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There seem to be two conflicting demands here:
(1) How to best model a crystal structure for refinement against
experimental data.
(2) How to present this model in an objective, generic way to convey
something about the protein in the real (non-crystalline) world to
non-specialists.
As the discussion shows, this is the best forum to discuss (1) and an
NMR or EM forum will be the best place to discuss modelling issues with
those techniques.
I don't think, however, that we're necessarily the experts in part (2),
but rather, for example, the various curators of the PDB.
For instance, the MSD produce 'biological unit' files which are
extremely useful for bioinformaticians, biochemists (and structural
biologists for that matter). It's not that our refined PDB files don't
encode that information already, just that we don't present it in an
intuitive way in our refinement model. I don't see any obvious reason to
change this.
I'm not sure that the issue of disordered side-chains is much different:
if we work out how best to model (or not) these atoms for refinement,
maybe the MSD folks etc. can determine the most appropriate,
user-friendly way to intuitively present the information to
non-specialists.
Cheers,
Charlie
--
Charlie Bond
Professorial Fellow
University of Western Australia
School of Biomedical, Biomolecular and Chemical Sciences
M310
35 Stirling Highway
Crawley WA 6009
Australia
[EMAIL PROTECTED]
+61 8 6488 4406
