[phenixbb] joint xn refinement question
pafonine at lbl.gov
Fri Jan 30 08:25:40 PST 2009
> 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
> 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
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