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Molecular Visualization Workshop - Explore, Model, and Share 3D Macromolecular Structures

Join our workshop to learn about molecular visualization and modeling techniques. Explore existing molecular models, create new ones, and understand the structure-function relationships. Learn to use tools like PyMOL, Chimera, and Jmol to visualize and manipulate macromolecular structures. Share your findings with others using Proteopedia and create stunning animations with Polyview-3D. Optional: Keep an annotated record of your explorations.

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Molecular Visualization Workshop - Explore, Model, and Share 3D Macromolecular Structures

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  1. Let’s get started! Go to workshops.molviz.org Find today’s workshop and click on Syllabus Today’s syllabus will remain online for years. In our Syllabus, do steps 1-7. Step 8, installing Java, is optional. Eric will be happy to help you at any time! Martz – June 2016

  2. Introductions • Name • Whose lab you work in • Research interest (very brief)

  3. Structural Biologists • X-ray crystallography • NMR spectroscopy • High-resolution electron microscopy • Theoretical modeling

  4. Terminology Visualization: Exploring an existing molecular model. Modeling: Creating a new molecular model or changing the conformation or composition of an existing model.

  5. Visualization software you have used • PyMOL? • Chimera? • Jmol? Today • Something else? • RasMol? • Chime? • Protein Explorer? Obsolete

  6. Workshop Overview Obtaining 3D Macromolecular Models Understanding The Models Sharing Structure-Function Information

  7. Workshop Overview Obtaining 3D Macromolecular Models Published Empirical (Crystallographic or NMR) Homology Models (Theoretical Models Are Unreliable) Understanding The Models Sharing Structure-Function Information

  8. Workshop Overview Obtaining 3D Macromolecular Models Understanding The Models FirstGlance in Jmol (has links and guidance for other Resources) Sharing Structure-Function Information

  9. FirstGlance in Jmol ≠ Jmol! • Jmol (jmol.org) is a large international open-source project active since before 2000. • Lead developer since 2006 is Robert Hanson (St. Olaf College, Northfield MN). • Jmol is no easier to use than PyMOL, etc. • FirstGlance in Jmol (firstglance.jmol.org) is a user interface that makes Jmol’s power accessible to a wide range of users. • First available in 2006, FirstGlance is developed by Eric Martz, building upon his previous project Protein Explorer. It is linked to the buttons in Nature. Martz – May 2015

  10. Workshop Overview • Molecular Scenes from FirstGlance • a) Save images or presentation-ready animations. • Customized Molecular Scenes without Tears • b) Polyview-3D: publication quality images & presentation-ready animations. • c) Proteopedia: a wiki; create custom molecular scenes to share on-line. Obtaining 3D Macromolecular Models Understanding The Models Sharing Structure-Function Information: Martz – June 2016

  11. Mechanosensitive channel Animation by Polyview-3D: “PyMOL without tears” (Morph between 2oau & 2vv5) FirstGlance.Jmol.Org

  12. Optional: Keep an annotated record of your explorations. • Save static images or animations from FirstGlance. • Drop them into Powerpoint (or Google Slides, or Libre Office). • Add notes. See 497L.MolviZ.Org for questions assigned in an undergraduate class, plus a demo report of the answers.

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