Hi Emily,

Is it possible to use the neutron data only for refining hydrogen atom positions and the X-ray data for all other atoms?

yes, easily in phenix.refine. Though this may not be the world's greatest refinement strategy. Do you have specific reasons for wanting to do this?

I used the option to add hydrogen atoms to model and refine H/D at exchangable sites and H elsewhere.

Yes, this is a good thing to do when refining against neutron data set.

This worked for many of the exchangeable hydrogen atoms. However, for some side chains, especially Lysine, the program has placed a hydrogen and deuterium atom (with refined occupancies) in the same position as the atom it is supposed to be bonded to.

Hm.. this should not happen if file comes out of any Phenix program... Could you please send me the PDB file (off list, to my email directly), indicate residue(s) in trouble and explain how you obtained this file, then I'll have a look. Pavel