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. Eric will be happy to help you at any time!

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

Structural Biologists X-ray crystallography NMR spectroscopy High-resolution cryo-electron microscopy Theoretical modeling

Structural Biologists X-ray crystallography NMR spectroscopy High-resolution electron microscopy Theoretical modeling (unreliable) Empirical Methods

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

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

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

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

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

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 much wider 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.

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

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

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.

Workshop Schedule After Workshop: Individual Appointments Three 70 minute blocks each day 9:00 – 10:10 15 min break 10:10-11:25 10:25 – 11:35 15 min break 11:35-11:50 11:50-1:00 After Workshop: Individual Appointments