Re: [PyMOL] mutagenesis script

[Andreas H. <ah...@bi...>]

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
01307 Dresden, Germany

Phone: +49 351 463 40063
EMail: ah...@bi...