Dear Kristian,
Thank you for your quick answer concerning pymol and python scripts.
You answered questions 1-3, indeed. Generator functions are described
at http://www.python.org/doc/2.2.2/whatsnew/node5.html and require
python 2.2.
Questions 4 and 6 I can now answer myself:
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?
The spawn command does the trick. I did not check out this ScriptBox
Utility yet.
6) How do I generate symmetry molecules for one selected state of a
molecule only? I have a molecule with 144 states and generating
symmetry objects for all states simultaneously takes too long time and
finally crashes pymol, because all memory is used up.
Copy the desired state into a new object and generate the symmetry
molecules of this new object:
def sym_state(s):
cmd.delete("sym*")
cmd.delete("tmp")
cmd.create("tmp", "MyObject", s, 1)
cmd.symexp("sym", "tmp", "tmp", 30)
cmd.do("show cell")
print("Generated symmetry objects for state " + `s`)
return
Cheers,
Markus
On Wednesday, March 26, 2003, at 02:51 pm, Kristian Rother wrote:
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
Markus Meier
M. E. Müller Institut
Biozentrum der Universität Basel
Klingelbergstrasse 70
CH-4056 Basel
Tel.: +41 61 267 20 91
Fax: +41 61 267 21 09
