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Hi Ravindra,<br>
<br>
didn't you report the exact same problem? I think so, and my reply was
contained two suggestions:<br>
<br>
- try the latest PHENIX from nightly builds:<br>
<a class="moz-txt-link-freetext"
href="http://www.phenix-online.org/download/nightly_builds.cgi">http://www.phenix-online.org/download/nightly_builds.cgi</a><br>
<br>
Note, 1.4-3 is not the latest.<br>
<br>
- 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.<br>
<br>
Pavel.<br>
<br>
<br>
On 9/19/09 1:02 PM, RAVINDRA D MAKDE wrote:
<blockquote cite="mid:1253390573l.1183790l.0l@psu.edu" type="cite">
<div>
<div>Hi all,</div>
<div><br>
</div>
<div>I will highly appreciate your help
to resolve the following bugs encountered during running phenix.refine
on GUI
as well as on command lines.</div>
<div><br>
</div>
<div>My version of Phenix and
platform are: </div>
<div>PHENIX: Python-based Hierarchical ENvironment for
Integrated Xtallography</div>
<div> Version:
1.4</div>
<div> Release tag: 3</div>
<div> cctbx tag:
2008_12_07_1353</div>
<div> Platform: mac-intel-osx
osx-10.5.8</div>
<div><br>
</div>
<div><br>
</div>
<div><b>The error encountered
using phenix refinement GUI (phenix.refine_gui) is as
follows:</b></div>
<div><br>
</div>
<div>A Python error was detected. This
is almost certainly a bug; please send an email containing this message
to
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a> so we can fix it.
Thanks!</div>
<div>RuntimeError : min() argument is an empty
array</div>
<div>Traceback:</div>
<div>Traceback (most recent call
last):</div>
<div> File
"/usr/local/phenix-1.4-3/phenix/wxGUI2/Base.py", line 274, in
OnBrowse</div>
<div>
self.file_text_field.SetValue(new_path)</div>
<div> File
"/usr/local/phenix-1.4-3/phenix/wxGUI2/Controls.py", line 974, in
SetValue</div>
<div>
self.phil_handler.propagate_update(self.phil_def_name,
new_value)</div>
<div> File
"/usr/local/phenix-1.4-3/phenix/wxGUI2/PhilInterfaceHandler.py", line
103, in
propagate_update</div>
<div>
self._update_handlers[def_name](self, def_name,
value)</div>
<div> File
"/usr/local/phenix-1.4-3/phenix/wxGUI2/Extensions.py", line 28, in
extract_xray_neutron_params</div>
<div> phil_def_name =
phil_object_name)</div>
<div> File
"/usr/local/phenix-1.4-3/phenix/wxGUI2/Reflections.py", line 155, in
__init__</div>
<div> self.load_reflection_file(file_name,
phil_def_name)</div>
<div> File
"/usr/local/phenix-1.4-3/phenix/wxGUI2/Reflections.py", line 159, in
load_reflection_file</div>
<div> self.hkl_server =
self.hkl_handler.add_hkl_file(file_name,
phil_def_name)</div>
<div> File
"/usr/local/phenix-1.4-3/phenix/wxGUI2/Reflections.py", line 66, in
add_hkl_file</div>
<div>
err=sys.stderr)</div>
<div> File
"/usr/local/phenix-1.4-3/iotbx/reflection_file_utils.py", line 393, in
__init__</div>
<div>
force_symmetry=self.force_symmetry))</div>
<div> File
"/usr/local/phenix-1.4-3/iotbx/reflection_file_reader.py", line 197, in
as_miller_arrays</div>
<div>
base_array_info=base_array_info)</div>
<div> File
"/usr/local/phenix-1.4-3/iotbx/mtz/__init__.py", line 434, in
as_miller_arrays</div>
<div> and
flex.min(column_group.sigmas()) >
0):</div>
<div><br>
</div>
<div><br>
</div>
<div><b>The error encountered using
phenix refinement on command line (phenix.refine coordinate.pdb
reflection.mtz)
is as follows:</b></div>
<div><br>
</div>
<div>Traceback (most recent call
last):</div>
<div> File
"/usr/local/phenix-1.4-3/phenix/phenix/command_line/refine.py", line 9,
in
<module></div>
<div>
command_line.run(command_name="phenix.refine",
args=sys.argv[1:])</div>
<div> File
"/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py",
line 68, in
run</div>
<div> log=log)</div>
<div> File
"/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py",
line 231,
in __init__</div>
<div> reflection_file_server =
self.reflection_file_server()</div>
<div> File
"/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py",
line 566,
in reflection_file_server</div>
<div>
err=self.log)</div>
<div> File
"/usr/local/phenix-1.4-3/iotbx/reflection_file_utils.py", line 393, in
__init__</div>
<div>
force_symmetry=self.force_symmetry))</div>
<div> File
"/usr/local/phenix-1.4-3/iotbx/reflection_file_reader.py", line 197, in
as_miller_arrays</div>
<div>
base_array_info=base_array_info)</div>
<div> File
"/usr/local/phenix-1.4-3/iotbx/mtz/__init__.py", line 434, in
as_miller_arrays</div>
<div> and
flex.min(column_group.sigmas()) > 0):</div>
<div>RuntimeError: min() argument
is an empty array</div>
<div><br>
</div>
<div>N.B. Earlier, I had encountered the
similar error (using command line) using PHENIX version 1.3 on the same
platform.</div>
<div><br>
</div>
<div>Thanks in
advance.</div>
<div><br>
</div>
<div>Regards,</div>
<div><br>
</div>
<div>Ravi</div>
<div><br>
</div>
<br>
Ravindra D. Makde, PhD<br>
Postdoctoral fellow, Tan lab,<br>
The Department of Biochemistry and Molecular Biology,<br>
The Pennsylvania State University,<br>
University Park, PA 16802<br>
USA<br>
<br>
<br>
</div>
</blockquote>
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