aonghus wrote: > 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.
Very good. > 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? I do not know what a thermal ellipsoid is. > 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. The notional unitcell coordinates should also be read (if present). The Jmol engine is also capable of supporting formal and partial charges, although, I do not remember if that is happening for .cif or .res files. > 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. I am neither a crystallographer nor a chemist ... you need to explain in simpler terms :-) > 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. I see the picture with ellipsoids instead of spheres. Those shapes look familiar ... it now seems to me that perhaps someone asked about this last year. Q: In 25 words or less, what do the ellipsoids represent? Q: How is the orientation determined? Q: Are the ellipsoids in a constant orientation relative to the molecule, or do the move/vibrate/animate? Rendering ellipsoids would be much slower than rendering spheres. Q: Do you want to do this with macromolecules, or just little ones ... say, less than 500 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? Are you saying that you want to replicate the unitcell? There was some serious discussion on this topic a few months ago. But at this point I would say that this will *not* make it into Jmol v10. So I don't think any work would start on this until late 2004 (at the earliest). > I am not a crystallographer- I'm not even a chemist :-) > are there many crystallographers using > Jmol? Are there plans to implement these features? I think that there are a growing number of crystallographers using Jmol ... but not sure how many. Egon, the other principal Jmol developer, is a crystallographer. 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
