[Chimera-users] question about using swapaa in Chimera

[Elaine Meng]

Hi David,
I forgot to mention that swapaa and SCWRL do not move the backbone.   
Further modeling approaches would be needed if you intend to examine  
conformational changes in the backbone.
Elaine

On Nov 22, 2006, at 2:34 PM, Elaine Meng wrote:

> 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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> Chimera-users at cgl.ucsf.edu
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-----
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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