Hi Ravindra,

didn't you report the exact same problem? I think so, and my reply was contained two suggestions:

- try the latest PHENIX from nightly builds:
http://www.phenix-online.org/download/nightly_builds.cgi

Note, 1.4-3 is not the latest.

- if you get the same error using the latest installer, then please send me the data, model and the exact command including all parameter files (if any), so I can do further diagnostics and suggest a work-around.

Pavel.


On 9/19/09 1:02 PM, RAVINDRA D MAKDE wrote:
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@phenix-online.org so we can fix it.  Thanks!
RuntimeError : min() argument is an empty array
Traceback:
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