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PointSuite - v.0.7
-

- - - - - - - - - - - - - - - - -
labelled icosahedronPointSuite 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

-
    -
  1. The approximate center of mass - ("reference atom") is calculated from Calpha and P atom - positions.
    2. -
  2. 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.
    3. -
  3. 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. 
    -
    4. -
  4. 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).
    -
    5. -
  5. 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).
    -
    6. -
  6. The five-fold, two-fold, and - three-fold closest to the reference atom are identified.
    -
    7. -
  7. 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.
    8. -
  8. 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.
    9. -
  9. 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.
    10. -
-
- -

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
-

-
    -
  1. 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].
    2. -
  2. 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).
    3. -
  3. 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.
    4. -
-

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 deleted file mode 100644 index 4accd72..0000000 --- a/html/multiparticle.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - - 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
-
1AL01998
- 		Rossmann
- 		2 - partial particles/a.u.
1C8H2000
- 		Rossmann
-
1CD31999
- 		Rossmann
-
1DWN2000
- 		Liljas
-
-
1LP32002
- 		Chapman
- 		only - example with 3 particles/a.u.
2GTL2006
- 		Royer
- 		only - non-virus example (D6 earthworm hemoglobin)
-
2VF92008
- 		Liljas
-
-
2XGK
- 		2011
- 		Rossmann
-
3CJI2008
- 		Reddy
-
-
3DPR2009
- 		Verdaguer
-
-
4AED
- 		2012
- 		Rossmann
-
-
- - diff --git a/html/virusproc-tutorial.html b/html/virusproc-tutorial.html deleted file mode 100644 index f101b06..0000000 --- a/html/virusproc-tutorial.html +++ /dev/null @@ -1,290 +0,0 @@ - - - - - pointsuite tutorial - - -

PROCESSING VIRUSES USING - POINTSUITE
-

-
-

TWO - STEPS: 
-

-
    -
  1. USE runpt.csh SCRIPT TO CREATE BIOLOGICAL - ASSEMBLY CIF
    -
    2. -
  2. USE runchimera.csh TO CHECK - RESULT
    -
    3. -
-
-

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.
-
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
AUTHOR vs PTSUITE
- runchimera.csh
- 		EXAMPLE
- 		Procedure
- 		result
-
2xd8 - image2xd8 image
- (A) 2XD8 - -- EM virus
-
- runpt.csh 2xd8.cif 2xd8.biomt
- runchimera.csh
-
- runpt.log assembly.cif
-
-
2w0c - image2w0c image
- (B) 2W0C - -- X-ray 1 particle/crystal au
- coordinates in crystal frame (usually true)
-
-
- runpt.csh  2w0c.cif - 2w0c.biomt
- runchimera.csh
-
-
- runpt.log assembly.cif
-
2vf9 - image2vf9 image
- (C) 2VF9 - -- X-ray 2 - particles/crystal au 
- coordinates in crystal frame
-
- runpt.csh  2vf9.cif - 2vf9.biomt1* - ident  x1.mat**
- *(1st 60 BIOMT matrices in current public file)
- **(61st BIOMT matrix in current public file)
- runchimera.csh
-
- runpt.log assembly.cif
-
3n7x - image3n7x image
- (D) 3N7X - -- X-ray 1/2 particle/crystal au
- coordinates in NONCRYSTAL frame
-
-
- runpt.csh  3n7x.cif - 3n7x.biomt  x0.mat
- runchimera.csh
-
-
- runpt.log assembly.cif
-
-
-

-

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
-
-
-
- -