Hi Tim,

You can use two dashes on the command line, like:
pymol -r get_neighbors.py -- ALA

And then access them using sys.argv in your script.

For example: save the following as tmp_pymol.py and run: 'pymol -r tmp_pymol.py -- ALA' ( without quotes)

>>>>
from pymol import cmd
import sys


def foo(string):
        print string
        return

cmd.extend('foo',foo)


if __name__ == '__main__':
        foo(sys.argv[1])

>>>
Hope this helps,
Matt

      

      On 02/22/2013 10:50 AM, Someone Else wrote:
Hi everyone,

I would like my PyMOL script take a command line parameters, e.g:

pymol get_neighbors.py ALA

How to extract "ALA" from inside my neighbors.py?

Best regards,
Tim




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