Fixmultcoords

Copyright 2001 Stephen Graham

Synopsis

Small python program intended to be run after alternate.inp which restores co-ordinates of alternate conformers.  This is required as alternate.inp generates the mtf file for multiple conformers and appends these conformers to the bottom of your pdb file, but it resets their co-ordinates to that of the first conformer (the one present in the pdb file that goes through generate.inp).

Usage

$ fixmultcoords <main.pdb> <alt_conformer.pdb>

where <main.pdb> is your main pdb file (the one which went through generate.inp) and <alt_conformer.pdb> is a file containing the co-ordinates of your multiple conformers.  Output is directed to stdout.  This program is most effective when used in conjunction with Gerard's aconio program which splits a CNS pdb file with multiple conformations into several files (one for the main conformer and additional files for the alternates).  These files may then be loaded into O as different molecules.  As such, when finished with manual refinement one needs only sam_atom_out a few different files (one for the main conformer and one or more for the alternate conformers) in order to be ready for CNS refinement (well, you still have to split the main file for generate, but this is still easier than manually re-typing co-ordinates!).  Example:

$ fixmultocc main.pdb alternate_conf.pdb > main_correct_coords.pdb

Known Bugs

Currently only works when you have two conformers, and their names are AC1 and AC2.  If anyone needs I could extend the program to cope with more than two confs and different alternate conformer segids - I have just not been bothered as of yet.

Download

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