[phenixbb] Question

Louis Lazar louisl at brandeis.edu
Mon Oct 18 07:30:24 PDT 2010


Hello,

I am seeing an internal error while trying to conduct joint x-ray/neutron
refinement, and any help with the issue below would be greatly appreciated.
Thank you very much in advance:

================================ ADP refinement
===============================

Traceback (most recent call last):
  File
"/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/command_line/refine.py",
line 11, in <module>
    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
  File
"/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/command_line.py",
line 89, in run
    call_back_handler=call_back_handler)
  File
"/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/driver.py",
line 1182, in run
    call_back_handler       = call_back_handler)
  File
"/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/strategies.py",
line 735, in refinement_machine
    h_params               = h_params)
  File
"/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/refinement/adp_refinement.py",
line 192, in __init__
    all_params = all_params)
  File
"/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/refinement/adp_refinement.py",
line 216, in refine_adp
    model.set_refine_individual_adp()
  File
"/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/model.py",
line 1035, in set_refine_individual_adp
    iselection = selection_iso.iselection())
RuntimeError: cctbx InternalError:
/net/anaconda/scratch1/phenix/phenix-1.6.4-486/cctbx_project/cctbx/xray/scatterer_flags.h(417):
CCTBX_ASSERT(f.use_u_iso()) failure.



This error occurs during the 2nd macro cycle of refinement using this
general command:

phenix.refine model.pdb data_xray.hkl
neutron_data.file_name=data_neutron.hkl
input.xray_data.labels=FOBSx input.neutron_data.labels=FOBSn



Thanks again.

Regards,

Louis
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