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
