User:Wayne Decatur/UNH CME Workshop March 11 2011

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Introduction to Authoring Pages and Creating Scenes in Proteopedia



  • Overview of the workshop


Protein Data Bank


  • 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

Types of Proteopedia pages

Topic Pages

User Pages

  • Other users cannot edit pages in this space

PDB Entry Pages

  • Proteopedia has an entry for every PDB entry (over 70,000) with interactive scene links and links to useful resources

FirstGlance 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

Assessing structure

Structural Biology for Non-structural Biologists

Proteopedia 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 Pub-Med, PMID all that is needed for references in text, combined with a reference list at end
  • Help:Getting Started in Proteopedia
  • 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 Authoring

  • Proteopedia's Scene Authoring Tools
    • Load a structure 2zi0 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 permitting



Macromolecular Visualization

Small Molecule Visualization and Model Kits

Topic Pages - Education

Authoring Scenes and Views in Proteopedia and beyond



  1. B. Bienfait and P. Ertl, JSME: a free molecule editor in JavaScript, Journal of Cheminformatics 5:24 (2013) article

Class Sandboxes

Sandbox Reserved 171 Sandbox Reserved 181
Sandbox Reserved 172 Sandbox Reserved 182
Sandbox Reserved 173 Sandbox Reserved 183
Sandbox Reserved 174 Sandbox Reserved 184
Sandbox Reserved 175 Sandbox Reserved 185
Sandbox Reserved 176
Sandbox Reserved 177
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Sandbox Reserved 179
Sandbox Reserved 180

Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur

Personal tools