Hello,
It is much easier than that.
Make a pymol script, for example, test.pml:
#
load 3gbn.pdb
select Selection1, resi 80:115
save Selection1.cif, Selection1
quit
#
then run it with the -c option :
pymol test.pml -c
If you want to pass an argument, like the filename of a pdb file to be directly
opened, then use the -cp option.
Florian
> On 9 Dec 2024, at 22:38, Yarrow Madrona <yarrowmadr...@gmail.com> wrote:
>
> I'm trying to run pymol in batch mode without launching the window. I am
> running PyMOL 3.1.1.
>
> Here is my code for an example script (test.py). I'm trying to run before
> running the real script. In the command line I enter:
> pymol -cq test.py
>
>
> from pymol import cmd
> import time
>
> def main():
> print("Starting PyMOL batch processing...")
> cmd.load("3gbn.pdb")
> do_stuff()
> print("Loaded 3gbn.pdb")
> time.sleep(25) # Ensure commands are processed
> cmd.quit()
>
> if __name__ == "__main_":
> main()
> I don't get any output. If I type:
> pymol -c test.py
> It appears that pymol starts and closes:
>
> <image.png>
>
> Any help on how to run a python script with pymol in batch without opening
> the GUI would be appreciated.
> Yarrow
>
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