Hi Qun,

- I agree with Ralf: the version you use is really old and I would suggest using the latest available that you can download from this web page: http://www.phenix-online.org/download/

- When you run joint XN refinement, you need to explicitly specify which data is neutron and which is X-ray (there is no (reliable) way for phenix.refine to figure this out automatically). So, I would correct your command below as following and run again:

phenix.refine xray_data.file_name=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

The fraction of your file "refine_default.params" looks good to me. The choice for scattering dictionary is automatically adjusted given the input data. I agree it is a bit confusing the way it's reported in parameters file, I'm making a note of this right now and I will make it clearer in future.

A few points to keep in mind doing joint XN refinement:
- you can automatically add H atoms as well as exchangeable H/D using phenix.ready_set. Example:
phenix.ready_set model.pdb

- when doing joint XN refinement, try using "optimize_wxc=true optimize_wxu=true". This might be essential to get a good result.

- also, I would recommend running separate X-ray and Neutron refinements to compare with.

Please let me know if you have any questions or problems with this; I will be happy to help with any issues.

Cheers,
Pavel.


On 1/1/2009 9:15 PM, crystallogrphy wrote:
Deall all:

I have a question about xray and neutron joint refinement.

When I start phenix joint refinement like this, phenix gave the wrong message:
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):
    call_back_after_monitor_collect=call_back_after_monitor_collect)
  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
AssertionError

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: [email protected]
lab phone: 216-368-3337

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