1. Go to workshops.molviz.org Find today’s workshop and click on Syllabus Today’s syllabus will remain online indefinitely. In our Syllabus, do steps 1-4:

2. Introductions 1.Name 2.Whose lab you work in 3.Research interest (very brief)

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

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

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

6. Workshop Overview 1.Obtaining 3D Macromolecular Models 2.Understanding The Models 3.Sharing Structure-Function Information Martz – May 2010

7. Workshop Overview 1.Obtaining 3D Macromolecular Models a)Published Empirical (Crystallographic or NMR) b)Homology Models (Theoretical Models Are Grossly Inaccurate) 2.Understanding The Models 3.Sharing Structure-Function Information Martz – May 2010

8. Workshop Overview 1.Obtaining 3D Macromolecular Models 2.Understanding The Models a)Proteopedia b)FirstGlance in Jmol ( + links to Key Resources) 3.Sharing Structure-Function Information Martz – May 2010

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, it is developed by Eric Martz, following his experience with Protein Explorer. It is used in 3D View links in Nature Structure.

10. Workshop Overview 1.Obtaining 3D Macromolecular Models 2.Understanding The Models 3.Sharing Structure-Function Information: Custom Molecular Scenes without Tears a)Proteopedia: a wiki; rotating molecules; on-line b)Polyview-3D: publication quality; animations for Powerpoint Martz – May 2010

11. Gal 4 Transcriptional Regulator Protein. DNA Double Helix (Chain / Chain). Lysine 18 sits in DNA Major Groove recognizing CGG. Martz – May 2010 – 1d66

12. Animation Created by Polyview-3D (using PyMOL) Martz – May 2010 – 1d66