Computer coding automates computational tasks for reproducibility, efficiency and reliability. Unfortunately, many undergraduate chemistry and biochemistry majors encounter very little in the way of computer coding. Furthermore, essential programming fundamentals such as variables, do loops and if/then statements can be confusing abstractions to beginning programmers. To introduce programming concepts and their practical applications, we have developed a one-day introduction to coding for the Physical Chemistry Laboratory using the open-source molecular visualization package Jmol.1 Jmol is employed by web-based repositories of structural data such as the Protein Data Bank2 and the Cambridge Crystallographic Data Centre.3 Jmol has powerful scripting capabilities for molecular animation and display. During the laboraory, students download Jmol to their computers, select a molecule or protein of interest from a class or research project, and then employ introductory coding concepts to write code that animates, re-colors and re-scales molecular structural features, as selected via commands using Boolean logic. The success or failure of implementing variables, for loops and if/then statements are immediately visualized by color and movement of the computer models. The exercise includes anaglyph 3D computer imaging. The lab exercise culminates with students exporting a file for 3D printing, allowing students to contrast in physical and computer-based molecular models.

Molecular visualization as motivation for learning computer programming basics

255th National Meeting (2018)

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