Dear Markus,
> 1) How can I supply arguments to a python script,
> when I invoke it from
> the pymol command line?
Write the python script like
def bla(arg1,arg2):
any.python.commands(arg1,arg2)
return
from pymol import cmd
cmd.extend('blacommand',bla)
Now you can call your function 'bla' from the PyMOL
command line:
PyMOL> blacommand pdb1cso,42
Which would be like in Python:
bla('pdb1cso','42')
> 2) Can I set user variables in the pymol command
> line and access them
> in a python script?
same answer as for 1).
> 3) Can I rerun a python script and use generator
> functions that I
> initialised in the run before?
Sorry, I did not understand this question completely
(might be same answer as above two).
> 4) Can I temporarily return control to pymol from
> within a running a
> python script and continue running the script after
> I have finished
> interacting with pymol?
You should probably check out the Script Box utility,
if You have not already (http://www.rubor.de/bioinf
> 5) Can I query the active state of a pymol object
> (and other properties
> as well) from withing a python script?
Yes. Look at:
http://www.rubor.de/bioinf/pymol_tips.html#getcoord
> 6)
dunno
> 7)
also.
Good luck,
Kristian Rother
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