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

[Shu-Hsien S. <sh...@bu...>]

Dear Dr.DeLano,

Thanks! That really helps!

Two more questions:
Does the 'pymol -qc' takes command line variables (os.argv in python)?
For example, the first line of my script would be:
cmd.do('load %s' %os.argv[1])

Second question might be off a little bit.
Is it possible to wrap PyMol as a module of Python? I know can be 
installed as a Python module, but that doesn't seem to be able to let me 
do things like:

# Sample Python script
import PyMol
PyMol.cmd.do('......')
distance = PyMol.cmd.do('distance ......')

Does it make any difference whether or not I installed PyMol independant 
of Python?

I am a bit confused with cmd.do vs cmd.select.
So, if I am writing a script for running in PyMol(using @some_script.py),
I should use:
import PyMol
cmd.select('...')

If I am writing a script for running PyMol in command line,
I should use:
from PyMol import cmd
cmd.do('...')

Kind of confused...

-shuhsien

>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
>  
>