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PyMOL Script

PyMOL scripts are plain text files containing PyMOL commands, one per line, appearing as they would be entered at the PyMOL command prompt. The standard extension for a PyMOL script is `.pml`.

Basic usage

Save your commands in a plain text file (using e.g. Notepad, TextEdit, or a text editor of your choice) with a `.pml` extension, e.g. `script.pml`.

Run the script by either "File > Run script..." in the GUI menu bar, or via the command