RE: [ccp4bb]: B factors

["Vondelft, Frank" <Frank.Vondelft@syrrx.com>]

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> > I would also be interested in the current opinion(s). Speaking for
> > myself, I think that 80 or 100 is a very reasonable average atomic B
> > for structures diffracting to low resolution, and the relative
scarcity
> > of such high B-factors in the PDB is due to questionable practices
used
> > in the past which did not preserve the overall B-factor information
> > present in the original data.
> .....
> .....
> 
> noticed (anecdotally) more frequent occurrences of B-factors that we 
> once would have called abnormally high based on our strange old rules
of 
> thumb, such as that main-chain B's should be around 20.  


Routine use of TLS refinement does, however, seem to restore credibility
to those strange old rules;  in particular, it generates a far more
satisfactory model of why my density sucks (i.e. global and concerted
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...

Further idle musings and some vague hand-gestures lead me to wonder
whether this may point us to that elusive automatic definition of the
TLS group, or indeed to a way to transition smoothly from grouped to
individual B-factors with increasing resolution;  it's seems almost as
if TLS groups should allow us to apply chemical restraints to the
uncertainties as well as XYZ. 

*sigh* maybe when I have more time ;-)

Of course, the _combined_ Bfactor (individual + TLS, alla TLSANAL) can
and should be high if that's what the data says. 

phx.


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