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
