See http://www.ornl.gov/sci/ortep/doc/ for definitive material. Note that the ORTEP code is ca 175K FORTRAN lines. I suspect that using vecmath will make some operations easier but it's not trivial.-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
Peter Murray-Rust wrote: | At 15:41 18/05/2004 +0100, aonghus wrote: | | | We are working on much of this at present. We have an alpha version of | cif2cml converted that is able to read CIFs into CML, apply symmetries, | compute the chemically reasonable fragments, use CDK to generate 2D | structures and write out the results. | |> It would seem that displaying thermal ellipsoids should be relatively |> easy- the information is already in the file- have a look at |> |> http://www.chem.gla.ac.uk/~louis/software/ortep3/ |> |> for an example.
My feeling is that it will be useful for Jmol to display various user-defined primitives but that in many cases the user will have to precompute them. For example I might want to display the inertial ellipsoid of a molecule - essentially the ellipsoid which best describes the mass distribution of the molecule at quadratic approximation. This might be computed elsewhere. Many other physical properties give rise to ellipsoids - e.g. refractive index - and again these could be precomputed. Jmol might then get an XML (CML) input such as:
<ellipsoid id="ell23" title="refIndex" x3="1" y3="7.2" z3="1.2"> <matrix rows="3" columns="3"> 1 2 3 2 5 1 7 4 1</matrix> </ellipsoid>
and could plot it independently of the physical meaning.
P.
| | | It is not quite trivial. The ellipsoids are defined wrt crystal axes and | you also have to be able to apply symmetry elements to symmetry related | ellipsoids. However if you are prepared to hack though the matrix | algebra (which is standard in many books) you can deduce the semiaxes of | the ellipsoids. The Jmol has to be able to draw an ellipsoid. This | should be easier than ORTEP because the hidden line algorithm is not | required. |
yes, I see. Crystallographers very sensibly do everything with respect to the crystal axes- but, the space group is given in the .cif file and it can't be too hard to compute the thermal ellipsoid information (or anisotropic displacement parameters- are they just direction cosines?)
They are weighted direction cosines (eigenvectors) and are symmetry-dependent.
when the file is read. I don't think it is necessary to do anything really fancy here- rendering the ellipsoidal isosurface is probably overkill- what would be very useful is 3 'thin' ellipses, aligned along the 3 axes to give some indication of the size and direction. This is what most of the other programs do (and then perhaps something more sophisticated could be done for povray output for eg.).
I would expect that Jmol would have styles for display just as it has for atoms.
|> It might also be possible to display the symmetry elements- perhaps by |> reading the symmetry information from the file, constructing the "extra" |> atoms and maybe making them into a special selection that can be toggled |> on/off? | | | Again not trivial, but possible. | |> I am not a crystallographer- are there many crystallographers using |> Jmol? Are there plans to implement these features? | | | We hope to make our CIF2CML software available fairly soon as | OpenSource. It concentrates on the chemistry rather than the | crystallographic experiment. I don't think Jmol should be become a CIF | viewer, but it could reasonably display crystal+symmetry+atoms |
Yes, thats a good idea cif -> cif2cml -> Jmol especially if it can handle reconstructing the symmetry elements.
CML holds the symmetry elements explicitly without loss. What is more problematic (and perhaps what you are alluding to) is the generation of symmetry-related molecules are fragments. There are several problems which we are working on and none are completely trivial.
- generation of the unique set of disjoint molecules. This depends on bonding criteria
- elimination of duplicate atoms (on symmetry elements)
- generation of symmetry related molecules for packing. The problem is that everyone wants a different set! and there is no algorithm which produces a beautiful result for every molecule.
So, we await the release of CIF2CML. It seems to me that Jmol (with some small(?) extensions) could make a very nice cif viewer- is there some other free/open source software which can do all these things?
Try Mercury at www.ccdc.ac.uk
It's not Open but it's free and has useful tutorials
P.
many thanks
aonghus
- -- Aonghus Lawlor [EMAIL PROTECTED] 00 353 1 7062418 http://fiachra.ucd.ie/ Irish Centre for Colloid Science & Biomaterials Department of Chemistry University College Dublin GPG Public Key http://fiachra.ucd.ie/~aonghus/public.gpg -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.4 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org
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