Peter wrote: >>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
I suspect that rendering them as isosurfaces will be rather expensive. That may not be a problem if you are talking about a small number of ellipsoids. > 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. Good. Then Jmol can read the CML output. >>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. I would probably be willing to provide an ellipsoid rendering primitive if someone else wanted to take the lead on this. >>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. At this point I am not that interested in undertaking new features unless they are trivial :-) Miguel ------------------------------------------------------- This SF.Net email is sponsored by: SourceForge.net Broadband Sign-up now for SourceForge Broadband and get the fastest 6.0/768 connection for only $19.95/mo for the first 3 months! http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
