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On Wednesday 23 August 2006 10:54 am, Gerard Bricogne wrote:
>
> One option is to model that disorder, e.g. by TLS - and there,
> it is well known that this kind of disorder can interfere with ideal
> distances (see Willis & Pryor).
I think you have stated that in a confusing manner.
Let me attempt to clarify, and hope I add more light than smoke.
TLS is inherently a rigid-body model, so the ideal distances are
unperturbed.
However, when individual atoms are modelled anisotropically, there
is an apparent bond-length compression that arises from failing to
apply a correction to the distance between the centroids of two
ellipsoids. Programs such as shelx apply this correction when
reporting bond lengths.
Now if you approximate a TLS model in terms of individual ellipsoids,
which is what e.g. refmac does internally during refinement, the
same issue would arise when applying bond-length restraints.
I do not recall whether refmac does or does not correct for the
apparent compression in this case. Perhaps Garib will speak up.
Ethan
> However one can expect that the final answer will be more
> complicated: in the theory of TLS, it is not only the variance of an
> apparent bond length (in the smeared density) which needs resetting,
> but its expectation value as well (again, see Willis and Pryor).
>
>
> With best wishes,
>
> Gerard.
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle WA
