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 <[email protected]> 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 <[email protected]> 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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