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)
James
2013/11/11 Ron Jacak <ron.ja...@gmail.com>
> Hi James,
>
> SCWRL is a good suggestion. You may also want to take a look at Rosetta (
> https://www.rosettacommons.org/). 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 (
> http://rosettadesign.med.unc.edu/), since the installation and
> compilation can take some time.
>
> Best,
> -Ron
>
> 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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