Alan, Thomas, Brian, Rich, others, OK, progress. I have just uploaded code introducing the ELLIPSOID command. All it does at this point is draw the axes. But that's enough to convince me I do have the Uij --> ellipsoid axes conversion correct, and that is no small achievement! The ellipsoid axes are determined by first transforming the Uij to Bij, then expressing the B matrix in terms of cartesian coordinates. Then solving the eigenvector problem to find the rotation that sets all nondiagonal elements 0 so that the characteristic equation is of the form
a11 x^2 + a22 y^2 + a33 z^2 = constant For the record, this required adding a small eigenvector/eigenvalue solver class (public domain, NIST - JAMA; org/jmol/symmetry/Eigen.java). Still to do are (a) symmetry considerations and (b) footballs. I hope to look at this later today. Symmetry should be no problem. I'm pretty sure just have to make sure I'm multiplying matrices properly. Some nice examples with different symmetries and poor data (lots of anisotropy) would be helpful. Alan, do you have any BAD data??? (Feel free to send it to me off line if you would prefer.) Once we have symmetry, we will at least have visualizations to check. Footballs can come later. At some point we need to confirm that the axes are the correct absolute length. I think I can do footballs without isosurfaces. Tricky, though. We need to find out how to draw ellipsoids in POV-Ray. We might even get the POV-Ray output going first if that turns out to be a relatively easy operation. Colors -- for now let's just stick with what Jmol can do with colors already. This includes temperature, which I believe can be calculated from Uij using: bFactor = (U11 + U22 + U33)/3 but I'm not 100% sure that is correct. Bob Thomas Stout wrote: > > Yes, Bob - I believe that is correct! > -Tom > > On Tue, Apr 15, 2008 at 1:47 PM, Bob Hanson <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>> wrote: > > Thank you, Thomas. That's very interesting information. I hope > that Jmol > can be at the forefront of visualizing whatever is needed in that > area. > > Am I correct that the PDB ANISOU records are coefficients for the > equation > > U11 x^2 + U22 y^2 + U33 z^2 + U12 xy + U13 xz + U23 yz - c = 0 > > where x, y, and z are not Cartesian coordinates but, rather, > coordinates > in the reciprocal lattice space: > > x a* + y b* + z c* > > ? This means also that the space group must be read properly so > that the > unit cell parameters and reciprocal axes can be determined. Correct? > > Bob > > > Thomas Stout wrote: > > > > > I too am very supportive of adding this functionality! For > > macromolecules however, I would like to comment though that the > number > > of "ultra-high-resolution" (sub 1.0-1.4Angstrom) structures is > > continuing to increase rapidly. This is due to both better crystals > > and much more powerful synchrotron X-ray sources (amongst other > > factors). Therefore, the number of macromolecular structures with > > anisotropic thermal parameters is also greatly on the rise. One > > caveat however is that the entire issue of the aniso-Bs (or Us) is > > currently under debate in the macromolecular field. The recent rise > > of TLS refinement (essentially, anisotropic motion of domains) is > > proving a distinct advantage in the refinement of moderate (and > lower) > > resolution structures. There is not yet a consensus on how those > > modified Bs (or Us) should be properly represented within the PDB > > format, and as a result there is considerable "variety" amongst > > structures in the PDB with ANISO records. (Some are the "raw" > (whole) > > nine components of the atomic thermal parameter, others are the > > directional modifications to the isotropic thermal parameter). > > However, the format is fixed so I would still encourage the > inclusion > > of PDB structures in the anisotropic thermal ellipsoid > representations > > (and leave it up to the macromolecular crystallographers to sort out > > what those fields actually mean). > > > > This would be a very useful addition! > > Cheers, > > Tom > > > > On Tue, Apr 15, 2008 at 7:06 AM, Alan Hewat <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> > > <mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>> wrote: > > > > I strongly support Brian's request for drawing anisotropic > temperature > > ellipsoids, and agree with Rich that the full ellipsoid surface > > should be > > drawn, with an option for showing axial lengths. Actually, near > > the end of > > last year we discussed standards for output of anisotropic > temperature > > factors from the Inorganic Crystal Structure Database ICSD, > and at > > that > > time Brian pointed out the IUCr CIF recommendations, which > are for > > Uij: > > > > On Fri, Nov 16, 2007 at 6:32 PM, Brian McMahon <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> > > <mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>> wrote: > > > For structural papers (e.g. Acta C and E) there is a list of > > > required items > > (http://journals.iucr.org/services/cif/reqditems.html) > > > which stipulates _atom_site_U_iso_or_equiv. Does this answer > > > your question? I think the biological crystallography > journals > > > accept Bij values in line with that community's normal > practice. > > > > Bob, you may obtain CIFs containing Uij anisotropic temperature > > factors > > from the ICSD on http://icsd.ill.fr/ The IUCr published CIFs > are also > > freely available to download, and definitions of Uij are > contained > > on the > > IUCr website. Let me know if you have any specific questions. > > Anisotropic > > temperature factors would be really great for inorganic and > small > > organic > > structures. They are perhaps less useful for large organic > > molecules where > > PDB format usually applies. > > > > Alan. > > ______________________________________________ > > Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE > > <[EMAIL PROTECTED]> +33.476.98.41.68 > > http://www.NeutronOptics.com/hewat > > ______________________________________________ > > > > > > > ------------------------------------------------------------------------- > > This SF.net email is sponsored by the 2008 JavaOne(SM) > Conference > > Don't miss this year's exciting event. There's still time to > save > > $100. > > Use priority code J8TL2D2. > > > > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone > > _______________________________________________ > > Jmol-users mailing list > > [email protected] > <mailto:[email protected]> > > <mailto:[email protected] > <mailto:[email protected]>> > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > >------------------------------------------------------------------------ > > > >------------------------------------------------------------------------- > >This SF.net email is sponsored by the 2008 JavaOne(SM) Conference > >Don't miss this year's exciting event. There's still time to save > $100. > >Use priority code J8TL2D2. > > >http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone > > > >------------------------------------------------------------------------ > > > >_______________________________________________ > >Jmol-users mailing list > >[email protected] > <mailto:[email protected]> > >https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference > Don't miss this year's exciting event. There's still time to save > $100. > Use priority code J8TL2D2. > > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone > _______________________________________________ > Jmol-users mailing list > [email protected] > <mailto:[email protected]> > https://lists.sourceforge.net/lists/listinfo/jmol-users > > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >This SF.net email is sponsored by the 2008 JavaOne(SM) Conference >Don't miss this year's exciting event. There's still time to save $100. >Use priority code J8TL2D2. >http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
