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hi,
The beta version of Jmol is looking very impressive.
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? 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.
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 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?
I am not a crystallographer- are there many crystallographers using Jmol? Are there plans to implement these features?
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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