Chandan,
 
PyMOL's mutagenesis wizard is purely geometric, and is intended to offer up Dunbrack rotamers as per:
 
http://dunbrack.fccc.edu/bbdep/bbdepdownload.php
 
Cheers,
Warren

From: Chandan Choudhury [mailto:iitdckc@gmail.com]
Sent: Wednesday, September 09, 2009 5:01 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] help about mutation


I am querious to know on what mathematical basis does the software mutates the amino acids.
--
Chandan kumar Choudhury
NCL, Pune
INDIA