[Chimera-users] Automatic mutations

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 12 09:37:28 PST 2013


Hi James,
You can use the Chimera command "swapaa" in a script.  Its various options include backbone-dependent rotamer library and basically all of the other functionality of the Rotamers tool.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>

This page outlines how to loop through multiple proteins and execute Chimera commands:
<http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

However, I don't know how you would get the specific residue numbers into the commands.  Another approach would be to generate (possibly with another script) a large Chimera command script that explicitly opens, mutates, saves to file (see the "write" command), and closes each structure.

I hope this helps,
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 Nov 10, 2013, at 11:29 AM, James Starlight <jmsstarlight at gmail.com> wrote:

> Dear Chimera users!
> 
> I'm looking for the possible python script which using the Chimera's source would introduce selected mutations in the defined PDB file and produce PDB output containing such protein with the selected substitution residues. It would be also good if rotamers for mutation residues would be backbone dependent or taken from the existing rotamer libraries (although its not essence because I can run minimization on the mutants)
> 
> Previously I've done such tasks with selectivity mutations via Chimera-GUI rotamer plugin but now I'd like to obtain big series of the mutant of studied protein for further examinations of such mutants by means of molecular dynamics simulation. 
> Could someone provide me with such script if it could not be very complicated to make it? 
> 
> Thanks for help,
> 
> James




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