This is an error in map calculation - I have a few suspicions about
what is breaking but I need to see what's happening internally. Can
you please send me the logfile?
thanks,
Nat
On Wed, Dec 26, 2012 at 1:56 PM, 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
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