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
>>
>>
>>
>>_______________________________________________
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>>[email protected]
>>https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>>
>>
>>
>
>
>
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