Hi Gazal,
Generally when I want to do batch operations using PyMOL I wrote a Python
script and I call PyMOL from within that script. I prefer this way because
I think is more flexible and simple than using PyMOL from the command line.
In those cases I start the Python script with the following imports:
import *main*
*main*.pymol_argv = [‘pymol’,’-qc’] # Pymol: quiet and no GUI
import pymol
from pymol import cmd, stored
pymol.finish_launching()
Nevertheless, if you want to call PyMOL from the command line you have several
options <http://www.pymolwiki.org/index.php/Command_Line_Options> that you
can pass to PyMOL like “-qc” , i.e. quiet and no GUI
Let us know if this answer your question, or if you still have doubts.
Cheers,
Osvaldo.
On Fri, Jul 10, 2015 at 9:44 AM, Gazal <gazal...@gmail.com> wrote:
Hi,
>
> I'm trying to find the RMSD values for batch purposes. The command which I
> found works for the Pymol-command line.
> I was hoping if I could get an idea about using the python script
> fitting.py in my shell script without triggering the Pymol GUI.
>
> Thanks in advance.
>
> Gazal
>
>
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