr('transform', `translate(-93,202)`)
+                    .append('g')
+                    .attr('transform', `translate(6,0)`)
+                    .call(xAxis);
+
+                axisContainer.append('svg:svg')
+                    .attr('width', 50)
+                    .attr('height', 220)
+                    .attr('class', 'pae-y-axis')
+                    .style('z-index', '1')
+                    .style('position', 'absolute')
+                    .attr('transform', `translate(-123,0)`)
+                    .append('g')
+                    .attr('transform', `translate(36,4)`)
+                    .call(yAxis);
+
+            }
+        });
+
+
+    }
+
+    formatTicks(d: any) {
+        return d > 999 ? d / 1000 + 'k' : d;
+    }
+
+    renderControls() {
+        const superpositionState = PluginCustomState(this.plugin).superpositionState;
+        if (!superpositionState || !superpositionState.alphafold) return null;
+
+        const errorScale = [0, 5, 10, 15, 20, 25, 30];
+
+        return 

+
+            

+            Aligned residue
+
+            

+                

+                    PAE
+                

+                
Scored residue

+
+                PAE Scale
+                
    
+                    {errorScale.map((errValue) => 
  • {errValue}
    • )}
+                

+
+                
Expected position error (Ångströms)

+
+            

+        
;
+    }
+}
+
+export class AlphafoldSuperpositionControls extends CollapsableControls {
+    defaultState() {
+        return {
+            isCollapsed: false,
+            header: 'AlphaFold Superposition',
+            brand: { accent: 'gray' as const, svg: SuperpositionSvg },
+            isHidden: true
+        };
+    }
+
+    componentDidMount() {
+        this.subscribe(this.plugin.managers.structure.hierarchy.behaviors.selection, sel => {
+            const superpositionState = PluginCustomState(this.plugin).superpositionState;
+            if (superpositionState && superpositionState.alphafold.apiData.cif && superpositionState.alphafold.apiData.cif !== '') {
+                this.setState({ isHidden: false });
+            }
+        });
+    }
+
+    rmsdTable() {
+        const spData = PluginCustomState(this.plugin).superpositionState;
+        if (!spData) throw new Error('customState.superpositionState has not been initialized');
+        const { activeSegment } = spData;
+        const { rmsds } = spData.alphafold;
+        return 

+            {(rmsds.length === 0 || !rmsds[activeSegment - 1]) && 

+                No overlap found!
+            

+            }
+            {rmsds[activeSegment - 1] && 

+                
Entry

+                
RMSD (Å)

+            

+            }
+            {rmsds[activeSegment - 1] && rmsds[activeSegment - 1].map((d: string) => {
+                const details = d.split(':');
+                return details[1] !== '-' ? 

+                    
{details[0]}

+                    
{details[1]}

+                
 : null;
+            })}
+        
;
+    }
+
+    renderControls() {
+        const superpositionState = PluginCustomState(this.plugin).superpositionState;
+        if (!superpositionState) throw new Error('customState.superpositionState has not been initialized');
+        return <>
+            {superpositionState.alphafold.ref !== '' && this.rmsdTable()}
+            {superpositionState.alphafold.ref === '' && }
+        ;
+    }
+}
+
+export const AlphafoldSuperpositionParams = {
+    // alignSequences: PD.Boolean(true, { isEssential: true, description: 'For Chain-based 3D superposition, perform a sequence alignment and use the aligned residue pairs to guide the 3D superposition.' }),
+    traceOnly: PD.Boolean(true, { description: 'For Chain- and Uniprot-based 3D superposition, base superposition only on CA (and equivalent) atoms.' })
+};
+const DefaultAlphafoldSuperpositionOptions = PD.getDefaultValues(AlphafoldSuperpositionParams);
+export type AlphafoldSuperpositionOptions = PD.ValuesFor
+
+// const SuperpositionTag = 'SuperpositionTransform';
+
+type AfSuperpositionControlsState = {
+    isBusy: boolean,
+    action?: 'byChains' | 'byAtoms' | 'options',
+    canUseDb?: boolean,
+    options: AlphafoldSuperpositionOptions
+}
+
+export class AfSuperpositionControls extends PurePluginUIComponent<{}, AfSuperpositionControlsState> {
+    state: AfSuperpositionControlsState = {
+        isBusy: false,
+        canUseDb: true,
+        action: undefined,
+        options: DefaultAlphafoldSuperpositionOptions
+    };
+
+    componentDidMount() {
+        this.subscribe(this.plugin.behaviors.state.isBusy, v => {
+            this.setState({ isBusy: v });
+        });
+    }
+
+    get selection() {
+        return this.plugin.managers.structure.selection;
+    }
+
+    get customState() {
+        return PluginCustomState(this.plugin);
+    }
+
+    superposeDb = async () => {
+        this.setState({ isBusy: true });
+        const spData = this.customState.superpositionState;
+        if (!spData) throw new Error('customState.superpositionState has not been initialized');
+        spData.alphafold.traceOnly = this.state.options.traceOnly;
+        superposeAf(this.plugin, this.state.options.traceOnly);
+    };
+
+    toggleOptions = () => this.setState({ action: this.state.action === 'options' ? void 0 : 'options' });
+
+    superposeByDbMapping() {
+        return <>
+            
+        ;
+    }
+
+    private setOptions = (values: AlphafoldSuperpositionOptions) => {
+        this.setState({ options: values });
+    };
+
+    render() {
+        return <>
+            
New Feature!

+            

+                
Load and superpose AlphaFold structure against representative chains.

+            

+            

+                {this.state.canUseDb && this.superposeByDbMapping()}
+                
+            

+            {this.state.action === 'options' && 

+                
+            
}
+        ;
+
+    }
+}
\ No newline at end of file
diff --git a/frontend/venome-molstar/src/app/ui/alphafold-tranparency.tsx b/frontend/venome-molstar/src/app/ui/alphafold-tranparency.tsx
new file mode 100644
index 00000000..9dbcb041
--- /dev/null
+++ b/frontend/venome-molstar/src/app/ui/alphafold-tranparency.tsx
@@ -0,0 +1,52 @@
+import { CollapsableControls } from 'molstar/lib/mol-plugin-ui/base';
+import { SuperpositionSvg } from 'molstar/lib/mol-plugin-ui/controls/icons';
+import { ParameterControls } from 'molstar/lib/mol-plugin-ui/controls/parameters';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
+import { applyAFTransparency, clearStructureTransparency } from '../alphafold-transparency';
+import { PluginCustomState } from '../plugin-custom-state';
+
+
+const TransparencyParams = {
+    score: PD.Numeric(70, { min: 0, max: 100, step: 1 }, { label: 'pLDDT less than', description: 'pLDDT score value in the range of 0 to 100' }),
+    opacity: PD.Numeric(0.2, { min: 0, max: 1, step: 0.01 }, { description: 'Opacity value in the range 0 to 1' })
+};
+type TransparencyParams = PD.Values
+
+export class AlphafoldTransparencyControls extends CollapsableControls<{}, { transpareny: any }> {
+    defaultState() {
+        return {
+            isCollapsed: false,
+            header: 'AlphaFold Structure Opacity',
+            brand: { accent: 'gray' as const, svg: SuperpositionSvg },
+            isHidden: true,
+            transpareny: {
+                score: 70,
+                opacity: 0.2
+            }
+        };
+    }
+
+    componentDidMount() {
+        this.subscribe(this.plugin.managers.structure.hierarchy.behaviors.selection, sel => {
+            const superpositionState = PluginCustomState(this.plugin).superpositionState;
+            if (superpositionState && superpositionState.alphafold.ref && superpositionState.alphafold.ref !== '') {
+                this.setState({ isHidden: false });
+            }
+        });
+    }
+
+    updateTransparency = async (val: any) => {
+        this.setState({ transpareny: val });
+        const superpositionState = PluginCustomState(this.plugin).superpositionState;
+        if (!superpositionState) throw new Error('customState.superpositionState has not been initialized');
+        const afStr: any = this.plugin.managers.structure.hierarchy.current.refs.get(superpositionState.alphafold.ref!);
+        await clearStructureTransparency(this.plugin, afStr.components);
+        await applyAFTransparency(this.plugin, afStr, 1 - val.opacity, val.score);
+    };
+
+    renderControls() {
+        return <>
+            
+        ;
+    }
+}
\ No newline at end of file
diff --git a/frontend/venome-molstar/src/app/ui/annotation-controls.tsx b/frontend/venome-molstar/src/app/ui/annotation-controls.tsx
new file mode 100644
index 00000000..fcf2d726
--- /dev/null
+++ b/frontend/venome-molstar/src/app/ui/annotation-controls.tsx
@@ -0,0 +1,199 @@
+import { PDBeStructureQualityReport } from 'molstar/lib/extensions/pdbe/structure-quality-report/behavior';
+import { StructureQualityReportColorThemeProvider } from 'molstar/lib/extensions/pdbe/structure-quality-report/color';
+import { StructureHierarchyManager } from 'molstar/lib/mol-plugin-state/manager/structure/hierarchy';
+import { PurePluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { Button } from 'molstar/lib/mol-plugin-ui/controls/common';
+import { ArrowDropDownSvg, ArrowRightSvg, Icon } from 'molstar/lib/mol-plugin-ui/controls/icons';
+import { StateSelection, StateTransform } from 'molstar/lib/mol-state';
+import { PDBeDomainAnnotations } from '../domain-annotations/behavior';
+import { DomainAnnotationsColorThemeProvider } from '../domain-annotations/color';
+import { PluginCustomState } from '../plugin-custom-state';
+import { AnnotationRowControls } from './annotation-row-controls';
+import { SymmetryAnnotationControls, isAssemblySymmetryAnnotationApplicable } from './symmetry-annotation-controls';
+
+
+const _TextsmsOutlined = ;
+export function TextsmsOutlinedSvg() { return _TextsmsOutlined; }
+
+type AnnotationType = 'validation' | 'domains' | 'symmetry'
+
+interface AnnotationsComponentControlsState {
+    isCollapsed: boolean,
+    validationApplied: boolean,
+    validationOptions: boolean,
+    validationParams: any,
+    domainsApplied: boolean,
+    domainsOptions: boolean,
+    domainsParams: any,
+    showSymmetryAnnotation: boolean,
+    description?: string,
+}
+
+
+export class AnnotationsComponentControls extends PurePluginUIComponent<{}, AnnotationsComponentControlsState> {
+    state: AnnotationsComponentControlsState = {
+        isCollapsed: false,
+        validationApplied: false,
+        validationOptions: false,
+        validationParams: undefined,
+        domainsApplied: false,
+        domainsOptions: false,
+        domainsParams: undefined,
+        showSymmetryAnnotation: false,
+    };
+
+    componentDidMount() {
+        this.subscribe(this.plugin.managers.structure.hierarchy.behaviors.selection, () => {
+            this.initOptionParams();
+            this.forceUpdate();
+        });
+        this.subscribe(this.plugin.managers.structure.hierarchy.behaviors.selection, c => this.setState({
+            description: StructureHierarchyManager.getSelectedStructuresDescription(this.plugin)
+        }));
+    }
+
+    initOptionParams = () => {
+        const initParams = PluginCustomState(this.plugin).initParams;
+        const validationAnnotationCtrl = !!initParams?.validationAnnotation;
+        const domainAnnotationCtrl = !!initParams?.domainAnnotation;
+        const symmetryAnnotationCtrl = !!initParams?.symmetryAnnotation && isAssemblySymmetryAnnotationApplicable(this.plugin);
+        this.setState({ showSymmetryAnnotation: symmetryAnnotationCtrl });
+
+        if ((validationAnnotationCtrl && !this.state.validationParams) || (domainAnnotationCtrl && !this.state.domainsParams)) {
+
+            const structure = this.getStructure()?.data;
+            if (structure) {
+                const themeDataCtx = { structure };
+
+                if (validationAnnotationCtrl && !this.state.validationParams) {
+                    const validationActionsParams = StructureQualityReportColorThemeProvider.getParams(themeDataCtx);
+                    if (validationActionsParams) {
+                        this.setState({
+                            validationParams: {
+                                params: validationActionsParams,
+                                values: { type: validationActionsParams.type.defaultValue }
+                            }
+                        });
+                    }
+                }
+
+                if (domainAnnotationCtrl && !this.state.domainsParams) {
+                    const domainActionsParams = DomainAnnotationsColorThemeProvider.getParams(themeDataCtx);
+                    if (domainActionsParams) {
+                        this.setState({
+                            domainsParams: {
+                                params: domainActionsParams,
+                                values: { type: domainActionsParams.type.defaultValue }
+                            }
+                        });
+                    }
+                }
+
+            }
+        }
+    };
+    getStructure = () => {
+        const groupRef = StateSelection.findTagInSubtree(this.plugin.state.data.tree, StateTransform.RootRef, 'structure-component-static-polymer');
+        return groupRef ? this.plugin.state.data.select(groupRef)[0]?.obj : undefined;
+    };
+
+    toggleCollapsed = () => {
+        this.setState({ isCollapsed: !this.state.isCollapsed });
+    };
+
+    applyAnnotation = (type: 'validation' | 'domains', visibleState: boolean, params?: any) => {
+        // Defaults
+        let themeName: any = 'chain-id';
+        let themePropsToAdd = PDBeStructureQualityReport;
+        let themePropsToRemove = this.state.domainsParams ? PDBeDomainAnnotations : void 0;
+
+        // Set Theme Params
+        if (type === 'validation') {
+            if (visibleState) {
+                themeName = 'pdbe-structure-quality-report';
+            }
+            this.setState({ validationApplied: visibleState });
+            this.setState({ domainsApplied: false });
+        } else if (type === 'domains') {
+            themePropsToAdd = PDBeDomainAnnotations;
+            themePropsToRemove = this.state.validationParams ? PDBeStructureQualityReport : void 0;
+            if (visibleState) themeName = 'pdbe-domain-annotations';
+            this.setState({ domainsApplied: visibleState });
+            this.setState({ validationApplied: false });
+        }
+
+        // Update Tooltip
+        if (visibleState && themeName !== 'chain-id') {
+            const addTooltipUpdate = this.plugin.state.behaviors.build().to(themePropsToAdd.id).update(themePropsToAdd, (old: any) => { old.showTooltip = true; });
+            this.plugin.runTask(this.plugin.state.behaviors.updateTree(addTooltipUpdate));
+
+            if (themePropsToRemove) {
+                const removeTooltipUpdate = this.plugin.state.behaviors.build().to(themePropsToRemove.id).update(themePropsToRemove, (old: any) => { old.showTooltip = false; });
+                this.plugin.runTask(this.plugin.state.behaviors.updateTree(removeTooltipUpdate));
+            }
+        }
+
+        let polymerGroup: any;
+        const componentGroups = this.plugin.managers.structure.hierarchy.currentComponentGroups;
+        componentGroups.forEach((compGrp) => {
+            if (compGrp[0].key === 'structure-component-static-polymer') polymerGroup = compGrp;
+        });
+        if (polymerGroup) {
+            this.plugin.managers.structure.component.updateRepresentationsTheme(polymerGroup, { color: themeName, colorParams: params ? params : void 0 });
+        }
+    };
+
+    toggleAnnotation = (type: AnnotationType) => {
+        if (type === 'validation') this.applyAnnotation('validation', !this.state.validationApplied, this.state.validationParams.values);
+        if (type === 'domains') this.applyAnnotation('domains', !this.state.domainsApplied, this.state.domainsParams.values);
+    };
+
+    updateValidationParams = (val: any) => {
+        const updatedParams = { ...this.state.validationParams };
+        updatedParams.values = val;
+        this.setState({ validationParams: updatedParams });
+        if (this.state.validationApplied) this.applyAnnotation('validation', this.state.validationApplied, val);
+    };
+    updateDomainParams = (val: any) => {
+        const updatedParams = { ...this.state.domainsParams };
+        updatedParams.values = val;
+        this.setState({ domainsParams: updatedParams });
+        if (this.state.domainsApplied) this.applyAnnotation('domains', this.state.domainsApplied, val);
+    };
+
+    render() {
+        if (!this.state.validationParams && !this.state.domainsParams && !this.state.showSymmetryAnnotation) return <>;
+
+        const brand = {
+            accent: 'green',
+            svg: TextsmsOutlinedSvg
+        };
+
+        const wrapClass = this.state.isCollapsed
+            ? 'msp-transform-wrapper msp-transform-wrapper-collapsed'
+            : 'msp-transform-wrapper';
+
+        return 

+            

+                
+            

+
+            {!this.state.isCollapsed && <>
+                 this.toggleAnnotation('validation')} />
+                 this.toggleAnnotation('domains')} />
+                {this.state.showSymmetryAnnotation &&
+                    }
+            }
+        
;
+    }
+}
diff --git a/frontend/venome-molstar/src/app/ui/annotation-row-controls.tsx b/frontend/venome-molstar/src/app/ui/annotation-row-controls.tsx
new file mode 100644
index 00000000..03080da5
--- /dev/null
+++ b/frontend/venome-molstar/src/app/ui/annotation-row-controls.tsx
@@ -0,0 +1,74 @@
+import { Button, IconButton } from 'molstar/lib/mol-plugin-ui/controls/common';
+import { MoreHorizSvg, VisibilityOffOutlinedSvg, VisibilityOutlinedSvg } from 'molstar/lib/mol-plugin-ui/controls/icons';
+import { ParameterControls, ParameterControlsProps } from 'molstar/lib/mol-plugin-ui/controls/parameters';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
+import React from 'react';
+
+
+type AnnotationRowControlsProps
 = ParameterControlsProps
 & {
+    shortTitle?: string,
+    title: string,
+    applied?: boolean,
+    onChangeApplied?: (applied: boolean) => void,
+}
+
+type AnnotationRowControlsState = {
+    applied: boolean,
+    optionsExpanded: boolean,
+}
+
+
+/** UI controls for a single annotation source (row) in Annotations section */
+export class AnnotationRowControls
 extends React.PureComponent, AnnotationRowControlsState> {
+    state = { applied: false, optionsExpanded: false };
+
+    // componentDidMount() {
+    //     this.subscribe(this.plugin.state.events.cell.stateUpdated, e => {
+    //         if (State.ObjectEvent.isCell(e, this.pivot.cell)) this.forceUpdate();
+    //     });
+    // }
+
+    isApplied() {
+        return this.props.applied ?? this.state.applied;
+    }
+
+    toggleApplied(applied?: boolean) {
+        const newState = applied ?? !this.isApplied();
+        if (this.props.applied === undefined) {
+            this.setState({ applied: newState });
+        }
+        this.props.onChangeApplied?.(newState);
+    }
+
+    toggleOptions() {
+        this.setState(s => ({ optionsExpanded: !s.optionsExpanded }));
+    }
+
+    render() {
+        if (!this.props.params) return null;
+        return <>
+            

+                
+                 this.toggleApplied()} toggleState={false}
+                    svg={!this.isApplied() ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg}
+                    title={`Click to ${this.isApplied() ? 'hide' : 'show'} ${this.props.title}`} small className='msp-form-control' flex />
+                 this.toggleOptions()} svg={MoreHorizSvg} title='Options' toggleState={this.state.optionsExpanded} className='msp-form-control' flex />
+            

+            {this.state.optionsExpanded &&
+                

+                    

+                        

+                            {this.renderOptions()}
+                        

+                    

+                

+            }
+        ;
+    }
+
+    renderOptions() {
+        return ;
+    }
+}
\ No newline at end of file
diff --git a/frontend/venome-molstar/src/app/ui/export-superposition.tsx b/frontend/venome-molstar/src/app/ui/export-superposition.tsx
new file mode 100644
index 00000000..c1be9fee
--- /dev/null
+++ b/frontend/venome-molstar/src/app/ui/export-superposition.tsx
@@ -0,0 +1,63 @@
+import { useState } from 'react';
+import { CollapsableControls, CollapsableState } from 'molstar/lib/mol-plugin-ui/base';
+import { Button } from 'molstar/lib/mol-plugin-ui/controls/common';
+import { GetAppSvg } from 'molstar/lib/mol-plugin-ui/controls/icons';
+import { ParameterControls } from 'molstar/lib/mol-plugin-ui/controls/parameters';
+import { useBehavior } from 'molstar/lib/mol-plugin-ui/hooks/use-behavior';
+import { PluginContext } from 'molstar/lib/mol-plugin/context';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
+import { superpositionExportHierarchy } from '../superposition-export';
+
+export class SuperpositionModelExportUI extends CollapsableControls<{}, {}> {
+    protected defaultState(): CollapsableState {
+        return {
+            header: 'Export Models',
+            isCollapsed: true,
+            brand: { accent: 'cyan', svg: GetAppSvg }
+        };
+    }
+    protected renderControls(): JSX.Element | null {
+        return ;
+    }
+}
+
+const Params = {
+    format: PD.Select<'cif' | 'bcif'>('cif', [['cif', 'mmCIF'], ['bcif', 'Binary mmCIF']])
+};
+const DefaultParams = PD.getDefaultValues(Params);
+
+function SuperpositionExportControls({ plugin }: { plugin: PluginContext }) {
+    const [params, setParams] = useState(DefaultParams);
+    const [exporting, setExporting] = useState(false);
+    useBehavior(plugin.managers.structure.hierarchy.behaviors.selection); // triggers UI update
+    const isBusy = useBehavior(plugin.behaviors.state.isBusy);
+    const hierarchy = plugin.managers.structure.hierarchy.current;
+
+    let label: string = 'Nothing to Export';
+    if (hierarchy.structures.length === 1) {
+        label = 'Export';
+    } if (hierarchy.structures.length > 1) {
+        label = 'Export (as ZIP)';
+    }
+
+    const onExport = async () => {
+        setExporting(true);
+        try {
+            await superpositionExportHierarchy(plugin, { format: params.format });
+        } finally {
+            setExporting(false);
+        }
+    };
+
+    return <>
+        
+        
+    ;
+}
\ No newline at end of file
diff --git a/frontend/venome-molstar/src/app/ui/pdbe-left-panel.tsx b/frontend/venome-molstar/src/app/ui/pdbe-left-panel.tsx
new file mode 100644
index 00000000..0c42f3ba
--- /dev/null
+++ b/frontend/venome-molstar/src/app/ui/pdbe-left-panel.tsx
@@ -0,0 +1,205 @@
+import { Canvas3DParams } from 'molstar/lib/mol-canvas3d/canvas3d';
+import { PluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { IconButton, SectionHeader } from 'molstar/lib/mol-plugin-ui/controls/common';
+import { AccountTreeOutlinedSvg, DeleteOutlinedSvg, HelpOutlineSvg, HomeOutlinedSvg, TuneSvg } from 'molstar/lib/mol-plugin-ui/controls/icons';
+import { ParameterControls } from 'molstar/lib/mol-plugin-ui/controls/parameters';
+import { StateObjectActions } from 'molstar/lib/mol-plugin-ui/state/actions';
+import { RemoteStateSnapshots, StateSnapshots } from 'molstar/lib/mol-plugin-ui/state/snapshots';
+import { StateTree } from 'molstar/lib/mol-plugin-ui/state/tree';
+import { HelpContent, HelpGroup, HelpText } from 'molstar/lib/mol-plugin-ui/viewport/help';
+import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
+import { StateTransform } from 'molstar/lib/mol-state';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
+import * as React from 'react';
+import { PluginCustomState } from '../plugin-custom-state';
+import { SegmentTree } from './segment-tree';
+
+
+const _WavesIcon = ;
+export function WavesIconSvg() { return _WavesIcon; }
+
+type LeftPanelTabName = 'none' | 'root' | 'data' | 'states' | 'settings' | 'help' | 'segments'
+
+export class LeftPanelControls extends PluginUIComponent<{}, { tab: LeftPanelTabName }> {
+    state = { tab: this.plugin.behaviors.layout.leftPanelTabName.value as LeftPanelTabName };
+
+    componentDidMount() {
+        this.subscribe(this.plugin.behaviors.layout.leftPanelTabName, tab => {
+            if (this.state.tab !== tab) this.setState({ tab });
+            if (tab === 'none' && this.plugin.layout.state.regionState.left !== 'collapsed') {
+                PluginCommands.Layout.Update(this.plugin, { state: { regionState: { ...this.plugin.layout.state.regionState, left: 'collapsed' } } });
+            }
+        });
+
+        this.subscribe(this.plugin.state.data.events.changed, ({ state }) => {
+            if (this.state.tab !== 'data') return;
+            if (state.cells.size === 1) this.set('root');
+        });
+    }
+
+    set = (tab: LeftPanelTabName) => {
+        if (this.state.tab === tab) {
+            this.setState({ tab: 'none' }, () => this.plugin.behaviors.layout.leftPanelTabName.next('none'));
+            PluginCommands.Layout.Update(this.plugin, { state: { regionState: { ...this.plugin.layout.state.regionState, left: 'collapsed' } } });
+            return;
+        }
+
+        this.setState({ tab }, () => this.plugin.behaviors.layout.leftPanelTabName.next(tab as any));
+        if (this.plugin.layout.state.regionState.left !== 'full') {
+            PluginCommands.Layout.Update(this.plugin, { state: { regionState: { ...this.plugin.layout.state.regionState, left: 'full' } } });
+        }
+    };
+
+    tabs: { [K in LeftPanelTabName]: JSX.Element } = {
+        'none': <>,
+        'root': <>
+            
+            
+            {this.plugin.spec.components?.remoteState !== 'none' && }
+        ,
+        'data': <>
+             State Tree} />
+            
+        ,
+        'segments': <>
+            {/*  */}
+            
+        ,
+        'states': ,
+        'settings': <>
+            
+            
+        ,
+        'help': <>
+            
+            
+            
+        
+    };
+
+    render() {
+        const tab = this.state.tab;
+        const customState = PluginCustomState(this.plugin);
+        return 

+            

+                {/*  this.set('root')} title='Home' /> */}
+                {/*  */}
+                {/*  this.set('states')} title='Plugin State' /> */}
+                 this.set('help')} title='Help' />
+                {customState && customState.initParams && customState.initParams.superposition &&  this.set('segments')} title='Superpose segments' />}
+                

+                     this.set('settings')} title='Settings' />
+                

+            

+            

+                {this.tabs[tab]}
+            

+        
;
+    }
+}
+
+// class DataIcon extends PluginUIComponent<{ set: (tab: LeftPanelTabName) => void }, { changed: boolean }> {
+//     state = { changed: false };
+
+//     get tab() {
+//         return this.plugin.behaviors.layout.leftPanelTabName.value;
+//     }
+
+//     componentDidMount() {
+//         this.subscribe(this.plugin.behaviors.layout.leftPanelTabName, tab => {
+//             if (this.tab === 'data') this.setState({ changed: false });
+//             else this.forceUpdate();
+//         });
+
+//         this.subscribe(this.plugin.state.data.events.changed, state => {
+//             if (this.tab !== 'data') this.setState({ changed: true });
+//         });
+//     }
+
+//     render() {
+//         return  this.props.set('data')} title='State Tree'
+//             style={{ position: 'relative' }} extraContent={this.state.changed ? 
 : void 0} />;
+//     }
+// }
+
+class FullSettings extends PluginUIComponent {
+    private setSettings = (p: { param: PD.Base, name: string, value: any }) => {
+        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { [p.name]: p.value } });
+    };
+
+    componentDidMount() {
+        this.subscribe(this.plugin.events.canvas3d.settingsUpdated, () => this.forceUpdate());
+        this.subscribe(this.plugin.layout.events.updated, () => this.forceUpdate());
+
+        this.subscribe(this.plugin.canvas3d!.camera.stateChanged, state => {
+            if (state.radiusMax !== undefined || state.radius !== undefined) {
+                this.forceUpdate();
+            }
+        });
+    }
+
+    render() {
+        return <>
+            {this.plugin.canvas3d && <>
+                
+                
+            }
+            {/* 
+             */}
+        ;
+    }
+}
+
+class RemoveAllButton extends PluginUIComponent<{}> {
+    componentDidMount() {
+        this.subscribe(this.plugin.state.events.cell.created, e => {
+            if (e.cell.transform.parent === StateTransform.RootRef) this.forceUpdate();
+        });
+
+        this.subscribe(this.plugin.state.events.cell.removed, e => {
+            if (e.parent === StateTransform.RootRef) this.forceUpdate();
+        });
+    }
+
+    remove = (e: React.MouseEvent) => {
+        e.preventDefault();
+        PluginCommands.State.RemoveObject(this.plugin, { state: this.plugin.state.data, ref: StateTransform.RootRef });
+    };
+
+    render() {
+        const count = this.plugin.state.data.tree.children.get(StateTransform.RootRef).size;
+        if (count === 0) return null;
+        return ;
+    }
+}
+
+function HelpSection(props: { header: string }) {
+    return 
{props.header}
;
+}
+
+class SuperpositionHelpContent extends PluginUIComponent {
+    componentDidMount() {
+        this.subscribe(this.plugin.events.canvas3d.settingsUpdated, () => this.forceUpdate());
+    }
+    render() {
+        return 

+            
+            
+                
+                    
Discrete UniProt sequence range mapped to the structure

+                
+            
+            
+                
+                    
Structural chains that possess significantly close superposition Q-score

+                
+            
+            
+                
+                    
The best-ranked chain within a cluster chosen based on the model quality, resolution, observed residues ratio and UniProt sequence coverage

+                
+            
+        
;
+    }
+}
\ No newline at end of file
diff --git a/frontend/venome-molstar/src/app/ui/pdbe-screenshot-controls.tsx b/frontend/venome-molstar/src/app/ui/pdbe-screenshot-controls.tsx
new file mode 100644
index 00000000..7b18a01b
--- /dev/null
+++ b/frontend/venome-molstar/src/app/ui/pdbe-screenshot-controls.tsx
@@ -0,0 +1,109 @@
+import * as React from 'react';
+import { PluginContext } from 'molstar/lib/mol-plugin/context';
+import { ParameterControls } from 'molstar/lib/mol-plugin-ui/controls/parameters';
+import { PluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { ScreenshotPreview } from 'molstar/lib/mol-plugin-ui/controls/screenshot';
+import { Button, ToggleButton } from 'molstar/lib/mol-plugin-ui/controls/common';
+import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
+import { useBehavior } from 'molstar/lib/mol-plugin-ui/hooks/use-behavior';
+import { GetAppSvg, CopySvg, CropOrginalSvg, CropSvg, CropFreeSvg } from 'molstar/lib/mol-plugin-ui/controls/icons';
+
+interface ImageControlsState {
+    showPreview: boolean,
+    isDisabled: boolean,
+    imageData?: string
+}
+
+export class DownloadScreenshotControls extends PluginUIComponent<{ close: () => void }, ImageControlsState> {
+    state: ImageControlsState = {
+        showPreview: true,
+        isDisabled: false
+    } as ImageControlsState;
+
+    private download = () => {
+        this.plugin.helpers.viewportScreenshot?.download();
+        this.props.close();
+    };
+
+    private copy = async () => {
+        try {
+            await this.plugin.helpers.viewportScreenshot?.copyToClipboard();
+            PluginCommands.Toast.Show(this.plugin, {
+                message: 'Copied to clipboard.',
+                title: 'Screenshot',
+                timeoutMs: 1500
+            });
+        } catch {
+            return this.copyImg();
+        }
+    };
+
+    private copyImg = async () => {
+        const src = await this.plugin.helpers.viewportScreenshot?.getImageDataUri();
+        this.setState({ imageData: src });
+    };
+
+    componentDidMount() {
+        this.subscribe(this.plugin.state.data.behaviors.isUpdating, v => {
+            this.setState({ isDisabled: v });
+        });
+    }
+
+    componentWillUnmount() {
+        this.setState({ imageData: void 0 });
+    }
+
+    open = (e: React.ChangeEvent) => {
+        if (!e.target.files || !e.target.files![0]) return;
+        PluginCommands.State.Snapshots.OpenFile(this.plugin, { file: e.target.files![0] });
+    };
+
+    render() {
+        const hasClipboardApi = !!(navigator.clipboard as any)?.write;
+
+        return 

+            {this.state.showPreview && 

+                
+                
+            
}
+            

+                {!this.state.imageData && }
+                {this.state.imageData && }
+                
+            

+            {this.state.imageData && 

+                
Right click below + Copy Image

+                
+            
}
+            
+        
;
+    }
+}
+
+function ScreenshotParams({ plugin, isDisabled }: { plugin: PluginContext, isDisabled: boolean }) {
+    const helper = plugin.helpers.viewportScreenshot!;
+    const values = useBehavior(helper.behaviors.values);
+
+    return  helper.behaviors.values.next(v)} isDisabled={isDisabled} />;
+}
+
+function CropControls({ plugin }: { plugin: PluginContext }) {
+    const helper = plugin.helpers.viewportScreenshot;
+    const cropParams = useBehavior(helper?.behaviors.cropParams!);
+    useBehavior(helper?.behaviors.relativeCrop);
+
+    if (!helper) return null;
+
+    return 

+         helper.toggleAutocrop()} label={'Auto-crop ' + (cropParams.auto ? 'On' : 'Off')} />
+
+        {!cropParams.auto && 
;
+}
\ No newline at end of file
diff --git a/frontend/venome-molstar/src/app/ui/pdbe-structure-controls.tsx b/frontend/venome-molstar/src/app/ui/pdbe-structure-controls.tsx
new file mode 100644
index 00000000..374f57fe
--- /dev/null
+++ b/frontend/venome-molstar/src/app/ui/pdbe-structure-controls.tsx
@@ -0,0 +1,77 @@
+import { PluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { StructureComponentControls } from 'molstar/lib/mol-plugin-ui/structure/components';
+import { StructureMeasurementsControls } from 'molstar/lib/mol-plugin-ui/structure/measurements';
+import { StructureSourceControls } from 'molstar/lib/mol-plugin-ui/structure/source';
+import { VolumeStreamingControls, VolumeSourceControls } from 'molstar/lib/mol-plugin-ui/structure/volume';
+import { AnnotationsComponentControls } from './annotation-controls';
+import { Icon, BuildSvg } from 'molstar/lib/mol-plugin-ui/controls/icons';
+import { SuperpositionComponentControls } from './superposition-components';
+import { StructureQuickStylesControls } from 'molstar/lib/mol-plugin-ui/structure/quick-styles';
+import { AlphafoldPaeControls, AlphafoldSuperpositionControls } from './alphafold-superposition';
+import { SuperpositionModelExportUI } from './export-superposition';
+import { AlphafoldTransparencyControls } from './alphafold-tranparency';
+import { AssemblySymmetry } from 'molstar/lib/extensions/rcsb/assembly-symmetry/prop';
+
+
+export class PDBeStructureTools extends PluginUIComponent {
+    render() {
+        const AssemblySymmetryKey = AssemblySymmetry.Tag.Representation;
+        return <>
+            
Structure Tools

+
+            
+            
+            
+            
+            
+            
+            
+            
+        ;
+    }
+}
+
+export class CustomStructureControls extends PluginUIComponent<{ initiallyCollapsed?: boolean, takeKeys?: string[], skipKeys?: string[] }> {
+    componentDidMount() {
+        this.subscribe(this.plugin.state.behaviors.events.changed, () => this.forceUpdate());
+    }
+
+    render() {
+        const takeKeys = this.props.takeKeys ?? Array.from(this.plugin.customStructureControls.keys());
+        const result: JSX.Element[] = [];
+        for (const key of takeKeys) {
+            if (this.props.skipKeys?.includes(key)) continue;
+            const Controls = this.plugin.customStructureControls.get(key);
+            if (!Controls) continue;
+            result.push();
+        }
+        return result.length > 0 ? <>{result} : null;
+    }
+}
+
+export class PDBeLigandViewStructureTools extends PluginUIComponent {
+    render() {
+        return <>
+            
Structure Tools

+            
+            
+            
+            
+        ;
+    }
+}
+
+export class PDBeSuperpositionStructureTools extends PluginUIComponent {
+    render() {
+        return <>
+            
Structure Tools

+            
+            
+            
+            
+            
+            
+            
+        ;
+    }
+}
\ No newline at end of file
diff --git a/frontend/venome-molstar/src/app/ui/pdbe-viewport-controls.tsx b/frontend/venome-molstar/src/app/ui/pdbe-viewport-controls.tsx
new file mode 100644
index 00000000..5d9f9c91
--- /dev/null
+++ b/frontend/venome-molstar/src/app/ui/pdbe-viewport-controls.tsx
@@ -0,0 +1,40 @@
+import { ViewportControls } from 'molstar/lib/mol-plugin-ui/viewport';
+import { PluginCustomState } from '../plugin-custom-state';
+
+
+export class PDBeViewportControls extends ViewportControls {
+    private isBlack(): boolean {
+        const bgColor = PluginCustomState(this.plugin).initParams?.bgColor;
+        return bgColor !== undefined && bgColor.r === 0 && bgColor.g === 0 && bgColor.b === 0;
+    }
+
+    render() {
+        const initParams = PluginCustomState(this.plugin).initParams;
+        const showPDBeLink = initParams?.moleculeId && initParams?.pdbeLink && !initParams?.superposition;
+        const pdbeLinkColor = this.isBlack() ? '#fff' : '#555';
+        const pdbeLink = {
+            parentStyle: { width: 'auto' },
+            bgStyle: { position: 'absolute', height: '27px', width: '54px', marginLeft: '-33px' },
+            containerStyle: { position: 'absolute', right: '10px', top: '10px', padding: '3px 3px 3px 18px' },
+            style: { display: 'inline-block', fontSize: '14px', color: pdbeLinkColor, borderBottom: 'none', cursor: 'pointer', textDecoration: 'none', position: 'absolute', right: '5px' },
+            pdbeImg: {
+                src: 'https://www.ebi.ac.uk/pdbe/entry/static/images/logos/PDBe/logo_T_64.png',
+                alt: 'PDBe logo',
+                style: { height: '12px', width: '12px', border: 0, position: 'absolute', margin: '4px 0 0 -13px' }
+            }
+        } as const;
+
+        return <>
+            {showPDBeLink && 

+                }
+            

+                {super.render()}
+            

+        ;
+    }
+}
\ No newline at end of file
diff --git a/frontend/venome-molstar/src/app/ui/segment-tree.tsx b/frontend/venome-molstar/src/app/ui/segment-tree.tsx
new file mode 100644
index 00000000..03e03d72
--- /dev/null
+++ b/frontend/venome-molstar/src/app/ui/segment-tree.tsx
@@ -0,0 +1,785 @@
+import { Mat4 } from 'molstar/lib/mol-math/linear-algebra';
+import { StructureComponentRef, StructureRepresentationRef } from 'molstar/lib/mol-plugin-state/manager/structure/hierarchy-state';
+import { PluginStateObject } from 'molstar/lib/mol-plugin-state/objects';
+import { StateTransforms } from 'molstar/lib/mol-plugin-state/transforms';
+import { PluginUIComponent, PurePluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { ActionMenu } from 'molstar/lib/mol-plugin-ui/controls/action-menu';
+import { Button, ExpandGroup, IconButton, SectionHeader } from 'molstar/lib/mol-plugin-ui/controls/common';
+import { ArrowDropDownSvg, ArrowRightSvg, CheckSvg, CloseSvg, VisibilityOffOutlinedSvg, VisibilityOutlinedSvg } from 'molstar/lib/mol-plugin-ui/controls/icons';
+import { ParameterControls } from 'molstar/lib/mol-plugin-ui/controls/parameters';
+import { UpdateTransformControl } from 'molstar/lib/mol-plugin-ui/state/update-transform';
+import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
+import { MolScriptBuilder as MS } from 'molstar/lib/mol-script/language/builder';
+import { State, StateObjectRef, StateSelection } from 'molstar/lib/mol-state';
+import { Color } from 'molstar/lib/mol-util/color';
+import { ColorLists } from 'molstar/lib/mol-util/color/lists';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
+import * as React from 'react';
+import { Subject } from 'rxjs';
+import { debounceTime, filter } from 'rxjs/operators';
+import { ClusterMember, PluginCustomState, Segment } from '../plugin-custom-state';
+import { renderSuperposition, superposeAf } from '../superposition';
+
+
+const SuperpositionTag = 'SuperpositionTransform';
+
+export class SegmentTree extends PurePluginUIComponent<{}, { segment?: any, isBusy: boolean }> {
+
+    componentDidMount() {
+        this.subscribe(PluginCustomState(this.plugin).events!.superpositionInit, () => {
+            const customState = this.customState;
+            if (customState && !customState.superpositionError) {
+                this.getSegmentParams();
+            }
+            this.forceUpdate();
+        });
+
+        this.subscribe(PluginCustomState(this.plugin).events!.isBusy, (e: boolean) => {
+            this.setState({ isBusy: e });
+            if (e) {
+                PluginCommands.Toast.Show(this.plugin, {
+                    title: 'Process',
+                    message: 'Loading / computing large dataset!',
+                    key: 'is-busy-toast'
+                });
+            } else {
+                PluginCommands.Toast.Hide(this.plugin, { key: 'is-busy-toast' });
+            }
+        });
+
+        this.subscribe(this.plugin.behaviors.layout.leftPanelTabName, (e: string) => {
+            if (e !== 'segments') return;
+            this.getSegmentParams();
+            this.forceUpdate();
+        });
+    }
+
+    get customState() {
+        return PluginCustomState(this.plugin);
+    }
+
+    getSegmentParams = () => {
+        const customState = this.customState;
+        if (!customState.superpositionState || !customState.superpositionState.segmentData) return;
+
+        const segmentData: Segment[] = customState.superpositionState.segmentData;
+
+        const segmentArr: [string, string][] = segmentData.map((segment, i: number) => {
+            const segmentLabel = `${i + 1} ( ${segment.segment_start} - ${segment.segment_end} )`;
+            return [segmentLabel, segmentLabel];
+        });
+
+        const segmentOptions = {
+            segment: PD.Select('', segmentArr, { label: 'Select Segment', description: 'Select segment to view its clusters below' })
+        };
+
+        const segmentIndex = customState.superpositionState.activeSegment - 1;
+        this.setState({
+            segment: {
+                params: segmentOptions,
+                value: { segment: segmentArr[segmentIndex][0] }
+            }
+        });
+        this.setState({ isBusy: false });
+    };
+
+    updateSegment = async (val: any) => {
+        if (!this.state.segment) return;
+        if (!this.state.segment) return;
+        const customState = this.customState;
+        if (!customState.superpositionState) throw new Error('customState.superpositionState has not been initialized');
+        customState.events?.isBusy.next(true);
+
+        // Hide pervious segement structures
+        this.hideStructures(customState.superpositionState.activeSegment - 1);
+
+        // Set current segment params
+        const updatedParams = { ...this.state.segment as any };
+        updatedParams.value = val;
+        this.setState({ segment: updatedParams });
+
+        setTimeout(async () => {
+            const updatedSegmentIndex = parseInt(val.segment.split(' ')[0]);
+            customState.superpositionState!.activeSegment = updatedSegmentIndex;
+
+            // Display current segment visible structures
+            await this.displayStructures(customState.superpositionState!.activeSegment - 1);
+            customState.events?.isBusy.next(false);
+            customState.events?.segmentUpdate.next(true);
+        }, 100);
+        return false;
+    };
+
+    hideStructures = (segmentIndex: number) => {
+        // clear selections
+        this.plugin.managers.interactivity.lociSelects.deselectAll();
+
+        // clear Focus
+        this.plugin.managers.structure.focus.clear();
+
+        // remove measurements
+        const measurements: any = this.plugin.managers.structure.measurement.state;
+        const measureTypes = ['labels', 'distances', 'angles', 'dihedrals'];
+        let measurementCell: any = void 0;
+        measureTypes.forEach((type: string) => {
+            if (measurementCell) return;
+            if (measurements[type][0]) {
+                measurementCell = this.plugin.state.data.cells.get(measurements[type][0].transform.parent)!;
+            }
+        });
+        if (measurementCell) {
+            PluginCommands.State.RemoveObject(this.plugin, { state: measurementCell.parent!, ref: measurementCell.transform.parent, removeParentGhosts: true });
+        }
+
+        // hide structures
+        const customState = this.customState;
+        if (!customState.superpositionState) throw new Error('customState.superpositionState has not been initialized');
+        customState.superpositionState.visibleRefs[segmentIndex] = [];
+        for (const struct of customState.superpositionState.loadedStructs[segmentIndex]) {
+            const structRef = customState.superpositionState.models[struct];
+            if (structRef) {
+                const structHierarchy: any = this.plugin.managers.structure.hierarchy.current.refs.get(structRef);
+                if (structHierarchy && structHierarchy.components) {
+                    for (const c of structHierarchy.components) {
+                        if (c && c.cell && !c.cell.state.isHidden) {
+                            customState.superpositionState.visibleRefs[segmentIndex].push(c.cell.transform.ref);
+                            PluginCommands.State.ToggleVisibility(this.plugin, { state: c.cell.parent!, ref: c.cell.transform.ref });
+                        }
+                    }
+                }
+            }
+        }
+
+        if (customState.superpositionState.alphafold.ref) {
+            const afStr: any = this.plugin.managers.structure.hierarchy.current.refs.get(customState.superpositionState.alphafold.ref);
+            if (afStr && afStr.components) {
+                for (const c of afStr.components) {
+                    if (c && c.cell && !c.cell.state.isHidden) {
+                        PluginCommands.State.ToggleVisibility(this.plugin, { state: c.cell.parent!, ref: c.cell.transform.ref });
+                    }
+                }
+            }
+        }
+    };
+
+    displayStructures = async (segmentIndex: number) => {
+        const customState = this.customState;
+        const spState = customState.superpositionState;
+        if (!spState) throw new Error('customState.superpositionState has not been initialized');
+        if (spState.visibleRefs[segmentIndex].length === 0) {
+            const loadStrs: any = [];
+            spState.segmentData?.[segmentIndex].clusters.forEach(cluster => {
+
+                let entryList = [cluster[0]];
+                if (customState.initParams?.superpositionParams?.superposeAll) {
+                    entryList = cluster;
+                }
+
+                entryList.forEach((str: ClusterMember) => {
+
+                    const structStateId = `${str.pdb_id}_${str.struct_asym_id}`;
+                    const structRef = spState.models[structStateId];
+                    if (structRef) {
+                        const cell = this.plugin.state.data.cells.get(structRef)!;
+                        const isHidden = cell.state.isHidden ? true : false;
+                        if (isHidden) {
+                            PluginCommands.State.ToggleVisibility(this.plugin, { state: cell.parent!, ref: structRef });
+                            // PluginCommands.State.ToggleVisibility(this.plugin, { state: cell.parent!, ref: cell.transform.parent });
+                        }
+                    } else {
+                        loadStrs.push(str);
+                    }
+                });
+            });
+            PluginCommands.Camera.Reset(this.plugin);
+
+            if (loadStrs.length > 0) {
+                await renderSuperposition(this.plugin, segmentIndex, loadStrs);
+                PluginCommands.Camera.Reset(this.plugin);
+            }
+
+        } else {
+            for (const ref of spState.visibleRefs[segmentIndex]) {
+                const cell = this.plugin.state.data.cells.get(ref)!;
+                if (cell && cell.state.isHidden) {
+                    PluginCommands.State.ToggleVisibility(this.plugin, { state: cell.parent!, ref });
+                }
+            }
+            PluginCommands.Camera.Reset(this.plugin);
+        }
+
+        if (spState.alphafold.ref) {
+            superposeAf(this.plugin, spState.alphafold.traceOnly);
+            PluginCommands.Camera.Reset(this.plugin);
+        }
+
+        if (spState.alphafold.ref && spState.alphafold.visibility[segmentIndex]) {
+            const afStr: any = this.plugin.managers.structure.hierarchy.current.refs.get(spState.alphafold.ref);
+            if (afStr && afStr.components) {
+                for (const c of afStr.components) {
+                    if (c && c.cell && c.cell.state.isHidden) {
+                        PluginCommands.State.ToggleVisibility(this.plugin, { state: c.cell.parent!, ref: c.cell.transform.ref });
+                    }
+                }
+            }
+        }
+    };
+
+    async transform(s: StateObjectRef, matrix: Mat4) {
+        const r = StateObjectRef.resolveAndCheck(this.plugin.state.data, s);
+        if (!r) return;
+        // TODO should find any TransformStructureConformation decorator instance
+        const o = StateSelection.findTagInSubtree(this.plugin.state.data.tree, r.transform.ref, SuperpositionTag);
+
+        const params = {
+            transform: {
+                name: 'matrix' as const,
+                params: { data: matrix, transpose: false }
+            }
+        };
+        // TODO add .insertOrUpdate to StateBuilder?
+        const b = o
+            ? this.plugin.state.data.build().to(o).update(params)
+            : this.plugin.state.data.build().to(s)
+                .insert(StateTransforms.Model.TransformStructureConformation, params, { tags: SuperpositionTag });
+        await this.plugin.runTask(this.plugin.state.data.updateTree(b));
+    }
+
+    render() {
+        let sectionHeader = ;
+        const customState = this.customState;
+        if (customState && customState.initParams && !customState.initParams.superposition) {
+            return <>
+                {sectionHeader}
+                
Functionality unavailable!

+            ;
+        } else {
+            if (customState && customState.initParams && customState.initParams.superposition) {
+
+                sectionHeader = ;
+
+                if (customState.superpositionError) {
+                    return <>
+                        {sectionHeader}
+                        
{customState.superpositionError}

+                    ;
+                } else if (!customState.superpositionState || !customState.superpositionState.segmentData) {
+                    return <>
+                        {sectionHeader}
+                        
Loading Segment Data!

+                    ;
+                }
+            }
+        }
+
+        if (this.state) {
+            const segmentIndex = parseInt(this.state.segment.value.segment.split(' ')[0]) - 1;
+            if (!customState.superpositionState?.segmentData) throw new Error('customState.superpositionState.segmentData has not been initialized');
+            const segmentData: Segment[] = customState.superpositionState.segmentData;
+            const fullSegmentRange = `( ${segmentData[0].segment_start} - ${segmentData[segmentData.length - 1].segment_end} )`;
+            sectionHeader = ;
+            return <>
+                {sectionHeader}
+                
+                {segmentData[segmentIndex].clusters.map((c: any[], i: number) => )}
+            ;
+        }
+
+        return <>;
+
+    }
+}
+
+class ClusterNode extends PluginUIComponent<{ cluster: any[], totalClusters: number, segmentIndex: number, clusterIndex: number }, { isCollapsed: boolean, showAll: boolean, showNone: boolean, showSearch: boolean, isBusy: boolean, searchText: string, cluster: any[] }> {
+
+    state = {
+        isCollapsed: false,
+        showAll: false,
+        showNone: false,
+        showSearch: false,
+        isBusy: false,
+        cluster: this.props.cluster,
+        searchText: ''
+    };
+
+    private inputStream = new Subject();
+    private handleInputStream = (inputStr: string) => {
+        this.setState({ searchText: inputStr });
+        const filteredRes = this.props.cluster.filter((item) => {
+            return item.pdb_id.toLowerCase().indexOf(inputStr.toLowerCase()) >= 0;
+        });
+        this.setState({ cluster: filteredRes });
+    };
+
+    componentDidMount() {
+        this.subscribe(PluginCustomState(this.plugin).events!.isBusy, (e: boolean) => {
+            this.setState({ isBusy: e, showAll: false, showNone: false });
+        });
+        this.subscribe(this.inputStream.pipe(debounceTime(1000 / 24)), (e: any) => this.handleInputStream(e));
+    }
+
+    get customState() {
+        return PluginCustomState(this.plugin);
+    }
+
+    toggleExpanded = (e: React.MouseEvent) => {
+        e.preventDefault();
+        this.setState({ isCollapsed: !this.state.isCollapsed });
+        e.currentTarget.blur();
+    };
+
+    selectAll = (e: React.MouseEvent) => {
+        e.preventDefault();
+        this.setState({ showAll: !this.state.showAll, showNone: false });
+        e.currentTarget.blur();
+    };
+
+    selectNone = (e: React.MouseEvent) => {
+        e.preventDefault();
+        this.setState({ showAll: false, showNone: !this.state.showNone });
+        e.currentTarget.blur();
+    };
+
+    applyAction = async (e: React.MouseEvent) => {
+        e.preventDefault();
+        e.currentTarget.blur();
+        const customState = this.customState;
+        customState.events?.isBusy.next(true);
+        const currentState = { ...this.state };
+        this.setState({ showAll: false, showNone: false });
+        setTimeout(async () => {
+            const loadStrs: any = [];
+            for await (const str of this.state.cluster) {
+                const structStateId = `${str.pdb_id}_${str.struct_asym_id}`;
+                let structRef = undefined;
+                if (customState && customState.superpositionState && customState.superpositionState.models[structStateId]) {
+                    structRef = customState.superpositionState.models[structStateId];
+                }
+
+                if (structRef) {
+
+                    const cell = this.plugin.state.data.cells.get(structRef)!;
+                    if (cell) {
+                        const isHidden = cell.state.isHidden ? true : false;
+                        if ((isHidden && currentState.showAll) || (!isHidden && currentState.showNone)) {
+                            await PluginCommands.State.ToggleVisibility(this.plugin, { state: cell.parent!, ref: structRef });
+                            // await PluginCommands.State.ToggleVisibility(this.plugin, { state: cell.parent!, ref: cell.transform.parent });
+                        }
+                    }
+                } else {
+                    if (currentState.showAll) loadStrs.push(str);
+                }
+            };
+            PluginCommands.Camera.Reset(this.plugin);
+            if (loadStrs.length > 0) {
+                await renderSuperposition(this.plugin, this.props.segmentIndex, loadStrs);
+            }
+            customState.events?.isBusy.next(false);
+        });
+    };
+
+    cancelAction = (e: React.MouseEvent) => {
+        e.preventDefault();
+        this.setState({ showAll: false, showNone: false });
+        e.currentTarget.blur();
+    };
+
+    clearSearch = (e: React.MouseEvent) => {
+        e.preventDefault();
+        this.setState({ searchText: '' });
+        this.inputStream.next('');
+        e.currentTarget.blur();
+    };
+
+    render() {
+        const customState = this.customState;
+        if (!customState.superpositionState || !customState.superpositionState.segmentData) return <>;
+        const expand = ;
+        const title = `Segment ${customState.superpositionState.activeSegment} Cluster ${this.props.clusterIndex + 1}`;
+        const label = ;
+
+        const selectionControls = <>
+            
+            
+        ;
+
+        const mainRow = 

+            {expand}
+            {label}
+            {this.props.cluster.length > 1 && selectionControls}
+        
;
+
+        const searchControls = 

+            

+                Search PDB ID
+                

+                     this.inputStream.next(e.target.value)} value={this.state.searchText} maxLength={4} />
+                

+            

+            
+        
;
+
+        return <>
+            {mainRow}
+            {(this.state.showAll || this.state.showNone) && 

+                

+                    {this.state.showAll ? 'Display' : 'Hide'} {this.state.cluster.length < this.props.cluster.length ? `${this.state.cluster.length} / ` : 'all '}{this.props.cluster.length} chains
+                    
+                    
+                

+            

+            }
+            {(!this.state.isCollapsed && this.props.cluster.length > 5) && searchControls}
+            {!this.state.isCollapsed && 
 1) ? '330px' : '87%', overflowY: 'auto' }}>
+                {this.state.cluster.map((s: any, i: number) => )}
+            

+            }
+        ;
+    }
+
+}
+
+class StructureNode extends PluginUIComponent<{ structure: any, isRep: boolean, segmentIndex: number }, { showControls: boolean, isBusy: boolean, isProcessing: boolean, isHidden: boolean }> {
+
+    state = {
+        showControls: false,
+        isBusy: false,
+        isProcessing: false,
+        isHidden: true,
+    };
+
+    get customState() {
+        return PluginCustomState(this.plugin);
+    }
+
+    get ref() {
+        if (this.customState && this.customState.superpositionState && this.customState.superpositionState.models[`${this.props.structure.pdb_id}_${this.props.structure.struct_asym_id}`]) {
+            return this.customState.superpositionState.models[`${this.props.structure.pdb_id}_${this.props.structure.struct_asym_id}`];
+        } else {
+            return undefined;
+        }
+    }
+
+    get modelCell() {
+        if (this.ref) {
+            return this.plugin.state.data.cells.get(this.ref);
+        } else {
+            return undefined;
+        }
+    }
+
+    get isAllHidden() {
+        let isHidden = true;
+        if (this.ref) {
+            const structHierarchy: any = this.plugin.managers.structure.hierarchy.current.refs.get(this.ref!);
+            if (structHierarchy && structHierarchy.components) {
+                for (const c of structHierarchy.components) {
+                    if (c && c.cell && !c.cell.state.isHidden) {
+                        isHidden = false;
+                        break;
+                    }
+                }
+            } else {
+                isHidden = false;
+            }
+        }
+        return isHidden;
+    }
+
+    checkRelation(ref: string) {
+        let isRelated = false;
+        const cell = this.plugin.state.data.cells.get(ref)!;
+        if (cell && cell.transform.parent) {
+            if (cell && cell.transform.parent === this.ref) {
+                isRelated = true;
+            } else {
+                const pcell = this.plugin.state.data.cells.get(cell.transform.parent)!;
+                if (pcell && pcell.transform.parent === this.ref) isRelated = true;
+            }
+        } else {
+            const currentNodeCell = this.plugin.state.data.cells.get(this.ref!)!;
+            if (currentNodeCell && currentNodeCell.transform.parent === cell.transform.parent) {
+                isRelated = true;
+            }
+        }
+        return isRelated;
+    }
+
+    is(e: State.ObjectEvent) {
+
+        if (!this.ref) return false;
+        let isRelated = false;
+        if (this.ref && e.ref !== this.ref) {
+            isRelated = this.checkRelation(e.ref);
+        }
+        if (e.ref === this.ref || isRelated) {
+            return true;
+        } else {
+            const id = `${this.props.structure.pdb_id}_${this.props.structure.struct_asym_id}`;
+            const invalidStruct = this.customState.superpositionState?.invalidStruct.includes(id) ?? false;
+            return invalidStruct;
+        }
+    }
+
+    componentDidMount() {
+        this.setState({ isHidden: this.isAllHidden });
+        this.subscribe(PluginCustomState(this.plugin).events!.isBusy, (e: boolean) => {
+            this.setState({ isBusy: e, showControls: false });
+        });
+        this.subscribe(this.plugin.state.events.cell.stateUpdated.pipe(filter(e => this.is(e)), debounceTime(33)), e => {
+            this.setState({ isHidden: this.isAllHidden });
+            // this.forceUpdate();
+        });
+    }
+
+    toggleVisible = async (e: React.MouseEvent) => {
+        e.preventDefault();
+        e.currentTarget.blur();
+        this.setState({ isProcessing: true, showControls: false });
+        if (this.ref) {
+
+            const structHierarchy: any = this.plugin.managers.structure.hierarchy.current.refs.get(this.ref!);
+            if (structHierarchy && structHierarchy.components) {
+                for (const c of structHierarchy.components) {
+                    const currentHiddenState = c.cell.state.isHidden ? true : false;
+                    if (currentHiddenState === this.state.isHidden) {
+                        PluginCommands.State.ToggleVisibility(this.plugin, { state: c.cell.parent!, ref: c.cell.transform.ref });
+                    }
+                }
+                this.setState({ isHidden: !this.state.isHidden });
+            }
+
+        } else {
+            await renderSuperposition(this.plugin, this.props.segmentIndex, [this.props.structure]);
+        }
+        this.setState({ isProcessing: false });
+        PluginCommands.Camera.Reset(this.plugin);
+    };
+
+    selectAction: ActionMenu.OnSelect = item => {
+        if (!item) return;
+        this.setState({ showControls: false });
+        (item?.value as any)();
+    };
+
+    getTagRefs(tags: string[]) {
+        const TagSet: Set = new Set(tags);
+        const tree = this.plugin.state.data.tree;
+        return StateSelection.findUniqueTagsInSubtree(tree, this.modelCell!.transform.ref, TagSet);
+    };
+
+    getRandomColor() {
+        const clList: any = ColorLists;
+        const spState = PluginCustomState(this.plugin).superpositionState;
+        if (!spState) throw new Error('customState.superpositionState has not been initialized');
+        let palleteIndex = spState.colorState[this.props.segmentIndex].palleteIndex;
+        let colorIndex = spState.colorState[this.props.segmentIndex].colorIndex;
+        if (clList[spState.colorPalette[palleteIndex]].list[colorIndex + 1]) {
+            colorIndex += 1;
+        } else {
+            colorIndex = 0;
+            palleteIndex = spState.colorPalette[palleteIndex + 1] ? palleteIndex + 1 : 0;
+        }
+        const palleteName = spState.colorPalette[palleteIndex];
+        spState.colorState[this.props.segmentIndex].palleteIndex = palleteIndex;
+        spState.colorState[this.props.segmentIndex].colorIndex = colorIndex;
+        return clList[palleteName].list[colorIndex];
+    }
+
+    async addChainRepr() {
+        const uniformColor1 = this.getRandomColor();
+        const strInstance = this.plugin.state.data.select(this.ref!)[0];
+        const query = MS.struct.generator.atomGroups({
+            'chain-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.label_asym_id(), this.props.structure.struct_asym_id])
+        });
+        const chainSel = await this.plugin.builders.structure.tryCreateComponentFromExpression(strInstance, query, `Chain-${this.props.segmentIndex}`, { label: `Chain`, tags: [`superposition-sel`] });
+        if (chainSel) {
+            await this.plugin.builders.structure.representation.addRepresentation(chainSel, { type: 'cartoon', color: 'uniform', colorParams: { value: uniformColor1 } }, { tag: `superposition-visual` });
+        }
+    }
+
+    updates() {
+        const structHierarchy: any = this.plugin.managers.structure.hierarchy.current.refs.get(this.ref!);
+        if (structHierarchy && structHierarchy.components) {
+            const representations: any = [];
+            let showAddChainBtn = true;
+            structHierarchy.components.forEach((comps: any) => {
+                const gKeys = comps.key!.split(',');
+                const cId1Arr = gKeys[0].split('-');
+                if (cId1Arr[2] === 'Chain') showAddChainBtn = false;
+
+                if (comps.representations) {
+                    comps.representations.forEach((repr: any) => {
+                        representations.push(repr);
+                    });
+                }
+            });
+
+            const customState = PluginCustomState(this.plugin);
+            if (customState.initParams?.superpositionParams && !customState.initParams.superpositionParams.ligandView) {
+                showAddChainBtn = false;
+            }
+
+            if (representations.length > 0) {
+                return 

+                    {representations.length > 0 && representations.map((r: any, i: number) => )}
+                    {showAddChainBtn && 

+                        
+                    
}
+                
;
+            }
+        }
+        return <>;
+    }
+
+    highlight = (e: React.MouseEvent) => {
+        e.preventDefault();
+        if (this.ref) {
+            const cell = this.plugin.state.data.cells.get(this.ref)!;
+            PluginCommands.Interactivity.Object.Highlight(this.plugin, { state: cell.parent!, ref: this.ref });
+        }
+        e.currentTarget.blur();
+    };
+
+    clearHighlight = (e: React.MouseEvent) => {
+        e.preventDefault();
+        PluginCommands.Interactivity.ClearHighlights(this.plugin);
+        e.currentTarget.blur();
+    };
+
+    toggleControls = (e: React.MouseEvent) => {
+        e.preventDefault();
+        this.setState({ showControls: !this.state.showControls });
+        e.currentTarget.blur();
+    };
+
+    getSubtitle() {
+        if (!this.customState.superpositionState) throw new Error('customState.superpositionState has not been initialized');
+        const hetList = this.customState.superpositionState.hets[`${this.props.structure.pdb_id}_${this.props.structure.struct_asym_id}`];
+        let subtitle: string | undefined;
+        if (hetList) {
+            const hetLimit = this.props.structure.is_representative ? 1 : 4;
+            const totalHets = hetList.length;
+            let hetStr = hetList.join(', ');
+            if (totalHets > hetLimit) {
+                hetStr = hetList.slice(0, hetLimit).join(', ');
+                hetStr += ` + ${totalHets - hetLimit}`;
+            }
+            subtitle = ` ( ${hetStr} )`;
+            if (this.props.structure.is_representative) subtitle = ` ${subtitle} ( Representative )`;
+        } else if (this.props.structure.is_representative) {
+            subtitle = ' ( Representative )';
+        }
+        return subtitle;
+    }
+
+    get panelColor() {
+        let panelColor = '#808080';
+        if (!this.state.isHidden) {
+            if (this.modelCell) {
+                const refs = this.getTagRefs([`superposition-visual`, `superposition-ligand-visual`]);
+                const visualRef = refs[`superposition-ligand-visual`] ? refs[`superposition-ligand-visual`] : refs[`superposition-visual`] ? refs[`superposition-visual`] : undefined;
+                if (visualRef) {
+                    const visualCell = this.plugin.state.data.cells.get(visualRef)!;
+                    if (visualCell.params && visualCell.params!.values && visualCell.params!.values.colorTheme) {
+                        const colorTheme = visualCell.params!.values!.colorTheme;
+                        if (colorTheme.params && colorTheme.params.value) {
+                            panelColor = `${Color.toStyle(colorTheme.params.value)}`;
+                        } else if (colorTheme.params && colorTheme.params.palette) {
+                            const colorList1 = colorTheme.params.palette.params.list.colors;
+                            panelColor = `${Color.toStyle(colorList1[0])}`;
+                        } else if (colorTheme.params && colorTheme.params.list) {
+                            const colorList2 = colorTheme.params.list.colors;
+                            panelColor = `${Color.toStyle(colorList2[0])}`;
+                        }
+                    }
+                }
+            }
+        }
+        return panelColor;
+    }
+
+    render() {
+        const superpositionParams = this.customState.initParams!.superpositionParams;
+        const strutStateId = `${this.props.structure.pdb_id}_${this.props.structure.struct_asym_id}`;
+        const invalidStruct = this.customState.superpositionState?.invalidStruct.includes(strutStateId);
+        const noMatrixStruct = this.customState.superpositionState?.noMatrixStruct.includes(strutStateId);
+        const subTitle = invalidStruct ? noMatrixStruct ? ` Matrix not available!` : ` No Ligand found!` : this.getSubtitle();
+
+        let strTitle = `${this.props.structure.pdb_id} chain ${this.props.structure.auth_asym_id}`;
+        if (superpositionParams && superpositionParams.ligandView) {
+            strTitle = `${this.props.structure.pdb_id} ${this.props.structure.struct_asym_id}`;
+        }
+        const label = ;
+
+        const expand = ;
+        const visibility = ;
+        const row = 

+            {!this.state.isHidden && expand}
+            {label}
+            {visibility}
+        
;
+
+        return 

+            {row}
+            {this.state.showControls && this.updates()}
+        
;
+    }
+
+}
+
+class StructureRepresentationEntry extends PurePluginUIComponent<{ group: StructureComponentRef[], representation: StructureRepresentationRef }> {
+    componentDidMount() {
+        this.subscribe(this.plugin.state.events.cell.stateUpdated, e => {
+            if (State.ObjectEvent.isCell(e, this.props.representation.cell)) this.forceUpdate();
+        });
+    }
+
+    toggleVisible = (e: React.MouseEvent) => {
+        e.preventDefault();
+        e.currentTarget.blur();
+        const cell = this.props.representation.cell;
+        PluginCommands.State.ToggleVisibility(this.plugin, { state: cell.parent!, ref: cell.transform.parent });
+    };
+
+    render() {
+        const repr = this.props.representation.cell;
+        let label = repr.obj?.label;
+        if (repr.obj?.data.repr && repr.obj?.data.repr.label) {
+            let sourceLabel = (repr.obj?.data.repr.label.indexOf('[Focus]') >= 0) ? '[Focus]' : repr.obj?.data.repr.label;
+            const isLargeLabel = sourceLabel.length > 10 ? true : false;
+            sourceLabel = `${isLargeLabel ? `${sourceLabel.substring(0, 28)}...` : sourceLabel}`;
+            if (isLargeLabel) {
+                label = sourceLabel;
+            } else {
+                label = `${sourceLabel} ${(label && label.length < 21) ? ' - ' + label : ''}`;
+            }
+        }
+        if (repr.obj?.data.repr && repr.obj?.data.repr.label === 'Custom Selection') label = 'Custom Selection';
+        return 

+            {repr.parent && 
+                
+            }
+            
+        
;
+    }
+}
\ No newline at end of file
diff --git a/frontend/venome-molstar/src/app/ui/superposition-components.tsx b/frontend/venome-molstar/src/app/ui/superposition-components.tsx
new file mode 100644
index 00000000..85ab67c1
--- /dev/null
+++ b/frontend/venome-molstar/src/app/ui/superposition-components.tsx
@@ -0,0 +1,498 @@
+import { StructureComponentRef, StructureRepresentationRef } from 'molstar/lib/mol-plugin-state/manager/structure/hierarchy-state';
+import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
+import { State, StateTransformer } from 'molstar/lib/mol-state';
+import { ParamDefinition } from 'molstar/lib/mol-util/param-definition';
+import { CollapsableControls, CollapsableState, PurePluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { Button, IconButton } from 'molstar/lib/mol-plugin-ui/controls/common';
+import { CubeOutlineSvg, VisibilityOffOutlinedSvg, VisibilityOutlinedSvg, MoreHorizSvg, CheckSvg, CloseSvg } from 'molstar/lib/mol-plugin-ui/controls/icons';
+import { ParameterControls } from 'molstar/lib/mol-plugin-ui/controls/parameters';
+import { StructureRepresentation3D } from 'molstar/lib/mol-plugin-state/transforms/representation';
+import { debounceTime } from 'rxjs/operators';
+import { Subject } from 'rxjs';
+import { PluginCustomState } from '../plugin-custom-state';
+
+interface StructureComponentControlState extends CollapsableState {
+    isDisabled: boolean
+}
+
+export class SuperpositionComponentControls extends CollapsableControls<{}, StructureComponentControlState> {
+    protected defaultState(): StructureComponentControlState {
+        return {
+            header: 'Components',
+            isCollapsed: false,
+            isDisabled: false,
+            brand: { accent: 'blue', svg: CubeOutlineSvg }
+        };
+    }
+
+    renderControls() {
+        return <>
+            
+        ;
+    }
+}
+
+interface ComponentGroups { nonLigGroups: StructureComponentRef[][], ligGroups: StructureComponentRef[][], carbGroups: StructureComponentRef[][], alphafold: StructureComponentRef[][] }
+
+interface ComponentListControlsState {
+    segmentWatch: boolean,
+    ligSearchText: string,
+    carbSearchText: string,
+    componentGroups: ComponentGroups,
+    ligGroups: StructureComponentRef[][],
+    isLigCollapsed: boolean,
+    carbGroups: StructureComponentRef[][],
+    isCarbCollapsed: boolean,
+    isBusy: boolean
+};
+
+class ComponentListControls extends PurePluginUIComponent<{}, ComponentListControlsState> {
+
+    state = {
+        segmentWatch: false,
+        ligSearchText: '',
+        carbSearchText: '',
+        componentGroups: { nonLigGroups: [], ligGroups: [], carbGroups: [], alphafold: [] },
+        ligGroups: [],
+        isLigCollapsed: false,
+        carbGroups: [],
+        isCarbCollapsed: false,
+        isBusy: false
+    };
+
+    private ligInputStream = new Subject();
+    private handleLigInputStream = (inputStr: string) => {
+        this.setState({ ligSearchText: inputStr });
+        const filteredRes = this.state.componentGroups.ligGroups.filter((g: StructureComponentRef[]) => {
+            const gKeys = g[0].key!.split(',');
+            const cId1Arr = gKeys[0].split('-');
+            return cId1Arr[2].toLowerCase().indexOf(inputStr.toLowerCase()) >= 0;
+        });
+        this.setState({ ligGroups: filteredRes });
+    };
+
+    private carbInputStream = new Subject();
+    private handleCarbInputStream = (inputStr: string) => {
+        this.setState({ carbSearchText: inputStr });
+        const filteredRes = this.state.componentGroups.carbGroups.filter((g: StructureComponentRef[]) => {
+            const gKeys = g[0].key!.split(',');
+            const cId1Arr = gKeys[0].split('-');
+            cId1Arr.splice(0, 2);
+            cId1Arr.pop();
+            return cId1Arr.join('-').toLowerCase().indexOf(inputStr.toLowerCase()) >= 0;
+        });
+        this.setState({ carbGroups: filteredRes });
+    };
+
+    componentDidMount() {
+        this.subscribe(this.plugin.managers.structure.hierarchy.behaviors.selection, () => {
+            this.categoriseGroups();
+            this.forceUpdate();
+        });
+        this.subscribe(this.plugin.behaviors.state.isBusy, v => {
+            this.setState({ isBusy: v });
+        });
+    }
+
+    componentDidUpdate() {
+        const customState = PluginCustomState(this.plugin);
+        if (customState.events && !this.state.segmentWatch) {
+            this.setState({ segmentWatch: true });
+            this.subscribe(customState.events.segmentUpdate, () => {
+                this.categoriseGroups();
+                this.forceUpdate();
+            });
+        }
+        this.subscribe(this.ligInputStream.pipe(debounceTime(1000 / 24)), e => this.handleLigInputStream(e));
+        this.subscribe(this.carbInputStream.pipe(debounceTime(1000 / 24)), e => this.handleCarbInputStream(e));
+    }
+
+    categoriseGroups() {
+        const componentGroupsVal: ComponentGroups = { nonLigGroups: [], ligGroups: [], carbGroups: [], alphafold: [] };
+        const componentGroups = this.plugin.managers.structure.hierarchy.currentComponentGroups;
+        const customState = PluginCustomState(this.plugin);
+        componentGroups.forEach((g: StructureComponentRef[]) => {
+            const superpositionState = customState.superpositionState;
+            if (!superpositionState) throw new Error('customState.superpositionState has not been initialized');
+            let isLigandView = false;
+            if (customState.initParams && customState.initParams.superpositionParams && customState.initParams.superpositionParams.ligandView) {
+                isLigandView = true;
+            }
+
+            if (isLigandView) {
+                const gKeys = g[0].key!.split(',');
+                const cId1Arr = gKeys[0].split('-');
+                if (gKeys.indexOf('superposition-focus-surr-sel') === -1) {
+                    if (cId1Arr[cId1Arr.length - 1] !== (superpositionState.activeSegment - 1) + '') return;
+                    if (gKeys.indexOf('superposition-ligand-sel') >= 0) {
+                        componentGroupsVal.ligGroups.push(g);
+                    } else if (gKeys.indexOf('superposition-carb-sel') >= 0) {
+                        componentGroupsVal.carbGroups.push(g);
+                    } else if (gKeys.indexOf('alphafold-chain') >= 0) {
+                        componentGroupsVal.alphafold.push(g);
+                    } else {
+                        componentGroupsVal.nonLigGroups.push(g);
+                    }
+                } else {
+                    componentGroupsVal.nonLigGroups.push(g);
+                }
+            } else {
+                const gKeys = g[0].key!.split(',');
+                if (gKeys.indexOf('superposition-focus-surr-sel') >= 0 || gKeys.indexOf(`Chain-${superpositionState.activeSegment - 1}`) >= 0) {
+                    componentGroupsVal.nonLigGroups.push(g);
+                } else if (gKeys.indexOf('alphafold-chain') >= 0) {
+                    componentGroupsVal.alphafold.push(g);
+                }
+            }
+        });
+        this.setState({ componentGroups: componentGroupsVal, ligGroups: componentGroupsVal.ligGroups, carbGroups: componentGroupsVal.carbGroups, ligSearchText: '', carbSearchText: '' });
+    }
+
+    toggleVisible = (e: React.MouseEvent, action: 'hide' | 'show', type: 'ligands' | 'carbohydrates') => {
+        e.preventDefault();
+        e.currentTarget.blur();
+
+        const customState = PluginCustomState(this.plugin);
+        customState.events?.isBusy.next(true);
+
+        const visualEntites = (type === 'ligands') ? this.state.ligGroups : this.state.carbGroups;
+
+        setTimeout(async () => {
+            for await (const visualEntity of visualEntites) {
+                this.plugin.managers.structure.hierarchy.toggleVisibility(visualEntity, action);
+            };
+            customState.events?.isBusy.next(false);
+        });
+
+    };
+
+    showHideAllControls = (type: 'ligands' | 'carbohydrates') => {
+        return <>
+            
+            
+        ;
+    };
+
+    clearLigSearch = (e: React.MouseEvent) => {
+        e.preventDefault();
+        this.setState({ ligSearchText: '' });
+        this.ligInputStream.next('');
+        e.currentTarget.blur();
+    };
+
+    clearCarbSearch = (e: React.MouseEvent) => {
+        e.preventDefault();
+        this.setState({ carbSearchText: '' });
+        this.carbInputStream.next('');
+        e.currentTarget.blur();
+    };
+
+    collapseSection = (e: React.MouseEvent, type: 'ligands' | 'carbohydrates') => {
+        e.preventDefault();
+        e.currentTarget.blur();
+        if (type === 'ligands') {
+            this.setState({ isLigCollapsed: !this.state.isLigCollapsed });
+        } else {
+            this.setState({ isCarbCollapsed: !this.state.isCarbCollapsed });
+        }
+    };
+
+    sectionHeader = (type: 'ligands' | 'carbohydrates') => {
+        const showHideAllControls = (type === 'ligands') ? this.showHideAllControls('ligands') : this.showHideAllControls('carbohydrates');
+        const title = (type === 'ligands') ? 'Ligand' : 'Carbohydrates';
+        const visibleVisuals = (type === 'ligands') ? this.state.ligGroups.length : this.state.carbGroups.length;
+        const totalVisuals = (type === 'ligands') ? this.state.componentGroups.ligGroups.length : this.state.componentGroups.carbGroups.length;
+        return 

+            
+            {visibleVisuals > 1 && showHideAllControls}
+        
;
+    };
+
+
+
+    render() {
+
+        const ligSearchControls = 

+            

+                Search Ligand
+                

+                     this.ligInputStream.next(e.target.value)} value={this.state.ligSearchText} maxLength={3} />
+                

+            

+            
+        
;
+
+        const carbSearchControls = 

+            

+                Search Carbohydrate
+                

+                     this.carbInputStream.next(e.target.value)} value={this.state.carbSearchText} maxLength={3} />
+                

+            

+            
+        
;
+
+        const ligSectionHeader = this.sectionHeader('ligands');
+        const carbSectionHeader = this.sectionHeader('carbohydrates');
+
+        return <>
+            {(this.state.componentGroups.nonLigGroups.length > 0) && 

+                {this.state.componentGroups.nonLigGroups.map((g: any) => )}
+            
}
+            {(this.state.componentGroups.alphafold.length > 0) && 

+                {this.state.componentGroups.alphafold.map((g: any) => )}
+            
}
+            {(this.state.componentGroups.ligGroups.length > 0) && ligSectionHeader}
+            {(!this.state.isLigCollapsed && this.state.componentGroups.ligGroups.length > 5) && ligSearchControls}
+            {(this.state.componentGroups.ligGroups.length > 0) && 

+                {!this.state.isLigCollapsed && this.state.ligGroups.map((g: any) => )}
+            
}
+            {(this.state.componentGroups.carbGroups.length > 0) && carbSectionHeader}
+            {(!this.state.isCarbCollapsed && this.state.componentGroups.carbGroups.length > 5) && carbSearchControls}
+            {(this.state.componentGroups.carbGroups.length > 0) && 

+                {!this.state.isCarbCollapsed && this.state.carbGroups.map((g: any) => )}
+            
}
+        ;
+    }
+}
+
+type StructureComponentEntryActions = 'action' | 'label'
+
+class StructureComponentGroup extends PurePluginUIComponent<{ group: StructureComponentRef[], boldHeader?: boolean, type?: string }, { action?: StructureComponentEntryActions, isHidden: boolean, isBusy: boolean }> {
+    state = {
+        action: void 0 as StructureComponentEntryActions | undefined,
+        isHidden: false,
+        isBusy: false
+    };
+
+    get pivot() {
+        return this.props.group[0];
+    }
+
+    checkAllHidden = async () => {
+        let allHidden = true;
+        for (const c of this.props.group) {
+            if (!c.cell.state.isHidden) {
+                allHidden = false;
+                break;
+            }
+        }
+        if (allHidden) this.setState({ isHidden: true });
+    };
+
+    componentDidMount() {
+        this.checkAllHidden();
+        this.subscribe(this.plugin.state.events.cell.stateUpdated, e => {
+            // if (State.ObjectEvent.isCell(e, this.pivot.cell)) this.forceUpdate();
+            if (this.pivot.cell.obj?.label === e.cell.obj?.label) {
+                if (!e.cell.state.isHidden) {
+                    this.setState({ isHidden: false });
+                } else {
+                    this.checkAllHidden();
+                }
+            }
+        });
+
+        this.subscribe(this.plugin.behaviors.state.isBusy, v => {
+            this.setState({ isBusy: v });
+        });
+
+        this.subscribe(PluginCustomState(this.plugin).events!.isBusy, (e: boolean) => {
+            this.setState({ isBusy: e });
+        });
+    }
+
+    toggleVisible = (e: React.MouseEvent) => {
+        e.preventDefault();
+        e.currentTarget.blur();
+        this.plugin.managers.structure.component.toggleVisibility(this.props.group);
+        this.setState({ isHidden: !this.state.isHidden });
+        if (this.props.type === 'alphafold') {
+            const spState = PluginCustomState(this.plugin).superpositionState;
+            if (!spState) throw new Error('customState.superpositionState has not been initialized');
+            spState.alphafold.visibility[spState.activeSegment - 1] = this.state.isHidden;
+        }
+    };
+
+    toggleAction = () => this.setState({ action: this.state.action === 'action' ? void 0 : 'action' });
+
+    highlight = (e: React.MouseEvent) => {
+        e.preventDefault();
+        if (!this.props.group[0].cell.parent) return;
+        PluginCommands.Interactivity.Object.Highlight(this.plugin, { state: this.props.group[0].cell.parent!, ref: this.props.group.map(c => c.cell.transform.ref) });
+    };
+
+    clearHighlight = (e: React.MouseEvent) => {
+        e.preventDefault();
+        PluginCommands.Interactivity.ClearHighlights(this.plugin);
+    };
+
+    focus = () => {
+        let allHidden = true;
+        for (const c of this.props.group) {
+            if (!c.cell.state.isHidden) {
+                allHidden = false;
+                break;
+            }
+        }
+
+        if (allHidden) {
+            this.plugin.managers.structure.hierarchy.toggleVisibility(this.props.group, 'show');
+        }
+
+        this.plugin.managers.camera.focusSpheres(this.props.group, e => {
+            if (e.cell.state.isHidden) return;
+            return e.cell.obj?.data.boundary.sphere;
+        });
+    };
+
+    render() {
+        const component = this.pivot;
+        const cell = component.cell;
+        const label = cell.obj?.label;
+        const labelEle = this.props.boldHeader ? {label} : label;
+
+        return <>
+            

+                
+                
+                
+            

+            {this.state.action === 'action' && 

+                

+                    {component.representations.map(r => )}
+                

+            
}
+        ;
+    }
+}
+
+class StructureRepresentationEntry extends PurePluginUIComponent<{ group: StructureComponentRef[], representation: StructureRepresentationRef }, { isBusy: boolean, clusterVal?: any }> {
+
+    state = {
+        isBusy: false,
+        clusterVal: { cluster: 'All' }
+    };
+
+    remove = () => this.plugin.managers.structure.component.removeRepresentations(this.props.group, this.props.representation);
+    toggleVisible = (e: React.MouseEvent) => {
+        e.preventDefault();
+        e.currentTarget.blur();
+        this.plugin.managers.structure.component.toggleVisibility(this.props.group, this.props.representation);
+    };
+
+    componentDidMount() {
+        this.subscribe(this.plugin.state.events.cell.stateUpdated, e => {
+            if (State.ObjectEvent.isCell(e, this.props.representation.cell)) this.forceUpdate();
+        });
+        this.subscribe(this.plugin.behaviors.state.isBusy, v => {
+            this.setState({ isBusy: v });
+        });
+        this.subscribe(PluginCustomState(this.plugin).events!.isBusy, (e: boolean) => {
+            this.setState({ isBusy: e });
+        });
+    }
+
+    updateRepresentations(components: ReadonlyArray, pivot: StructureRepresentationRef, params: StateTransformer.Params) {
+
+        if (components.length === 0) return Promise.resolve();
+        const index = components[0].representations.indexOf(pivot);
+        if (index < 0) return Promise.resolve();
+
+        const superpositionState = PluginCustomState(this.plugin).superpositionState;
+        if (!superpositionState) throw new Error('customState.superpositionState has not been initialized');
+        let filteredComps: any = [];
+        if (this.state.clusterVal.cluster !== 'All') {
+            if (!superpositionState.segmentData) throw new Error('customState.superpositionState.segmentData has not been initialized');
+            const clusterData = superpositionState.segmentData[superpositionState.activeSegment - 1].clusters[parseInt(this.state.clusterVal.cluster) - 1];
+
+            filteredComps = clusterData.map((s: any) => {
+                return `${s.pdb_id}_${s.struct_asym_id}`;
+            });
+
+            if (filteredComps.length === 0) return;
+
+        }
+
+        const update = this.plugin.state.data.build();
+
+        for (const c of components) {
+            // TODO: is it ok to use just the index here? Could possible lead to ugly edge cases, but perhaps not worth the trouble to "fix".
+            const repr = c.representations[index];
+            if (!repr) continue;
+            if (repr.cell.transform.transformer !== pivot.cell.transform.transformer) continue;
+
+            if (this.state.clusterVal.cluster !== 'All') {
+                const rmIndex = filteredComps.indexOf(superpositionState.refMaps[repr.cell.transform.parent]);
+                if (rmIndex === -1) continue;
+            }
+
+            const updatedParams = {
+                type: params.type ? params.type : repr.cell.params?.values.type,
+                colorTheme: params.colorTheme ? params.colorTheme : repr.cell.params?.values.colorTheme,
+                sizeTheme: params.sizeTheme ? params.sizeTheme : repr.cell.params?.values.sizeTheme
+            };
+
+            update.to(repr.cell).update(updatedParams);
+        }
+
+        return update.commit({ canUndo: 'Update Representation' });
+    }
+
+    update = (params: any) => {
+        return this.updateRepresentations(this.props.group, this.props.representation, params);
+    };
+
+    selectCluster = (params: any) => {
+        this.setState({ clusterVal: { cluster: params.cluster } });
+    };
+
+    render() {
+        const repr = this.props.representation.cell;
+
+        const superpositionState = PluginCustomState(this.plugin).superpositionState;
+        const clusterSelectArr: any = [['All', 'All']];
+        if (!superpositionState?.segmentData) throw new Error('customState.superpositionState.segmentData has not been initialized');
+        superpositionState.segmentData[superpositionState.activeSegment - 1].clusters.forEach((c: any, i: number) => {
+            clusterSelectArr.push([(i + 1) + '', (i + 1) + '']);
+        });
+        const clusterOptions = {
+            cluster: ParamDefinition.Select('All', clusterSelectArr, { label: 'Select Cluster' })
+        };
+
+        let isSurrVisual = false;
+        let isAlphafold = false;
+        if (repr && repr.obj) {
+            const reprObj: any = repr.obj;
+            if (reprObj.tags && reprObj.tags.indexOf('superposition-focus-surr-repr') >= 0) isSurrVisual = true;
+            if (reprObj.tags && reprObj.tags.indexOf('af-superposition-visual') >= 0) isAlphafold = true;
+        }
+
+        return 

+            {repr.parent && 

+                {(clusterSelectArr.length > 2 && !isSurrVisual && !isAlphafold) && 

+                    
+                
}
+                

+                    
+                

+                

+                    
+                

+                

+                    
+                

+            
}
+        
;
+    }
+}
\ No newline at end of file
diff --git a/frontend/venome-molstar/src/app/ui/superposition-viewport.tsx b/frontend/venome-molstar/src/app/ui/superposition-viewport.tsx
new file mode 100644
index 00000000..98240cb0
--- /dev/null
+++ b/frontend/venome-molstar/src/app/ui/superposition-viewport.tsx
@@ -0,0 +1,25 @@
+import { PluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { LociLabels, StateSnapshotViewportControls, SelectionViewportControls } from 'molstar/lib/mol-plugin-ui/controls';
+import { BackgroundTaskProgress } from 'molstar/lib/mol-plugin-ui/task';
+import { Toasts } from 'molstar/lib/mol-plugin-ui/toast';
+import { Viewport, ViewportControls } from 'molstar/lib/mol-plugin-ui/viewport';
+
+export class SuperpostionViewport extends PluginUIComponent {
+    render() {
+        const VPControls = this.plugin.spec.components?.viewport?.controls || ViewportControls;
+
+        return <>
+            
+            

+                
+            

+            
+            
+            
+            

+                
+                
+            

+        ;
+    }
+}
\ No newline at end of file
diff --git a/frontend/venome-molstar/src/app/ui/symmetry-annotation-controls.tsx b/frontend/venome-molstar/src/app/ui/symmetry-annotation-controls.tsx
new file mode 100644
index 00000000..d93ae450
--- /dev/null
+++ b/frontend/venome-molstar/src/app/ui/symmetry-annotation-controls.tsx
@@ -0,0 +1,250 @@
+import { AssemblySymmetry3D, getRCSBAssemblySymmetryConfig, tryCreateAssemblySymmetry } from 'molstar/lib/extensions/rcsb/assembly-symmetry/behavior';
+import { AssemblySymmetry, AssemblySymmetryDataProps, AssemblySymmetryDataProvider, AssemblySymmetryParams, AssemblySymmetryProps, AssemblySymmetryProvider } from 'molstar/lib/extensions/rcsb/assembly-symmetry/prop';
+import { StructureRef } from 'molstar/lib/mol-plugin-state/manager/structure/hierarchy-state';
+import { PurePluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { PluginContext } from 'molstar/lib/mol-plugin/context';
+import { StateSelection } from 'molstar/lib/mol-state';
+import { Task } from 'molstar/lib/mol-task';
+import { UUID } from 'molstar/lib/mol-util';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
+import { AnnotationRowControls } from './annotation-row-controls';
+
+
+type SymmetryParams = {
+    /** State of the visibility button */
+    on: PD.BooleanParam,
+    /** Index of the currently selected symmetry (in case there a more symmetries for an assembly), regardless of whether visibility is on of off */
+    symmetryIndex: PD.Select,
+    /** `true` if symmetry data have been retrieved but do not contain any non-trivial symmetry */
+    noSymmetries: PD.BooleanParam,
+}
+
+type SymmetryParamValues = PD.ValuesFor
+
+interface SymmetryControlsState {
+    params: SymmetryParams,
+    values: SymmetryParamValues,
+}
+
+const DefaultSymmetryControlsState: SymmetryControlsState = {
+    params: {
+        on: PD.Boolean(false, { isHidden: true }),
+        symmetryIndex: PD.Select(0, [[0, 'Auto']]),
+        noSymmetries: PD.Boolean(false, { isHidden: true }),
+    },
+    values: {
+        on: false,
+        symmetryIndex: 0,
+        noSymmetries: false,
+    },
+};
+
+
+/** UI controls for showing Assembly Symmetry annotations (a row within Annotations section) */
+export class SymmetryAnnotationControls extends PurePluginUIComponent<{}, SymmetryControlsState> {
+    state = DefaultSymmetryControlsState;
+
+    currentStructureId: UUID | undefined = undefined;
+
+    componentDidMount() {
+        // Reset state when the pivot structure changes
+        this.subscribe(this.plugin.managers.structure.hierarchy.behaviors.selection, c => {
+            const structureObj = c.structures[0]?.cell.obj;
+            const structureId = structureObj?.id;
+            if (structureId !== this.currentStructureId) {
+                this.currentStructureId = structureId;
+                this.syncParams();
+            }
+        });
+        // Synchronize params when AssemblySymmetry3D changes
+        this.subscribe(this.plugin.state.events.cell.stateUpdated, e => {
+            if (e.cell.transform.transformer === AssemblySymmetry3D) {
+                this.syncParams();
+            }
+        });
+        // Synchronize params when AssemblySymmetry3D is removed
+        this.subscribe(this.plugin.state.events.cell.removed, e => {
+            this.syncParams();
+        });
+    }
+
+    /** Synchronize parameters and values in UI with real parameters currently applied in `AssemblySymmetryProvider` */
+    syncParams() {
+        if (this.hasAssemblySymmetry3D()) {
+            const noSymmetries = this.noSymmetriesAvailable();
+            const realParams = this.getRealParams();
+            const realValues = this.getRealValues();
+            const options = noSymmetries ?
+                [[0, 'None']] as const
+                : realParams.symmetryIndex.options.filter(([index, label]) => index >= 0); // Removing the 'off' option (having index -1)
+            const params = {
+                ...this.state.params,
+                symmetryIndex: PD.Select(0, options),
+            };
+            const values = (realValues.symmetryIndex >= 0) ? {
+                on: true,
+                symmetryIndex: realValues.symmetryIndex,
+                noSymmetries: noSymmetries,
+            } : {
+                on: false,
+                symmetryIndex: this.state.values.symmetryIndex,
+                noSymmetries: noSymmetries,
+            };
+            this.setState({ params, values });
+        } else {
+            this.setState({
+                params: DefaultSymmetryControlsState.params,
+                values: DefaultSymmetryControlsState.values,
+            });
+        }
+    }
+
+    /** Return `true` if symmetry data have been retrieved and do not contain any non-trivial symmetry. */
+    noSymmetriesAvailable() {
+        const structure = this.getPivotStructure()?.cell.obj?.data;
+        const symmetryData = structure && AssemblySymmetryDataProvider.get(structure).value;
+        return symmetryData !== undefined && symmetryData.filter(sym => sym.symbol !== 'C1').length === 0;
+    }
+
+    /** Get the first loaded structure, if any. */
+    getPivotStructure(): StructureRef | undefined {
+        return getPivotStructure(this.plugin);
+    }
+
+    /** Get parameters currently applied in `AssemblySymmetryProvider` */
+    getRealParams(): AssemblySymmetryParams {
+        const structure = this.getPivotStructure()?.cell.obj?.data;
+        let params: AssemblySymmetryParams;
+        if (structure) {
+            params = AssemblySymmetryProvider.getParams(structure);
+        } else {
+            params = AssemblySymmetryProvider.defaultParams;
+        }
+        return params;
+    }
+
+    /** Get parameter values currently applied in `AssemblySymmetryProvider` */
+    getRealValues(): AssemblySymmetryProps {
+        const structure = this.getPivotStructure()?.cell.obj?.data;
+        if (structure) {
+            return AssemblySymmetryProvider.props(structure);
+        } else {
+            return { ...PD.getDefaultValues(AssemblySymmetryProvider.defaultParams), symmetryIndex: -1 };
+        }
+    }
+
+    /** Return `true` if an `AssemblySymmetry3D` node existing in the   */
+    hasAssemblySymmetry3D(): boolean {
+        const struct = this.getPivotStructure();
+        const state = struct?.cell.parent;
+        return state !== undefined && !!StateSelection.findTagInSubtree(state.tree, struct!.cell.transform.ref, AssemblySymmetry.Tag.Representation);
+    }
+
+    /** Run changes needed to set visibility on or off, and set UI accordingly */
+    async apply(applied: boolean) {
+        if (applied) {
+            if (this.hasAssemblySymmetry3D()) {
+                await this.changeParamValues({ ...this.state.values, on: true });
+            } else {
+                await this.initSymmetry();
+            }
+            this.setState(old => ({ values: { ...old.values, on: true } }));
+        } else {
+            if (this.hasAssemblySymmetry3D()) {
+                await this.changeParamValues({ ...this.state.values, on: false });
+            } else {
+                // no action needed
+            }
+            this.setState(old => ({ values: { ...old.values, on: false } }));
+        }
+    }
+
+    /** Run changes needed to change parameter values, and set UI accordingly*/
+    async changeParamValues(values: SymmetryParamValues) {
+        const struct = this.getPivotStructure();
+        if (!struct) return;
+        const currValues = this.getRealValues();
+        const newValues = { ...currValues, symmetryIndex: values.on ? values.symmetryIndex : -1 };
+
+        if (struct.properties) {
+            const b = this.plugin.state.data.build();
+            b.to(struct.properties.cell).update(old => {
+                old.properties[AssemblySymmetryProvider.descriptor.name] = newValues;
+            });
+            await b.commit();
+        } else {
+            const pd = this.plugin.customStructureProperties.getParams(struct.cell.obj?.data);
+            const params = PD.getDefaultValues(pd);
+            params.properties[AssemblySymmetryProvider.descriptor.name] = newValues;
+            await this.plugin.builders.structure.insertStructureProperties(struct.cell, params);
+        }
+        if (!values.on) { // if values.on, parameters will be updated via subscription
+            this.setState({ values });
+        }
+    }
+
+    /** Try to retrieve symmetry data and create `AssemblySymmetry3D` representation */
+    async initSymmetry(initialSymmetryIndex?: number) {
+        await Task.create('Initialize Assembly Symmetry', async ctx => {
+            const struct = this.getPivotStructure();
+            const data = struct?.cell.obj?.data;
+            if (!data) return;
+            try {
+                const propCtx = { runtime: ctx, assetManager: this.plugin.managers.asset };
+
+                const config = getRCSBAssemblySymmetryConfig(this.plugin);
+                const symmetryDataProps: AssemblySymmetryDataProps = {
+                    serverType: config.DefaultServerType,
+                    serverUrl: config.DefaultServerUrl,
+                };
+                await AssemblySymmetryDataProvider.attach(propCtx, data, symmetryDataProps);
+
+                const assemblySymmetryData = AssemblySymmetryDataProvider.get(data).value;
+                const symmetryIndex = initialSymmetryIndex ?? (assemblySymmetryData ? AssemblySymmetry.firstNonC1(assemblySymmetryData) : -1);
+                const symmetryProps: AssemblySymmetryProps = { ...symmetryDataProps, symmetryIndex };
+                await AssemblySymmetryProvider.attach(propCtx, data, symmetryProps);
+            } catch (e) {
+                this.plugin.log.error(`Assembly Symmetry: ${e}`);
+                return;
+            }
+            await tryCreateAssemblySymmetry(this.plugin, struct.cell);
+        }).run();
+    }
+
+    render() {
+        const shortTitle = 'Assembly Symmetry' + (this.state.values.noSymmetries ? ' [Not Available]' : '');
+        const title = 'Assembly Symmetry' + (this.state.values.noSymmetries ? ' [Not Available]\nSymmetry information for this assembly is not available' : '');
+        return <>
+             this.apply(applied)}
+                params={this.state.params} values={this.state.values} onChangeValues={v => this.changeParamValues(v)} />
+        ;
+    }
+}
+
+
+class SymmetryAnnotationRowControls extends AnnotationRowControls {
+    renderOptions() {
+        if (this.props.values.noSymmetries) {
+            return 

+                
Symmetry information not available

+            
;
+        }
+        return super.renderOptions();
+    }
+}
+
+/** Get the first loaded structure, if any. */
+function getPivotStructure(plugin: PluginContext): StructureRef | undefined {
+    return plugin.managers.structure.hierarchy.selection.structures[0];
+}
+
+export function isAssemblySymmetryAnnotationApplicable(plugin: PluginContext) {
+    const struct = getPivotStructure(plugin);
+    const isAssembly = struct?.cell.obj?.data?.units[0].conformation.operator.assembly !== undefined;
+    return isAssembly && AssemblySymmetry.isApplicable(struct?.cell.obj?.data);
+    // It would be nice to disable the default `AssemblySymmetry.isApplicable` behavior
+    // (i.e. hiding Assembly Symmetry controls for non-biological assemblies, e.g. 1smv assembly 3)
+    // by `AssemblySymmetry.isApplicable = struct => struct?.units[0].conformation.operator.assembly !== undefined;`
+    // But we cannot easily override the `fetch` function which calls the original `isApplicable`.
+}
diff --git a/frontend/venome-molstar/src/overlay.scss b/frontend/venome-molstar/src/overlay.scss
new file mode 100644
index 00000000..d47fb070
--- /dev/null
+++ b/frontend/venome-molstar/src/overlay.scss
@@ -0,0 +1,46 @@
+.pdbemolstar-overlay {
+    z-index: 1000;
+    position: fixed;
+    top: 0px;
+    bottom: 0px;
+    left: 0px;
+    right: 0px;
+    display: flex;
+    justify-content: center;
+    align-items: center;
+    pointer-events: none;
+}
+
+.pdbemolstar-overlay-box {
+    width: 25%;
+    height: 25%;
+}
+
+svg.pdbe-animated-logo {
+    background-color: transparent;
+    width: 100%;
+    height: 100%;
+    opacity: 80%;
+
+    .path-fg {
+        stroke-dasharray: 1812 250;
+        stroke-dashoffset: -250;
+        animation: dash linear normal infinite;
+        animation-duration: 5s;
+        animation-delay: 1s;
+    }
+    @keyframes dash {
+        0% {
+            stroke-dashoffset: 1812;
+        }
+        80% {
+            stroke-dashoffset: -250;
+        }
+        100% {
+            stroke-dashoffset: -250;
+        }
+    }
+}
+.msp-plugin .msp-viewport-controls-buttons .msp-btn-link-toggle-off {
+	background: black !important;
+}
diff --git a/frontend/venome-molstar/src/web-component/index.js b/frontend/venome-molstar/src/web-component/index.js
new file mode 100644
index 00000000..370a5173
--- /dev/null
+++ b/frontend/venome-molstar/src/web-component/index.js
@@ -0,0 +1,19 @@
+import { LitElement } from 'lit-element';
+
+class PdbeMolstar extends LitElement {
+    connectedCallback() {
+        super.connectedCallback();
+        this.viewerInstance = new PDBeMolstarPlugin();
+        this.initParams = PDBeMolstarPlugin.initParamsFromHtmlAttributes(this);
+        console.log('PdbeMolstar initParams:', this.initParams);
+        this.viewerInstance.render(this, this.initParams);
+    }
+
+    createRenderRoot() {
+        return this;
+    }
+}
+
+export default PdbeMolstar;
+
+customElements.define('pdbe-molstar', PdbeMolstar);
diff --git a/frontend/venome-molstar/tsconfig.json b/frontend/venome-molstar/tsconfig.json
new file mode 100644
index 00000000..4c930ae1
--- /dev/null
+++ b/frontend/venome-molstar/tsconfig.json
@@ -0,0 +1,27 @@
+{
+	"compilerOptions": {
+		"declaration": true,
+		"target": "ESNext",
+		"alwaysStrict": true,
+		"noImplicitAny": true,
+		"noImplicitThis": true,
+		"sourceMap": false,
+		"noUnusedLocals": true,
+		"strictNullChecks": true,
+		"strictFunctionTypes": true,
+		"module": "ESNext",
+		"esModuleInterop": true,
+		"moduleResolution": "node",
+		"importHelpers": true,
+		"noEmitHelpers": true,
+		"allowSyntheticDefaultImports": true,
+		"jsx": "react-jsx",
+		"lib": ["ESNext", "es6", "dom", "esnext.asynciterable", "es2016"],
+		"rootDir": "src/app",
+		"outDir": "lib",
+		"composite": true, // required if we want to set "tsBuildInfoFile"
+		"tsBuildInfoFile": "tsconfig.tsbuildinfo", // default setting would place this file out of the repo directory
+		"baseUrl": "./"
+	},
+	"include": ["src/app"]
+}
diff --git a/frontend/venome-molstar/webpack.config.development.js b/frontend/venome-molstar/webpack.config.development.js
new file mode 100644
index 00000000..d4c054a9
--- /dev/null
+++ b/frontend/venome-molstar/webpack.config.development.js
@@ -0,0 +1,21 @@
+const path = require('path');
+
+const PACKAGE_ROOT_PATH = process.cwd();
+const PACKAGE = require(path.join(PACKAGE_ROOT_PATH, 'package.json'));
+
+function removeKey(obj, key) {
+    if (typeof obj !== 'object') return obj;
+    const result = { ...obj };
+    delete result[key];
+    return result;
+}
+
+const productionConfig = require('./webpack.config.production.js');
+
+const developmentConfig = productionConfig.map(conf => ({
+    ...conf,
+    devtool: 'eval-source-map',
+    entry: removeKey(conf.entry, `${PACKAGE.name}-light`),  // skip building pdbe-molstar-light in dev mode
+}));
+
+module.exports = developmentConfig;
diff --git a/frontend/venome-molstar/webpack.config.production.js b/frontend/venome-molstar/webpack.config.production.js
new file mode 100644
index 00000000..b97d3b94
--- /dev/null
+++ b/frontend/venome-molstar/webpack.config.production.js
@@ -0,0 +1,140 @@
+const path = require("path");
+const webpack = require("webpack");
+const ExtraWatchWebpackPlugin = require("extra-watch-webpack-plugin");
+const MiniCssExtractPlugin = require("mini-css-extract-plugin");
+
+const PACKAGE_ROOT_PATH = process.cwd();
+const PACKAGE = require(path.join(PACKAGE_ROOT_PATH, "package.json"));
+
+/** Webpack configuration for building the plugin bundle (pdbe-molstar-plugin-*.js, pdbe-molstar-*.css).
+ * Also builds the light-skin version (pdbe-molstar-light-plugin-*.js, pdbe-molstar-light-*.css). */
+const molstarConfig = {
+	entry: {
+		[PACKAGE.name]: path.resolve(__dirname, "lib/index.js"),
+		[PACKAGE.name + "-light"]: path.resolve(
+			__dirname,
+			"lib/index(light).js"
+		),
+	},
+	output: {
+		filename: `[name]-plugin-${PACKAGE.version}.js`,
+		path: path.resolve(__dirname, "build/"),
+	},
+	target: "web",
+	module: {
+		rules: [
+			{
+				test: /\.(html|ico)$/,
+				use: [
+					{
+						loader: "file-loader",
+						options: { name: "[name].[ext]" },
+					},
+				],
+			},
+			{
+				test: /\.(s*)css$/,
+				use: [
+					MiniCssExtractPlugin.loader,
+					{ loader: "css-loader", options: { sourceMap: false } },
+					{ loader: "sass-loader", options: { sourceMap: false } },
+				],
+			},
+		],
+	},
+	plugins: [
+		new ExtraWatchWebpackPlugin({
+			files: ["./lib/**/*.scss", "./lib/**/*.html"],
+		}),
+		new webpack.DefinePlugin({
+			"process.env.DEBUG": JSON.stringify(process.env.DEBUG),
+			__MOLSTAR_DEBUG_TIMESTAMP__: webpack.DefinePlugin.runtimeValue(
+				() => `${new Date().valueOf()}`,
+				true
+			),
+		}),
+		new MiniCssExtractPlugin({
+			filename: `[name]-${PACKAGE.version}.css`,
+		}),
+	],
+	resolve: {
+		modules: ["node_modules", path.resolve(__dirname, "lib/")],
+		fallback: {
+			fs: false,
+			crypto: require.resolve("crypto-browserify"),
+			path: require.resolve("path-browserify"),
+			stream: require.resolve("stream-browserify"),
+		},
+		alias: {
+			Molstar: "molstar/lib/lib",
+		},
+	},
+	watchOptions: {
+		aggregateTimeout: 750,
+	},
+};
+
+/** Webpack configuration for building a part of the web-component bundle,
+ * which will be concatenated with the plugin bundle to build the full
+ * web-component bundle (pdbe-molstar-component-*.js) */
+const componentConfig = {
+	entry: path.resolve(__dirname, `src/web-component/index.js`),
+	output: {
+		filename: `${PACKAGE.name}-component-build-${PACKAGE.version}.js`,
+		path: path.resolve(__dirname, "lib/"),
+	},
+	target: "web",
+	resolve: {
+		extensions: [".js"],
+	},
+	externals: {
+		PDBeMolstarPlugin: "PDBeMolstarPlugin",
+	},
+	module: {
+		rules: [
+			{
+				test: /\.css$/,
+				use: [
+					"style-loader",
+					{ loader: "css-loader", options: { importLoaders: 1 } },
+				],
+			},
+			{
+				test: /.(jpg|jpeg|png|svg)$/,
+				use: ["url-loader"],
+			},
+			{
+				test: /\.(js)$/,
+				exclude: function excludeCondition(path) {
+					const nonEs5SyntaxPackages = ["lit-element", "lit-html"];
+
+					// DO transpile these packages
+					if (nonEs5SyntaxPackages.some((pkg) => path.match(pkg))) {
+						return false;
+					}
+
+					// Ignore all other modules that are in node_modules
+					if (path.match(/node_modules\\/)) {
+						return true;
+					} else return false;
+				},
+				use: {
+					loader: "babel-loader",
+					options: {
+						babelrc: false,
+						plugins: [
+							[
+								"@babel/plugin-transform-runtime",
+								{
+									regenerator: true,
+								},
+							],
+						],
+					},
+				},
+			},
+		],
+	},
+};
+
+module.exports = [molstarConfig, componentConfig];