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.

AUTHOR vs PTSUITE runchimera.csh	EXAMPLE	Procedure	result
	(A) 2XD8 -- EM virus	runpt.csh 2xd8.cif 2xd8.biomt runchimera.csh	runpt.log assembly.cif
	(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
	(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
	(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