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
>______________________________________________
>
>
>-------------------------------------------------------------------------
>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
