> It strikes me that there is a variance here between the atomic coordinates
> being a *model* that best attempts to represent the data, and something
> that is sugar-coated and always works when one pulls it up in Rasmol. The
unfortunately, this is something even crystallographers sometimes forget ...
> occupancy is, to quote RCSB "the fraction of the atom type present at this
> site". It would seem quite legitimate to set that to zero if one felt the
this is intended for (discrete) alternative conformations. the sum of the
occupancies in that case should still be one
> side-chains that are rotationally disordered around chi1, what is the
> best *model* ? An occupancy of zero or a B-factor of 200+ ?
we would need a different way of describing such models, e.g. with
internal coordinates (where the chi-1 torsion would get a high
variance or 'B-factor', or a multi-modal distribution, but the other
distances, angles and torsions could still be well-determined and
unimodal). in the absence of such a model, go for high B-values
> A logical extension of "they are *there* after all" would lead us to use a
> complete solvent model in 3.5 Angstrom structures, because the water
> molecules are *there* even if we can't reliably position them. We
silly sophistry. if we observe residues 1 to 324 with the exeception
of the sidechain atoms of lysine 123, occam's razor tells us we can
reasonably assume them to be there, albeit disordered (no matter what the
resolution, by the way). this argument does not apply to solvent molecules
> A practical matter: at moderate resolution one typically refines B-factors
> with relatively tight restraints across geometry, at least as an
> end-point. This tends to dampen the desired effect (large B-factors for
this is precisely why grouped B-factors are so useful at moderate and
low resolution (e.g., one B per residue, or one for the main-chain
and one for the side-chain atoms of each residue)
--dvd
******************************************************************
Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:gerard@xray.bmc.uu.se
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The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
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