[phenixbb] RuntimeError : min()

RAVINDRA D MAKDE rdm19 at psu.edu
Sat Sep 19 13:02:53 PDT 2009


Hi all,
I will highly appreciate your help to resolve the following bugs encountered
during running phenix.refine on GUI as well as on command lines.
My version of Phenix and platform are: PHENIX: Python-based Hierarchical
ENvironment for Integrated Xtallography  Version: 1.4  Release tag: 3  cctbx
tag: 2008_12_07_1353  Platform: mac-intel-osx osx-10.5.8

The error encountered using phenix refinement GUI (phenix.refine_gui) is as
follows:
A Python error was detected.  This is almost certainly a bug; please send an
email containing this message to phenixbb at phenix-online.org so we can fix it. 
Thanks!RuntimeError : min() argument is an empty arrayTraceback:Traceback (most
recent call last):  File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Base.py", line
274, in OnBrowse    self.file_text_field.SetValue(new_path)  File
"/usr/local/phenix-1.4-3/phenix/wxGUI2/Controls.py", line 974, in SetValue   
self.phil_handler.propagate_update(self.phil_def_name, new_value)  File
"/usr/local/phenix-1.4-3/phenix/wxGUI2/PhilInterfaceHandler.py", line 103, in
propagate_update    self._update_handlers[def_name](self, def_name, value) 
File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Extensions.py", line 28, in
extract_xray_neutron_params    phil_def_name = phil_object_name)  File
"/usr/local/phenix-1.4-3/phenix/wxGUI2/Reflections.py", line 155, in __init__  
 self.load_reflection_file(file_name, phil_def_name)  File
"/usr/local/phenix-1.4-3/phenix/wxGUI2/Reflections.py", line 159, in
load_reflection_file    self.hkl_server =
self.hkl_handler.add_hkl_file(file_name, phil_def_name)  File
"/usr/local/phenix-1.4-3/phenix/wxGUI2/Reflections.py", line 66, in
add_hkl_file    err=sys.stderr)  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):

The error encountered using phenix refinement on command line (phenix.refine
coordinate.pdb reflection.mtz) is as follows:
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
N.B. Earlier, I had encountered the similar error (using command line) using
PHENIX version 1.3 on the same platform.
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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