Dan, I wasn't 100% sure you got this. Two questions:
1) Are ORTEP anisotropy parameters just three scalars that are Cartesion x,y,z-based? 2) Same question for your work. If (1) is "yes", heck, we can basically now render Orteps with what I just added. If (2) is "yes", your question is probably answered as well. I suspect your answers are (1) yes, (2) no, in which case we need to figure out how to orient those ellipses. I think this is an added Axisangle that then gets applied to the voxel transformation matrix. I need that anyway for orienting cartoon orbitals properly, so that's coming as well. Bob -------- Original Message -------- Subject: Re: [Jmol-developers] ellipsoids Date: Tue, 13 Jun 2006 22:18:42 -0500 From: Bob Hanson <[EMAIL PROTECTED]> Reply-To: [email protected] To: [email protected] References: <[EMAIL PROTECTED]> <[EMAIL PROTECTED]> <[EMAIL PROTECTED]> addendum. See http://www.stolaf.edu/people/hansonr/jmol/test/proto/isosurface.htm command: isosurface center {x y z} anisotropy {a b c} orbital 1 0 0 2; for discussion. Hokey way to make a sphere, but, hey, it works! Bob Bob Hanson wrote: >The simplest way of implementing ellipsoids just might be with >isosurfaces. All one needs is the surface for a simple sphere, but >because we have vectors that define x, y, and z, independently scalable, >those would handle all the distortion needed. If it were considered like >an orbital, then perhaps the two solutions will converge -- both require >centering, scaling, and (even in the case of orbitals, depending upon >one's aesthetics) possible stretching. The remaining piece would be >orienting the ellipsoid properly. We could even provide the ortep-like >quarter-ellipse cutout if desired. > >Q: How are these anisotropic parameters generally described? Does each >atom just require three vectors that describe its ellipse? > >I might play with this a bit. > >Bob > > > >Miguel wrote: > > > >>>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 >> >> >> >> > > > >_______________________________________________ >Jmol-developers mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-developers > > _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
