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 See http://jmol.sourceforge.net/technotes/ (maybe a bit out of date -- it's a bit more complicated than that now, since we have Maya, VMRL, and PovRAY exporters) 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
