I am a RNA and protein crystallographer that works on problems in RNA editing. I am an associate professor of biochemistry and molecular biology at the University of Oklahoma Health Sciences Center in Oklahoma City. I have taught about 350 first-year graduate students in the biomedical sciences how to use the molecular graphics program PyMOL over the past 12 years. PyMOL is very popular for making images of protein structures for publication. It also provides strong support for making movies of moving molecules. PyMOL is written in C but wrapped with Python. My first Python scripts automated tasks in PyMOL. I developed a collection of functions mapped to aliases for my students [(Mooers 2016)] (https://doi.org/10.1002/pro.2996). I extended this collection ten-fold recently (Mooers 2020). These shortcuts extended the work that can be done in PyMOL. I made these shortcuts to help students overcome their fear of the command line in PyMOL. I also designed and lead for ten years a 15-hour team-taught course that used PyMOL as the central tool. A number of our graduate students have used PyMOL to make images and movies for their seminar presentation, posters, publications, and dissertations.
I started using Python in my research about 10 years ago. I have been a frequent user of Ipython Notebooks and then Jupyter Notebooks. I find that these notebooks are a fun platform for developing new code. Jupyter Notebooks are addictive because the rapid feedback provides instant gratification.
I am interested in reproducible research. Jupyter Notebooks are a viable platform for supporting literate programming in structural biology. To help support doing structural biology research in Jupyter Notebooks, I developed a snippet library of PyMOL code (pymolsnips). This library is the subject of my talk proposal.
Tuesday Oct. 13, 2020, 4 p.m.–Oct. 13, 2020, 4:30 p.m. in Jupyter in Scientific Research