At 4/15/2007, Joan Slonczewski wrote: > Has anyone seen an interface similar to Protein Explorer based on > Jmol? > > Joan L. Slonczewski > Kenyon College Dear Joan, To the best of my knowledge, the Jmol tool closest to Protein Explorer is FirstGlance in Jmol (http://firstglance.jmol.org ) -- but it lacks most of the help and much of the power of PE. Probably you have seen the brief comparison at http://proteinexplorer.org Since Feb 1, 2007, FirstGlance in Jmol has been used in 670 sessions/ week, while 580 PE sessions/week get into QuickViews. For the same interval of last year, the numbers were 325/week and 600/week respectively. Jmol itself is evolving at an amazing pace (thanks recently largely to Bob Hanson). It now has dozens of powerful capabilities lacking in Chime, and more every week it seems. I am waiting a bit until Jmol's capabilities have settled down before beginning to design and implement a PE-Jmol. Eventually I do hope to do that, but it seems to me a large project that will take several years to do well, and I hope to apply for new funding first. So nothing that I know about is in the offing near term. Meanwhile, anyone who wishes is free to begin a port of PE to Jmol without me! (I'm happy to help people find relevant portions of PE's javascript.) Incidentally, the primary public FirstGlance in Jmol (version 1.0, released early in 2006) still uses Jmol 10.2 because there are many issues that need to be revisited in considerable detail, with the javascript and help in FirstGlance being revised as needed, before I can certify that FirstGlance will work "as advertised" with the current Jmol version 11+. And the current Jmol offers many new opportunities for FirstGlance. Meanwhile FirstGlance in Jmol has been adapted to color a protein by evolutionary conservation at the ConSurf server (http:// consurf.tau.ac.il). Protein Explorer remains alive and well for now, working best in Firefox on Windows. Intel Mac OSX users can run Windows on their OSX desktop (using parallels.com), then run Protein Explorer much better than in the old Mac Classic mode. Although not free, installation of Windows into Parallels.Com Desktop for Mac is a breeze (automated by Parallels). Regards, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://workshops.proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.proteinexplorer.org PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://bioinformatics.org/mailman/listinfo/molvis-list - - - - - - - - - - - - - - - - - - - - - - - - - - - */