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MooersLab/README.md

MooersLab

This site contains the public repositories of the Dr. Blaine Mooers Lab, Department of Biochemistry and Molecular Biology, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA. My lab determines the structures of biomolecular molecules and their complexes with drugs using mostly X-ray crystallography and sometimes small angle X-ray scattering, a method that does not require crystals. We grow crystals using advanced experimental design methods and collect X-ray diffraction data in-house and frequently at the Stanford Synchrotron Radiation LightSource and sometimes at the four other major light sources in the US. We also do structure-based drug design using supercomputers.

We are not computer scientists, but we do write some code from time-to-time. We made some software tools to ease the writing of PyMOL scripts for making molecular images. These tools are available for the top 19 text editors and for the Jupyter, Colab, and R Markdown notebooks. All of these text editors can make your work lighter and have many wonderful features, but Emacs is our favorite because it is by far the most customizable, thanks to Emacs Lisp.

The repositories are grouped by category. Some repositories are listed in several categories. This listing is still a work in progress. Many repositories have yet to be added. Seventeen repos are forks to other people's repositories. Go to the repositories tab to see the full list of repositories.

Index of repositories

ACA talks

Bash related

Bayeisan Data Analysis

  • JointProb R Markdown and jupyter notebooks for the Saturday JointProb study group.

Blog

Clojure

  • quizzes about clojure These are useful for improving command recall after a break in using Clojure for several months.

Crystallographic computing

CCTBX related

For use in notebooks

For use in text editors

Curvefiting software

Emacs related

Jupyter and Colab related

PyMOL specific

CCTBX specific

LaTeX related

Note that I currently write alot in Emacs on 750words.com via GhostText. I configured the atomic-chrome package for Emacs to go into LaTeX mode when GhostText connects to 750words. I can also use Emacs to write and edit text in Overleaf via atomic-chrome and GhostText. This is a very cool way of extending Emacs to websites that have weaker support for editing text.

Molecular Graphics related

Collection of links for a 15-hour course on Molecular Graphics

PyMOL

  • pymolrc My pymolrc file.
  • pymolsnips A large collection of PyMOL macro language (pml) code snippets. Contains link to a webpage with extensive instructions on installing 19 text editors.
  • pymolshortcuts A large collection of functions mapped to aliases or shortcuts. This colleciton of functions is very useful for non-coders.
  • EasyPyMOL Support for horizontal scripting in PyMOL.
  • orgpymolpysnips Support for literate programming in org-mode with PyMOL.
  • rstudiopymolpysnips Support for literate programming in Rstuido with PyMOL.
  • taggedpymolpysnips Support for literate programming in JuptyerLab Lab with tagged snippets with the elyra-snippets extension and with PyMOL.
  • jupyterlabpymolpysnips PyMOL Python snippets for use in JupyterLab with the jupyterlab-snippets extension.
  • colabOpenSourcePyMOLpySnips PyMOL Python snippets for use in Colab with open source PyMOL.
  • colabPyMOLpySnips PyMOL Python snippets for use in Colab with the incentive version of PyMOL.
  • PyMOL wall hangings Protocol for making oversized images to be framed and hung on a wall.

R statistical program

Small Angle Scattering

Time management

  • TimeSpent Time tracking by project with Google Sheets.

Supercomputing related (includes high performance computing (HPC), cluster computing, cloud computing)

Vim (and Neovim)

Writing productivity tools

YouTube Videos of relevance to these repos

MooersLab/MooersLab is a special repository because its README.md (this file) appears on his GitHub profile 👋.

Pinned

  1. The repository pymolschortucts contains the a collection of shortcuts that are loaded on startup of PyMOL. These shortcuts enable websearches from within PyMOL as well as many other convienent func…

    Python 50 15

  2. pymolsnips Public

    Pymolsnips is a library of PyMOL scripting language code fragments for several popular text editors.

    Vim Snippet 29 6

  3. EasyPyMOL Public

    Script to facilitate the making of horizontal scripts

    Python 11 12

  4. Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.

    HTML 13 3

  5. Code snippets for colab-notebooks running open-source PyMOL

    Jupyter Notebook 1

  6. Workbook for tracking minutes spent and words written per day per writing project.

    HTML 1

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Contribution activity

June 2023

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