Drag the .pml script from Explorer/Finder/Dolphin etc. into PyMOL window.
Using a terminal (e.g. xterm):
# run a PyMOL command script (opens PyMOL GUI) pymol script.pml # run a Python script pymol script.py # batch mode (no PyMOL GUI) pymol -c script.pml # use absolute path if "pymol" is not in $PATH /opt/pymol-2.2.3/pymol -c script.pml
Register .pml extension with PyMOLWin.exe
Using Windows Explorer:
Load PML scripts with @:
Load Python scripts with run:
PyMOL> run example.py
PyMOL> run /tmp/PyMOLScripts/example.py
PyMOL> run C:\PyMOLScripts\example.py
Download the PyMOL (PML) script example.pml and open it with PyMOL by dragging it into the PyMOL window.
Run the same example.pml script on the PyMOL command line with @.
Hints: The commands cd, pwd and ls are useful to first navigate to the right directory. Filename auto-completion speeds up typing and avoids typos. You can also use environemnt variables (e.g. $HOME) and ~ (home directory).
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