Fixmultocc

Copyright 2001 Stephen Graham

Synopsis

Small python program to reset the occurances of multiple conformers to 1/n where n is the number of conformers present in the pdb file.  Designed to be used after alternate.inp which has the annoying habit of dividing all occupancies of multiple conformers by the afforementioned n.

Usage

$ fixmultocc <pdb_file> <chain_prefix> <# of conformers>

where <pdb_file> is the pdb file you are interested in, <chain_prefix> is the prefix used to denote multiple conformers (by default AC in CNS) and <# of conformers> is the number of multiple conformers present.  Output is directed to stdout.  Example:

$ fixmultocc alternate.pdb AC 2 > alternate_goodocc.pdb

Known Bugs / Workarounds

Currently works only when the PDB file has a fixed number of multiple conformers for each prefix.  The easiest way to work around this is to have separate alternate.inp files for each number of multiple conformers, and give each set a different prefix.  Example:

alternate_2.inp for residues with 2 conformers (prefix = AA)
alternate_3.inp for residues with 3 conformers (prefix = AB)

then just run fixmultocc twice

$fixmultocc alternate.pdb AA 2 > tmp
$fixmultocc tmp AB 3 > alternate_goodocc.pdb

Download

Latest version last modified 17/7/01 and available here.