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diff --git a/2021/talks/molecular.md b/2021/talks/molecular.md new file mode 100644 index 00000000..ecfaec10 --- /dev/null +++ b/2021/talks/molecular.md @@ -0,0 +1,94 @@ +[[!meta title="Reproducible molecular graphics with Org-mode"]] +[[!meta copyright="Copyright © 2021 Blaine Mooers"]] +[[!inline pages="internal(2021/info/molecular-nav)" raw="yes"]] + +<!-- You can manually edit this file to update the abstract, add links, etc. ---> + + +# Reproducible molecular graphics with Org-mode +Blaine Mooers + +Research papers in structural biology should include the code used +to make the images of molecules in the article in the supplemental +materials. Some structural bioinformaticists have started to include +their computer code in the supplemental materials to allow readers +to reproduce their analyses. However, authors of papers reporting new +structures have overlooked the inclusion of the code that makes the +images of the molecules in their articles. Nonetheless, this aspect of +reproducible research needs to become the standard practice to improve +the rigor of the science. + +In a literate programming document, the author interleaves the code +that makes the images of molecules in the explanatory text. Such a +document allows the reader to reproduce the images in the manuscript. +The reader can also explore the effect of altering the parameters in +the code. Org files are one alternative for making such literate +programming documents. + +We developed a yasnippet library called orgpymolpysnips for structural +biologists (<https://github.com/MooersLab/orgpymolpysnips>). This +library facilitates the assembly of literate programming documents +with molecular images made by PyMOL. PyMOL is the most popular +molecular graphics program for making images for publication; it has +over 100,000 users, which is a lot of users in the sciences. PyMOL was +used to make many of the striking images of biological molecules on +the cover of Nature and Science. We use the emacs-jupyter package to +send commands from a code block in Org files to PyMOL's Python API. +PyMOL returns the molecular image to the output block below the +code block. Of course, an Emacs user can convert the Org file into a +PDF, convert the code blocks to script files, and submit these for +non-Emacs users. We describe the content of the library and provide +examples of the running PyMOL from Org-mode. We compare using Org, +Jupyter Notebook, Jupyter Lab, and RStudio with PyMOL to do +literate programming in structural biology. + + + +# Outline + +- 5-10 minutes: (brief description/outline) + - Title slide + - Structural Biolog Workflow in the Mooers Lab + - Cover images made with PyMOL + + - Why develop a snippet library for your field? + - PyMOL in Org: kernel specification + - Creating a conda env and installing PyMOL + - Example code block in Org to make DSSR block model of tRNA + - Resulting image + - Summary + - Acknowledgements + +<!-- +- 20 minutes: (brief description/outline) + + I would prefer to give a 20-minute talk because this allows time to develop the context. + +- Title slide +- Structural Biology Workflow in the Mooers Lab +- Cover images made with PyMOL +- Bar graph of PyMOL's popularity +- Origin story of PyMOL +- PyMOL's hybrid open-source model +- PyMOL's GIU +- Default molecular representations in PyMOL +- Example of the PyMOL macro language +- Same commands in Python +- Corresponding code in yasnippet snippet +- Extension of molecular representations with orgpymolpysnips +- Hermann Ebbinghaus's Forgetting Curve +- Why develop a snippet library for your field? +- PyMOL in Org: kernel specification +- Anatomy of kernel file +- Creating a conda env and installing PyMOL +- Example code block to make DSSR block model of tRNA +- Resulting image +- Org vs. JuptyerNotebook, Juptyer Lab, and RStudio +- Summary +- Acknowledgements + +--> + +[[!inline pages="internal(2021/info/molecular-schedule)" raw="yes"]] + +[[!inline pages="internal(2021/info/molecular-nav)" raw="yes"]] |