At 17:12 14/10/2004 -0400, Miguel wrote:
> 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?
fractional normally
Q: Can you send me a small sample file off-list?
done
> 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' ?
where all atoms are translated so they are bonded to as many others as possible
Q: Does anyone know any reason why we should not leave the coordinates alone ... as in the file?
No
> - 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)
an atom which can "oscillate" between two or more different positions, not necessarily with equal weight
Q: What do you mean by 'group' in this context?
Sometimes a whole group is disordered
> Also disordered atoms in different groups should probably never be joined > to each other
How are 'disordered' atoms denoted in the file.
_atom_site_distorder_assembly and _atom_site_distorder_group have values that are not "."
> I think everyone was impressed with the Jmol display
P.
Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069
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