[phenixbb] RuntimeError : min()

Pavel Afonine PAfonine at lbl.gov
Sat Sep 19 14:51:14 PDT 2009


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 at 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
>
>
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