go to workshops.molviz.org find today’s workshop and click on syllabus today’s syllabus will...
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Structural Biologists X-ray crystallography NMR spectroscopy High-resolution electron microscopy Theoretical modelingTRANSCRIPT
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• 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:
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Introductions
1. Name2. Whose lab you work in3. Research interest (very brief)
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Structural Biologists
• X-ray crystallography• NMR spectroscopy• High-resolution electron microscopy• Theoretical modeling
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Visualization:Exploring an existing molecular model.
Modeling:Creating a new molecular model or
changing the conformation or composition of an existing model.
Terminology
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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 Models2. Understanding The Models3. Sharing Structure-Function Information
Martz – May 2010
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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
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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
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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 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.
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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
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Gal 4 Transcriptional Regulator Protein.DNA Double Helix (Chain / Chain).Lysine 18 sits in DNA Major Grooverecognizing CGG.
Martz – May 2010 – 1d66
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Animation Created by Polyview-3D(using PyMOL)
Martz – May 2010 – 1d66