User:Wayne Decatur/NASCE2011: Difference between revisions
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General Introduction
Introduction to Proteopedia
Under the Hood
Jmol
The Structure Data
Protein Data Bank
Proteopedia
Types of Proteopedia pages
Topic Pages
User Pages
PDB Entry Pages
FirstGlance in Jmol
Structural Biology for Non-structural Biologists
Proteopedia Page Authoring
Proteopedia Scene Authoring
Time permitting
Resources
Macromolecular Visualization
Small Molecule Visualization and Model Kits
Topic Pages - Education
Authoring Scenes and Views in Proteopedia and beyond
Modeling
Class Sandboxes
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*Conveniences | *Conveniences | ||
**Buttons for 3D structure windows and other commonly used items | **Buttons for 3D structure windows and other commonly used items | ||
**Since a large amount of references are from | **Since a large amount of references are from PubMed, PMID all that is needed for references in text, combined with a reference list at end | ||
* [[Proteopedia:How to Make a Page]] | * [[Proteopedia:How to Make a Page]] | ||
*[[Help:Editing|How to edit pages in Proteopedia]] | *[[Help:Editing|How to edit pages in Proteopedia]] | ||
Revision as of 00:03, 13 July 2011
General IntroductionGeneral Introduction
- Thanks to the organizers of the NASCE2011
- About me
- Overview of the workshop planned
- Gauge Audience, Adjust plan?
Introduction to ProteopediaIntroduction to Proteopedia
- Main Page
- Sightseeing by way of example "Case Studies" / ""User Narratives"
- Topics
- main page--->Ribosome structure, spin, toggles, list, contributors --->page particular section ---> another page green links
- via search---> The Glutamate Receptor (GluA2) quality, popup, section window
- Open-ended Gateway
- learn of a structure in a meeting (Robert Milllar talk on Saturday) ---> Pubmed search result---> 2rh1
- Sites
- ConSurf
- Firstglance in Jmol
- new publication ---> 3rze Sites
- note where link to 3D structure at Nature publication goes
- learn of a structure in a meeting (Robert Milllar talk on Saturday) ---> Pubmed search result---> 2rh1
- Student aid - Proteopedia:Table of Contents -->Metabolism -->Carbohydrate Metabolism -->Citric Acid Cycle--> Citrate Synthase morphs and reaction steps in second section
- Lecturing
- User:Eric Martz/Nucleosomes
- resources for this workshop as listed under Workshops and Seminars on my user page as Workshop for the NASCE Meeting at the University of Michigan, Ann Arbor, MI July 13 2011
- Structural Biology Resource
- Student Projects
- Journal Club --> RecG Bound to Three-Way DNA Junction
- Communicating specific ideas in context of structure --> e-mail a link to a Sandbox, e.g. Sandbox CsrA
- Group meeting ---> Proteopedia:Workbench, also good for preparing for publication
- Publications
- Topics
Under the HoodUnder the Hood
- Wiki implementation, very specialized
- references
- Create a page for example with references
- other technical aspects related to Jmol and other media
- references
- Jmol
JmolJmol
- Jmol
- The Application
- The Java Applet - Demonstration with Human Follicle-Stimulating Hormone Complexed with its Receptor
- Advanced Options
- Console
- Compare Command Demonstration
- Sculpting - Simple example of that here
- 3D options - Demo with Hormone
The Structure DataThe Structure Data
- everything centers around an Atomic coordinate file
- Experimental vs theoretical sources
Protein Data BankProtein Data Bank
- nearly 75,000 X-ray crystallography, NMR, and cryo-EM structures
- PDB statistics
- about 85% are crystallographic structures
- Isomesh of electron density helps illustrate how crystallographic models get built using a portion of one
- Caveat: Keep in mind these are models - Not all models created equally
- one gauge [Resolution]] noted with a link on each PDB entry page
ProteopediaProteopedia
- Proteopedia - interactive 3D encylopedia of macromolecular structures and structural biology resources to which scientists contribute and use to share structural biology content
- User or Sandbox login
- We encourage you all to become users of any sort. If you become a registered, you can save information in your userspace regardless of your overall contribution to public spaces.
Types of Proteopedia pagesTypes of Proteopedia pages
- Topic Pages
- Macromolecular Structures
- About Macromolecular Structure
- PDB Entry Pages
- User space Pages
- Sandbox Pages
- Workbench Pages
- Interactive 3D Complements (I3DC) - Journal of Biological Inorganic Chemistry
- Administrative
- How To/Guides
- Organizational/Table of Contents
- Main Page - the main gateway
Topic PagesTopic Pages
- Additional examples of topic pages concerning structures
- Hemolysin
- Proteopedia pages can be exported for offline viewing using the toolbox on the left.
- Hemolysin
- Information and Resource Collection, as well
User PagesUser Pages
- Other users cannot edit pages in this space
PDB Entry PagesPDB Entry Pages
- Proteopedia has an entry for every PDB entry (nearly 75,000) with interactive scene links and links to useful resources
- Example 1p3v (PDB 4 digit alphanumeric accession number)
- Conservation: , explanation, and see also The ConSurf Database and The ConSurf Server Other examples: 4enl or 5cyt
- Show how to use ConSurf
- Example 1p3v (PDB 4 digit alphanumeric accession number)
FirstGlance in JmolFirstGlance in Jmol
- Views and Convenience buttons
- How many chains? - Use 3pla
- Key Resources:
- Biological Unit
- Missing pieces?; PDBsum link on Proteopedia entry pages helpful for this as well
- Under adoptions on main page , there is Orientations of Proteins in Membranes (OPM) database from the University of Michigan (Ann Arbor, Michigan, USA), which could be useful for several proteins involved in endocrinology, example 2rh1
- Also accessible via Membrane proteins from within Proteopedia
Structural Biology for Non-structural BiologistsStructural Biology for Non-structural Biologists
- MolviZ "Top 5" by Eric Martz
- Polyview-3D = fancy PyMol views and animations made super easy via a web server with forms.
- Example for 2rh1
- Use overall structure with ligands off; under chain and color rendering chain a as cartoon and hide remaining; under individual residue highlight enter a:408:cf,a:290:ms from converter
- 2rh1 from Polyview-3D
- Makes animations too and/or morphs as well using a file with multiple models
- Example for 2rh1
Proteopedia Page AuthoringProteopedia Page Authoring
- Model of a wiki
- Sandbox - there is a "student" login that can be used by groups for editing these for teaching purposes
- Conveniences
- Buttons for 3D structure windows and other commonly used items
- Since a large amount of references are from PubMed, PMID all that is needed for references in text, combined with a reference list at end
- Proteopedia:How to Make a Page
- 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
Proteopedia Scene AuthoringProteopedia Scene Authoring
- Proteopedia's Scene Authoring Tools
- Load a structure 3ciy or previous scene
- Set your scene. Undo/Redo features.
- Save your scene
- Add the scene to the page
- Try it out and then add and improve. Repeat.
Time permittingTime permitting
- Advanced scenes/toggles - Human Follicle-Stimulating Hormone Complexed with its Receptor has several examples
- Morphing allows displaying the visual transition between two molecular conformations.
- Pymol to Jmol conversion built into Proteopedia's Scene Authoring Tools
- Jmol works with small molecules too
- Works with small molecules too and even can do energy minimization with them
- Can be used to show chemical reactions
- Recalling the Caveat: Keep in mind these are models -Not only are not all models models created equally, not even all portions of models are created equally
- Assessing structure
- Resolution noted with a link on each PDB entry page
- Temperature factors, also see demonstration here
- Gaps, i.e. missing pieces (see above)
ResourcesResources
Macromolecular VisualizationMacromolecular Visualization
- Eric Martz's recent workshop at his list of workshops.
- 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
- About Macromolecular Structure
- FirstGlance in Jmol is very useful for exploring PDB entries or upload structure files.
- Jmol Protein Explorer's powerful Quickviews approach really helps quickly generate useful views. This effort is building Chime-based Protein Explorer to work with Jmol, and a few features may still not yet work.
- MolviZ "Top 5"
- MolviZ.Org
- Protein Explorer's Glossary
- Jmol Application
- PyMol
- 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.
Small Molecule Visualization and Model KitsSmall Molecule Visualization and Model Kits
- CheMagic Virtual Molecular Model Kit
- The Jmol Interface by Mike Evans at University of Illinois has a model kit interface and easy ways to arrows and items.
- ChemCanvas, an open source chemical diagram editor
- ChemTube3D has interactive animations and structures of molecules and reactions important in chemistry.
- Service allowing young people to look up a molecule and blow it up and put it back together
Topic Pages - EducationTopic Pages - Education
Authoring Scenes and Views in Proteopedia and beyondAuthoring Scenes and Views in Proteopedia and beyond
- Proteopedia:Video Guide
- Proteopedia:How to Make a Page
- 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
- 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.
- Jmol Command Reference Manual for advanced scene authoring.
- Jmol Wiki
- Morphing allows displaying the visual transition between two molecular conformations.
- Polyview-3D, fancy PyMol views and animations made super easy via a web server with forms.
ModelingModeling
- See the end of Eric Martz's recent workshop syllabus where he covers homology (more accurately, comparative) modeling.
- A Feb. 1st 2011 news item about Yang Zhang and his work.
- Mutating an amino acid in a proteins - here with PyMOL and here with Swiss PDB-Viewer
- Homology modeling
- Comparative Modeling
- Ab Initio and Molecular Dynamics