Hi, 

I am doing joint X-ray and neutron refinement for my structure. 

I found a few residues with two alternate conformations. After I generated alternation conformations, I used phenix.readyset to generate hydrogen and deuterium atoms for D/H atoms. However, phenix.readyset only gives H atoms for exchangable H atoms, such as the amide H atoms. The reason is that A and B letters have been assigned for the alternate conformation, not for the D/H atoms for particular conformations. 

Could anyone know how to solve this problem? 

The second question is that I found one Glu residue is protonated at OE1 atom of its carboxylate side chain. How could I generate protonated Glu? Do I need a strain file for this?

Thanks!

Qun