Hi Walter,
I added H positions using reduce and have been switching to Ds as the density suggests for exchangeable positions.
You can use this command below that will automatically add H or exchangeable H/D to your molecule: phenix.ready_set model.pdb neutron_exchange_hydrogens=true
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.
Which version of PHENIX you use? Yes, a few pictures may help (if they will be large, please don't send them to the bb but to my email directly, otherwise the email might get stuck), since I don't see what exactly is happening. Several months ago I added automatic real-space fitting of H/D atoms into density which is supposed to happen during refinement. For example, this is meant to help in cases like this: if tyrosine's O-H/D sticks out of density peak and the density is not strong enough to guide moving H/D into it, then this procedure should help. Also, could it be that X-ray data outweigh the neutron data? Could you try refining against neutron data only to see if it helps? A few comments about the command you use:
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 \
You most likely don't need "rigid_body", but I would definitely add "occupancies" since it will refined occupancies of H/D atoms at unchangeable positions which is important.
simulated_annealing=False \
This is False by default, so you san simply remove this line.
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 \
OK. I would also add "ordered_solvent=true" to automatically add and refined water.
switch_to_isotropic_high_res_limit=2.5 \
This is used only if you have anisotropic atoms. If not, you can remove this line too.
optimize_wxc=true \ optimize_wxu=true \
This might take a while to run. What happens if you don't use these two above? Pavel.