Jason -- I forgot that you are creating your own JVXL files. Though not yet
documented, the JVXL 2.0 format does allow specification of exactly what you
want -- an arbitrary number of lines of arbitrary color through the triangle
set. Let me know if that interests you.
Bob
On Fri, Oct 16, 2009 at 10:56 AM, Robert Hanson <[email protected]> wrote:
> Jason, more thoughts on this on the plane last night....
>
> 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 to Jmol. I'd like the oblivious part to be in the use interface
> and let Jmol take care of anisotropic scaling.
>
> As for access to the triangles, if I tell you a few secrets, will you
> promise me not to spread it around too much? (yeah, yeah, that's a joke...)
>
> After creating a surface on a web page (say, for example,
> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
> with
>
> load 1crn.pdb;isosurface molecular
>
> then issue from the address line of the browser:
>
>
> javascript:alert(jmolGetPropertyAsJavaObject("JmolViewer").getModelSet().getShape(22).getMesh("isosurface1").vertices)
>
> or, for example:
>
>
> javascript:alert(jmolGetPropertyAsJavaObject("JmolViewer").getModelSet().getShape(22).getMesh("isosurface1").polygonIndexes)
>
> That "22" is subject to change at the whim of the developer. But that's all
> the information you are looking for, I think. So you could, in principle,
> draw any lines now using the DRAW LINE command (which draws any number of
> connected segments)
>
> But that's not necessarily that efficient, and we should talk about what
> you think would be really great to have. The way we would do this would be
> to create a new package called "math" and load it up with the coolest Java
> you can find. It would not be a load on any other user, because unless you
> accessed the "plot" object or whatever we call it, that package would not be
> delivered.
>
> Bob
>
>
>
>
>
> On Wed, Oct 14, 2009 at 4:51 PM, <[email protected]> wrote:
>
>> I've been using jmol quite a bit lately in Sage for drawing 3d
>> mathematical surfaces. One thing I really miss is the ability to have
>> nice meshes (including arbitrary meshes) on a surface. Currently Jmol
>> allows a mesh option to pmesh surfaces, but that only draws a specific
>> grid that is hard to see (it is the same color as the surface, but
>> lighter or something).
>>
>> Probably the easiest change would be to make the mesh default to black
>> lines (like the black lines for contour plots on cut planes). That
>> would make the mesh lines much easier to see. Seeing the mesh lines
>> often really helps us mathematicians (especially those of us teaching).
>>
>> A very nice functionality to add would be the ability to draw arbitrary
>> meshes on surfaces, similar to what is implemented here (but as black
>> lines on the surface, rather than the crude approximation constructed
>> here):
>>
>> http://trac.sagemath.org/sage_trac/attachment/ticket/5511/mesh_function.jpeg
>> .
>> I think Mathematica has a nice interface to these sorts
>> of things:
>> http://reference.wolfram.com/mathematica/ref/MeshFunctions.html
>>
>> We (Sage) can take care of the interface to draw meshes. What we'd need
>> from jmol is the ability to draw a line *on* a surface and have it look
>> like the contour lines look like on a plane. Maybe for each triangle in
>> the surface, we could give a list of lines to draw on that triangle by
>> specifying (for each line) the two edges the line crosses and the
>> fraction of the distance along the edge to make the intersection between
>> the line and the edge of the triangle.
>>
>> What do you think?
>>
>> Thanks,
>>
>> Jason
>>
>>
>>
>> ------------------------------------------------------------------------------
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>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
------------------------------------------------------------------------------
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is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9 - 12, 2009. Register now!
http://p.sf.net/sfu/devconference
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