Thanks! I'll try all pf this possibilities- especially I'm interesting in Modeller because its 1) python-based and 2) produce suitable input for MD (fixing side-chains or loops missed in the X-ray input data)


2013/11/11 Ron Jacak <>
Hi James,

SCWRL is a good suggestion.  You may also want to take a look at Rosetta (  It uses the Dunbrack 2010 rotamer library but also includes a dozen or so other score terms to aid in repacking and minimizing mutations.  There's also a server (, since the installation and compilation can take some time.


On Nov 10, 2013, at 2:27 PM, James Starlight wrote:

> 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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