[phenixbb] joint xn refinement question

Pavel Afonine pafonine at lbl.gov
Fri Jan 30 08:25:40 PST 2009

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 


More information about the phenixbb mailing list