error: running phenix.refine
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, Regards, Ravi Ravindra D. Makde, PhD Postdoctoral fellow, Tan lab, The Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 USA
Hi Ravi, - version 1.3 is old and it is the best to try one of the latest ones: http://www.phenix-online.org/download/nightly_builds.cgi - if you get the same error using the latest installer, I will need to see the inputs you used: data file, command line parameters. It would be helpful if you send me those. Pavel. On 9/16/09 8:04 PM, RAVINDRA D MAKDE wrote:
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,
Regards,
Ravi
Ravindra D. Makde, PhD Postdoctoral fellow, Tan lab, The Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 USA
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