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