On Tue, 18 May 2004, Miguel wrote: > > Peter wrote: > > | I don't think Jmol should be become a CIF > > | viewer, but it could reasonably display crystal+symmetry+atoms > > Aonghus wrote: > > It seems to me that Jmol (with some small(?) extensions) could > > make a very nice cif viewer- > > It is not clear to me what features/functions would be required/desired of > a 'cif viewer'. > > Like I said, I am not particularly interested in biting off anything > particularly complicated at this time. > > But, out of curiosity > > Q: Can someone give me a short list of things that would be > required/expected of a 'cif viewer' >
hi, It seems a "cif viewer" might be a nice idea;) but way beyond what is needed for the moment. Maybe we can do something a bit simpler- like display the 'full' molecule from a .cif file, along with some extra information like the thermal ellipsoids. For molecules that don't have a symmetry axis, the shelx program outputs a complete atom list and jmol display the full molecule. For molecules with a symmetry axis, it outputs only the list of atoms related by symmetry along with the symmetry operators needed to reconstruct the full molecule. For these molecules, jmol is currently only displaying the molecule fragment- and people really want to see their molecule in 'full'. I would think this is a similar level of functionality to 'automatically compute bonds' - in the case of .cif files jmol would read the atom list and the symmetry operators from the file, and then apply the symmetry operators to generate the full molecule. The thermal ellipsoids also give very useful information. There is no necessity to draw the complete isosurface- it would be much too slow and all that is needed is an indication of the size along a given direction. What would be involved in drawing 3 orthogonal ellipses along the coordinate directions? Does anyone know the precise meaning of the thermal ellipsoid data (there are 6 fields- I guess 3 directions relative to the crystal axes and 3 lengths?). What is the status of plugins under jmol- it might be an idea to keep the rendering core of jmol small and fast, and implement some of the 'fancier' things in plugins? I would like to see jmol do these things- and I certainly offer to help implement them. There are a few options- modify jmol, wait for cif2cml, or maybe a write plugin- any thoughts or suggestions on this? 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
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