Go to workshops.molviz.org

1

• Go to workshops.molviz.org
• Find todays workshop and click on Syllabus
• Todays 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
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?
• 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

• Obtaining 3D Macromolecular Models
• Published Empirical (Crystallographic or NMR)
• Homology Models
• (Theoretical Models Are Grossly Inaccurate)
• Understanding The Models
• Sharing Structure-Function Information

Martz May 2010
8
Workshop Overview

• Obtaining 3D Macromolecular Models
• Understanding The Models
• Proteopedia
• FirstGlance in Jmol ( links to Key Resources)
• 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 Jmols 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

• Obtaining 3D Macromolecular Models
• Understanding The Models
• Sharing Structure-Function Information Custom
  Molecular Scenes without Tears
• Proteopedia a wiki rotating molecules on-line
• 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