OK, from the exchanges of 12/14/07 and since, you guys are pretty fast. I'm impressed. Allow me to introduce myself. http://www.stolaf.edu/people/hansonr. Professor of Chemistry, St. Olaf College; Current Principal Developer, Jmol.
What can I tell you about Jmol? Sounds like you have found the documentation and experimented a bit with at least writing some pmesh files that Jmol can read. Also take a look at the HTML files in http://chemapps.stolaf.edu/jmol/docs/examples-11, particularly: http://chemapps.stolaf.edu/jmol/docs/examples-11/pmesh.htm http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm http://chemapps.stolaf.edu/jmol/docs/examples-11/new2.htm http://chemapps.stolaf.edu/jmol/docs/examples-11/new0.htm We are just about to deliver Jmol 11.4.0, so a lot of recent work has been going into detailed testing of functionality. I see you are talking about pmesh. And if you like that, fine. It works great, but the script interface is a bit slow because of all the string parsing. We could set up a direct Java interface, or even a binary file format if that would help. Realize that there are two Jmol components -- the stand-alone application and the applet. The Jmol application has some interesting features, like command-line creation of JPG and PovRAY output, and generic "exporter" capability that is easily expanded. The applet has tremendous interactive capability, but not so much with pmesh objects as of now. Still, that could be possible, and the 3D annotation capabilities are really outstanding. (You can create 3D annotations ("echo"s) that can serve as hypertext links, for example, and you can create points in space that visible or not can be clicked on and will allow callbacks to the web page. The whole thing is connected with LiveConnect and scriptable via JavaScript. A very interesting capability of Jmol that has arisen in the past year is the capability to save and restore the current state of the applet - everything. So if you set up a "scene" in the application you can just write the state file to disk and open it with the applet, and you will be right where you left off. This has been used in a variety of contexts to good effect. I've been interested in exploring it in terms of collaborative visualization. (I do something, save a state, send it to you, you load it and see the exact same thing.) You might be interested in that. Recent work you might also be interested in is in the area of synchonization -- multiple applets can be synchronized so that commands or mouse actions on one drive the others. This is working perfectly now, and it is just one step away from being able to script remotely so that, for instance, multiple people viewing the same page could see the same real-time 3D manipulations of a mathematical object. I'd be very interested in your feedback relating to the JVXL format for isosurface compression. We think we have a winner there. It really makes isosurfaces deliverable over the web for the first time. This has started to see use for the delivery of protein surfaces. See http://chemapps.stolaf.edu/jmol/docs/misc/JVXL_format.pdf I put together a little page for you guys to experiment with. It's at http://chemapps.stolaf.edu/jmol/docs/examples-11/math.htm Try a few things there; see what you think. The example uses 100,000 quadrilaterals, and it's pretty fast in terms of rendering. Just to set the record straight -- the graphics engine was written by Michael Howard, a software engineer, not a chemist. Everyone who has looked at this cannot believe this is Java, and it's because Michael did such an outstanding job with the rasterization methods. No Java3D here; no OpenGL. Just bare-bones write-the-pixels coding. Unbelievable. I came on board a couple of years ago as a chemist with lots of software experience, but by then the Java primitives for graphics rendering were all in place. Credit for that goes exclusively to Michael (aka Miguel). I'm now the principal developer. My focus has been on expanding Jmol's capability within the molecular visualization world. But I'm thrilled that you folks are interested in it as well. Very cool. Q: What do you have now in the area of Java applets? Q: Is pmesh the right delivery mechanism? Or is there something else that can be delivered to Jmol, such as primitive function that let Jmol query for the values of x(u,v), y(u,v), z(u,v) and thus build its own pmesh internally? Something like: Point3f xyzFromUv(float u, float v); Could you build that into an accompanying applet, so the two could talk to each other? That could be fun. Q: Are you most interested in command-line/file-based interaction with the Jmol application? Or are you more interested in the possibilities involving the applet? Q: What are you using right now for the cool graphics I see at your site? In short, Jmol's success is all about collaboration and interdisciplinary discussion. In that spirit, I am quite excited that you might be interested in integrating Jmol with Sage. Looking forward to hearing from you, Bob Hanson (Current) Principal Developer, Jmol Professor of Chemistry, St. Olaf College [EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr --~--~---------~--~----~------------~-------~--~----~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://sage.scipy.org/sage/ and http://modular.math.washington.edu/sage/ -~----------~----~----~----~------~----~------~--~---
