go to workshops.molviz.org find today’s workshop and click on syllabus today’s syllabus will...
DESCRIPTION
Structural Biologists X-ray crystallography NMR spectroscopy High-resolution electron microscopy Theoretical modelingTRANSCRIPT
• 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