[Chimera-users] when will NoResidueRotamersError be raised?

Xiao-Bo Li x22li at cs.uwaterloo.ca
Wed Feb 12 10:45:55 PST 2014


Hi Elaine,

If I have two different protein structure open (not models), how can I 
reference one of them using the commandline?  I want to mutate one of 
them not the other.

Best,

XBL

On 02/12/14 13:07, Elaine Meng wrote:
> Hi XBL,
> Do you really need to use python?  You can just use the Chimera command "swapaa" to mutate between any of the standard amino acid types.  It does the hard work of calling the right code for you, the same code as the Rotamers tool.  Here is more information on that command and its options:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>
>
> Most users prefer to use the command and/or graphical interfaces, when possible.  These are more thoroughly documented than the code.  (If you are doing a lot with the python code, it might be a question for chimera-dev at cgl.ucsf.edu instead of chimera-users at cgl.ucsf.edu)
> Best,
> 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 Feb 12, 2014, at 5:45 AM, Xiao-Bo Li wrote:
>
>> I would like to mutate one residue to another.  So far, the only way I found is to use the rotamers of the other residues on the original.
>>
>> I'm using chimera's python script.  I would like to know if the NoResidueRotamersError will only be raised for residues that don't have rotamers like GLY.
>>
>> If not, then how can I replace the amino acid residue that I want to mutate?  I am using the "getRotamers" function, which returns this error.
>>
>>
>>
>> XBL
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



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