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<p>​Hi Greg,<br>
</p>
<p>I'm sorry for this crash of fit_loops! </p>
<p><br>
</p>
<p>It looks like somehow a map_coeffs array that has anomalous information was given to fit loops. That seems like a bug, so if you can send me the input files and full log I will try to fix it. <br>
</p>
<p><br>
</p>
<p>In the meantime, if you run with a file that has only non-anomalous data in it perhaps that will get around the problem.<br>
</p>
<p><br>
</p>
<p>All the best,<br>
</p>
<p>Tom T<br>
</p>
<p><br>
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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 Greg Bowman <gdbowman@jhu.edu><br>
<b>Sent:</b> Thursday, April 21, 2016 10:28 AM<br>
<b>To:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> [phenixbb] fit_loops using loop_lib</font>
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<div>Hi all -
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<div class="">I’m having a problem getting phenix.fit_loops to run using the loop library (loop_lib=True). The phenix.fit_loops seems to work fine without this keyword (I get a good solution for a test case), but I have 3A density and wanted to restrict solutions
to the loop library for the poorer density regions. I am running this from the command line, with this input:</div>
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phenix.fit_loops pdb_in=refine_35-delloop1170to1172.pdb mtz_in=refine_35.mtz \</div>
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seq_file=KRJmonomer.seq start=1170 end=1172 chain_id=B \</div>
<div class="" style="margin:0px; font-size:11px; line-height:normal; font-family:Menlo">
loop_lib=True >> fit_loops-1170to1172-looplibrary.log</div>
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<div class="">I am using OSX ElCapitan (10.11.3) and get this error:</div>
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File "/Applications/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/fit_loops.py", line 962, in <module></div>
<div class="" style="margin:0px; font-size:11px; line-height:normal; font-family:Menlo">
fit_loops=fit_loops(args=sys.argv[1:])</div>
<div class="" style="margin:0px; font-size:11px; line-height:normal; font-family:Menlo">
File "/Applications/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/fit_loops.py", line 598, in __init__</div>
<div class="" style="margin:0px; font-size:11px; line-height:normal; font-family:Menlo">
target_time=target_time,</div>
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File "/Applications/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/fit_loops.py", line 760, in run_fit</div>
<div class="" style="margin:0px; font-size:11px; line-height:normal; font-family:Menlo">
target_time=target_time,</div>
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File "/Applications/phenix-1.10.1-2155/modules/phenix/phenix/autosol/UserMethods.py", line 3671, in Build_fit_gaps</div>
<div class="" style="margin:0px; font-size:11px; line-height:normal; font-family:Menlo">
starting_residue_number=starting_residue_number)</div>
<div class="" style="margin:0px; font-size:11px; line-height:normal; font-family:Menlo">
File "/Applications/phenix-1.10.1-2155/modules/phenix/phenix/loop_lib/clustering.py", line 2063, in apply_clusters</div>
<div class="" style="margin:0px; font-size:11px; line-height:normal; font-family:Menlo">
d=get_density_map(map_coeffs_array=map_coeffs_array)</div>
<div class="" style="margin:0px; font-size:11px; line-height:normal; font-family:Menlo">
File "/Applications/phenix-1.10.1-2155/modules/phenix/phenix/utilities/get_density_map.py", line 54, in __init__</div>
<div class="" style="margin:0px; font-size:11px; line-height:normal; font-family:Menlo">
assert not map_coeffs_array.anomalous_flag()</div>
<div class="" style="margin:0px; font-size:11px; line-height:normal; font-family:Menlo">
AssertionError</div>
</div>
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<div class="">The last lines of the log file are:</div>
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<div class="" style="margin:0px; font-size:11px; line-height:normal; font-family:Menlo">
Fitting loop with loop-library...</div>
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loop_lib length (including 3 on each end): 9</div>
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DATABASE: /Applications/phenix-1.10.1-2155/modules/chem_data/loop_library/loops_9_2.5/loop_lib CLUSTER_FILE: split_clusters.pkl.gz</div>
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<div class="">Thanks,</div>
<div class="">Greg</div>
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