[phenixbb] Problem with anomalous scattering factor refinement

[Subhani Bandara]

Hi all,

I've been trying to refine a structure with anomalous data with anomalous
scattering factors. After some refinements without anomalous scattering
factor refinement, I used the data.mtz file and original reflection file in
reflection file editor to get the anomalous data merged with Rfree flags.
When I tried to use this file with a pdb file (deleted hexadigest remark)
and a cif file for ligands, the refinement ends with the following error at
the end of the 3rd refinement cycle (I have only 3 cycles for a refinement).

I was able to run a similar refinement with anomalous scattering factors
for another structure without a problem. One difference in this structure
is that this has NCS and the previous one didn't. I am using dev-1243 GUI.

RuntimeError : scitbx array_family range error

Traceback:

  File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/libtbx/thread_utils.py",
line 234, in run

    return_value = self._target(self._args, self._kwargs, self._c)



  File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/libtbx/runtime_utils.py",
line 87, in __call__

    result = self.target()



  File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/libtbx/runtime_utils.py",
line 66, in __call__

    result = self.run()



  File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/runtime.py",
line 69, in run

    refine_object = self._run(args, callback)



  File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/runtime.py",
line 85, in _run

    call_back_handler=callback)



  File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/command_line.py",
line 169, in run

    map_manger.write_files()



  File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/driver.py",
line 1735, in write_files

    map_coeff_dataset=self.write_mtz_file(),



  File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/driver.py",
line 1724, in write_mtz_file

    pdb_hierarchy=self.refine_object.model.pdb_hierarchy())



  File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/mmtbx/maps/__init__.py",
line 500, in __init__

    pdb_hierarchy = pdb_hierarchy)



  File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/mmtbx/maps/__init__.py",
line 428, in map_coefficients_from_fmodel

    sharp      = params.sharpening).map_coeffs



  File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/mmtbx/map_tools.py",
line 55, in __init__

    data = self.map_coeffs.data()*scale)





Thanks in advance for any help


Subhani
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20121226/c7c836ae/attachment.htm>