Apart from others' reply, I believe pymol will run .pml files while python will run .py files.
Regards, Saurabh Gayali ------------------------------ *Saurabh Gayali* Business Analyst [Excelra], Former Research Scientist [IGIB] saurabh.gay...@gmail.com / +91 8800412916 <http://example.com/>Bangalore, India On Tue, Dec 10, 2024 at 3:11 AM 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: image.png] > > Any help on how to run a python script with pymol in batch without opening > the GUI would be appreciated. > Yarrow > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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