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]> 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]> 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
> ______________________________________________
>
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