After tracking these extra hydrogens further, I now realize the source is
Phenix.ready_set, not COOT as I had first thought. Phenix.ready_set adds an
alternate amide hydrogen (ATOM H) for each instance where the residue is not
itself in two alternate conformations, but the preceding residue has
alternate carbonyl atoms (ATOM C and ATOM O). This makes sense so as to
maintain planar peptide bonds for both carbonyl moieties.
Martin
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