README.pdbcns Home Page: Richardsons' Laboratory J. Michael Word - 5/2001


Introduction

Perl script to convert atom names for common amino acids and nucleic acid bases from PDB format to CNS (or XPLOR) style atom names.



Installation

You will probably need to change the location of the perl on the first line to reflect your site's configuration.



Use

In addition to changing atom names, the chain id can be mapped to a given segID string and vice versa.

To convert from pdb to cns/xplor:

pdbcns pdbinput=a,sega,b,segb inputfile.pdb > outputfile.cns

To convert from cns/xplor to pdb:

pdbcns cnsinput=sega,a,segb,b inputfile.cns > outputfile.pdb

The mapping "c,ssss..." or "ssss,c..." cannot contain spaces but may contain as many pairs as required, separated by commas; use quotes if neccessary.



e-mail:
J. Michael Word or
David C. Richardson
URL: http://kinemage.biochem.duke.edu
Biochemistry Department
Duke University
Durham, NC USA 27710