I got tired of having to add chain names, renumber residues in chains and removing the .B99990001 for MODELLER output structures. So I created a small script to do it for me.
########################################################################
FILE: RenameRenumber
PURPOSE: Rename chains and renumber residues. Also removes the MODELLER file extension.
If launched from within DS using a structure in a 3D window, the chains will be named A and B by default
(in that order) and residues in each chain will be renumbered from 1.
If the script window is opened, the user may specify the name and starting numbers using the Arguments window.
Characters will be taken as chain names and numerals as residue starting number.
Open script in Script Window, write e.g. the next line in the Argument window and right-click 'Run':
> A 1 B 234
If launched from the command line it will take the first argument as the protein structure input file.
Chains will be named A and B as standard, from 1. If additional input is given characters will be taken as chain name
and numerals as residue starting number.
"C:\Program Files\Accelrys\Discovery Studio 2.1\bin\perl.bat" "My Documents\RenameRenumber.pl" file.pdb A 1 B 234
Additionally, renamed chains without specified starting positions will start from 1.
The script does not renumber any more chains than there are chain names.
Author: Andreas Arnell @ Lonza APT
Date: 12/02/2009
Discovery Studio is Copyright (C) 2007 by Accelrys Software Inc., All rights reserved.
The author is not affiliated with Accelrys Inc in any way and takes no responsibilty for any use,
misuse, malfunctions, bugs or results of any thereof relating to this script.
Use at your own risk.
Enjoy!
/Andreas
