[Chimera-users] Choose a specific rotamer

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 11 18:56:26 PST 2011

Hi Elisabeth,
If you just want to replace the current sidechain with one rotamer,  
you could do it with the command "swapaa."  To use criterion (a) least  
clashes, and if a tie (b) most H-bonds, then you would indicate that  
with the "criteria" option.  Example:

swapaa ile #0:33.a criteria ch

Description of "swapaa" and its options:

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

On Feb 11, 2011, at 7:56 AM, Elisabeth Ortega wrote:

> Hi all,
> I'm trying to do a script to display the "best" rotamer of all the  
> rotamers that the funcion getRotamers give to me. I use the function  
> useRotamers to display them but now I only want to display the  
> rotamer with the less number of clashes and the highest number of h- 
> bonds. I know that getRotamers return to us a list with all the  
> rotamers of an aminoacid sorted by probability but I don't have any  
> idea about how display only one of the rotamers. Anyone know how I  
> can do it?
> Thanks in advance.
> Elisabeth

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