[Molvis-list] Proteopedia.Org: A Jmol wiki with scene authoring tools

Eric Martz emartz at microbio.umass.edu
Sat May 3 20:45:57 EDT 2008

http://Proteopedia.Org is a new Jmol-based server developed primarily 
by Joel L. Sussman (an eminent crystallographer and former Head of 
the Protein Data Bank), Jaime Prilusky (author of The OCA PDB Browser 
and Head of the Bioinformatics Unit at the Weizmann Institute), and 
Eran Hodis (developer of the eMovie PyMol plugin for macromolecular 
movie making) at the Weizmann Institute in Israel. I think it is one 
of the most exciting uses of Jmol that I have seen, and a 
breakthrough in molecular visualization accessibility.

Proteopedia is a good place to start exploring a macromolecule. 
All >50,000 published macromolecules already have pages, each with 
the molecule in Jmol, the abstract from the publication plus "green 
links" that highlight the ligands (showing their full names) and 
functional sites in Jmol. Under each molecule are links to 
FirstGlance in Jmol and other salient resources.

Proteopedia is a wiki on macromolecular structure, so anyone can 
contribute (as in Wikipedia). Its most exciting innovation is a 
"Scene Authoring Tool" that makes it easy for those unfamiliar with 
the Jmol scripting language to develop custom molecular views, or 
scenes, in Jmol. These scenes are then automatically saved (as state 
scripts), and played back in Jmol from "green links" in the text. 
There can be as many applets per page as needed.

You are invited to add pages about your favorite molecules, 
incorporating interactive scenes that show key features.

Educators and students can develop interactive macromolecular 
structure tutorials in Proteopedia far more easily than in any other 
system presently available. Proteopedia can also be used for 
supplementary materials for journal publications, or laboratory websites.

For lecture presentations, supplementary materials or lab websites, 
those who contribute the content need to be able to guarantee that 
their pages will not be edited by others. Unlike Wikipedia, 
Proteopedia provides an easy solution. Each user has the option of 
creating protected pages that only s/he can edit. Others can copy, 
edit, and adapt the content from protected pages, since all content 
(including protected content) is bound to the GNU Free Document License.

I recently taught a course to 40-some researchers in which I 
introduced Proteopedia. I had the entire group try out the scene 
authoring tools concurrently on their laptops. I assigned each 
student a number from one to 40 by counting and pointing. Each 
student then used (or created) a page "Sandbox N", where N is that 
student's number (for example, "Sandbox 15" for the student assigned 
number 15). As in Wikipedia, Sandbox pages are places to practice. 
Their content is periodically cleared. Several ambitious students 
wanted to begin adding permanent content immediately, so they were 
given permanent login accounts immediately, during the class. Please 
get in touch with me if you will be needing student logins for Sandboxes.

Have fun! -Eric

Eric Martz, Professor Emeritus, Dept Microbiology
University of Massachusetts, Amherst MA US

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