Re: [Jmol-developers] PyMOL geometry in Jmol

[Miguel <mi...@jm...>]

> Miguel,
>
> Okay, with Sascha making it look so easy, I couldn't resist playing aro=
und
> with g3d a bit tonight in order to explore just how feasible it would b=
e
> to
> use PyMOL as an optional JNI extension to generate molecular geometry
> inside
> Jmol (or g3d).
>
> Here's what I've been able to accomplish in a few hours, simply by havi=
ng
> PyMOL directly write out Java source code to message Jmol (contrived ye=
s,
> but nevertheless a quick way to test the concept without creating any r=
eal
> glue).
>
>>From the original geometry in PyMOL...
>
> http://delsci.com/jmol/pymol040104.jpg
>
> The following can be obtained inside of Jmol (well, actually just
> org.jmol.g3d.Graphics3D inside a JPanel).
>
> http://delsci.com/jmol/jmol040104.jpg

Very good=21

> No color yet, and the lighting is different, but otherwise it is
> remarkably
> close.  However, the spheres aren't clipping each other quite right and=

> the
> triangles are flat shaded.  Questions:
>
> 1) I've set the slab and depth values to 1000 & 4000 respectively, whic=
h
> covers the full Z range of the scene, but still the spheres aren't
> intersecting one another correctly.  The fillSphereCentered method is u=
sed
> to draw them one by one.  If that's okay to do, then what's missing?

slab values in RasMol/Chiime/Jmol run from 100 to 0

100'% visible, 0% visible

> 2) Is there a way to provide a normal vector for each triangle vertex?
> That's pretty much essential for HQ surface rendering.  Clearly Jmol ca=
n
> do
> smooth shading correctly with the ribbons, but unless I'm overlooking
> something obvious, that isn't possible right now for individual triangl=
es.
> What's the outlook for this?

There is currently no mechanism to handle this ... so don't waste any tim=
e
looking for it.

I plan to implement some type of phong shading across the faces of
triangles some time with the next two weeks.

I have been thinking about it for a few weeks and have a high-performance=

design planned out.

Q: How is performance?

> By the way, when you said that g3d was clean and standalone...you weren=
't
> kidding=21  It took me just 15 minutes to get that first 3D sphere draw=
n in
> a simple Java app, sans OpenGL.  Fantastic work=21

Excellent=21

> I've also discovered a convenient little coincidence:  PyMOL's built-in=

> ray
> tracer uses input geometry in almost exactly the same form as g3d.  So
> while
> I am currently taking PyMOL ray tracing geometries into Jmol, the rever=
se
> should also be quite easy: with just a few changes, PyMOL could be used=
 as
> a
> photorealistic rendering engine for Jmol -- though of course only in ca=
ses
> where Jmol has access to native extensions, such as when running under
> WebStart.

Very good.

I must say that I am impressed and quite excited that you were able to
slap this quick-and-dirt-demo together so easily.

> Cheers,
> Warren
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist

This bodes well for potential collabaration between PyMOL and Jmol.

Miguel