[Jmol-developers] ellipsoids and isosurfaces From: Bob Hanson - 2006-06-27 15:05:30 ```Dan Gezelter: Please check at http://www.stolaf.edu/people/hansonr/jmol/test/proto and let me know if what I have done there in relation to ellipsoids is sufficient for you. The basic format is: isosurface center {x y z} ellipsoid {cx cy cz f_ab} or isosurface center (some_atom_expression) ellipsoid {cx cy cz f_ab} where {x y z} is a coordinate in molecular coordinates, (some_atom_expression) is something like (atomno=34) or (oxygen and connected(hydrogen)), and {cx cy cz f_ab} describes the axis and magnitude of the c axis of the ellipsoid along with the factor f_ab, which is the ratio a/c = b/c. If more than one atom is described by the atom expression, then the geometric center of those atoms is used for the center. (I notice now that my "f_ab" is 1 divided by your "ecc". Sorry about that -- if it's a major problem or just too weird, I will reverse it.) If f_ab is negative, then this is saying "normalize cx cy cz so that it has unit length" thus allowing simple orientation of "unit" ellipsoids. These unit ellipsoids can then be scaled using the additional "scale" keyword: isosurface center (atomno=3) scale 2.0 ellipsoid {1 1 1 -0.5} All: The isosurface command is proving to be quite rich in its generality. The basic sequence of all isosurface commands is: isosurface [surface-construction-parameters] [surface-type-and-parameters] [mapping-parameters] [mapping-type-and-parameters] [display-parameters] Here is a quick rundown of what these options involve. I realize it's quite a large collection of options. Not all are compatible with each other. See ; for details. [surface-construction-parameters] include: anisotropy {ax ay az} eccentricity {cx cy cz f_ab} center {x y z} center (atom expression) cutoff gridpoints debug/nodebug insideout fixed (not attached to the current model) modelbased (attached to the current model) fileindex [surface-type-and-parameters] includes: "cube or jvxl file name" "" (use the currently loaded file) ellipsoid {cx cy cz f_ab} functionXY "function-name-to-call" {xyz origin} {ni ix iy iz} {nj jx jy jz} {nk kx ky kz} lobe {cx cy cz f_ab} orbital n l m Zeff(optional) pts_per_angstrom(optional) solvent sphere [mapping-parameters] include color absolute contour contour <-n (specific contour)> plane {a b c d} remappable (still working on this -- would allow JVXL color mappings to be remappable) sign (the two colors for - and +, respectively) [mapping-type-and-parameters] include "cube or jvxl file name" "" (use the currently loaded file) phase [display-parameters] background/nobackground dots/nodots fill/nofill mesh/nomesh Dan Gezelter wrote: >>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 >************************************************ > > > > >_______________________________________________ >Jmol-developers mailing list >Jmol-developers@... >https://lists.sourceforge.net/lists/listinfo/jmol-developers > > ```