Literature DB >> 33967632

A PyMOL snippet library for Jupyter to boost researcher productivity.

Blaine H M Mooers1,2,3.   

Abstract

Snippets - code templates one line or longer - boost researcher productivity because they are faster to insert than writing the code from scratch and because they reduce debugging time. Several extensions support the use of snippets in Jupyter. We developed a Python version of the pymolsnips library and customized it for use in the jupyterlab-snippets-multimenus extension for JupyterLab. The extension provides access to the snippets by pull-down menus. Each snippet performs one task. Each task often requires many lines of code. This library's availability in Jupyter enables PyMOL users to run PyMOL efficiently inside Jupyter while storing the code and the associated molecular graphics images next to each other in one notebook document. This proximity of code and images supports reproducible research in structural biology, and the use of one computer file facilitates collaborations.

Entities:  

Year:  2021        PMID: 33967632      PMCID: PMC8104305          DOI: 10.1109/mcse.2021.3059536

Source DB:  PubMed          Journal:  Comput Sci Eng        ISSN: 1521-9615            Impact factor:   2.080


  8 in total

1.  Scripting Wizards for Chime and RasMol.

Authors:  R M Horton
Journal:  Biotechniques       Date:  1999-05       Impact factor: 1.993

2.  Warren L. DeLano 21 June 1972-3 November 2009.

Authors:  Axel T Brunger; James A Wells
Journal:  Nat Struct Mol Biol       Date:  2009-12       Impact factor: 15.369

3.  Shortcuts for faster image creation in PyMOL.

Authors:  Blaine H M Mooers
Journal:  Protein Sci       Date:  2019-11-27       Impact factor: 6.725

4.  An introduction to biomolecular graphics.

Authors:  Cameron Mura; Colin M McCrimmon; Jason Vertrees; Michael R Sawaya
Journal:  PLoS Comput Biol       Date:  2010-08-26       Impact factor: 4.475

5.  Collaboration gets the most out of software.

Authors:  Andrew Morin; Ben Eisenbraun; Jason Key; Paul C Sanschagrin; Michael A Timony; Michelle Ottaviano; Piotr Sliz
Journal:  Elife       Date:  2013-09-10       Impact factor: 8.140

6.  DSSR: an integrated software tool for dissecting the spatial structure of RNA.

Authors:  Xiang-Jun Lu; Harmen J Bussemaker; Wilma K Olson
Journal:  Nucleic Acids Res       Date:  2015-07-15       Impact factor: 16.971

7.  Structural basis of resistance of mutant RET protein-tyrosine kinase to its inhibitors nintedanib and vandetanib.

Authors:  Simon S Terzyan; Tao Shen; Xuan Liu; Qingling Huang; Peng Teng; Mi Zhou; Frank Hilberg; Jianfeng Cai; Blaine H M Mooers; Jie Wu
Journal:  J Biol Chem       Date:  2019-05-22       Impact factor: 5.157

8.  Templates for writing PyMOL scripts.

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

  8 in total
  1 in total

1.  Diterpenes/Diterpenoids and Their Derivatives as Potential Bioactive Leads against Dengue Virus: A Computational and Network Pharmacology Study.

Authors:  Rasel Ahmed Khan; Rajib Hossain; Abolghasem Siyadatpanah; Khattab Al-Khafaji; Abul Bashar Ripon Khalipha; Dipta Dey; Umma Hafsa Asha; Partha Biswas; Abu Saim Mohammad Saikat; Hadi Ahmadi Chenari; Polrat Wilairatana; Muhammad Torequl Islam
Journal:  Molecules       Date:  2021-11-11       Impact factor: 4.411

  1 in total

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