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