期刊
PROTEIN SCIENCE
卷 30, 期 1, 页码 262-269出版社
WILEY
DOI: 10.1002/pro.3997
关键词
computer artwork; computer graphics; molecular artwork; molecular graphics; molecular illustration; molecular visualization; reproducible research; scientific illustration; scripting
资金
- National Cancer Institute [R01 CA242845]
- National Institute of Allergy and Infectious Diseases [R01 AI088011]
- National Institute of General Medical Sciences [P20 GM103640]
- National Science Foundation [MCB1616845]
- Oklahoma Center for the Advancement of Science and Technology [HR20-002]
- Schrodinger, Inc
PyMOL commands allow precise control over molecular model appearance, but many users struggle with poor command recall. In response, pymolsnips library was developed to provide code templates for easier PyMOL script writing, increasing productivity for users across various text editors and operating systems.
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.
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