Dear Ed,
> Riding hydrogens are *not* part of your model, they are part of the
> algorithm used to predict observations.
<snip>
As a diversion from PDB-ology I would point out that, according to
Bayesian statistics, of which the maximum-likelihood method is a rough
specialisation and approximation, "the model" and "the algorithm used to
predict observations" are identical notions, if the results of that
prediction are understood to be given by probability distributions over
possible observations, and not just as numbers. It is just our habit of
worshipping 3D graven images in the form of PDB files that make us give a
peculiar meaning to the work "model": it is the whole mechanism by which
that file gives rise to a prediction of structure factors (including the
insertion of riding hydrogens, if desired; but also a solvent model and an
error model via the sigmaa parameter) that constitutes "the model" in the
Bayesian sense of the word.
In any case - it was too good an opportunity to be missed to put a drop
of Bayesian oil into the old crystallographic cogs.
With best wishes,
Gerard.
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