Pavel,

> - In general you are free to decide what you name a domain: it can be
> a residue, its part or the whole structure.
> - What would be "main" and "side" for non-amino acid molecule, like a
> whatever ligand?

I don't see how my freedom to explicitly define the terms I use in a
post is relevant.  I was just emphasizing that I use "grouped" in "CNS
sense".  Your question obviously has no answer, neither I intended to
propose any general definition of a side chain.  It is quite clear that
one can only define main chain/side chain in a meaningful way for
*polymers*.

> It boils down to similar point that tightly restrained refinement of
> individual coordinates would be equivalent to rigid body refinement.
> In practice, it is not. You can prove it by doing simple numeric
> experiments. I did this sometime ago when working on this paper
> (Automatic multiple-zone rigid-body refinement with a large
> convergence radius. Afonine et al), but I didn't include the results
> since it was out of scope of that paper. 

Oh no it does not.  Tightly restrained refinement will be equivalent to
torsion angle parametrization, since bonds and angles are essentially
fixed (but dihedrals are not).  Similarly, properly tight restraints on
individual B-factors are not equivalent to grouped B-factors (in
whatever sense) because they can capture the distribution throughout the
structure.

> Each data quality requires proper model parameterization. Otherwise,
> why don't we do multipolar refinement at 2A resolution, or refine
> individual anisotropic B-factors at 3A resolution? Simply because it
> would be improper model parameterization given the data quality. It
> would be the same nonsense as refining individual isotropic B-factors
> at 4A resolution. Although technically, using proper weights, you
> probably could -:)

I think the example that Jose Antonio originally provided (at 3.1A, not
4A) clearly demonstrates that it makes more sense to do properly
restrained individual B-factor refinement than
two-adp-groups-per-residue refinement.  Do you disagree specifically on
this issue?  Are you suggesting that there is nothing wrong that
B-factors go from 85 to 132 between CA and CB in R178 and then from 162
*down* to 101 in L183 in his model?  Look at C-N bond between I180 and
K181.  I don't think a model that provides 82/164 jump in adp between
covalently bonded atoms is realistic.  Not at 3.1A, and probably not
even at 4A.

I think you are too quick to dismiss properly restrained individual
B-factor refinement at low resolution as nonsense.  The existing
two-adp-groups-per-residue implementation (CNS and phenix) is, imho, an
example of *improper* parametrization.  It disregards the perfectly
valid observation that B-factors of covalently bonded atoms can't differ
much.  It is similar to modeling every residue as two dummy atoms,
representing the backbone and the side chain, but without distance
restraints between them and between backbone elements of neighbor
residues. 

I think your examples of multipolar refinement at 2A and anisotropic
adps at 3A are somewhat more extreme compared to tightly restrained
individual B-factors at 3.1A.  It's an argument by exaggeration, so to
speak.


> > 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.
> >   
> 
> Yes, this is what is implemented in phenix.refine. See formula in the
> reference above -:)

Thanks for pointing this out.  Shall RTDM.

Cheers,

Ed.


-- 
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 /