From CCP4 wiki
==== Hydrogens ====
Use phenix.ready_set to add hydrogens to your PDB file, and (except at ultra-high resolution)
the riding hydrogen model in phenix.refine (this is the default so you do not have to specify anything).
phenix.ready_set internally uses phenix.elbow for ligands and phenix.reduce for the protein. phenix.pdbtools can also add hydrogens (FIXME: what are the differences?).
Hydrogens should not be used in NCS and TLS groups - it might be a good idea to add <font face="Courier"> and not (element H or element D)</font> to all selection strings.