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<div style="direction: ltr;font-family: Arial;color: #0000FF;font-size: 10pt;">Hi Pavel,
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<div>On another issue, yet related to real space refinement: is it possible to do real space refinement against the FEM map? It would be nice to test the model against features observed in the FEM map via real-space refinement, wouldn't it? A<span style="font-size: 10pt;"> while
ago you told me that it was in the works.</span><span style="font-size: 10pt;"> </span><span style="font-size: 10pt;">Or am I missing the purpose of the FEM map?</span></div>
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<div>Cheers,</div>
<div><br>
</div>
<div> Boaz<br>
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<div><font color="#000080" face="Times New Roman" size="3"><em>Boaz Shaanan, Ph.D.
<br>
Dept. of Life Sciences <br>
Ben-Gurion University of the Negev <br>
Beer-Sheva 84105 <br>
Israel <br>
<br>
E-mail: bshaanan@bgu.ac.il<br>
Phone: 972-8-647-2220 Skype: boaz.shaanan <br>
Fax: 972-8-647-2992 or 972-8-646-1710 </em></font></div>
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<div id="divRpF45734" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Pavel Afonine [pafonine@lbl.gov]<br>
<b>Sent:</b> Friday, May 16, 2014 7:36 AM<br>
<b>To:</b> Gino Cingolani; PHENIX user mailing list<br>
<b>Subject:</b> Re: [phenixbb] phenix.real_space_refine<br>
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<div>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" target="_blank">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>
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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>
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<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>
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<div style="font-family:Tahoma; font-size:13px"><font size="3" style="font-family:Helvetica">******************************************************************************<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" target="_blank">
gino.cingolani@jefferson.edu</a><br>
Website: <a class="moz-txt-link-freetext" href="http://www.cingolanilab.org" target="_blank">
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>
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