I know I can run my PyMOL scripts if I specify a valid path from the current working directory and also using absolute paths, but can I have a central script repository, so I don't always need to specify the full path or copy my scripts around from project to project?

Environment info:

Kernel: Linux 5.6.8-1-MANJARO x86_64
Python: 3.8.2
Python2: 2.7.18
PyMOL: 2.3.0 Open-Source

1 Answer 1


You can use pymolrc and create aliases to your scripts.

If your script is located e.g. in


Just enter this line to your pymolrc:

alias myscript1, run /Users/tillyboy/pymolscripts/script1.pml

Now myscript1 is available for all your Pymol sessions independent of your current working directory.


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