Re: [PyMOL] Running pymol without launching window in batch

[Gruber, K. (<kar...@un...>]

Dear Yarrow,

The problem in your script is the `if __name__ == "__main__"` clause.

When the script is run using `pymol -cqk test.py`, __name__ refers to the string "pymol".

The following script fetches a structure from the PDB and saves a PNG image. Run it using `pymol -cqk test.py -- <PDB-ID>`. (The flag -k prevents loading pymolrc and plugins.)

```python
from pymol import cmd


def main(pdb_id: str) -> None:
    print(f"Loading PDB-ID {pdb_id.upper()}")
    cmd.fetch(pdb_id)
    png_file_name = f"{pdb_id}.png"
    print(f"Writting image to {png_file_name}")
    cmd.png(png_file_name)


if __name__ == "pymol":
    import sys

    pdb_id = sys.argv[1]
    main(pdb_id)
```

Best regards,

Karl

On 06.01.2025, at 18:04, Florian Nachon <mai...@na...> wrote:


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 <yar...@gm...> 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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