DISCLAIMER: When I say "grouped B-factor refinement" I mean CNS-style,
Bmain/Bside refinement. Not to be confused with more general "domain
B-factor refinement" where single B-factor is assigned to some part of
the structure.
> Apart from improving data-to-parameters ratio, another argument for
> going from individual isotropic ADP to group isotropic ADP, is that at
> low resolution you don't see atoms individually and therefore there is
> not much sense in refining parameters for them individually.
Which is in some way redundant argument, since your ability to "see
atoms individually" (i.e. optical resolution) is correlated with
data-to-parameter ratio. And such argument would also be misleading
because "individual B-factor refinement" does *not* refine parameters
individually, due to presence of restraints. In a way, the term itself
is misleading (there goes semantic issue again).
> That's exactly why ("effective number of parameters in presence of
> restraints") individual B-factor refinement works well in phenix.refine
> at lower resolutions, where people traditionally tempt to switch to
> group isotropic ADP. Going to lower resolution, I only switch to group
> ADP refinement if I really have to.
Just as it worked well in CNS and works well in REFMAC (which doesn't
even have the grouped B-factor refinement). It may be an extreme point
of view, but I think grouped B-factor refinement is useless distraction.
Unlike domain B-factor refinement coupled with thoughtful decision as to
which parts of the molecule may move together. Which again is not
necessarily better than refining one B-factor per atom with tight
restraints.
> Group B-factor refinement is a constrained refinement: indeed, you
> constrain all B-factors to be identical within the group (similarly, as
> TLS refinement is a group constrained anisotropic refinement). It is
> "unrestrained" in a sense that there is no restraints used to make the
> group B-factors similar between adjacent residues. I will add this
> functionality to phenix.refine at some point.
It is rather obvious that I meant restraints between groups, not inside.
As for implementation of such restraints, it may be easier said than
done. While it's reasonable to apply the same restraints to every pair
of covalently bonded atoms, restraints between groups are not
necessarily identical. For instance, main-chain/side-chain restraints
in the same residue may need to be weaker than those applied to backbone
atoms when restraining neighboring residues. Side-chains on the surface
apparently will be less correlated with the backbone than those in the
core.
With the broader definition of the grouped B-factor refinement things
get even more ambiguous. Let's say I select one B-factor for every
secondary structure element. Two helices, while adjacent in the
sequence, may be totally uncorrelated, while those close in the
structure may be far apart in the sequence. I have a feeling that I've
seen/heard somewhere the idea of imposing B-factor restraints based on
interatomic distances, may be applicable here.
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------ / Lao Tse /
