From Proteopedia

Jump to: navigation, search


For users: browsing and displaying

You can use Proteopedia as a reference resource, without authoring any content yourself.

Generic help in using Proteopedia

  • For assistance with searching for something in Proteopedia, try Help:Searching.
  • Browse Proteopedia's Table of Contents.
  • Check out the Structure Index.
  • Each of the ~150,000 macromolecular models in the Protein Data Bank has a page in Proteopedia. To see some examples, click on Random in the navigation box on the left side of this page.
    • To keep this page visible, right-click on Random (Ctrl-click on Macs) and then click on Open Link in New Tab.
  • For definitions of terms, and explanations of concepts in structural biology, see About Macromolecular Structure. Many articles are listed there, for example Amino Acids and Resolution.

Proteopedia Speed

  • Render faster: If you have Java available on your computer, molecular models in Proteopedia pages will be rendered faster:

Teaching and Education

Software for use with Proteopedia

For authors: contributing content

The sections below concern authoring new content, or improving existing content, in Proteopedia.

Getting Started Authoring (including Beginners Primer)

Creating Molecular Scenes

  • For step-by-step instructions on creating example molecular scenes, try Proteopedia:DIY:Scenes.
  • If your molecular scenes require a model that is not published in the Protein Data Bank, see Help:Uploading molecules. See also Biological Unit: Showing and instructions for hiding portions of a model at Getting Started.
  • If you save a page and get XML Error: Mismatched tag at line 1, don't worry, you can recover your page: see Help:Errors.
  • If rotating model looks different than the still rendering read Rotating vs still models
  • For simple recipes for including Flash, Imagemap, Floating quote Box, Movies (.mov, .mpeg) etc., try Proteopedia:Cookbook.
  • If you do not see the Scene Authoring Tool (SAT) when editing a page: please disable 'Show preview on first edit' in the 'Editing' tab within 'my preferences'. Additionally, the SAT will never be displayed while the editing changes are being previewed (you clicked on the 'Show Preview' button).

Static Images

Interactive 3D "Supplementary Materials" for Journal Publications

Protecting Pages


  • For examples of Proteopedia articles in non-English languages, and for the rules and policies for such articles, please see Proteopedia:Languages. *For instructions for translating articles to other languages, see Help:Language Translation.
  • See also Text Directionality regarding right-to-left languages such as Arabic or Hebrew.

Proteopedia Speed

  • Proteopedia will render faster in your computer if you enable the use of Java (see above).
  • Create fast pages: Following these simple tips your Proteopedia pages might load and render faster.


Users of Proteopedia are invited to comment on published structures. Comments can raise questions about the interpretation, validity or quality of the model, cite other pertinent resources, congratulate the authors on a job well done, discuss implications of the model, etc.

How to comment on articles or published structures: Log in to Proteopedia and add your comment by editing the discussion tab associated with each page. You can comment on any page in Proteopedia.


See Help:Errors for guidelines on how to proceed when your page seems gone forever.


Feel free to contact us with any questions or suggestions.

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Jaime Prilusky, Joel L. Sussman, Angel Herraez, Eran Hodis, Wayne Decatur

Personal tools