[phenixbb] error: running phenix.refine

RAVINDRA D MAKDE rdm19 at psu.edu
Wed Sep 16 20:04:03 PDT 2009

Hello all,
I will greatly appreciate the help for the following:
I am getting the error "RuntimeError: min() argument is an empty array" (more
details error message given below) while running phenix.refine. I am using
PHENIX:  Version: 1.3 on  Platform: mac-intel-osx osx-10.5.7
My error message is as follows: 
Traceback (most recent call last):  File
"/usr/local/phenix-1.3-final/phenix/phenix/command_line/refine.py", line 5, in
<module>    command_line.run(command_name="phenix.refine", args=sys.argv[1:]) 
File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/command_line.py",
line 68, in run    log=log)  File
"/usr/local/phenix-1.3-final/phenix/phenix/refinement/command_line.py", line
231, in __init__    reflection_file_server = self.reflection_file_server() 
File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/command_line.py",
line 566, in reflection_file_server    err=self.log)  File
"/usr/local/phenix-1.3-final/iotbx/iotbx/reflection_file_utils.py", line 379,
in __init__    force_symmetry=self.force_symmetry))  File
"/usr/local/phenix-1.3-final/iotbx/iotbx/reflection_file_reader.py", line 197,
in as_miller_arrays    base_array_info=base_array_info)  File
"/usr/local/phenix-1.3-final/iotbx/iotbx/mtz/__init__.py", line 424, in
as_miller_arrays    and flex.min(column_group.sigmas()) > 0):RuntimeError:
min() argument is an empty array

Thanks in advance,

Ravindra D. Makde, PhD
Postdoctoral fellow, Tan lab,
The Department of Biochemistry and Molecular Biology,
The Pennsylvania State University,
University Park, PA 16802

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