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: Modeling:
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 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.
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.