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

[April Bednarski]

Hi Eric,
I just wanted to say that we would definitely be interested in using  
the Jmol interactive protein structure tutorial you mentioned.  We  
would actually like to use something like that for both our intro  
course and our nonmajors course.  If you would like assessment data  
from us on using the tutorial, we would also do that!  When do you  
think this would be ready for testing in classrooms?
April

On Nov 23, 2004, at 2:02 PM, Eric Martz wrote:

>
>
> >---------------------------- 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
> duplication.
>
> -Eric Martz
>
> /* - - - - - - - - - - - - - - - - - - - - - - - - - - -
>  Protein Explorer - 3D Visualization: http://proteinexplorer.org
> Workshops: http://www.umass.edu/molvis/workshop
> Biochem Structure Tutorials http://MolviZ.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://molvis.sdsc.edu/atlas/atlas.htm
> PDB Lite Macromolecule Finder: http://pdblite.org
> Molecular Visualization EMail List (molvis-list):
>         http://bioinformatics.org/mailman/listinfo/molvis-list
>
> Eric Martz, Professor Emeritus, Dept Microbiology
>  U Mass, Amherst MA US  413-545-2325/FAX 413-545-2532
>                 http://www.umass.edu/molvis/martz
> - - - - - - - - - - - - - - - - - - - - - - - - - - - */
>
> _______________________________________________
> Molvis-list mailing list
>  Molvis-list at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/molvis-list