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]>> 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]>> 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]> > 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
