Hi Martin,
you can get hints about how to script wizard functions if you log your
activities while running the wizard.
A python script (mutate.py) that makes use of the mutagenesis wizard
could look like this:
## run through pymol, eg.:
## pymol -qc mutate.py 1god A/94/ ASN
from pymol import cmd
import sys
pdb, selection, mutant = sys.argv[-3:]
cmd.wizard("mutagenesis")
cmd.fetch(pdb)
cmd.refresh_wizard()
cmd.get_wizard().do_select(selection)
cmd.get_wizard().set_mode(mutant)
cmd.get_wizard().apply()
cmd.set_wizard()
cmd.save("%s_m.pdb" % pdb, pdb)
This is pretty no-frills, as no rotamer stuff is taken into account.
I wrote it in Python, because it allows to parameterize from command
line, you can add loops easily etc.
Beware, the error message you get is because pymol unsuccessfully tries
to open the command line arguments as files.
Hope that helps.
Best regards,
Andreas
Martin Höfling wrote:
Hi there,
does anybody of you has an idea, if the mutagenesis stuff is available for use
inside scripts too?
I wanna load a pdb, mutate a resid and save the resulting pdb via commandline.
The only thing I found was modifying atoms, when I searched via "help" and
also checked the wiki, i hope that I didn't miss sth.
Cheers
Martin
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Andreas Henschel
Bioinformatics Group
TU Dresden
Tatzberg 47-51
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Phone: +49 351 463 40063
EMail: [email protected]
