very good news from the jmol project leader - see below - William
(Sent from my iPhone.) Begin forwarded message: > From: Bob Hanson <[EMAIL PROTECTED]> > Date: December 24, 2007 4:19:58 PM MST > To: [EMAIL PROTECTED] > Subject: Re: [Jmol-developers] Jmol and Mathematics Visualization > Reply-To: [EMAIL PROTECTED] > > Dear William, > > William Stein wrote: > >> Hello Jmol-Devel, >> >> I'm the project directory of Sage (http://sagemath.org), an open >> source mathematics software project, >> which -- among other things -- has a web-browser based graphical >> interface. See screenshots here: >> >> http://sagemath.org/screen_shots/ >> >> After searching for a long time for a good open source option for 3d >> *interactive* graphics embedded >> in the Sage notebook it seems that jmol is -- oddly enough -- the >> best option, even though you guys >> designed it for chemistry. >> > Oh, I am not surprised. Jmol has some very nice capabilities that have > nothing to do with chemistry. We are delighted to see this expanded > use. > > >> We've been adapting it for doing general >> mathematical visualization, and >> just included it standard in sage-2.9.1, which was released today. >> >> >> > I would be very interested in hearing about some of your adaptations. > >> 1. What is the relation between javaview and jmol? >> >> > what is javaview? --OK (see below) > >> 2. What is the relation between java3d and jmol? >> >> > jmol uses no java3d. See http://jmol.sourceforge.net/technotes/ > (maybe a > bit out of date -- it's a bit more complicated than that now, since we > have Maya, VMRL, and PovRAY exporters) > >> 3. Are you aware of jmol being used for applications outside of >> chemistry? E.g., applications >> to general mathematical visualization? >> >> > I am not > >> 4. Do you have any advice as to how jmol could be best used for >> more general >> mathematical visualization? We can use/abuse the existing >> molecular modeling >> interface, but perhaps we should somehow coordinate with you and >> modify >> jmol itself to have more general functionality? >> >> > I would love to collaborate with you on this, either to incorporate > generally useful mathematical functionality or help you develop a > "JmolMath" adaptation. Isosurfaces in particular have been worked on > quite a bit, and you can map f(x,y) at least onto an isosurface > directly. > > One of the nice aspects of how Jmol is set up is that we can now add > functionality with virtually no expense to general users. The > functionality is all modularized into separate Jar files so that only > that functionality that is used is loaded. You get a basic package, > then > only if you use biomolecular systems, for example, does the browser > download those. If you create math-related functionality, we can add > it > in that way as well. > > >> 5. Viewing examples here: >> http://www.javaview.de/demo/index.html >> Do you think we can do as good -- or better -- then they do, but >> using jmol? >> >> >> > I don't see anything at http://sagemath.org/screen_shots/misc/ that > couldn't be done today in Jmol. One thing we don't have is nice > graphical axis rendering. But that should be pretty easy to implement. > All the surfaces would be no problem. You would want to add a > calculation engine that runs the mathematical calculation and creates > either the isosurface itself or a scalar field that can be used to > generate an isosurface based on it. > > The demo animations at javaview's site could be more involved, but > that > just means they would be an interesting challenge. > Objects such as I see at http://www.javaview.de/demo/ > PaParmSurface.html > would look WAY better in Jmol, because you wouldn't have them be so > grainy. We can run 100s of thousands of triangles with almost no delay > in real-time rotations. > > I think the hardest part would be the translation of a string like > "2./(1.+(u*sin(v))^2)*sqrt(1.+u*u)*sin(v)*cos(u-atan(u))" into real > math. But maybe that's not a big deal for you. > > Bob Hanson > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > --- > ---------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Jmol-developers mailing list > [EMAIL PROTECTED] > https://lists.sourceforge.net/lists/listinfo/jmol-developers --~--~---------~--~----~------------~-------~--~----~ 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/ -~----------~----~----~----~------~----~------~--~---
