On Friday, January 06, 2012 09:30:22 am Nat Echols wrote:
> 2012/1/6 Pete Meyer <pame...@mcw.edu>:
> > However, at 3.2 Angstroms I'd recommend against using atomic B-factors -
> > the "rule of thumb" for this is 2.8 Angstroms for atomic B-factors (or
> > at least it was back in the day). �It might help to use an overall
> > B-factor combined with one (or a few) TLS groups.
>
> This may be true for older software which restraints B-factors only to
> bonded atoms, but it is not the case in Phenix*, which takes into
> account all nearby atoms, not just bonded ones. The result is that
> individual B-factor refinement is very stable at low resolution - we
> don't know what the limit is, but it routinely works very well at 4A.
Unfortunately, "stable" and "statistically correct" are two very different
criteria. It is quite possible to have a stable refinement that produces
nonsensical, or at least unjustifiable, B factors. Actually this caveat
applies to things other than B factors as well, but I'll stay on topic.
At last year's CCP4 Study Weekend I presented a statistical approach to
deciding what treatment of B could be justified at various resolutions.
"To B or not to B?" The presentations from that meeting should appear in a
special issue of Acta D soon.
Based on the set of representative cases I have examined, I am willing
to bet that with the limited obs/parameter ratio in the case at hand,
a model with individual Bs would turn out to be statistically unjustified
even if the refinement is "stable". A TLS model is more likely to be
appropriate.
cheers,
Ethan
> Of course the performance is still dependent on solvent content, NCS,
> etc., but it is very rare that grouped B-factor refinement actually
> works better.
>
> -Nat
>
> * I think Refmac may do something similar, but I haven't tried this
> recently. I would be very surprised if it did not work well at 3.2A,
> however.
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
