A Semester-Long Learning Path Teaching Computational Skills via Molecular Graphics in PyMOL

Abstract

Structural biology describes biological processes at the molecular level and is an integral part of undergraduate study programs in molecular biosciences. Students are often fascinated by the visualizations created by molecular graphics software, which allow them to see the molecular world for the first time. Today, molecular visualization and structural analysis do not require expensive high-end computers but can be performed on the students' own laptops and are therefore highly suited for active learning approaches. We have designed a semester-long learning path that integrates molecular graphics and structural analysis using PyMOL into an undergraduate course in biomolecular structure and function. Compared to stand-alone PyMOL introductions, the semester-long learning path allows for an improved pedagogical design. The path progressively introduces more advanced functions in relevant scientific contexts and allows for spaced repetition. Advanced analysis functions in PyMOL are available only via the command line, so the learning path also teaches basic scripting and serves as an accessible introduction to computational thinking because a few lines of code can produce stunning results. Student surveys carried out at the end of the course suggest that the learning path supported the ability to perform structural analysis to a high degree. Moreover, a simulated exam showed that almost all students were able to carry out basic visualization tasks using PyMOL scripts, while three-quarters could undertake advanced structural analysis after following the course. In summary, integration of molecular graphics software with teaching of structural biochemistry allows a hands-on approach to analyzing molecular mechanisms and introduces biologically oriented students to computational thinking.