User:Wayne Decatur/Biochem642 Molecular Visualization Sessions

From Proteopedia

Revision as of 22:18, 26 October 2009

Introduction

• Nobel prizes 2009 studies of the structure and function of the ribosome structure.
• Structures:
  • X-ray crystallography and resolution
  • NMR
  • Cryo-EM
  • Theoretical Models
• The Protein Data Bank
  • PDB Statistics
  • search 1d66 - display text of PDB file
• MolviZ "Top 5" item III shows us how we can explore structures.
  • FirstGlance in Jmol
  • Proteopedia allows viewing scenes, as well as creating and saving scenes. Hosts a lot of resources in information too.
    • Example of resources and information: About Macromolecular Structure
    • Searching: 2 means - example net charge

Viewing Strucutues

• Proteopedia: 1d66
  • Conservation: 5cyt, explanation, and see also The ConSurf Database and The ConSurf Server
  • Quality toggle
  • Popup
  • FirstGlance in Jmol from 1d66 entry in Proteopedia
    • Views and Convenience buttons
      • How many chains?
      • Spin
      • Water
      • Labels
      • N→C Rainbow
      • Composition
      • Cartoon
      • Charge/Hydrophobic
      • Slab
      • Be aware when Ligands are on or off; ligands are often interesting moieties in the structure.
    • Center atom
    • Gaps - I'd suggest helpful PDBSum linked to at Proteopedia vs. less clear Sequence at PDB or S2C (compare 2ace)
    • More Views
      • Distance measuring
      • Cation-Pi interactions
    • Contacts

• Polyview-3D for when you need an animation or extremely high-quality (most times the high quality button on Jmol is sufficient) static image.

Authoring pages and scenes

• Proteopedia:Video Guide
• How to edit pages in Proteopedia
• Special:Upload List of allowed file types: png, jpg, jpeg, tiff, tif, gif, mgif, pdb, cif, mmcif, cml, mol, xyz, kin, mmol
• LOGIN AND GO TO YOUR SANDBOX
• Proteopedia's Scene Authoring Tools
• Load molecule: 1d66
• Make a scene (view) and add it to your Sandbox page.
• Load that same scene again in the Scene Authoring Tools using the load scene tab, modify it, and save a new scene.
• Copying FirstGlance Scenes into Proteopedia
• Proteopedia pages can be exported for offline viewing using the toolbox on the left.

Resources

Molecular Visualization

• About Macromolecular Structure
• Proteopedia - a scientific 'wiki' bridging the rift between 3D structure and function of biomacromolecules, Eran Hodis, Jaime Prilusky, Eric Martz, Israel Silman, John Moult and Joel L Sussman. Genome Biology 9:R121, August 2008 or doi:10.1186/gb-2008-9-8-r121
• MolviZ "Top 5"
• MolviZ.Org
• Protein Explorer's Glossary
• Eric Martz's recent workshop at his list of workshops.
• Jmol Application
• Pymol
• Polyview-3D, fancy Pymol views and animations made super easy.
• Swiss-pdb Viewer a.k.a Deep View
• Protein Explorer

Authoring Scenes and Views in Proteopedia and beyond

• Proteopedia:Video Guide
• Proteopedia's Scene Authoring Tools
• Example of scenes without and with transitions
• User:Tom Gluick/glutamine synthetase (University of Maryland, Baltimore County). Includes instructions for using Jmol commands in the Jmol console for advanced scene authoring.
• Comparison of Jmol tutorial-authoring systems
• Taking a View in FirstGlance in Jmol and making a Proteopedia Scene
• Copying FirstGlance Scenes into Proteopedia
• Jmol Protein Explorer's powerful Quickviews approach really helps quickly generate particular scenes or ideas for scenes to generate elsewhere. Using the information detailed here or at the JTAT site on extracting state scripts, it is possible to go from these views to Proteopedia scenes; however, as the version of Jmol differs there may be discrepancies and issues.
• Jmol Command Reference Manual for advanced scene authoring in Jmol using commands because direct scripting works for Proteopedia too.
• Jmol Tutorial-Authoring Template (JTAT) describes and works for developing and viewing scenes offline or developing and viewing privately.
• Polyview-3D, fancy Pymol views and animations made super easy.
• eMovie,a PyMOL plug-in for macromolecular movie-making.

Class Sandboxes