[PyMOL] Trouble with mutagenesis script

[Dan P. <dan...@gm...>]

Dear all,

I'm trying to write a script to perform mutagenesis on a pdb
coordinate file via the command line. When I run the script, it
produces the expected output on the terminal and even creates the
desired output PDB file, but the output file is exactly identical to
the input file other than the name.

I am running the PyMOL 1.3 educational version on Windows 7 64 bit. My
working directory contains the PyMOL.exe executable, my mutate.py
script, and my digly.pdb coordinate file of a simple GLY-GLY peptide.

The mutate.py script appears as follows:

from pymol import cmd
import sys

pdb = sys.argv[1]
name = sys.argv[2]
selection = sys.argv[3]
mutant = sys.argv[4]

print "pdb: " + pdb
print "name: " + name
print "selection: " + selection
print "mutant: " + mutant

cmd.load(pdb)

cmd.wizard("mutagenesis")
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" % name, name)


I launch the script via the command line from the working directory
using the following command:

PyMOL.exe -qc mutate.py -- digly.pdb digly A/2 ASN

This produces the following output:

pdb: digly.pdb
name: digly
selection: A/2/
mutant: ASN

It also creates the digly_m.pdb file in the working directory.
However, this file is exactly identical to the digly.pdb file.

Could someone please point out the mistake in my script? I have
attached the diglycine peptide to this message. Thanks a lot for any
help.

-Dan