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+[[!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"]]