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Hi Gino,<br>
<br>
phenix.real_space_refine is actively developing tool; a week old
version is an obsolete one. So please try the latest one from
nightly builds:<br>
<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/download/nightly_builds.cgi">http://phenix-online.org/download/nightly_builds.cgi</a><br>
<br>
and if this does not work please send me input files so I
investigate.<br>
<br>
Specifically in this case the program crashed because the origin of
input map is not zero. In recent versions this is fixed.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 5/15/14, 2:58 PM, Gino Cingolani
wrote:<br>
</div>
<blockquote cite="mid:1400191136250.89514@jefferson.edu" type="cite">
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<p>Hi all,</p>
<p><br>
</p>
<p>I'm trying to refine a pdb against an EM map using
phenix.real_space_refine using default parameters (e.g.
phenix.real_space_refine model1.pdb map.ccp4).
</p>
<div>
<p>The program starts OK but quickly stops with the following
output (see below)</p>
<p><br>
</p>
<p>Any thoughts? Thanks so much!</p>
<p><br>
</p>
<p>Gino<br>
</p>
<p><br>
</p>
<p>###########################################################################</p>
<p>Add C-beta restraints<br>
*********************<br>
Adding C-beta torsion restraints...<br>
num c-beta restraints: 11832<br>
-------------------------------------------------------------------------------<br>
Getting target map<br>
******************<br>
Traceback (most recent call last):<br>
File
"/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py",
line 494, in <module><br>
o = run(sys.argv[1:])<br>
File
"/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py",
line 273, in __init__<br>
self.caller(func = self.get_target_map, prefix="Getting
target map")<br>
File
"/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py",
line 298, in caller<br>
func(prefix=prefix)<br>
File
"/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py",
line 372, in get_target_map<br>
number_of_macro_cycles =
self.params.refinement.macro_cycles)<br>
File
"/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py",
line 153, in extract_target_map_data_and_crystal_gridding<br>
crystal_symmetry =
inputs.xray_structure.crystal_symmetry())<br>
File
"/usr/local/phenix-dev-1615/cctbx_project/mmtbx/utils/__init__.py",
line 3094, in structure_factors_from_map<br>
use_sg = True)<br>
File
"/usr/local/phenix-dev-1615/cctbx_project/cctbx/miller/__init__.py",
line 1309, in structure_factors_from_map<br>
assert map.focus_size_1d() > 0 and map.nd() == 3 and
map.is_0_based()<br>
AssertionError<br>
</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
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<div style="font-family:Tahoma; font-size:13px"><font
style="font-family:Helvetica" size="3">******************************************************************************<br>
Gino Cingolani, Ph.D.<br>
Associate Professor<br>
Thomas Jefferson University<br>
Dept. of Biochemistry & Molecular Biology<br>
233 South 10th Street - Room 826<br>
Philadelphia PA 19107<br>
Office (215) 503 4573<br>
Lab (215) 503 4595<br>
Fax (215) 923 2117<br>
E-mail: <a class="moz-txt-link-abbreviated" href="mailto:gino.cingolani@jefferson.edu">gino.cingolani@jefferson.edu</a><br>
Website: <a class="moz-txt-link-freetext" href="http://www.cingolanilab.org">http://www.cingolanilab.org</a><br>
******************************************************************************<br>
"Nati non foste per viver come bruti, ma per seguir
virtute e canoscenza"<br>
("You were not born to live like brutes, but to follow
virtue and knowledge") <br>
Dante, The Divine Comedy<i><b> </b></i>(<i>Inferno</i>,
XXVI, vv. 119-120)<br>
</font><br>
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