PyMOL Users & Friends, There is a new kid on the block and he packs quite a punch. His name is Jmol v10 and all who have been looking to put molecular graphics content into a browser or Java applet need to take a close look at this cool new tool. It is a well-engineered free and open-source replacement to Chime available under the LGPL license. Unlike PyMOL, Jmol supports Chime scripts out of the box. Plus, Jmol has a fast software-based renderer that even Roger Sayle would be proud of. Probably the best way to try Jmol is to head on over to the PDB's new beta site:
<http://pdbbeta.rcsb.org/pdb/Welcome.do> and type in the 4-digit PDB code of your favorite structure at the top of the screen. One that's submitted, click on the Jmol tab right below the structure image. Jmol will open up momentarily. http://www.jmol.org is the main site where you can find more info and demos. One might ask why I draw so much attention to a product that could ostensibly compete with PyMOL. Well, here at DeLano Scientific LLC we utterly reject the notion that competitive concerns could ever provide a legitimate excuse to promote an inferior product we offer over something better from another source. That kind of customer dis-service provides no lasting benefit to anyone, especially within the scientific community. However, I am NOT saying that PyMOL is inferior to Jmol -- they just have different strengths. If you need fast live 3D molecules in a Web page or Java app today, DeLano Scientific does not even offer a solution for that yet. Jmol is a great tool you can adopt right now, and it is ideal if you already have Chime-based content ready to go. It's also worth pointing out that Jmol is one of the few compelling choices that fully complies with the same open-source principles that the PyMOL Open-Source Project adheres to: unrestricted usage, modification, and redistribution for all parties and for all purposes. PyMOL and Jmol aren't about competition, they're about addressing important unmet needs in industry and academia through open-source development and mutually-beneficial relationships between developers and users. There are no legal, business, or philosophical barriers to prevent creation of substantial interoperability between these two packages, either before or after the marketplace demands it. Delano Scientific LLC salutes Miguel, Egon, Chris, and the other Jmol developers for a job well done. There is a lot to the success of the Jmol project that the PyMOL effort could learn from -- whole number releases being just one small example ; ). I hope that Jmol and PyMOL can be used together with other tools like GROMACS, APBS, and MMTK to build new and more flexible ways of meeting your important scientific software needs. Furthermore, I think I can safely speak for all of us in asking that you all follow through when you are presented with the opportunity to help support open-source development, whether through subscription purchases, donations, capital contributions, grant approvals, or by simply citing the open-source tools you use in publications and presentations. Happy Holidays everyone! Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com Subject: Jmol version 10.00 - RELEASED Jmol version 10.00 was officially released on Friday 17 December 2004. I encourage you to visit http://www.jmol.org, download it, and take a look at it. Jmol is now a viable, fully functional, high performance, open source replacement for the Chime plugin. Those of you who have made investments in RasMol/Chime scripts over the years should now take a serious look at Jmol ... especially those of who who have build web tutorials and applications around the Chime plugin. On a personal note ... I have been working on this release full-time for two years ... so this is clearly a very important milestone for me. And I believe that it is important for the molecular visualization community. Those of you who have made investments in RasMol/Chime scripts, and especially in Chime web courseware, now have a migration path to an open source alternative, an applet written in Java, that does not require installation on the client, that runs on most major web browsers. I undertook this project under the encouragement of Dr. Jose Luis Lopez Perez at the University of Salamanca. Those who will use Jmol and benefit from it owe Jose Luis a debt of gratitude. !Gracias amigo! Miguel
