Seeing the Invisible: Learning to Teach with Biomolecular Visualization

The BioMolViz Working Group

doi:doi.org/10.15781/m4zd-7691

Book Title: Seeing the Invisible: Learning to Teach with Biomolecular Visualization

by The BioMolViz Working Group

Edited by Kristen Procko and Roderico Acevedo

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An Introduction to Teaching with Biomolecular Visualization
Matthew Flagg and Henry V. Jakubowski
Contributors and Funding
Citing this Book
Cover Art
Walter Novak
Pedagogical Approaches to Teaching Biomolecular Visualization
1. 1. Taking the First Steps Toward Teaching with Visualization
  Julie Himmelberger; Youngjoo Kim; and Christin Monroe
2. 2. Essential Resources for Pre-Rendered Structures
  James Nolan and Josh Beckham
3. 3. The Biomolecular Visualization Framework
  Pamela Mertz
4. 4. Opinion: Choosing a Molecular Modeling Program
  Kristen Procko
Program Versions and Documentation
Structure Databases and Files
1. 5. A Guide to PDB Structures and the RCSB PDB
  Brianna Bibel
2. 6. Advanced Search through the RCSB PDB
  Walter Novak
3. 7. Evaluating Structure Quality
  Kristin Fox
I. Getting Started: Modeling Program Basics
1. I.A. Getting Started with ChimeraX
  Walter Novak and Josh Beckham
2. I.B. Getting Started with iCn3D
  Henry V. Jakubowski and Kristen Procko
3. I.C. Getting Started with Mol* (Molstar)
  Didem Vardar-Ulu and Shane Austin
4. I.D. Getting Started with PyMOL
  Roderico Acevedo and Kristen Procko
II. Changing Color and Representation: Exploring Alternative Renderings
1. II.A. ChimeraX Changing Color and Representation (Alternative Renderings)
  Walter Novak and Josh Beckham
2. II.B. iCn3D Changing Color and Representation (Alternative Renderings)
  Henry V. Jakubowski and Kristen Procko
3. II.C. Mol* Changing Color and Representation (Alternative Renderings)
  Didem Vardar-Ulu and Shane Austin
4. II.D. PyMOL Changing Color and Representation (Alternative Renderings)
  Roderico Acevedo and Kristen Procko
III. Visualizing Molecular Surfaces & Properties (e.g., Electrostatic, Hydrophobic)
1. III.A. ChimeraX Molecular Surface/Properties
  Walter Novak and Josh Beckham
2. III.B. iCn3D Molecular Surface/Properties
  Henry V. Jakubowski and Kristen Procko
3. III.C. Mol* Molecular Surface/Properties
  Didem Vardar-Ulu and Shane Austin
4. III.D. PyMOL Molecular Surface/Properties
  Roderico Acevedo and Kristen Procko
IV. Viewing Biological vs. Asymmetric Units
1. IV.A. ChimeraX Viewing Biological vs. Asymmetric Units
  Walter Novak and Josh Beckham
2. IV.B. iCn3D Viewing Biological vs. Asymmetric Units
  Ning Sui
3. IV.C. Mol* Viewing Biological vs. Asymmetric Units
  Didem Vardar-Ulu and Shane Austin
4. IV.D. PyMOL Viewing Biological vs. Asymmetric Units
  Roderico Acevedo and Kristen Procko
V. Selecting with the Mouse or Trackpad
1. V.A. ChimeraX Mouse/Trackpad Selection
  Walter Novak and Josh Beckham
2. V.B. iCn3D Mouse/Trackpad Selection
  Henry V. Jakubowski and Kristen Procko
3. V.C. Mol* Mouse/Trackpad Selection
  Didem Vardar-Ulu and Shane Austin
4. V.D. PyMOL Mouse/Trackpad Selection
  Roderico Acevedo and Kristen Procko
VI. Selecting from the Sequence & Adding Labels
1. VI.A. ChimeraX Selecting on the Sequence and Labeling
  Walter Novak and Josh Beckham
2. VI.B. iCn3D Selecting on the Sequence and Labeling
  Henry V. Jakubowski and Kristen Procko
3. VI.C. Mol* Selecting on the Sequence and Labeling
  Didem Vardar-Ulu and Shane Austin
4. VI.D. PyMOL Selecting on the Sequence and Labeling
  Roderico Acevedo and Kristen Procko
VII. Selecting Groups Within 5Å
1. VII.A. ChimeraX 5Å Selection
  Walter Novak and Josh Beckham
2. VII.B. iCn3D 5Å Selection
  Henry V. Jakubowski and Kristen Procko
3. VII.C. Mol* 5Å Selection
  Didem Vardar-Ulu and Shane Austin
4. VII.D. PyMOL 5Å Selection
  Roderico Acevedo and Kristen Procko
VIII. Displaying Molecular Interactions
1. VIII.A. ChimeraX Molecular Interactions
  Walter Novak and Josh Beckham
2. VIII.B. iCn3D Molecular Interactions
  Henry V. Jakubowski and Kristen Procko
3. VIII.C. Mol* Molecular Interactions
  Didem Vardar-Ulu and Shane Austin
4. VIII.D. PyMOL Molecular Interactions
  Roderico Acevedo and Kristen Procko
IX. Manual Measurement (for Displaying Interactions & Distances)
1. IX.A. ChimeraX Manual Measurement
  Walter Novak and Josh Beckham
2. IX.B. iCn3D Manual Measurement
  Henry V. Jakubowski and Kristen Procko
3. IX.C. Mol* Manual Measurement
  Didem Vardar-Ulu and Shane Austin
4. IX.D. PyMOL Manual Measurement
  Roderico Acevedo and Kristen Procko
X. Showing Interactions at a Protein–Protein Interface
1. X.A. ChimeraX Protein–Protein Interface
  Walter Novak and Josh Beckham
2. X.B. iCn3D Protein–Protein Interface
  Henry V. Jakubowski and Kristen Procko
3. X.C. Mol* Protein–Protein Interface
  Didem Vardar-Ulu; Youngjoo Kim; and Shane Austin
4. X.D. PyMOL Protein–Protein Interface
  Julie Himmelberger and Pamela Mertz
XI. Superimposing Two Macromolecules
1. XI.A. ChimeraX Superimposition
  Walter Novak and Josh Beckham
2. XI.B. iCn3D Superimposition
  Henry V. Jakubowski and Kristen Procko
3. XI.C. Mol* Superimposition
  Didem Vardar-Ulu and Shane Austin
4. XI.D. PyMOL Superimposition
  Roderico Acevedo and Kristen Procko
Acknowledgements

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The BioMolViz Working Group

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Education / Educational sciences / Pedagogy

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Title: Seeing the Invisible: Learning to Teach with Biomolecular Visualization
Author: The BioMolViz Working Group
Editors: Kristen Procko and Roderico Acevedo
Primary Subject: Education / Educational sciences / Pedagogy
Additional Subject(s): Other graphic or visual art forms, Biochemistry, Molecular biology, Information visualization
Digital Object Identifier (DOI): https://doi.org/doi.org/10.15781/m4zd-7691

Book Title: Seeing the Invisible: Learning to Teach with Biomolecular Visualization

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