I am in Chicago and don't have full access to my data, but I'd like to contribute to this discussion.
CIF Symmetry: The key here should be loop_ _symmetry_equiv_pos_site_id _symmetry_equiv_pos_as_xyz 1 '-x, y, -z+1/2' etc. ---- I'm guessing that any CIF file showing only fractional coordinates must contain this record. Someone should look into that. I have written code for another program that parses these and can share that. -translation: Yes, this is an issue. There is no need to "modularize" the coordinates in [0,0,0:1,1,1]. Are we doing that? -disorder: One can see, for example, sometimes a CH3 showing up as a CH6. It might be nice to show disorder visually. -missing atoms: (Peter didn't mention this.) We need to be able to ignore atoms that are present in the file but have no coordinates listed. They simply can't be put in as 0,0,0 just because parseFloat() returns 0. Bob > I spent a very useful day with the International Union of Crystallography > staff and have looked at ca 60 recent CIFs in detail. The main challenges > that we face are: > - symmetry. How do we apply symmetry so that the exact molecule is built? > e.g. if a water sits on a 2-fold axis, only one O and one H are reported. > - translation. By default Jmol moves all the atoms into the unit cell > (0,0,0)-> (1,1,1). In fact most authors create a joined-up molecule. Could > the default be to use the authors coordinates rather than this > translation? > - disorder. Many structures have disordered atoms. The authors often > annotate them, fairly consistently, into disorder groups. Thus just one > group can be selected. It could be useful to have a visual display that an > atom had been selected as disordered (perhaps darker or > semi-transparent?). > Also disordered atoms in different groups should probably never be joined > to each other > > I think everyone was impressed with the Jmol display > > P. > > > >>Miguel > > Peter Murray-Rust > Unilever Centre for Molecular Informatics > Chemistry Department, Cambridge University > Lensfield Road, CAMBRIDGE, CB2 1EW, UK > Tel: +44-1223-763069 > > > > ------------------------------------------------------- > This SF.net email is sponsored by: IT Product Guide on ITManagersJournal > Use IT products in your business? Tell us what you think of them. Give us > Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out > more > http://productguide.itmanagersjournal.com/guidepromo.tmpl > _______________________________________________ > Jmol-developers mailing list > [EMAIL PROTECTED] > https://lists.sourceforge.net/lists/listinfo/jmol-developers > ------------------------------------------------------- This SF.net email is sponsored by: IT Product Guide on ITManagersJournal Use IT products in your business? Tell us what you think of them. Give us Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more http://productguide.itmanagersjournal.com/guidepromo.tmpl _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
