James,
What you want is something like SCWRL from the Dunbrack Lab. Minimization will
not get a sc out of an incorrect rotomer, and will not repack the protein in
the case of multiple mutations, SCWRL will. It can be downloaded for academic
use from here:
http://dunbrack.fccc.edu/SCWRL3.php/
There is also a web server if you only need to do this a few times.
http://www1.jcsg.org/prod/scripts/scwrl/serve.cgi
Best regards,
Mark
Mark Andrew White, Ph.D.
Associate Professor of Biochemistry & Molecular Biology,
Manager, SCSB X-ray Crystallography Laboratory
UTMB, Galveston, TX
409.747.4747
http://xray.utmb.edu
________________________________
From: James Starlight [[email protected]]
Sent: Sunday, November 10, 2013 1:27 PM
To: pymol-users
Subject: [PyMOL] Automatic mutation introduction
Dear PyMol users!
I'm looking for the possible python script which using the pymol 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 pymol-GUI 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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