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hi,
The beta version of Jmol is looking very impressive.
Agreed - it seems to shine.
The crystallographer in our department here is now using the applet to display the solved structures- staff can now view their structures with the applet embedded in a web pages. He does this with a little script which generates a small html page to display the .cif file which is the output of his crystal solving program.
This works fine but there are some things that Jmol does not do that would be very useful for people in crystallography. For example, are there any plans to display thermal ellipsoids?
We mentioned this as one object that could be algorithmically generated as an isosurface
From what I can see, there is actually a lot of structural information in the .cif/.res files that ShelX outputs- Jmol seems to only display the atom (x,y,z) positions. One thing that would be extremely useful is to have Jmol display the symmetry elements of a molecule- for certain outputs there is only a fragment of the molecule and some symmetry information. One of the programs the crystallographers use on windows has a "grow" button, which reads the symmetry axes from the .cif file (or perhaps based on picking an atom) and displays the full molecule.
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.
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.
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
P.
Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069
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