I am having an issue with running a simple phenix.refine that I have never encountered before. I get a list of issues and the program quits with: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/phenix/command_line/ refine.py", line 9, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/ command_line.py", line 68, in run log=log) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/ command_line.py", line 231, in __init__ reflection_file_server = self.reflection_file_server() File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/ command_line.py", line 566, in reflection_file_server err=self.log) File "/usr/local/phenix-1.4-3/iotbx/reflection_file_utils.py", line 393, in __init__ force_symmetry=self.force_symmetry)) File "/usr/local/phenix-1.4-3/iotbx/reflection_file_reader.py", line 197, in as_miller_arrays base_array_info=base_array_info) File "/usr/local/phenix-1.4-3/iotbx/mtz/__init__.py", line 434, in as_miller_arrays and flex.min(column_group.sigmas()) > 0): RuntimeError: min() argument is an empty array I have no idea if the issue is with my pdb or mtz. I'm sure it's something very simple that I just am not identifying. Thanks in advance, Dennis
I am having an issue with running a simple phenix.refine that I have never encountered before. I get a list of issues and the program quits with:
Sorry for the problem. It was fixed Apr 11 2009. Any installer built after this date should work. If you want to patch your 1.4-3 installation, edit the file /usr/local/phenix-1.4-3/iotbx/mtz/__init__.py and add one line as shown below. Ralf Index: __init__.py =================================================================== --- __init__.py (revision 8913) +++ __init__.py (revision 8914) @@ -430,6 +430,7 @@ if (merge_equivalents and isinstance(column_group.data(), flex.double) and isinstance(column_group.sigmas(), flex.double) + and column_group.sigmas().size() != 0 and flex.min(column_group.sigmas()) > 0): merged_column_group = column_group.merge_equivalents().array() if (merged_column_group.indices().size()
participants (2)
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Dennis Wolan
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Ralf W. Grosse-Kunstleve