Thank you Osvaldo.
However, as a beginner, I am having problems with getting this to work. I
pasted your script in a file (script.txt) and placed it in the same folder
where the pdb files are. Then I ran PyMol and typed "run
c:\somefolder\script.txt", but I all get is a black screen and no .png
files are generated.
On Sat, Jun 6, 2015 at 2:42 AM, Osvaldo Martin <aloctavo...@gmail.com>
wrote:
> 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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>>
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