> 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.
I don't understand this symmetry stuff yet. But I spent a good deal of time with someone on Tuesday who explained a lot to me about space groups. > - translation. By default Jmol moves all the atoms into the unit cell > (0,0,0)-> (1,1,1). Q: Do these files have cartesian coordinates or fractional coordinates? Q: Can you send me a small sample file off-list? > In fact most authors create a joined-up molecule. Could > the default be to use the authors coordinates rather than this > translation? I do not remember the details, but I *believe* that this translation is being done for a specific reason ... I suspect something messed-up having to do with PDB files ... or maybe I just didn't understand what I was doing when I was working on this. But when I think about it right now, it makes perfect sense that by default Jmol should show exactly what is in the file. Q: What do you mean by 'joined-up molecule' ? Q: Does anyone know any reason why we should not leave the coordinates alone ... as in the file? > - 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?). Q: What is a 'disordered' atom? (25 words or less) Q: What do you mean by 'group' in this context? > Also disordered atoms in different groups should probably never be joined > to each other How are 'disordered' atoms denoted in the file. > I think everyone was impressed with the Jmol display Good. Miguel ------------------------------------------------------- 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
