Education Corner
An Online Book to Create and Teach Through Molecular Visualization
By Kristen Procko and Roderico Acevedo
Figure 1. Book cover for Seeing the Invisible, designed by Wally Novak
Seeing the Invisible: Learning to Teach with Molecular Visualization is an open educational resource (OER) designed to support educators in creating their own biomolecular visualizations and bringing them into the classroom.
BioMolViz is a team of educators working to improve biomolecular visualization assessment and instruction. In 2021, the group developed an online workshop to help participants learn a molecular modeling program of their choice as part of an NSF-funded project. Capitalizing on team members’ expertise, training was offered in three popular molecular modeling programs. Last summer, an online working group revisited these materials with the goal of transforming them into an OER. Seeing the Invisible is the product of this work, incorporating the expertise of 18 contributors.
Figure 2. OER Coauthors from diverse backgrounds, institutions, and skillsets. From top, left to bottom, right: Josh Beckham, Wally Novak, Pamela Mertz, Henry Jakubowski, Didem Vardar-Ulu, Kristin Fox, Matthew Flagg, Brianna Bibel, James Nolan, Youngjoo Kim, Julie Himmelberger, Shane Austin, Ning Sui, Amanda Galán-Davila, Christin Monroe, and Keith Johnson.
An OER Designed by Educators for Educators
The OER is organized into three main sections. Following a preface to inspire instructors to understand the value of incorporating biomolecular visualization in their teaching, Seeing the Invisible opens with four chapters focused on pedagogy. The second section serves as a beginner’s guide to structural databases and navigating the information within the PDB. Finally, the reader is empowered to put the knowledge into practice, through stepwise lessons in using molecular modeling programs.
Pedagogy
In this section, the reader can expect to learn about backward design, alternative renderings, and incorporating accessibility into figure creation. Other chapters focus on how to choose the best molecular visualization program based on the instructor’s goals, and some of our favorite resources for visualizing PDB structures when self-created images are not required.
Figure 3. Viewing protein images through a colorblindness filter. Top, left illustrates a poor color scheme for accessibility, while the bottom, left is a more colorblind-friendly image.
Structural Databases
Authored by our working group’s structural biologists, the second section aims to demystify the data presented in structural databases by guiding a beginner in navigating the format of a PDB entry and understanding terminology. It provides basic background while leaning heavily on the RCSB PDB’s own resources for complimentary or deeper information, includes a straightforward guide to evaluating structure quality written for the non-structural biologist, and illustrates advanced RCSB PDB search techniques that we have found most useful when locating structures for our teaching. Overall, this section serves as a primer to the essentials of PDB navigation, interpretation, and search.
Molecular Modeling Lessons
At its core, Seeing the Invisible is designed to support educators in learning how to render their own biomolecular structures. Spanning twelve activities the team deemed essential for learning the basics of any molecular modeling program, each task is presented in four popular molecular visualization programs: ChimeraX, iCn3D, Mol*, and PyMOL. The step-by-step directions allow a novice to quickly produce a high quality rendering of a structure for use in teaching. Care was taken to ensure that each task could be completed with each visualization program. Where tasks could not be replicated exactly, creative measures were taken to provide analogous activities. For example, amino acid substitutions cannot be made in Mol*, therefore the mutagenesis chapter for Mol* leverages the utility of AlphaFold to predict a mutated structure that can be reloaded into the program. From generating a molecular surface to displaying interactions between enzyme and substrate, instructors now have the flexibility to create the images they need to illustrate the topics they are presenting in class.
Figure 4. Electrostatic potential map overlaid onto a surface representation of a protein using the four molecular modeling programs.
An OER for Any Learner
While the original intention of this book was to empower educators to learn a molecular modeling program, try a new one, or sample multiple programs to choose one for their classroom, members of our broader community have reported it is a valuable resource for teaching students directly. Michael Wolyniak, McGavacks Professor of Biology at Hampden-Sydney College, describes his experience using the OER in a classroom setting:
"Students went through the PyMOL sections of the book with a focus on the proteins we were looking at in class and generated renderings that served as the source of their research proposals as well as publication-quality images on final posters. Seeing the Invisible was very accessible to my students and enabled them to explore the world of protein imaging.”
Seeing the Invisible: Learning to Teach with Molecular Visualization is freely available to all learners online at https://utexas.pressbooks.pub/molviz-education/.
Roderico Acevedo is an Associate Professor of Chemistry at Westfield State University, a primarily undergraduate institution located in Western Massachusetts. His scholarly and pedagogical interests focus on helping students develop visual literacy in life science courses through hands-on engagement with structural data and molecular modeling tools.
A central component of his work is mentoring undergraduate researchers in projects that combine molecular visualization, computational modeling, and experimental biochemistry. He has supervised undergraduate research and honors projects spanning virtual reality–based molecular visualization, computational enzyme analysis, and course-based research experiences. Through his involvement with BioMolViz, including serving as Associate Director, he contributes to national efforts to support faculty and students in learning to create, interpret, and communicate biomolecular structures using resources such as the Protein Data Bank.
Kristen “KP” Procko holds dual appointments at The University of Texas at Austin (UT Austin). As Associate Professor of Instruction in the Department of Molecular Biosciences, her teaching emphasizes active learning, leveraging molecular visualization and physical manipulatives to deepen understanding of central metabolism and related biochemical concepts. She played a central role in modernizing the UT Austin biochemistry degree plan and created tools to assess student achievement of program learning outcomes. In her capacity as Faculty Director for Innovative Scholarship in the Office of STEM Education Excellence, she oversees programs that advance teaching excellence and foster innovation in STEM education. Since 2018, she has directed BioMolViz, an international initiative dedicated to improving instruction and assessment of students’ biomolecular visualization skills.