Bob, if you can render the Uij ellipsoids without drawing the axes for
now, that would already be very interesting. Anisotropic thermal
ellipsoids are useful because they indicate disorder of some kind, either
static or dynamic (or else a problem with the refinement :-) Of particular
interest is an indication of possible structural instability, and being
able to see which way those footballs are pointing can be very
instructive. BTW, with neutrons we can also obtain meaningful anisotropic
data for hydrogen, so that should not be systematically set to the
isotropic average - disordered hydrogen bonds are of interest in many
types of structures. When you have it working, I'll copy it to ICSD where
I have long had a 3D display of anisotropic temperature factors using VRML
(without ellipsoid axes :-)
Alan.
Bob Hanson said:
> Alan and Brian,
>
> At least for starters, here's what I have done:
>
> 1) programmed the CIF reader to read Uij data from CIF and mmCIF files
> 2) added an ISOSURFACE option to display Cartesian Uij' data:
>
> isosurface ellipsoid {[U11'],[U22'],[U33'],[U12'],[U13'],[U23']}
>
> 3) read Jeffery, Methods in X-Ray Crystallography (1971) Appendix VI.
>
> My plan is to do the {a*,b*,c*} coordinate transformation of the Uij
> data to cartesian Uij' today, so it appears as cartesian data ready for
> the isosurface command. Then we can do something like this:
>
> isosurface ellipsoid {not hydrogen} 50%
>
>
> (Do we need to be storing both the original Uij data and the
> cartesian-transformed parameters?) I don't fully understand how to get
> the eigenvectors,
>
> The problem are twofold: (1) transforming the Uij coefficients and (2)
> depicting the ellipsoids in appropriate ways. Now, here's the trick:
> Turns out I can do the rendering without ever figuring out what the
> actual axes are. The isosurface command accepts ANY function, and the
> function describing an arbitrary ellipsoid,
>
> a_1 x^2 + a_2 y^2 + a_3 z^2 + a_4 xy + a_5 xz + a_6 yz - c = 0
>
> is a perfectly fine surface. So that mechanism works now with just a few
> added lines to Jmol -- much like displaying an atomic orbital.
>
> Ultimately we may have the question as to whether we want to use
> isosurfaces to render these, but there are some nice advantages to doing
> it this way, at least at first. My overall plan would be to create a new
> "special" shape class, perhaps, "thermalEllipsoid":
>
> select model=3.1
> thermalEllipsoids 50%
>
> or something like that? If that's the case, and we want to visualize
> those axes, then I will have to figure out a completely different way to
> render these. So the compromize may be that initially all we have are
> the footballs, and later (this summer?) that may be upgraded.
>
> Bob
>
>
> Alan Hewat 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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>
>
> --
> 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
______________________________________________
Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE
<[EMAIL PROTECTED]> +33.476.98.41.68
http://www.NeutronOptics.com/hewat
______________________________________________
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