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-
-
-
-
-
- PointSuite
-
-
-
- PointSuite
- v.0.7
-
-
-
-
-  |
- PointSuite is a set of
- programs to process macromolecular assemblies described by
- point and helical symmetry operations, with the goals of
- uniform annotation, archiving, and viewing. In order
- to handle coordinates deposited in any orthogonal Cartesian
- frame, the relationships between the deposition, standard
- point and crystal frames are captured as frame
- transformations. For example, the transformation
- required to move icosahedral virus structures from deposited
- position to the standard frame shown at left is calculated
- and recorded. All point symmetries are fully handled;
- helical entries are handled only for non-crystal cases.
-
- Written/compiled by C. Lawson, with thanks to V.J. Reddy
- (TSRI) for sharing PDB2VIPER code (findframe); Tom
- Goddard (UCSF) for Chimera scripts (runchimera.csh);
- Huanwang Yang (RCSB PDB) for importmats and cif-handling
- subroutines.
-
- Please look at this open access article that describes how
- Pointsuite was used to remediate virus structures in the
- PDB: Lawson CL, Dutta SD, Westbrook JD, Henrick K, Berman HM
- (2008) Representation
-of
-viruses
-in
-the
-remediated
-PDB
-
- archive, Acta Cryst D, 874-882.
- |
-
-
- DOWNLOAD: pointsuite0.7.tgz
- (version date: January 15, 2013)
- |
-
-
- Virus Processing Tutorial
- |
-
-
- |
- Installation Instructions Documentation |
-
-
-
- INSTALL/COMPILE/CONFIGURE:
- Type the following commands in the directory where you want to
- install the software.
-
- tar xvzf
- pointsuite0.7.tgz
- cd pointsuite0.7
- make (to compile)
- The package is composed of programs written in C along with
- C-shell-based scripts.
- It has been extensively tested on linux and mac-intel osx
- operating systems.
-
- source
-
- setup.csh
- setup.csh script works for csh/tcsh shell. follow directions to
- set up your environment more permanently.
-
- To make
- full use of the package, the graphics program UCSF Chimera should
- also be installed and in your path.
-
- TEST:
- cd demo
- rundemo.csh 1RUG (runs the 1RUG demo)
- rundemo.csh all (runs all of the demos)
-
- browse the demos to view functionality
- 1RUG: Generate archival cif for icosahedral virus crystal
- structure.
- 1IFD: Generate archival cif for helical virus
- fiber diffraction structure.
-
- 1EI7: Generate archival cif for D17 symmetry particle.
-
- 1CGM: Generate matrix representation for ~900 A length
- helical TMV-like virus.
- 1M4X: Generate matrix representations for complex
- virus particle sub-assemblies.
- IMPORT: Generate BIOMT, CIF from typical
- author-uploaded example input files using importmats.
- Additional
- icosahedral virus examples: 2XD8 (EM), 2W0C, 2VF9, 3N7X
- (X-ray).
- See Virus processing tutorial for more info.
-
-
-
- RELEASE INFO:
- version
- 0.5.8 (12 June 2007) initial stable release
-
- version 0.6 (20 June 2011) minor updates:
- *importmats (from H. Yang) handles additional matrix type
- (xncsrel) from CNS ncs.def.
- *update of scripts automating image generation to work with v.1.4
- Chimera and higher
- *when run without arguments, runpt.csh autoscript now prints brief
- documentation
- *new
- virus processing tutorial
- *additional
- documentation now provided for utilities: importmats, autoscripts,
- multiplymats
- *RCSBvirusimages.csh script to generate set of virus images for
- web display.
-
- version 0.7 (15 January 2013):
- *improved cif parsing subroutines added by H. Yang (cifparse.c).
- *file input reading improvements in importmats, findframe,
- makeassembly
- *findframe single input file with matrices and coordinates can now
- be either PDB or CIF; optional 2nd file in BIOMT format (overrides 1st file matrices)
- *new program cif2pdb creates simple pdb file (matrices, cryst1
- record, coordinates) from cif (H. Yang).
- *simplified scripts, PDB-dependency removed for runpt.csh
- *RCSBvirusimages.csh script handles split entry cases
- (modifications by Ezra Peisach)
-
-
-
PROGRAM
- DOCUMENTATION:
-
-
-
-
- PROGRAM FINDFRAME
- Description
-
- The program FINDFRAME calculates the transformation matrix that
- moves the asymmetric unit of a particle with point symmetry in an
- arbitrary (skew) frame into a defined position within a standard
- point frame. The standard icosahedral
- frame is defined as having the 5-fold axis of the first pentamer
- centered on the vector (x=0,y=1, z=phi), where phi is the
- golden ratio (sqrt(5)+1)/2. This convention is also employed
- by the VIPER database and the is proposed convention of Belnap et.
- al. for cryoEM maps.
-
- FINDFRAME is an extension of the PDB2VIPER
- program from the VIPERdb (Shepherd, et al. (2006) Nucleic Acids
- Res, 34, D386-389) that incorporates the qikfit least-squares
- fitting routine from Bioplib
- (A.C.R. Martin, personal communication). Algorithm steps
- have been added to increase the precision of the calculated
- transformation matrix and to improve uniformity of coordinate
- placement relative to the standard icosahedron symmetry axes (see
- description below).
-
-
- Use
- on the command line:
-
- >findframe
-
- infile.pdb/cif
-
- The input file is expected to have all needed transformation
- matrices to build the icosahedral or other point group particle
- AND coordinates for the asymmetric unit . PDB
-
- matrices can be given either as REMARK 350 BIOMT or MTRIX records;
- in cif the matrices are given in _pdbx_struct_oper_list and must
- have type of "general operation", "point symmetry operation" or
- "helical symmetry operation". One of
- the transformation matrices must be the identity element. Optional:
- a second file can be provided with BIOMT records; in this case the
- matrices in the 2nd file override any present in the first file.
-
-
- Algorithm
-
- modifications to PDB2VIPER (from V.J. Reddy)
- are in italics
-
- - The approximate center of mass
- ("reference atom") is calculated from Calpha and P atom
- positions.
- - The set of matrix translation
- vectors are averaged to find the center of the particle relative
- to the coordinate origin. The reference atom is translated by
- the negated particle center and transformed into a unit vector.
- - The rotation matrices are
- decomposed into angle-axis form. The angle identifies the fold
- of the rotation (e.g. 72 or 144 degrees for 5-fold, 120 degrees
- for 3-fold). The axis vector defines the symmetry orientation.
-
- - The rotations are
- checked against their corresponding translation vectors to
- identify helical symmetry. If helical symmetry is
- detected, then the program attempts to identify all of the
- helical parameters from the matrices, and will print this info
- to findframe.cif and will then exit (currently, program only
- handles cases with helical axis on z).
-
- - If no helical operations are
- detected, then point symmetry is assumed and the program
- analyses the matrices to deduce the correct symmetry. The
- remainder of the algorithm description explains what happens for
- icosahedral symmetry, but essentially similar steps are taken
- for the other symmetries (circular,dihedral, tetrahedral,
- octahedral).
-
- - The five-fold, two-fold, and
- three-fold closest to the reference atom are identified.
-
- - The position of the reference
- atom unit vector relative to the 5-3 and 5-2 planes is
- evaluated. If the reference atom
- is closer to the 5-3 plane, the icosahedral a.u. is classified
- as "3-fold centric" and the closest 3-fold is selected for
- alignment in the next step. If
- the reference atom is closer to the 5-2 plane (typically true
- for T=3 viruses), the icosahedral a.u. is classified as
- "2-fold centric" and the 3-fold to the right of the 2-fold is
- selected for alignment.
- - The input structure's 5-fold
- and 3-fold are aligned onto the standard icosahedral frame
- 5-fold (0, 1, phi) and 3-fold (phi/3,
- 0, (2*phi+1)/3)
-axes
-in
-two
-steps.
-First,
-the
-rotation
-that
-
- superimposes the normal to the 5-3 plane of the deposited
- structure onto the normal to the 5-3 plane of the standard
- icosahedron 5-fold is found and applied. Second,
- the rotation around the aligned normals that superimposes the
- pair of 5-fold axes is found and applied. The
- initial estimate for the findframe matrix is based on these two
- rotation matrices and the translation vector determined in step
- 2.
- - Fitting/refinement: The
- input-supplied transformations are applied to the reference
- atom, and the resulting 60-atom constellation is transformed
- to the icosahedral frame by the initial findframe matrix. A reference set is generated by
- applying icosahedral symmetry operations to the 1st transformed atom.
- The 60-atom constellation is fitted to the icosahedral
- reference set, yielding a correction matrix. The final
- findframe matrix is generated by applying the correction
- matrix to the initial estimate. This
- step is particularly helpful for cases where the input
- file-supplied matrices have either low precision or small
- random errors, as these errors tend to be averaged out.
-
-
-
- Output
- General info about the calculation is provided
- in the standard output. On successful execution a cif file
- with symmetry and frame transformation info is also output
- called *findframe.cif*.
-
-
-
-
-
- PROGRAM POINTMATS
-
- Description
- Generates sets of transformations corresponding
- to point or helical symmetry provided in the input cif file (
- _pdbx_point_symmetry, _pdbx_helical_symmetry).
-
- If the input cif contains a "transform to point frame"
- matrix with _pdbx_struct_oper_list.id labelled 'P' (or a
- "transform to helical frame" matrix is given with
- _pdbx_struct_oper_list.id labelled 'H'), the matrix set is
- transformed such that it can be applied to coordinates away from
- the standard frame, e.g., [P-inv][std mats][P]. Use
- pointmats to obtain simple matrix set output files for
- point/helical symmetry operations; use makeassembly if you need
- full assembly and asymmetric unit descriptions.
-
-
-
- Use
- Commonly used after findframe, e.g.:
-
- pointmats findframe.cif
-
- will generate point or helical matrix set with standard order in the
- same frame as the matrices analysed by findframe.
-
-
-
- Output
- General info about the calculation is provided
- in the standard output; the matrices are written in CIF format to
- pointmats.cif and in BIOMT format to pointmats.biomt. Point
- symmetry operations follow a standard order. Helical
- symmetry operations are given as a continuous run centered around
- the identity element.
-
-
-
- PROGRAM
- MAKEASSEMBLY
-
- Description
- The set of point symmetry operations
- corresponding to a crystal asymmetric unit is identified, given
- the following input: CIF file with unitcell, spacegroup, asym_id,
- entity_id records , cif with _pdbx_point _symmetry or
- _pdbx_helical_symmetry and _pdbx_struct_oper_list with frame
- transformations (P for "transform to point frame" ; H for
- "transform to helical frame"; X0, X1, etc. for "transform to
- crystal frame"). The program will analyse the structure for
- ncs only if at least one "transform to crystal frame" matrix is
- given (X0) (this will frequently be the identity matrix). FROM
- v.5.7 onward, makeassembly outputs asym_id lists instead of
- author_asym id list.
-
- Use
- Crystal frame transformations are optional (e.g., for EM
- structures):
-
- >makeassembly uc_symtry_scale_.cif
- symm_transforms.cif
-
- Algorithm
-
-
- - For each independent particle
- position n defined by Xn, the full standard set of matrices for
- the point symmetry given in 2ptmat , **to be applied to
- coordinates transformed by X0**, are calculated as
- [Xn][2ptmat^-1][StdMats][2ptmat][X0^-1].
- - The crystal symmetry matrices in
- their fractional forms are transformed by the translation part
- of [Xn^-1]. This moves the
- origin of the crystal lattice to the particle center. Crystal symmetry operators
- passing through the particle center are identified by lack of
- fractional translation components (full unit translations are
- reset to 0).
- - Each crystal symmetry rotation
- identified in step 2 is applied to each of the rotations
- calculated in step 1. Symmetry-transformed
-
- rotations that are identical to untransformed rotations with
- lower index are eliminated from the list of ncs operations.
-
- Output
- General info about the calculation for each
- independent particle is provided in the standard output; an
- archival cif (assembly.cif) is generated, as well as biomt records
- for the full assembly (assembly.biomt). For crystal
- structures a bare-bones crystal frame pdb file is created that can
- be input to sfcheck or packing programs (assembly_xframe.pdb), and
- ncs records are generated (assembly.ncs).
-
-
- Utilities
-
- importmats:
-
- call with
- >importmats matfile
-
- Reads in and automatically detects a wide variety of matrix
- record formats including BIOMT, MTRIX, ncs.def.
- Outputs file with BIOMT records named "importmats.biomt" and file
- with CIF _pdbx_struct_assembly_oper records named "importmats.cif"
- Use importmats to prepare author.biomt file for runpt.csh
-
- autoscripts:
-
- (1) make assembly cif records:
- runpt.csh (prints out instructions for preparing script arguments)
- runpt.csh entry.cif author-upload-matfile (noncrystal and most
- crystal structures)
- runpt.csh entry.cif author-upload-matfile X0.mat (crystal out of
- frame or multiple positions in crystal a.u.)
- (2) makes pictures of files generated by runpt.csh:
- runchimera.csh
- (3) makes pictures from PDB file ready for release:
- RCSBvirusimages.csh file1.pdb
- RCSBvirusimages-split.csh file1.pdb file2.pdb file3.pdb ...
- (combined images for split entries)
-
- frac2orth:
- call with
- >frac2orth
-
- Interactively requests 6 parameters of unit cell and a position in
- fractional coordinates, outputs orthogonalization matrix,
- fractionalization matrix, and corresponding Cartesian coordinates of
- input position. Useful if the translation part of a skew
- matrix is provided in fractional coordinates.
-
- movecoords:
- call with
- >movecoords file1.pdb file2.matrix
-
- reads in pdb file and 4x4 matrix file, writes out "new.pdb" file
- that is identical to input file except with x,y,z coordinates
- tranformed by the 4x4 matrix.
-
- multiplymats:
-
- Performs complex matrix multiplications
- given a list of matrices in cif format and a string defining the
- desired multiplication.
- String can include numerical ranges and recursion.
- examples:
- "(1-2)(3,5,7-9)" creates the set of matrices 1*3, 1*5,
- 1*7, 1*8, 1*9, 2*3, 2*5, 2*7, 2*8, 2*9
- "(1)(2,(2)(2),(2)(2)(2))" creates the set of matrices 1*2,
- 1*2*2, 1*2*2*2
-
- call with
- >multiplymats <pointmats or assembly cif> <matrix
- multiplication string in double quotes>
-
- example (1m4x):
- multiplymats 1m4x.cif "(1-60)(61-88)"
- number of matrices read: 89
- Matrix multiplication expression to be parsed: (1-60)(61-88)
-
- result:
-
- 1*61
- 1*62
- 1*63
- 1*64
- 1*65
- 1*66
- 1*67
- 1*68
- 1*69
- 1*70
- 1*71
- ...
- 60*85
- 60*86
- 60*87
- 60*88
- Writing 1680 matrices to *mult.cif*
- Writing 1680 matrices to *mult.biomt*
-
-
-
- last modified 14 Jan 2013
- C. Lawson
-
-
-
diff --git a/html/multiparticle.html b/html/multiparticle.html
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-
-
-
-
- multiparticle
-
-
-
- Current PDB entries with 2 or more particle positions per crystal
- a.u. (11 as of Jan 2013, all viruses except one):
-
-
-
-
-
- id
- |
- release year
- |
- PI
- |
- notes
- |
-
-
- | 1AL0 |
- 1998
- |
- Rossmann
- |
- 2
- partial particles/a.u. |
-
-
- | 1C8H |
- 2000
- |
- Rossmann |
-
- |
-
-
- | 1CD3 |
- 1999
- |
- Rossmann |
-
- |
-
-
- | 1DWN |
- 2000
- |
- Liljas
- |
-
- |
-
-
- | 1LP3 |
- 2002
- |
- Chapman
- |
- only
- example with 3 particles/a.u. |
-
-
- | 2GTL |
- 2006
- |
- Royer
- |
- only
- non-virus example (D6 earthworm hemoglobin)
- |
-
-
- | 2VF9 |
- 2008
- |
- Liljas
- |
-
- |
-
-
- 2XGK
- |
- 2011
- |
- Rossmann |
-
- |
-
-
- | 3CJI |
- 2008
- |
- Reddy
- |
-
- |
-
-
- | 3DPR |
- 2009
- |
- Verdaguer
- |
-
- |
-
-
- 4AED
- |
- 2012
- |
- Rossmann |
-
- |
-
-
-
-
-
-
diff --git a/html/virusproc-tutorial.html b/html/virusproc-tutorial.html
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-
-
-
-
- pointsuite tutorial
-
-
- PROCESSING VIRUSES USING
- POINTSUITE
-
-
- TWO
- STEPS:
-
-
- - USE runpt.csh SCRIPT TO CREATE BIOLOGICAL
- ASSEMBLY CIF
-
- - USE runchimera.csh TO CHECK
- RESULT
-
-
-
- CREATING
-BIOMT/ASSEMBLY.CIF
-USING
-
-
- runpt.csh
- Input files (and
- what is read from them):
-
- <cif> : chain id list, crystal symmetry/unit
- cell info, coordinates
-
- <author matrix file>: author-provided matrix file
- in any format that can be read by importmats.
- The file
- must define ONE particle only, and must include one identity
- matrix.
- If needed
- can manually convert author-provided format file using "importmats
- <filename>"
-
- <ident or matfile>
- List of
- transformations required to place deposited coordinates into all
- particle positions in crystal
- ident tag signifies
- coordinates already in crystal frame (shorthand for identity
- matrix)
- matfile contains elements for
- one non-identity matrix: example
- #
- ident + matfiles = # of particles positioned in the crystal
- asymmetric unit
- if
- coordinates deposited in NONCRYSTAL frame, need to get at least
- one matrix from depositor
-
-
- Command:
-
- MOST CASES: runpt.csh <cif> <biomt>
-
- COMPLEX X-ray: runpt.csh <cif> <biomt>
- <matfile1> <matfile2> <matfile3>
- (either
- out-of-frame coordinates or multiple positions of point symmetry
- particle in the crystal a.u. )
-
-
- Output :
-
- On successful run command line will state "successful completion
- of script: check assembly.cif"
-
- runpt.log: log file with
- processing details.
-
- assembly.cif and assembly.biomt: files containing BIOMT
- information. CIF also describes how to move virus particle to
- standard icos frame, and how to generate standard icos virus
- subassemblies. PTSUITE BIOMT = author matrices adjusted
- for (1) standard icos. order; (2) exact icosahedral symmetry.
-
-
- build_auth.pdb, build_wwpdb.pdb : file
- with author-provided BIOMT + coordinates and file with
- final BIOMT + coordinates. These can be inspected/compared
- in chimera using pointsuite "runchimera.csh" script, or manually
- by applying Chimera multiscale model/biomt option.
-
- assembly.ncs (X-ray only): these files have
- pointsuite-calculated NCS. Useful to compare/check
- against author-provided NCS, but DO NOT INCLUDE IN PROCESSED
- ENTRY UNLESS AUTHOR NCS is determined to not be
- available. SEE BELOW.
-
-
-
-
-
- NCS/MTRIX
-
-
- RECORDS
- FOR ALL X-RAY
- ENTRIES, NCS/MTRIX records are handled separately from
- above. These matrices should be obtained from the deposited
- coordinate file and values placed in MTRIX (_struct_ncs_oper) records for SF
- validation. Because pointsuite-generated ncs are based on exact
- point symmetry operations, they can differ from
- author-refined values. Currently there is no specific
- pointsuite module for this.
-
-
-
-
- C. Lawson updated
- January 14, 2013
-
-
-
-
-
