http://Proteopedia.Org is a new Jmol-based server developed 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 -- perhaps the most exciting.
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 text about your favorite molecules, to add scenes that show key features, and to suggest ideas for technical improvements to best exploit Jmol. It is expected that, as visitors add content, Proteopedia will develop into one of the most useful on-line reference sites for structural information about macromolecules. Proteopedia already contains an automatically-generated page for each of the nearly 50,000 entries in the Protein Data Bank. This automatic page contains the molecule in Jmol, with green links to display every site and ligand in the PDB file (echoing their full names), the abstract of the paper, and links to a few other particularly useful structure services and resources. Students and Educators can develop macromolecular structure tutorials in Proteopedia far more easily than in any other system at present. 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 class 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. Proteopedia uses MediaWiki, and was greatly facilitated by Nico Vervelle's Jmol Extension. Have fun! -Eric ---- Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US http://www.umass.edu/molvis/martz ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Register now and save $200. Hurry, offer ends at 11:59 p.m., Monday, April 7! Use priority code J8TLD2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
