Dear Bob
At first glance, tested against a number of Acta Cryst. C structures
with relatively large or elongated ellipsoids, this is looking very
nice indeed.
So far the only issue I have come across is the logic of handling
mixed isotropic/anisotropic refinements; in the CIF
http://scripts.iucr.org/cgi-bin/sendcif?gd3149sup1
there are a number of atoms (O43, O53) which have been refined
isotropically and are listed in the main atom list with their
values of _atom_site_U_iso_or_equiv. They don't appear in the
separate list of atoms with anisotropic Uij values. So Jmol
doesn't display them at all in the "ellipsoid" mode. I guess
they should appear as suitably scaled spheres, perhaps with some
indication that they are U_equivalent's; or perhaps with a mode
that can switch on/off "ellipsoid" displays for isotropically
refined atoms.
My editorial colleagues are happy with the idea of using the
"temperature" colour scheme in association with these ellipsoids,
and in these examples that also works well.
I'll build some options arising from this into our enhanced
figures toolkit and encourage the technical editors here to
experiment some more.
The drop-down menu will benefit from having some of this functionality
added. An obvious extension would be to add "displacement ellipsoids"
to the list of Style>Scheme, but it might also be useful to have a
menu option to select between different styles of representation (axes,
footballs, etc.) when these become available.
Thank you very much for the work you've put into this: for our
small-molecule applications this will enormously increase the
impact of Jmol enhanced figures!
Best wishes
Brian
_________________________________________________________________________
Brian McMahon tel: +44 1244 342878
Research and Development Officer fax: +44 1244 314888
International Union of Crystallography e-mail: [EMAIL PROTECTED]
5 Abbey Square, Chester CH1 2HU, England
On Thu, Apr 17, 2008 at 02:14:06AM -0500, Bob Hanson wrote:
> Alright. Time to test. See
>
> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
> http://chemapps.stolaf.edu/jmol/docs/examples-11/ellipsoids.jpg
> http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11_5.zip
>
> Bob
>
>
>
> Bob Hanson wrote:
>
>> Alan, Thomas, Brian, Rich, others,
>>
>> OK, progress. I have just uploaded code introducing the ELLIPSOID
>> command. All it does at this point is draw the axes. But that's enough
>> to convince me I do have the Uij --> ellipsoid axes conversion correct,
>> and that is no small achievement! The ellipsoid axes are determined by
>> first transforming the Uij to Bij, then expressing the B matrix in terms
>> of cartesian coordinates. Then solving the eigenvector problem to find
>> the rotation that sets all nondiagonal elements 0 so that the
>> characteristic equation is of the form
>>
>> a11 x^2 + a22 y^2 + a33 z^2 = constant
>>
>> For the record, this required adding a small eigenvector/eigenvalue
>> solver class (public domain, NIST - JAMA; org/jmol/symmetry/Eigen.java).
>>
>> Still to do are (a) symmetry considerations and (b) footballs.
>>
>> I hope to look at this later today. Symmetry should be no problem. I'm
>> pretty sure just have to make sure I'm multiplying matrices properly.
>> Some nice examples with different symmetries and poor data (lots of
>> anisotropy) would be helpful. Alan, do you have any BAD data??? (Feel
>> free to send it to me off line if you would prefer.) Once we have
>> symmetry, we will at least have visualizations to check. Footballs can
>> come later.
>>
>> At some point we need to confirm that the axes are the correct absolute
>> length. I think I can do footballs without isosurfaces. Tricky, though.
>> We need to find out how to draw ellipsoids in POV-Ray. We might even get
>> the POV-Ray output going first if that turns out to be a relatively easy
>> operation.
>>
>> Colors -- for now let's just stick with what Jmol can do with colors
>> already. This includes temperature, which I believe can be calculated
>> from Uij using:
>>
>> bFactor = (U11 + U22 + U33)/3
>>
>> but I'm not 100% sure that is correct.
>>
>> Bob
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