[phenixbb] question about xn joint refinement

crystallogrphy qunwan1 at gmail.com
Thu Jan 1 21:15:48 PST 2009

Deall all:

I have a question about xray and neutron joint refinement.

When I start phenix joint refinement like this, phenix gave the wrong
phenix.refine dhfr-mtx-rt-xray.hkl neutron_data.file_name=newdhfr_un_change.hkl
xn_easy_080326a.pdb input.xray_data.labels=FOBSx
input.neutron_data.labels=FOBSn xray_data.r_free_flags.generate=True
neutron_data.r_free_flags.generate=True refine_default.params

===================== joint neutron/xray refinement start

Traceback (most recent call last):
  File "/usr/local/phenix-1.3-rc4/phenix/phenix/refinement/driver.py", line
1031, in run
    call_back_after_monitor_collect = call_back_after_monitor_collect)
  File "/usr/local/phenix-1.3-rc4/phenix/phenix/refinement/strategies.py",
line 184, in refinement_machine
   * assert not neutron_refinement

I guess in my default parameters, something is wrong, particularly the bold
word I highlighted. But I do not know how to fix. Does any one have a clue?\
Thanks and Happy New Year!

main {
    bulk_solvent_and_scale = True
    simulated_annealing = False
    ordered_solvent = False
    ncs = False
    ias = False
    number_of_macro_cycles = 3
    max_number_of_iterations = 25
    use_form_factor_weights = False
    tan_u_iso = False
    use_convergence_test = False
    target = *ml mlhl ml_sad ls
    min_number_of_test_set_reflections_for_max_likelihood_target = 50
    max_number_of_resolution_bins = 30
    reference_xray_structure = None
    use_experimental_phases = None
    compute_optimal_errors = False
    random_seed = 2679941
    *scattering_table = wk1995 it1992 *n_gaussian neutron*
    use_normalized_geometry_target = True
    target_weights_only = False
    use_f_model_scaled = False
    max_d_min = 0.25
    fake_f_obs = False

Qun Wan
Department of Pharmacology, Case Western Reserve University
10900 Euclid Avenue, Cleveland, OH 44106
email: qunwan1 at gmail.com
lab phone: 216-368-3337
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