[phenixbb] joint xn refinement question

Walter Novak wnovak at brandeis.edu
Fri Jan 30 08:00:19 PST 2009


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.


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 \

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

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