RE: [PyMOL] Accessing PyMol's commands from outside (or without viewer)

[Warren L. D. <wa...@de...>]

Shu-hsien

Sure, instead of cmd.select, use

cmd.do("select ligand, resn XYZ")
cmd.do("select protein, ! ligand ")

etc.

./pymol -qc select_box.py

Is the command line mode of PyMOL.  "pymol -qc" can be used like
"python" in most cases.

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Shu-Hsien Sheu
> Sent: Saturday, November 08, 2003 10:58 AM
> To: pym...@li...
> Subject: [PyMOL] Accessing PyMol's commands from outside (or without
> viewer)
> 
> Hi,
> 
> This should be a trial question though I cannot find a way of doing
it.
> I have a simple script that looks like this:
> (the original commands, rather than cmd.select......)
> select ligand, resn XYZ
> select protein, ! ligand
> select box, protein within 8 of ligand
> select box, box or byres box
> save box as box.pdb
> 
> I don't need the viewer at all and would be even more efficient if I
can
> call the PyMol API from the shell. Or, in a python script.
> For example, I would like to have something like:
> ./pymol select_box.py
> 
> thanks!
> 
> 
> 
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