• 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:

Introductions

1. Name2. Whose lab you work in3. Research interest (very brief)

Structural Biologists

• X-ray crystallography• NMR spectroscopy• High-resolution electron microscopy• Theoretical modeling

Visualization:Exploring an existing molecular model.

Modeling:Creating a new molecular model or

changing the conformation or composition of an existing model.

Terminology

Visualization software you have used

• PyMOL?• Chimera?• Jmol?• Something else?• RasMol?• Chime?• Protein Explorer?

Obsolete

Workshop Overview

1. Obtaining 3D Macromolecular Models2. Understanding The Models3. Sharing Structure-Function Information

Martz – May 2010

Workshop Overview

1. Obtaining 3D Macromolecular Modelsa) Published Empirical (Crystallographic or NMR)b) Homology Models(Theoretical Models Are Grossly Inaccurate)

2. Understanding The Models3. Sharing Structure-Function Information

Martz – May 2010

Workshop Overview

1. Obtaining 3D Macromolecular Models2. Understanding The Models

a) Proteopediab) FirstGlance in Jmol ( + links to Key Resources)

3. Sharing Structure-Function Information

Martz – May 2010

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.

Workshop Overview

1. Obtaining 3D Macromolecular Models2. Understanding The Models3. Sharing Structure-Function Information:

Custom Molecular Scenes without Tearsa) Proteopedia: a wiki; rotating molecules; on-lineb) Polyview-3D: publication quality; animations for

Powerpoint

Martz – May 2010

Gal 4 Transcriptional Regulator Protein.DNA Double Helix (Chain / Chain).Lysine 18 sits in DNA Major Grooverecognizing CGG.

Martz – May 2010 – 1d66

Animation Created by Polyview-3D(using PyMOL)

Martz – May 2010 – 1d66