[Chimera-users] multiple mutations

[Hernán Costa]

Hi Elaine, me again
Is this possible view around 4, 6, 8, etc angstroms (user defined) all residues or atoms around one residue or atom previously selected?
Thanks
 
Hernán
 
 
 
 


--- El vie, 3/18/11, Elaine Meng <meng at cgl.ucsf.edu> escribió:


De: Elaine Meng <meng at cgl.ucsf.edu>
Asunto: Re: [Chimera-users] multiple mutations
A: "Hernán Costa" <hcosta_1999 at yahoo.com>
Cc: chimera-users at cgl.ucsf.edu
Fecha: viernes, 18 de marzo de 2011, 02:56 am


Hi Hernan,
If you use the Rotamers tool (or command "swapaa") to mutate amino acids, only  one change is done at a time.   If mutating a very few residues that are near each other, you could still use Rotamers to change one at a time and see if the results for each residue are reasonable, based on clashes and H-bonds.  Since the output conformation of the sidechain is from a rotamer library, the conformation itself will be reasonable, but it may not interact well with its local environment.

However...
The Rotamers tool (or command "swapaa") in Chimera will NOT combinatorially search the rotamers of multiple interacting side chains to find the best possible set.  To do that, you would need to use a different program, such as SCWRL.

Rotamers details:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html>
The swapaa command:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>
SCWRL:
<http://dunbrack.fccc.edu/scwrl4/>

I hope this makes sense,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 17, 2011, at 8:29 AM, Hernán Costa wrote:

> Hi I need to obtain mutation on differents sites on a protein but i can´t. How can I create a mutual mutation an know if the rotamer selected is Ok?
> Thanks
> Hernán Costa
> 

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