> Greetings, Jmol team! > > I've become interested (for various reasons) in displaying > non-spherical atoms in Jmol. One possible application would > be to show thermal ellipsoids (i.e. to generate ORTEP-style plots > from x-ray data). The application I have in mind for ellipsoids > is to display atoms from a Gay-Berne simulation (the Gay-Berne potential > is an ellipsoidal generalization of Lennard-Jones that has become > common in the liquid crystal community.
A few years ago someone asked about displaying ORTEP ellipsoids. > Right now, we're using atom-associated vectors for visualization > within Jmol, and have modified the PovraySaver to construct > ellipsoids from the atom positions and the vectors. > > In your estimation, how difficult would it be to modify the classes > in g3d to render an ellipsoid within Jmol itself? Unfortunately, I think that it would be rather difficult. The beauty of a sphere is that it looks the same from every direction. That means that shape & shading information can be precalculated and cached, allowing relatively high performance rendering. An ellipsoid changes shape depending upon the viewing angle. Therefore, different techniques would need to be used. > In Povray, an > ellipsoid is simply a stretched (or squashed) sphere that is then > rotated and translated into the correct position. I imagine this is > somewhat more difficult in the g3d rendering scheme. Correct. > Any ideas if this is a feasible? It could be done ... but I don't think it would be easy. Some questions: It will be much more expensive than rendering a sphere. But, that may not be a problem if we are rendering relatively few ellipsoids ... Q: Do people want to render proteins with thousands of ellipsoids? Or is this generally applied to smaller molecules (or small portions of proteins)? Make a wild guess at completing the following sentences: Most molecules would have ---- ellipsoids. The largest reasonable molecule would have ---- ellipsoids. Q: Are all the ellipsoids the same shape, just scaled to different sizes? Or are some of them more elongated than others? Q: Within a given molecule, are there usually multiple ellipsoids that are the same size & shape? Miguel _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
