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## jmol-developers

 Re: [Jmol-developers] [Fwd: Re: ellipsoids] From: Dan Gezelter - 2006-06-14 13:08:18 ```> Dan, I wasn't 100% sure you got this. I get the digest once a day, but thanks anyway! > Two questions: > > 1) Are ORTEP anisotropy parameters just three scalars that are > Cartesion x,y,z-based? Umm... I'll answer with a qualified "yes", but getting those out of the ORTEP-style input files is sometimes a challenge. If you want a scary look at the most archaic way of getting data into a program, look here: http://www.ornl.gov/sci/ortep/doc/input.html#temp The thermal ellipsoid is specified with an upper triangular matrix: b11, b22, b33, b12, b13, b23, but the basis set for this matrix may be the crystal axes. > 2) Same question for your work. We've got uniaxial ellipsoids (a = b != c) , so a single vector is enough to specify the orientation of the c axis. Also, we've been packing the extra data on the eccentricity into the extended columns in the XYZ file format: atype x y z ecc cx cy cz Here, cx, cy, and cz specify the orientation of the "c" axis of the ellipsoid, and ecc is the length-to-breadth ratio (c/a). We can easily clone the XyzReader to make something more general that would specify two of the three axes: atype x y z a b c ax ay az bx by bz (or we could even specify all three, but we'd need to check for orthogonality of the vectors.) To answer Miguel's questions: >>> Q: Do people want to render proteins with thousands of >>> ellipsoids? Or is >>> this generally applied to smaller molecules (or small portions of >>> proteins)? Most ORTEP renderings are for smaller molecules (probably at most a hundred or so thermal ellipsoids). We're rendering liquid crystalline simulations with a few thousand ellipsoids (and a few thousand frames of the simulation), but we typically use atoms / vectors to find an orientation we like and then export to pov ray. >>> Q: Are all the ellipsoids the same shape, just scaled to >>> different sizes? >>> Or are some of them more elongated than others? In ORTEP, each atom has a different ellipsoid (with different eccentricities). In our stuff, there's a limited number of possible ellipsoidal geometries. >>> Q: Within a given molecule, are there usually multiple ellipsoids >>> that are >>> the same size & shape? In ORTEP? No. In our stuff? Sometimes. --Dan *********************************************** J. Daniel Gezelter Associate Professor Department of Chemistry and Biochemistry 251 Nieuwland Science Hall University of Notre Dame Notre Dame, IN 46556-5670 phone: +1 (574) 631-7595 fax: +1 (574) 631-6652 e-mail: gezelter@... web: http://www.nd.edu/~gezelter ************************************************ ```