I am refining with 1.14 Å data and have included riding hydrogen atoms. In
addition to (and perhaps related to) certain difficulties with real-space
refinement caused by nomenclature mismatch phenix/coot, the alpha-carbon
hydrogen is not removed when deleting an alternate conformation residue. For
each residue previously with two alternate conformations, reduced to one
conformation, the H atom retains A and B tags with partial occupancy. This
is easy to clean up with a text editor, or by running phenix.reduce -trim;
phenix.ready_set, however, if there are plans to smooth out model building
with hydrogens...
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