Hi, Tamas,
I agree with your assessment that there is a dilemma right now (thanks largely to Microsoft having removed java from Windows).
However, there is no question in my mind that jmol is the answer for the future, because it is under active development, has open source, and already works better than Chime/RasMol in some areas thanks to Miguel Howard's efforts. Chime in contrast has had no significant development for years, will apparently never be open source, and MDL has announced their intention to phase it out around 2007 in favor of something that may not have a free version.
Nevertheless, for 2005, I am continuing to develop Protein Explorer with Chime for several reasons. The main reason is that there is too much code involved to make a quick switch. I do intend to try to implement PE with jmol starting in 2006, but once I start that, it is unclear what big problems I may encounter, and how long there will be an eclipse with no released product. I am also hoping that some of the browser compatibility issues and limitations of jmol will be resolved before I start. In particular, it would be very useful to have the ability to render rolling-probe surfaces at least as well as Chime. Also I hope there will be a standard, well-tested and smooth solution to detecting the absence of java and guiding the user through java installation.
For new projects, unless there is a specific need that jmol does not and will not support soon, surely jmol is a safer bet. For upgrading existing Chime-based resources, I have no general recommendation since I have not yet worked with jmol myself and so have no experience to go on. For teaching, I think the best solution for 2005 is to be open minded and to use the best resources available, regardless of whether they use Chime, jmol, or some other underlying technology. Although they will complain, students need to learn how to install Chime and java and how to use Chime and jmol.
-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - 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
- - - - - - - - - - - - - - - - - - - - - - - - - - - */------------------------------------------------------- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
