Seeing the Invisible: Learning to Teach with Biomolecular Visualization

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Seeing the Invisible: Learning to Teach with Biomolecular Visualization

is a free, extensive online 2025 book by The BioMolViz Working Group, edited by Kristen Procko and Roderico Acevedo.
It explains how to use ChimeraX, iCn3D, Mol*, and PyMOL in teaching.

Chapters:

• An Introduction to Teaching with Biomolecular Visualization
• Contributors and Funding
• Citing this Book
• Cover Art

• Pedagogical Approaches to Teaching Biomolecular Visualization
• Structure Databases and Files
• Program Versions and Documentation

1. Getting Started: Modeling Program Basics
2. Changing Color and Representation: Exploring Alternative Renderings
3. Visualizing Molecular Surfaces & Properties (e.g., Electrostatic, Hydrophobic)
4. Viewing Biological vs. Asymmetric Units
5. Selecting with the Mouse or Trackpad
6. Selecting from the Sequence & Adding Labels
7. Selecting Groups Within 5Å
8. Displaying Molecular Interactions
9. Manual Measurement (for Displaying Interactions & Distances)
10. Showing Interactions at a Protein–Protein Interface
11. Superimposing Two Macromolecules
12. Mutagenesis

• Acknowledgements