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<p>Hi Charles,<br>
I'm sorry for the trouble! I think I fixed this bug ...Could you try updating it and try again? The use of map_to_model with mtz data is not as developed as using it with a map input file. Another approach is use phenix.cut_out_density to cut out density
for your structure which will then be in space group P1 and use cutout.mtz as input which should work more easily.<br>
</p>
<p>-Tom<br>
</p>
<p><br>
</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> phenixbb-bounces@phenix-online.org <phenixbb-bounces@phenix-online.org> on behalf of CPMAS Chen <cpmasmit@gmail.com><br>
<b>Sent:</b> Friday, March 3, 2017 3:15 PM<br>
<b>To:</b> PHENIX user mailing list (phenixbb@phenix-online.org)<br>
<b>Subject:</b> [phenixbb] map_to_model space group symbol not recognized</font>
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<div>Hi, All</div>
<div><br>
</div>
<div>when I try to using map_to_model tool to optimize my model from low-resolution map, </div>
<div><br>
</div>
<div>phenix.map_to_model refine_2.mtz seq_from_pdb.dat<br>
</div>
<div><br>
</div>
<div>I got the following error, even though I did not provide ncs file,</div>
<div><br>
</div>
<blockquote style="margin:0 0 0 40px; border:none; padding:0px">
<div>
<p class="gmail-p1"><span class="gmail-s1">Space group symmetry written as NCS operators to ncs_from_symmetry.ncs_spec</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1">Traceback (most recent call last):</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11-2567/build/../modules/phenix/phenix/command_line/map_to_model.py", line 9, in <module></span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> run(sys.argv[1:],out=sys.stdout)</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11-2567/modules/phenix/phenix/autosol/map_to_model.py", line 5729, in run</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> tracking_data=run_segment_and_split_map(params,out=out)</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11-2567/modules/phenix/phenix/autosol/map_to_model.py", line 4931, in run_segment_and_split_map</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> ncs_group_obj,remainder_ncs_group_obj,tracking_data=segment_map(args)</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/maptbx/segment_and_split_map.py", line 5795, in run</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> params,map_data,pdb_hierarchy,tracking_data=get_params(args,out=out)</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/maptbx/segment_and_split_map.py", line 2055, in get_params</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> params=get_params_from_args(args)</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/maptbx/segment_and_split_map.py", line 2051, in get_params_from_args</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> return command_line.work.extract()</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11-2567/modules/cctbx_project/libtbx/phil/__init__.py", line 1757, in extract</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> value = object.extract(parent=result)</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11-2567/modules/cctbx_project/libtbx/phil/__init__.py", line 1757, in extract</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> value = object.extract(parent=result)</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11-2567/modules/cctbx_project/libtbx/phil/__init__.py", line 1122, in extract</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> return self._type_from_words()(self.words, master=self)</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11-2567/modules/cctbx_project/iotbx/phil.py", line 40, in from_words</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> return sgtbx.space_group_info(symbol=str(symbol))</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/sgtbx/__init__.py", line 97, in __init__</span></p>
</div>
<div>
<p class="gmail-p1"><span class="gmail-s1"> symbols = space_group_symbols(symbol)</span></p>
</div>
<div>
<p class="gmail-p1">RuntimeError: cctbx Error: Space group symbol not recognized: <cctbx_sgtbx_ext.space_group object at 0x101836e20></p>
</div>
</blockquote>
<div>
<p class="gmail-p1"></p>
<p class="gmail-p1"><br>
</p>
<p class="gmail-p1">Would this be a bug or I simply missed something?</p>
<p class="gmail-p1"><br>
</p>
<p class="gmail-p1">Thanks!</p>
<p class="gmail-p1"><br>
</p>
<p class="gmail-p1">Charles</p>
</div>
-- <br>
<div class="gmail_signature">
<p></p>
<p>***************************************************</p>
<p>Charles Chen</p>
<p>Research Associate</p>
<p>University of Pittsburgh School of Medicine</p>
<p>Department of Anesthesiology</p>
<p>******************************************************</p>
<p></p>
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