On Dec 25, 2007 7:38 AM, Bob Hanson -- Jmol <[EMAIL PROTECTED]> wrote: > > 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
Offtopic: I guess it's not this one: http://en.wikipedia.org/wiki/Michael_Howard Nor this one: http://en.wikipedia.org/wiki/Michael_Howard_(Microsoft) :) I didn't find his page, if he has any. But anyway, we used jmol in: http://nanocrystallography.research.pdx.edu/ I was involved in this project a few years back and you did a tremendous job with jmol. Ondrej --~--~---------~--~----~------------~-------~--~----~ 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/ -~----------~----~----~----~------~----~------~--~---
