[phenixbb] phenix.refine issue

Dennis Wolan Dennis.Wolan at ucsf.edu
Mon Jul 27 16:02:08 PDT 2009


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





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