Hi Praz,
When I want to process several files, do complex or repetitive tasks I
prefer to write a Python script and access the PyMOL functions using the
PyMOL API, as in the code below.
This example will upload all the pdb files in the folder where the script
is located, one file at a time, save the current image as a png file and
then delete the uploaded molecule.
import __main__
__main__.pymol_argv = ['pymol','-qc']
import pymol
from pymol import cmd
pymol.finish_launching()
import glob
pdb_files = glob.glob('*.pdb')
for pdb in pdb_files:
cmd.load(pdb)
### insert your code here ###
cmd.png('%s' % pdb.split('.')[0])
cmd.delete('all')
Cheers,
Osvaldo.
On Fri, Jun 5, 2015 at 7:50 PM, Praz Nina <praz...@gmail.com> wrote:
> Hi all,
>
> I'm a beginner at PyMol, but I'm wondering if a batch action like this
> would be possible: If I have a bunch of .sdf and .pdb files in a folder,
> and I want to apply a specific "look" to all of them (I've written the
> parameters regarding light, field of view etc.), is it possible to batch
> process all of them and output a .png file of each of those structures?
>
> Likewise, if I want to make a movie from all of those structures (also
> have written a script, 450 frames, 360 rotation), can I process these files
> in a batch?
>
> Thanks,
> Praz
>
>
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