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.

(If using the shell/Awk version, the format for the directionality and mapping flags described below is either "pdbinput=a,sega,b,segb" or "cnsinput=sega,a,segb,b".)



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 -pm a,sega,b,segb inputfile.pdb > outputfile.cns

To convert from cns/xplor to pdb:

pdbcns -cm 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. If there is no chain id in the PDB file, you can specificy that with an underscore (e.g., "-pm _,sega").
If you do not want to add segIDs, just use a "-p" flag with no mapping parameters.



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