Literature DB >> 33179363

Templates for writing PyMOL scripts.

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

Abstract

PyMOL commands are used to exert exquisite control over the appearance of a molecular model. This control has made PyMOL popular for making images of protein structures for publications and presentations. However, many users have poor recall of the commands due to infrequent use of PyMOL. This poor recall hinders the writing of new code in scripts. One solution is to build the new script by using code fragments as templates for modular parts of the task at hand. The code fragments can be accessed from a library while writing the code from inside a text editor (e.g., Visual Studio Code, Vim, and Emacs). We developed a library of PyMOL code templates or snippets called pymolsnips to ease the writing of PyMOL code in scripts. We made pymolsnips available on GitHub in formats for 18 popular text editors. Most of the supported text editors are available for Mac, Windows, and Linux operating systems. The GitHub site includes animations that complement the instructions for installing the library for each text editor. We expect that the library will help many PyMOL users to be more productive when writing PyMOL script files.
© 2020 The Protein Society.

Entities:  

Keywords:  computer artwork; computer graphics; molecular artwork; molecular graphics; molecular illustration; molecular visualization; reproducible research; scientific illustration; scripting

Mesh:

Year:  2020        PMID: 33179363      PMCID: PMC7737772          DOI: 10.1002/pro.3997

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  13 in total

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Authors:  Blaine H M Mooers
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Authors:  S McNicholas; E Potterton; K S Wilson; M E M Noble
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Authors:  Artem Babaian; Anicet Ebou; Alyssa Fegen; Ho Yin Kam; German E Novakovsky; Jasper Wong; Dylan Aïssi; Li Yao
Journal:  BMC Bioinformatics       Date:  2018-08-22       Impact factor: 3.169

10.  Templates for writing PyMOL scripts.

Authors:  Blaine H M Mooers; Marina E Brown
Journal:  Protein Sci       Date:  2020-11-30       Impact factor: 6.725

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5.  Templates for writing PyMOL scripts.

Authors:  Blaine H M Mooers; Marina E Brown
Journal:  Protein Sci       Date:  2020-11-30       Impact factor: 6.725

  5 in total

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