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:[email protected]
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: [email protected] [mailto:pymol-users-
> [email protected]] On Behalf Of Shu-Hsien Sheu
> Sent: Saturday, November 08, 2003 10:58 AM
> To: [email protected]
> 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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