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Shortcuts for faster image creation in PyMOL

B. Mooers

Published 2019 in Protein Science

ABSTRACT

PyMOL is often used to generate images of biomolecular structures. Hundreds of parameters in PyMOL provide precise control over the appearance of structures. We developed 241 Python functions—called “shortcuts”—that extend and ease the use of PyMOL. A user runs a shortcut by entering its name at the PyMOL prompt. We clustered the shortcuts by functionality into 25 groups for faster look‐up. One set of shortcuts generates new styles of molecular representation. Another group saves files with time stamps in the file names; the unique filenames avoid overwriting files that have already been developed. A third group submits search terms in the user's web browser. The help function prints the function's documentation to the command history window. This documentation includes the PyMOL commands that the user can reuse by copying and pasting onto the command line or into a script file. The shortcuts should save the average PyMOL user many hours per year searching for code fragments in their computer or on‐line.

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