Re: [PyMOL] command-line and python scripts

Dear Kristian,

Thank you for your quick answer concerning pymol and python scripts.=20
You answered questions 1-3, indeed. Generator functions are described=20
at http://www.python.org/doc/2.2.2/whatsnew/node5.html and require=20
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=20=

> python script and continue running the script after I have finished=20
> interacting with pymol?
The spawn command does the trick. I did not check out this ScriptBox=20
Utility yet.

> 6) How do I generate symmetry molecules for one selected state of a=20
> molecule only? I have a molecule with 144 states and generating=20
> symmetry objects for all states simultaneously takes too long time and=20=

> finally crashes pymol, because all memory is used up.
Copy the desired state into a new object and generate the symmetry=20
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. M=FCller Institut
Biozentrum der Universit=E4t Basel
Klingelbergstrasse 70
CH-4056 Basel
Tel.: +41 61 267 20 91
Fax: +41 61 267 21 09