Re: [PyMOL] mutation

[Warren D. <wa...@de...>]

Chandan,

 

Apologies, but PyMOL can only mutate the standard 20 amino acids.  

 

Note that you have asked that second question before:

 

http://www.mail-archive.com/pym...@li.../msg07211.h
tml

 

Again, there is no special "theory" behind PyMOL's mutagenesis wizard:
the intent behind the implementation is to simply provide geometric
substitution as per the Dunbrack rotomer library.  No optimization is
performed.  Please follow the link below for a list of related
references covering the Dunbrack library and sidechain rotamer theory:

 

http://dunbrack.fccc.edu/bbdep/bbdepdownload.php

 

Cheers,

Warren

 

________________________________

From: Chandan Choudhury [mailto:ii...@gm...] 
Sent: Tuesday, September 22, 2009 9:28 PM
To: pym...@li...
Subject: [PyMOL] mutation

 

Hello all!!

I am required to mutate one of the atom of a protein (pdb file) with
some groups of atoms. Pymol features us to mutate a residu with another
amino acid, but I cannot mutate an atom with some other group that are
not amino acids. So, how can I do it. Please help.

Also I want to know the theory behind the mutation of residue done by
pymol.
Thanks

Chandan
-- 
Chandan kumar Choudhury
NCL, Pune
INDIA