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Related Experiment Videos

Templates for writing PyMOL scripts.

Blaine H M Mooers1,2,3, Marina E Brown1

  • 1Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.

Protein Science : a Publication of the Protein Society
|November 12, 2020
PubMed
Summary

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A new library of PyMOL code snippets, pymolsnips, helps users write scripts more efficiently. This tool aids researchers in recalling commands for molecular visualization, improving productivity in scientific image generation.

Area of Science:

  • Structural Biology
  • Computational Chemistry
  • Bioinformatics

Background:

  • PyMOL is widely used for creating high-quality images of protein structures for publications and presentations.
  • Infrequent use of PyMOL leads to poor command recall, hindering script development and reproducibility.
  • Writing custom scripts for molecular visualization requires precise and often complex command sequences.

Purpose of the Study:

  • To develop a solution for improving PyMOL script writing efficiency and command recall.
  • To create a reusable library of PyMOL code templates (snippets) for common visualization tasks.
  • To make this library easily accessible within popular text editors.

Main Methods:

  • Developed a library named pymolsnips, containing modular code fragments for PyMOL.
Keywords:
computer artworkcomputer graphicsmolecular artworkmolecular graphicsmolecular illustrationmolecular visualizationreproducible researchscientific illustrationscripting

Related Experiment Videos

  • Integrated pymolsnips with 18 popular text editors (e.g., VS Code, Vim, Emacs) across major operating systems.
  • Made the library publicly available on GitHub with installation guides and instructional animations.

    • Main Results:

    • pymolsnips provides readily accessible PyMOL code templates within text editors.
    • The library supports a wide range of popular text editors and operating systems.
    • Installation instructions and visual aids are available on the GitHub repository.

    Conclusions:

    • The pymolsnips library significantly eases the process of writing PyMOL script files.
    • This tool is expected to enhance productivity for researchers frequently using PyMOL for molecular visualization.
    • Improved script writing facilitates reproducible scientific image generation and data analysis.