Hi, I am new to the list, but I didn't see this issue in the list archive. I am doing a joint refinement using x-ray and neutron data (each set is ~2.0 Å). I added H positions using reduce and have been switching to Ds as the density suggests for exchangeable positions. My problem is that I cannot seem to get the H (or D) positions to refine into the neutron density. Perhaps I need an additional command, so I am attaching my refinement script. I can provide a few pictures from coot to demonstrate if helpful. Thanks! Wally phenix.refine prot_joint4_r8_001.pdb \ neutron_data.file_name=prot_best_mcH_D2O_2_data.mtz \ xray_data.file_name=prot_best_mcH_D2O_2_data.mtz \ output.prefix=prot_joint4_r9 \ strategy=rigid_body+individual_sites+individual_adp \ simulated_annealing=False \ input.xray_data.labels=F-obs input.neutron_data.labels=F-obs-neutron \ input.xray_data.r_free_flags.label=R-free-flags \ input.xray_data.r_free_flags.file_name=prot_best_mcH_D2O_2_data.mtz \ input.xray_data.r_free_flags.test_flag_value=1 \ input.neutron_data.r_free_flags.label=R-free-flags-neutron \ input.neutron_data.r_free_flags.file_name=prot_best_mcH_D2O_2_data.mtz \ input.neutron_data.r_free_flags.test_flag_value=1 \ main.number_of_macro_cycles=5 \ restraints_edits.params \ refinement.hydrogens.refine=individual \ find_and_add_hydrogens=True \ switch_to_isotropic_high_res_limit=2.5 \ optimize_wxc=true \ optimize_wxu=true \ --overwrite Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405