[phenixbb] Hirshfeld (rigid bond) test

Pavel Afonine pafonine at lbl.gov
Thu Jan 31 14:17:24 PST 2013


> I guess it is not terribly useful in most cases, but it would be a 
> valuable tool for
> comparing the outcomes of different refinement strategies for the same 
> macromolecule,
> especially as rigid-bond-test, unlike ADP values, should be in 
> principle independent
> from effects of different anisotropic scaling factors.
> Averaging rigid-bond-test values over domains, main chain/side chain 
> of a certain residue,
> or over certain bond-types (peptide, C-Cring a.s.o) would be a nice 
> validation tool too.

In case of isotropic atoms it's just |Bi-Bj|, where i and j are indices 
of bonded atoms, B are their isotropic B-factors. Often one considers 
<|Bi-Bj|>, where <> is average over all such pairs (or selected atoms), 
and I would expect as many opinions about what these values should be as 
many people are aware of such metric.

In case of anisotropic atoms the formula is the same, but B means 
projection of anisotropic vibration component onto bond vector i-j.

Hirshfeld's paper (Acta Cryst 197?, ?=6..7...8) discusses values for 
|Bi-Bj|, but it isn't clear whether that is transferable to macromolecules.

If memory serves correctly, Dale Tronrud uses tabulated |Bi-Bj| values 
for various atom types derived from well determined structures as 
targets for ADP restraints.

Some programs explicitly apply it as part of ADP restraints.


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