Welcome to Protein 3D Structure Visualization and Structural Bioinformatics!

1

• Welcome to Protein 3D Structure Visualization and
  Structural Bioinformatics!
• Please go ahead and get started
• Use the Google Chrome browser. If you dont have
  it, please install it now. Firefox and Safari
  are slower with the software well be using.
  Internet Explorer and Opera are unusably slow
  with this software.
• Go to workshops.molviz.org and click on our
  syllabus. (Our syllabus will remain online
  indefinitely.)
• Follow steps 1-6 under Get Started.

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Introductions

1. Name
2. Whose lab you work with
3. The protein you are working on/research interests
   (very brief)

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Structural Biologists

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

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Terminology

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

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Visualization software you have used

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

Obsolete
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Workshop Overview

1. Obtaining 3D Macromolecular Models
2. Understanding The Models
3. Sharing Structure-Function Information

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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
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Workshop Overview

• Obtaining 3D Macromolecular Models
• Understanding The Models
• FirstGlance in Jmol
• ( its links to Key Resources)
• Sharing Structure-Function Information

Martz May 2010
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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.

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Workshop Overview

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

Martz May 2010
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Gal 4 Transcriptional Regulator Protein. DNA
Double Helix (Chain / Chain). Lysine 18 sits in
DNA Major Groove recognizing CGG.
Martz May 2010 1d66
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Animation Created by Polyview-3D (using PyMOL)
Martz May 2010 1d66