From 886ae437fee6a674f7b2757062f1b8a91275457a Mon Sep 17 00:00:00 2001 From: Sacha Chua Date: Fri, 8 Oct 2021 01:58:03 -0400 Subject: Add talk pages for 2021 --- 2021/talks/molecular.md | 94 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 94 insertions(+) create mode 100644 2021/talks/molecular.md (limited to '2021/talks/molecular.md') 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"]] + + + + +# 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 (). 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 + + + +[[!inline pages="internal(2021/info/molecular-schedule)" raw="yes"]] + +[[!inline pages="internal(2021/info/molecular-nav)" raw="yes"]] -- cgit v1.2.3