<div dir="ltr">Thanks, Tom.<div><br></div><div>I downloaded 1.11.1-2575. the same error is still there as seen by the error msg attached at the end. Maybe you mean the nightly-build version? Let me try that too.</div><div><br></div><div>Actually, my real problem is to fit my data (3.75A) to my protein model. The Rwork/Rfree is about 0.4/0.45 and I can improve it to about 0.37/0.42. However, I can see there are quite some residues not fitting to the density. So, I am trying some methods provided in phenix to improve my fitting. Currently, what I am working is 1) phenix-rosetta, 2) map_to_model, 3) morph_model. Any other suggestions? </div><div><br></div><div>Thanks! </div><div><br></div><div>Charles</div><div><br></div><div>
<p class="gmail-p1"><span class="gmail-s1">Traceback (most recent call last):</span></p>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/map_to_model.py", line 9, in <module></span></p>
<p class="gmail-p1"><span class="gmail-s1"> run(sys.argv[1:],out=sys.stdout)</span></p>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/autosol/map_to_model.py", line 5729, in run</span></p>
<p class="gmail-p1"><span class="gmail-s1"> tracking_data=run_segment_and_split_map(params,out=out)</span></p>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/autosol/map_to_model.py", line 4931, in run_segment_and_split_map</span></p>
<p class="gmail-p1"><span class="gmail-s1"> ncs_group_obj,remainder_ncs_group_obj,tracking_data=segment_map(args)</span></p>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/cctbx/maptbx/segment_and_split_map.py", line 5795, in run</span></p>
<p class="gmail-p1"><span class="gmail-s1"> params,map_data,pdb_hierarchy,tracking_data=get_params(args,out=out)</span></p>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/cctbx/maptbx/segment_and_split_map.py", line 2055, in get_params</span></p>
<p class="gmail-p1"><span class="gmail-s1"> params=get_params_from_args(args)</span></p>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/cctbx/maptbx/segment_and_split_map.py", line 2051, in get_params_from_args</span></p>
<p class="gmail-p1"><span class="gmail-s1"> return command_line.work.extract()</span></p>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/libtbx/phil/__init__.py", line 1757, in extract</span></p>
<p class="gmail-p1"><span class="gmail-s1"> value = object.extract(parent=result)</span></p>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/libtbx/phil/__init__.py", line 1757, in extract</span></p>
<p class="gmail-p1"><span class="gmail-s1"> value = object.extract(parent=result)</span></p>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/libtbx/phil/__init__.py", line 1122, in extract</span></p>
<p class="gmail-p1"><span class="gmail-s1"> return self._type_from_words()(self.words, master=self)</span></p>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/iotbx/phil.py", line 40, in from_words</span></p>
<p class="gmail-p1"><span class="gmail-s1"> return sgtbx.space_group_info(symbol=str(symbol))</span></p>
<p class="gmail-p1"><span class="gmail-s1"> File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/cctbx/sgtbx/__init__.py", line 97, in __init__</span></p>
<p class="gmail-p1"><span class="gmail-s1"> symbols = space_group_symbols(symbol)</span></p>
<p class="gmail-p1"><span class="gmail-s1">RuntimeError: cctbx Error: <b><font size="4">Space group symbol not recognized</font></b>: <cctbx_sgtbx_ext.space_group object at 0x102805220></span></p></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Mar 3, 2017 at 5:39 PM, Terwilliger, Thomas Charles <span dir="ltr"><<a href="mailto:terwilliger@lanl.gov" target="_blank">terwilliger@lanl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" style="font-size:12pt;color:#000000;background-color:#ffffff;font-family:Calibri,Arial,Helvetica,sans-serif">
<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>
<div style="color:rgb(33,33,33)">
<hr style="display:inline-block;width:98%">
<div id="m_-2835120126137355667divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> <a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-<wbr>online.org</a> <<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-<wbr>online.org</a>> on behalf of CPMAS Chen <<a href="mailto:cpmasmit@gmail.com" target="_blank">cpmasmit@gmail.com</a>><br>
<b>Sent:</b> Friday, March 3, 2017 3:15 PM<br>
<b>To:</b> PHENIX user mailing list (<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a>)<br>
<b>Subject:</b> [phenixbb] map_to_model space group symbol not recognized</font>
<div> </div>
</div><div><div class="h5">
<div>
<div dir="ltr"><br clear="all">
<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="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1">Space group symmetry written as NCS operators to ncs_from_symmetry.ncs_spec</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1">Traceback (most recent call last):</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> File "/usr/local/phenix-1.11-2567/<wbr>build/../modules/phenix/<wbr>phenix/command_line/map_to_<wbr>model.py", line 9, in <module></span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> run(sys.argv[1:],out=sys.<wbr>stdout)</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> File "/usr/local/phenix-1.11-2567/<wbr>modules/phenix/phenix/autosol/<wbr>map_to_model.py", line 5729, in run</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> tracking_data=run_segment_and_<wbr>split_map(params,out=out)</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> File "/usr/local/phenix-1.11-2567/<wbr>modules/phenix/phenix/autosol/<wbr>map_to_model.py", line 4931, in run_segment_and_split_map</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> ncs_group_obj,remainder_ncs_<wbr>group_obj,tracking_data=<wbr>segment_map(args)</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> File "/usr/local/phenix-1.11-2567/<wbr>modules/cctbx_project/cctbx/<wbr>maptbx/segment_and_split_map.<wbr>py", line 5795, in run</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> params,map_data,pdb_hierarchy,<wbr>tracking_data=get_params(args,<wbr>out=out)</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> File "/usr/local/phenix-1.11-2567/<wbr>modules/cctbx_project/cctbx/<wbr>maptbx/segment_and_split_map.<wbr>py", line 2055, in get_params</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> params=get_params_from_args(<wbr>args)</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> File "/usr/local/phenix-1.11-2567/<wbr>modules/cctbx_project/cctbx/<wbr>maptbx/segment_and_split_map.<wbr>py", line 2051, in get_params_from_args</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> return command_line.work.extract()</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> File "/usr/local/phenix-1.11-2567/<wbr>modules/cctbx_project/libtbx/<wbr>phil/__init__.py", line 1757, in extract</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> value = object.extract(parent=result)</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> File "/usr/local/phenix-1.11-2567/<wbr>modules/cctbx_project/libtbx/<wbr>phil/__init__.py", line 1757, in extract</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> value = object.extract(parent=result)</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> File "/usr/local/phenix-1.11-2567/<wbr>modules/cctbx_project/libtbx/<wbr>phil/__init__.py", line 1122, in extract</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> return self._type_from_words()(self.<wbr>words, master=self)</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> File "/usr/local/phenix-1.11-2567/<wbr>modules/cctbx_project/iotbx/<wbr>phil.py", line 40, in from_words</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> return sgtbx.space_group_info(symbol=<wbr>str(symbol))</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> File "/usr/local/phenix-1.11-2567/<wbr>modules/cctbx_project/cctbx/<wbr>sgtbx/__init__.py", line 97, in __init__</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1"><span class="m_-2835120126137355667gmail-s1"> symbols = space_group_symbols(symbol)</span></p>
</div>
<div>
<p class="m_-2835120126137355667gmail-p1">RuntimeError: cctbx Error: Space group symbol not recognized: <cctbx_sgtbx_ext.space_group object at 0x101836e20></p>
</div>
</blockquote>
<div>
<p class="m_-2835120126137355667gmail-p1"></p>
<p class="m_-2835120126137355667gmail-p1"><br>
</p>
<p class="m_-2835120126137355667gmail-p1">Would this be a bug or I simply missed something?</p>
<p class="m_-2835120126137355667gmail-p1"><br>
</p>
<p class="m_-2835120126137355667gmail-p1">Thanks!</p>
<p class="m_-2835120126137355667gmail-p1"><br>
</p>
<p class="m_-2835120126137355667gmail-p1">Charles</p>
</div>
-- <br>
<div class="m_-2835120126137355667gmail_signature">
<p></p>
<p>******************************<wbr>*********************</p>
<p>Charles Chen</p>
<p>Research Associate</p>
<p>University of Pittsburgh School of Medicine</p>
<p>Department of Anesthesiology</p>
<p>******************************<wbr>************************</p>
<p></p>
</div>
</div>
</div>
</div></div></div>
</div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="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></div>
</div>