[Chimera-users] when will NoResidueRotamersError be raised?

Elaine Meng meng at cgl.ucsf.edu
Wed Feb 12 15:50:02 PST 2014


On Feb 12, 2014, at 10:45 AM, Xiao-Bo Li wrote:

> 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

Hi XBL,
The command-line specifications of different models are #0, #1, etc. You can see in the Model Panel (in Favorites menu) which number goes with which structure.  Also, there may be different chains even in one structure.  For example, residue 15 in chain A of model 0 is specified with:

#0:15.A

Please see the atom-specification documentation for more details and several examples.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

That page is also linked to "atom-spec" in the Usage line of the "swapaa" command description.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>

You might also want to take a look at the "getting started - command line" tutorial.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/getting_started.html>

Elaine

P.S. better to send Chimera questions to chimera-users at cgl.ucsf.edu than to only me - thanks!

> 
> 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
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




More information about the Chimera-users mailing list