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Dear Ethan,
Yes, thank you for this clarification to a rather "elliptic" statement.
As you explain, although TLS describes a rigid-body motion where the
distances within each moving molecule are left untouched, the
electron-density smeared by that rigid-body disorder is no longer
accountable in terms of a single model with the same geometric restraints as
are obeyed by each image of the molecule by a rigid-body motion.
I hope this is not bringing more smoke to obscure your light. My main
purpose was to rationalise why low-resolution structures may not necessarily
be amenable to exactly the same restraints as one would apply to
high-resolution ones, even after some fudging of weights.
With best wishes,
Gerard.
--
On Wed, Aug 23, 2006 at 11:26:31AM -0700, Ethan Merritt wrote:
> 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
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