<div dir="ltr">Well, while we&#39;re on this topic, I was just starting to try phenix-rosetta on a mac, and after following the instructions online I get this error message:<div><br></div><div><div>mcdbx-horowsah:120813/1to8p4122fromqinping/phenix_refine] horowsah% phenix.rosetta_refine 1to8norm10_refine_17-coot-1nohnoe.pdb zn-truncate-unique.mtz nproc=4 protocol=hires</div>

<div>Output directory:</div><div>  /Users/horowsah/Documents/Bardwell Lab Work/spy/xtalstrucs/120813/1to8p4122fromqinping/phenix_refine/rosetta_6</div><div><br></div><div>=========================== Importing data and flags ==========================</div>

<div><br></div><div><br></div><div>     ----------Scaling input intensities via French-Wilson Method----------    </div><div><br></div><div>Trying 60 bins...</div><div>Number of bins = 60</div><div>** Calculating bin mean intensity values for each intensity **</div>

<div>** Total # rejected intensities: 0 **</div><div><br></div><div>             ----------Setting up input files for Rosetta----------            </div><div><br></div><div>/rosetta/rosetta_2013wk49_bundle/main/source</div>

<div><br></div><div>                   ----------Loading model and data----------                  </div><div><br></div><div>Traceback (most recent call last):</div><div>  File &quot;//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/rosetta_refine.py&quot;, line 330, in &lt;module&gt;</div>

<div>    run(sys.argv[1:], create_dir=True)</div><div>  File &quot;//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/rosetta_refine.py&quot;, line 327, in run</div>

<div>    create_dir=create_dir)</div><div>  File &quot;//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/rosetta_refine.py&quot;, line 127, in __init__</div>

<div>    self.run_rosetta_scripts()</div><div>  File &quot;//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/rosetta_refine.py&quot;, line 181, in run_rosetta_scripts</div>

<div>    debug=self.params.runtime.debug)</div><div>  File &quot;//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/phenix/phenix/rosetta/refine.py&quot;, line 287, in __init__</div><div>    r_free_flags=r_free_flags)</div>

<div>  File &quot;//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/cctbx_project/mmtbx/utils/__init__.py&quot;, line 1802, in fmodel_simple</div><div>    ro = outliers_rejection,om=optimize_mask, ofp1=False)</div>

<div>  File &quot;//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/cctbx_project/mmtbx/utils/__init__.py&quot;, line 1788, in get_fmodel</div><div>    twin_law       = tl)</div><div>  File &quot;//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/cctbx_project/mmtbx/utils/__init__.py&quot;, line 1707, in fmodel_manager</div>

<div>    n_resolution_bins_output     = n_resolution_bins_output)</div><div>  File &quot;//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/cctbx_project/mmtbx/f_model.py&quot;, line 432, in __init__</div><div>    if(f_calc is None): f_calc = self.compute_f_calc(miller_array=f_obs)</div>

<div>  File &quot;//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/cctbx_project/mmtbx/f_model.py&quot;, line 518, in compute_f_calc</div><div>    exp_table_one_over_step_size = p.exp_table_one_over_step_size)</div>

<div>  File &quot;//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/cctbx_project/cctbx/miller/__init__.py&quot;, line 1374, in structure_factors_from_scatterers</div><div>    algorithm=algorithm)</div><div>  File &quot;//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/cctbx_project/cctbx/xray/structure_factors/from_scatterers.py&quot;, line 53, in __call__</div>

<div>    algorithm=algorithm) # passing algorithm allows f to decide on CPU/GPU implementation</div><div>  File &quot;//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/cctbx_project/cctbx/xray/structure_factors/from_scatterers_fft.py&quot;, line 18, in __init__</div>

<div>    manager, xray_structure, miller_set, algorithm=&quot;fft&quot;)</div><div>  File &quot;//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/cctbx_project/cctbx/xray/structure_factors/manager.py&quot;, line 234, in __init__</div>

<div>    assert xray_structure.space_group() == miller_set.space_group()</div><div>AssertionError</div></div><div><br></div><div><br></div><div>Anybody know what I did wrong?</div><div><br></div><div>Thanks,</div><div>Scott</div>

</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Dec 18, 2013 at 5:17 PM, Luca Jovine <span dir="ltr">&lt;<a href="mailto:Luca.Jovine@ki.se" target="_blank">Luca.Jovine@ki.se</a>&gt;</span> wrote:<br>

<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Ben,<br>
<br>
I have! What would you like to know?<br>
<br>
Best, Luca<br>
<div class="HOEnZb"><div class="h5"><br>
&gt; On Dec 18, 2013, at 19:47, &quot;Ben Eisenbraun&quot; &lt;<a href="mailto:bene@hkl.hms.harvard.edu">bene@hkl.hms.harvard.edu</a>&gt; wrote:<br>
&gt;<br>
&gt; Hi All,<br>
&gt;<br>
&gt; Has anyone run the Phenix-Rosetta refinement stuff on a Mac yet?<br>
&gt;<br>
&gt; Thanks.<br>
&gt;<br>
&gt; -ben<br>
&gt;<br>
&gt; --<br>
&gt; | Ben Eisenbraun<br>
&gt; | SBGrid Consortium                          | <a href="http://sbgrid.org" target="_blank">http://sbgrid.org</a>       |<br>
&gt; | Harvard Medical School                     | <a href="http://hms.harvard.edu" target="_blank">http://hms.harvard.edu</a>  |<br>
&gt; _______________________________________________<br>
&gt; phenixbb mailing list<br>
&gt; <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
&gt; <a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
_______________________________________________<br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><div style="font-family:Helvetica;word-wrap:break-word"><font>Scott Horowitz, Ph.D.<br></font></div><div style="font-family:Helvetica;word-wrap:break-word">

<font>Research Associate</font></div><div style="font-family:Helvetica;word-wrap:break-word"><font>Howard Hughes Medical Institute</font></div><div style="font-family:Helvetica;word-wrap:break-word"><font><br>University of Michigan<br>

Department of Molecular, Cellular, and Developmental Biology<br>Bardwell lab<br>830 N. University Ave, Room 4007<br>Ann Arbor, MI 48109<br>phone: <a value="+17346476683" style="color:rgb(17,85,204)">734-647-6683</a><br>fax: <a value="+17346154226" style="color:rgb(17,85,204)">734-615-4226</a></font></div>

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