[Chimera-users] question about using swapaa in Chimera

[Elaine Meng]

Hi David,
The swapaa command needs the 3-letter residue name, for example

swapaa pro #0:24

It should be noted, however, that swapaa is a fairly crude way of  
looking at mutations.  It will not adjust the positions of atoms in  
other residues, and the coordinates of the one you just "swapped" are  
not necessarily reasonable.  Situations where I would use "swapaa"  
are when I plan to rotate the sidechain of the new residue myself.

In the future, we plan to have Chimera know about reasonable  
conformations of amino acid side chains (rotamers) and possibly try  
to use a conformation that does not clash with the other atoms.  For  
now, you can look at clashes with the Find Contacts/Clashes tool  
(under Tools... Structure Analysis).

Apart from Chimera, you might want to take a look at the program  
SCWRL.  I believe it is free for noncommercial use from the Dunbrack  
group:

http://dunbrack.fccc.edu/SCWRL3.php

SCWRL isn't graphical, but you could view the output in Chimera.
Elaine

On Nov 22, 2006, at 10:57 AM, Ng, David ((NIH/NCI)) [E] wrote:

> Hi,
>
>
>
> I’m currently learning to use Chimera. I wish to look at specific  
> amino acid mutations in CDKN2A for effects in conformational  
> changes and changes in protein interactions with known partners.
>
>
>
> When I type the command “swapaa P #0:24” in chimera to mutate  
> arginine 24 to proline in CDKN2A, I get an error message that says  
> “Value error: No connectivity template for residue P”
>
>
>
> Can you help me with this issue? Thanks.
>
>
>
>
>
> David Ng, M.D.
>
> Staff Clinician
>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




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