Yes, Bob - I believe that is correct!
-Tom
On Tue, Apr 15, 2008 at 1:47 PM, Bob Hanson <[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]>> 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
> > ______________________________________________
> >
> >
> >
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>
> --
> 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
>
>
>
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