From: Thomas S. <tho...@gm...> - 2008-04-15 17:10:56
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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 <he...@il...> 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 <bm...@iu...> 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 > <Alan.Hewat@NeutronOptics.com> +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 > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |