[Molvis-list] Jmol version Protein Explorer?

[Eric Martz]

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
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