Jason, I think this is a great idea. As I use Sage a bit in my teaching, it would be nice to have a primitive with separate items for axes, axes' labels, axes scale (the numbers on the axes). Then buttons could be added to turn these on and off at the user request. If some things can be passed to Jmol as functions, they will render well at any zoom level. It would also be easier to use the slab function for slicing 3-D objects. That said there are some serious problems with how the notebook/ plot3D uses Jmol presently, that have little to do with whether a primitive exists or not. I'm willing to help fix them, but need to understand where in the code the html and javascript for Jmol is generated. The way it is presently done the following things are a problem:
1) It does not work in Firefox on Macs. Since I never have trouble with this, I'm assuming something abnormal is being done with the javascript that controls Jmol. Again, I bet I can help with this, but I could not easily find where the code was generated. All I can do is look at a web page. 2) Since people are running into memory problems, I suggest that only a limited number of live Jmols (present default JavaVM configurations support about 8 - 10 per page) be allowed in any given notebook. I provided some example code that does not require any server intervention that does this. I could help fold this in, if I could figure out how you are generating the javascript to control Jmol. 3) Since there is room next to Jmol in the notebook, I suggest that simple instructions on what Jmol can do and how to access the pop-up be added and maybe a link to more extensive documentation (the Jmol Site?). I'm an expert with Jmol and found it difficult to do anything but rotate the image without significant experimentation. 4) It also might be worth loading only a static image first with a link to make live. This saves a lot of bandwidth and will decrease the time users have to wait to see their plots. 5) It would probably be a good idea to upgrade Jmol to the latest stable release 11.8. I will try slipping that into a copy of 4.2 I just downloaded. These are just some thoughts. The key thing is I think I could help, but do not have time to wade through the code to figure out how everything is connected. Can someone just tell me were to look? Jonathan On Oct 22, 2:01 am, Jason Grout <jason-s...@creativetrax.com> wrote: > Jason Grout wrote: > > A few days ago I posted a query to thejmolmailing list about getting > > nice mesh lines injmolthat we could make pretty arbitrary, like in > >http://trac.sagemath.org/sage_trac/attachment/ticket/5511/mesh_functi... > > (see trac #5511 for the code for that figure). Two people have > > responded and it looks like we may be making progress; we are now > > looking for people with ideas about how to make everything work. If you > > would like to join the discussion (or comment here and I can forward it > > to thejmollist), please see: > > > http://www.mail-archive.com/jmol-us...@lists.sourceforge.net/msg13044.html > > In fact, Bob Hanson suggests creating a new mathematics plot type that > has things like arbitrary meshes, annotations, and whatever else we want: > > What you suggest might be possible -- even now -- but I suggest > we start talking about a new object type. Maybe a "plot3d" that > is an extended isosurface. We already have that for molecular > orbitals, LCAO cartoons, and pmesh. The way it works is that the > extended object has more capabilities -- in this case, to map > more than just contours onto an isosurface. Like you say, a > totally variable mesh, which would just be a set of lines of > variable width, color, and translucency. Possibly annotations. In > addition, possibly, automatic scaling. Right now you have to do > some transforms that are oblivious toJmol. I'd like the > oblivious part to be in the use interface and letJmoltake care > of anisotropic scaling. > > So, now is the time to dream about the perfectjmolprimitive for our > graphics. Any ideas? People that have worked on the 3d graphics in > Sage are especially encouraged to reply. > > Thanks, > > Jason > > -- > Jason Grout --~--~---------~--~----~------------~-------~--~----~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org -~----------~----~----~----~------~----~------~--~---
