RE: [ccp4bb]: B factors

[Ian Tickle <I.Tickle@astex-technology.com>]

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TLS refinement tells you nothing whatsoever about correlated atomic motions,
what it may do is tell you something about correlated mean-square
displacements - not the same thing at all!  In this respect TLS refinement
is not fundamentally different from restrained anisotropic displacement
parameter refinement: you still have to supply the chemical intuition that
the bonds and bond angles are very stiff (from IR spectroscopy the mean
square bond vibration amplitude of a single C-C bond is typically only ~
0.002 Ang^2, i.e. B ~ 0.16 Ang^2 at ambient temperature).  Hence virtually
all of the contributions to the atomic vibrations in a protein structure
must come from rigid body translational & librational motion.

-- Ian Tickle

-----Original Message-----
From: Vondelft, Frank [mailto:Frank.Vondelft@syrrx.com]
Sent: 16 December 2002 20:31
To: eaberry@lbl.gov
Cc: ccp4bb@dl.ac.uk
Subject: RE: [ccp4bb]: B factors


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> > disorder) than having to believe that one atom's positional
uncertainty
> > relative to its neighbours is in the order of its bondlengths to
those
> > self-same neighbours(*), which makes for somewhat awkward chemistry.
> > Our residual Bfactors do indeed end up in that range, even when the
> > WilsonB is 50+ (and I don't think that's simply the result of the
> > default in ccp4i).
> > 
> > (*) Yes, indeed: isotropic INDIVIDUAL Bfactors...
> 
> I would have thought the value we refine as individual B-factor
> says nothing about its motion being correlated or not with that
> of its neighbors, and of course if the rms movement is around 2A
> then it must be correlated with its neighbors, or bonds would
> be breaking?

Yes of course, that's the point, but it's nice to have these
correlations modelled explicitly, as opposed to them being merely
"understood", which is why I really like TLS.  And hence, too, the
improved R-factors after TLS(typically).

phx.


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