---------- Forwarded message ---------- From: Miguel <[EMAIL PROTECTED]> Date: Dec 26, 2007 7:36 PM Subject: Re: [Jmol-developers] [sage-devel] Re: Jmol and Mathematics Visualization To: [EMAIL PROTECTED], [EMAIL PROTECTED]
> We've run into some issues, > e.g., > > http://trac.sagemath.org/sage_trac/ticket/1537 > > involving "triangulation and shadow weirdness" whose fix might involve > having > to actually change jmol. I suspect that you will encounter other issues with lighting on very flat triangles and "cracking" in triangulated surfaces. As I understand it, these are typical problems with graphics engines ... and there was never much demand for these kinds of things within Jmol. > Oh, cool, you can do translucent surfaces! Translucent surfaces were originally done through 'screening', where every-other pixel was painted. I think that Bob Hanson was did some rework in this area about 6 months ago. > Nice. The moveto is > also frickin' cool. Yes, I always thought that it was very neat. Excellent when you want to show a specific detail of a molecule. > I think it's just the first thing we thought of that would work somewhat > for drawing surfaces. Should we be using something else? Passing a string to pmesh is OK for now ... that may be all there is. But longer term you will probably want a more efficient interface that allows you to pass binary data structures ... as a display list of triangles to be rendered. > Can you create callbacks like that using the java applet? This would be > great for Sage, I think. There is a callback mechanism that works OK for many applications. Bob certainly knows more about the current state of this. >> 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. > > Awesome! Bob ... that is beautiful! >> Q: What do you have now in the area of Java applets? > > Essentially nothing. The Sage notebook is an Ajax app -- lots of > javascript > and server-side code (in Python, using Twisted web2). We basically > don't use java applets at all in Sage, though it's always been my plan > to do so. Jmol is a pretty good example of a relatively complex applet that runs on lots of browsers. >> Could you build that into an accompanying applet, so the two could >> talk to each other? That could be fun. > > The Sage notebook is an ajax app, and evaluating a function like this to > have the mesh built in jmol would potentially be very slow: > 1. Jmol requests evaluation of a value > 2. Javascript notebook code queries the Sage server for the value > of the function > 3. The sage notebook server queries a running Sage compute process for > the value of a function. > 4. The Sage compute process calls some library function, maybe defined > in PARI or Maxima. > 5. The sage notebook server gets the value of the function > 6. The javascript notebook gets the value, then returns that two > the Jmol applet. > > This would not be good for building a mesh. If the Sage notebook were a > java > app and Sage were written in Java, it would be a different story, but > that's not > what Sage is. Hmmm ... well then maybe passing pmesh strings isn't so bad after all :) Miguel -- William Stein Associate Professor of Mathematics University of Washington http://wstein.org --~--~---------~--~----~------------~-------~--~----~ 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/ -~----------~----~----~----~------~----~------~--~---
