[Molvis-list] Re: [Jmol-users] Protein Explorer equivalent for Jmol

Eric Martz emartz at microbio.umass.edu
Tue Nov 23 15:02:08 EST 2004

>---------------------------- Mensaje original ----------------------------
>Asunto: [Jmol-users] Protein Explorer equivalent for Jmol
>De:     "Jeff Hansen" <jhansen at depauw.edu>
>Fecha:  Mar, 23 de Noviembre de 2004, 13:08
>Para:   jmol-users at lists.sourceforge.net
>Does anyone know if there is an equivalent to Protein Explorer for  Jmol?
>I know Protein Explorer is used by a lot of people for teaching  protein
>structure.  It would be nice to have a Jmol version since Chime  is not
>available on all platforms.

I am the principal developer of Protein Explorer (PE-Chime), and I 
certainly agree. I know of no equivalent in Jmol.

In the long range, I hope to port Protein Explorer to Jmol (PE-Jmol), 
eliminating the need for Chime. However, in the short range (on the order 
of a year) I first want to release some largely-completed enhancements to 
PE-Chime. I know these enhancements will be immediately widely used, and I 
suspect that once I begin serious work towards PE-Jmol, there will be a 
long (one year?) delay before I can release anything with functionality 
close to the present PE-Chime capabilities.

There are a number of issues. PE-Chime has been significantly constrained 
by the limitations of Chime. Jmol has a different and potentially 
less-constraining set of limitations. Therefore, some re-design should 
ideally be involved in PE-Jmol. Also it will probably be best to have 
PE-Jmol-unsigned-applet with more limitations than PE-Jmol-signed-applet 
(Jmol-signed-applet being not yet available, but planned).

All that being said, I am not opposed should someone else wish to undertake 
porting PE to Jmol now. However, I cannot devote a lot of time helping with 
a Jmol port at this stage. The PE source code (javascript) is available 
freely with every download. When time permits, I plan to make PE a truly 
open-source project. Already volunteers have contributed substantially to 
compatibility with Internet Explorer (Jean Philippe Demers, Paul Pillot -- 
released a couple of years ago), translation to Spanish (Gabriel Pons, 
released), and compatibility with Mozilla (Enrique Castro, not yet released).

By taking the time I need to ensure good quality and consistency throughout 
PE with each new version, I am a bottlneck as well as its principal 
developer. I am not opposed to parallel development by another party 
responsible for their own distribution, under an open source license. 
Parallel development of course leads to lots of problems. An example is the 
Spanish translation of PE-Chime which started with version 2.1 Alpha and 
then had later enhancements shoehorned into it. This is partly my fault for 
not designing PE to facilitate translation, and partly because PE-Chime is 
a moving target.

Along with many minor enhancements and cleaning up of documentation, the 
major enhancements I plan for the near future to PE-Chime are:
  - Compatibility with Mozilla/Netscape 7
  - Script recorder (already completed by Tim Driscoll, but not yet fully 
integrated into PE)
  - Support for Presentations in Protein Explorer (PiPE)

(Pre-alpha, in-development implementations of the latter two are already 
available, but not widely advertised.) Once these are released and in good 
shape, I expect to feel ready to tackle PE-Jmol, perhaps in late 2005 or 
early 2006.

Meanwhile, my team (Tim Driscoll, Frieda Reichsman, and Miguel Howard) have 
initiated development of a new, open source, Jmol-based tutorial on protein 
structure because the requirements for this tutorial precluded it being 
"within" PE-Chime. We plan to release the "shell" or "template" for the new 
tutorial in the hope that others will use it for new tutorials on other 
topics. A crucial component will be a javascript-based question-posing and 
response system. It is high time that molecular structure tutorials started 
to demand substantive responses from students. Although it is still in 
early stages, anyone interested in using such a question-posing and 
response system should contact us to collaborate and minimize unnecessary 

-Eric Martz

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Protein Explorer - 3D Visualization: http://proteinexplorer.org
Workshops: http://www.umass.edu/molvis/workshop
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World Index of Molecular Visualization Resources: http://molvisindex.org
ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm
PDB Lite Macromolecule Finder: http://pdblite.org
Molecular Visualization EMail List (molvis-list):

Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst MA US  413-545-2325/FAX 413-545-2532
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