[phenixbb] fit_loops using loop_lib

Terwilliger, Thomas Charles terwilliger at lanl.gov
Thu Apr 21 09:42:59 PDT 2016

?Hi Greg,

I'm sorry for this crash of fit_loops!

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.

In the meantime, if you run with a file that has only non-anomalous data in it perhaps that will get around the problem.

All the best,

Tom T

From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> on behalf of Greg Bowman <gdbowman at jhu.edu>
Sent: Thursday, April 21, 2016 10:28 AM
To: phenixbb at phenix-online.org
Subject: [phenixbb] fit_loops using loop_lib

Hi all -

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:

phenix.fit_loops pdb_in=refine_35-delloop1170to1172.pdb mtz_in=refine_35.mtz \
 seq_file=KRJmonomer.seq start=1170 end=1172 chain_id=B \
 loop_lib=True >> fit_loops-1170to1172-looplibrary.log

I am using OSX ElCapitan (10.11.3) and get this error:

File "/Applications/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/fit_loops.py", line 962, in <module>
  File "/Applications/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/fit_loops.py", line 598, in __init__
  File "/Applications/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/fit_loops.py", line 760, in run_fit
  File "/Applications/phenix-1.10.1-2155/modules/phenix/phenix/autosol/UserMethods.py", line 3671, in Build_fit_gaps
  File "/Applications/phenix-1.10.1-2155/modules/phenix/phenix/loop_lib/clustering.py", line 2063, in apply_clusters
  File "/Applications/phenix-1.10.1-2155/modules/phenix/phenix/utilities/get_density_map.py", line 54, in __init__
    assert not map_coeffs_array.anomalous_flag()

The last lines of the log file are:

Fitting loop with loop-library...
loop_lib length (including 3 on each end): 9
DATABASE:  /Applications/phenix-1.10.1-2155/modules/chem_data/loop_library/loops_9_2.5/loop_lib  CLUSTER_FILE:  split_clusters.pkl.gz


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