User:Wayne Decatur/Biochem642 Molecular Visualization 2010 Fall Sessions

From Proteopedia

Revision as of 17:25, 27 October 2010

Introduction

• Logistical information about class today and next week and problem sets
• Importance of Structural Biology
  • Important for understanding function
  • helpful representations and models for people learning
  • Nobel prizes 2009 studies of the structure and function of the ribosome structure.
• Structural Biology for Non-structural Biologists
  • MolviZ "Top 5"
  • items III-V pertinent today
  • particularly item III shows us how we can explore structures.
• Proteopedia - interactive 3D encylopedia of macromolecular structures and structural biology resources to which scientists contribute and use to share structural biology content
  • Proteopedia allows sharing of structural biology data in a 3D, interactive manner
    • Plant Viral Protein p19 Suppression of RNA Silencing
    • Glutamate receptor
  • Resources and information
    • About Macromolecular Structure
    • Searching
      • 2 means - example search net charge

• • Proteopedia has an entry for every PDB entry with links to useful items
    • PDB 4 digit alphanumeric accession number, similar to a PubMed ID or Genbank sequence accession number
    • Conservation: 5cyt, explanation, and see also The ConSurf Database and The ConSurf Server (Note: This is also item IV at MolviZ "Top 5".)
    • RCSB = Protein Data Bank - use link under 5cyt to RCSB

• Protein Data Bank
  • X-ray crystallography, NMR, and cryo-EM structures - total 68,840
  • From FAQ: "Since October 15, 2006, PDB depositions have been restricted to atomic coordinates that are substantially determined by experimental measurements on specimens containing biological macromolecules."
  • Slide on overview of crystallography, NMR, and cryo-EM structures
  • I'll point you to Eric Martz's recent workshop if you seek more information in 3D-interactive examples on on resolution, temperature (b-factors, and electron density maps.

• • • Plant Viral Protein p19 Suppression of RNA Silencing

• 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 Structures

• Proteopedia: 1d66
  • Spin
  • Quality toggle
  • Popup
  • Conservation: 5cyt, explanation, and see also The ConSurf Database and The ConSurf Server (Note: This is also item IV at MolviZ "Top 5".)
  • FirstGlance in Jmol from 1d66 entry in Proteopedia
    • Views and Convenience buttons
      • How many chains?
      • Spin
      • Hover (special to FirstGlance is ability to click and display identity; hover more general in Jmol. Model number would be shown if more than 1.)
      • Water
      • Labels
      • N→C Rainbow
      • Composition
      • Cartoon
      • Charge/Hydrophobic
      • Slab
      • Turn slab off and hit cartoon again. Where are the Ligands? 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 (salt bridges come up first)
    • Reset, Snapshot Gallery
    • 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. (Note: This is also item V at MolviZ "Top 5".)

Authoring pages and scenes

• Proteopedia:Video Guide
• How to edit pages in Proteopedia → Example 1, example 2, and example 3 of edited topic pages.
• Special:Upload List of allowed file types: png, jpg, jpeg, tiff, tif, gif, mgif, pdb, cif, mmcif, cml, mol, xyz, kin, mmol
• Proteopedia's Scene Authoring Tools
• Perform basic editing and creation of scenes in your Sandboxes
• 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 via a web server with forms.
• 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
• User:Tom Gluick/glutamine synthetase (University of Maryland, Baltimore County). Includes instructions for using Jmol commands in the Jmol console for advanced scene authoring.
• Jmol Command Reference Manual for advanced scene authoring in Jmol using commands because direct scripting works for Proteopedia too.
• Comparison of Jmol tutorial-authoring systems
• Copying FirstGlance in Jmol 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 Tutorial-Authoring Template (JTAT) describes and works for developing and viewing scenes offline or developing and viewing privately.
• Morphing allow displaying the visual transition between two molecular conformations.
• Polyview-3D, fancy PyMol views and animations made super easy via a web server with forms.
• eMovie,a PyMol plug-in for macromolecular movie-making.

Class Sandboxes