>---------------------------- 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */