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 # 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
+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.
+molecular structures often overlook the inclusion of the code that makes 
+the images of the molecules reported 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.
+In a literate programming document, the author interleaves between blocks 
+of prose the code that makes the images of molecules. The document allows 
+the reader to reproduce the images in the manuscript by running the code. 
+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
+We developed a yasnippet snippet 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.
+molecular graphics program for creating images for publication; it has
+over 100,000 users, which is a lot of users in molecular biology. PyMOL 
+has been used to make many of the images of biological molecules found 
+on the covers of many Cell, Nature, and Science issues. 
 
+We used the `jupyter' language in org-babel to send commands from 
+code blocks in Org files to PyMOL's Python API. PyMOL returns the 
+molecular image to the output block below the code block. An Emacs 
+user can convert the Org file into a PDF, `tangle' the code blocks 
+into a script file, and submit these for non-Emacs users. We describe 
+the content of the library and provide examples of the running PyMOL 
+from Org-mode documents. 
 
 
 # Outline