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Error when running ""

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Error when running ""

Dear all,

When I run the following command:


It gives the following error:

/bin/sh: /app/rosetta_src_2017.08.59291_bundle/main/source/bin/packing_angle.macosclangrelease: No such file or directory
Executing /app/rosetta_src_2017.08.59291_bundle/main/source/bin/packing_angle.macosclangrelease -database /app/rosetta_src_2017.08.59291_bundle/main/database/ -s model-0.relaxed.pdb -pack_missing_sidechains false -out:file:score_only model-0.relaxe_LHOCs.score...
Traceback (most recent call last):
  File "/app/rosetta_src_2017.08.59291_bundle/main/source/scripts/python/public/plot_VL_VH_orientational_coordinates/", line 120, in <module>
    score_file = ScoreFile(i, infiles, outpath, names).plot_for_all_coordinates(tempfiles, angles_file)
  File "/app/rosetta_src_2017.08.59291_bundle/main/source/scripts/python/public/plot_VL_VH_orientational_coordinates/", line 64, in plot_for_all_coordinates
  File "/app/rosetta_src_2017.08.59291_bundle/main/source/scripts/python/public/plot_VL_VH_orientational_coordinates/", line 73, in load_template_data
  File "/app/rosetta_src_2017.08.59291_bundle/main/source/scripts/python/public/plot_VL_VH_orientational_coordinates/", line 38, in calculate_angles
    assert rc == 0, "Command %s failed!" %(LHOC_cmd)
AssertionError: Command /app/rosetta_src_2017.08.59291_bundle/main/source/bin/packing_angle.macosclangrelease -database /app/rosetta_src_2017.08.59291_bundle/main/database/ -s model-0.relaxed.pdb -pack_missing_sidechains false -out:file:score_only model-0.relaxe_LHOCs.score failed!


It is strange that why the script calls the command "packing_angle.macosclangrelease" since my system is linux Centos. Is the a bug of

Best regards.


Yeping Sun

Post Situation: 
Sun, 2017-08-13 05:54

I would say it's closer to an "unimplemented feature" than a bug - it definitely hardcodes a mac path.  I encourage you to just open the script up in a text editor and fix it yourself.  You can even get away with `sed -i 's/macosclang/linuxgcc/'`.  (I am assuming you are using gcc, correct less for clang.)


The README in that directory does imply the hardcoding of the macos release.  I've filed a bug for you, but it's proably pretty low priority.

Sun, 2017-08-13 14:32

Hello, smlewis,

Thank for the replay and for filing the bug. 

However, I have opened the script with the text editor but cannot find where to fix, and there is no  "macosclangrelease" tag at all. And  `sed -i 's/macosclang/linuxgcc/'` changes nothing. The same error comes out after the "sed" substitution.

Maybe the "macosclangrelease" tag is in some other script called by the script? By what is it?

Best regards,



Sun, 2017-08-13 18:05

Yeah, you're right, it's line 42 in in the same directory.  When I searched for the string I did the whole directory, instead of just the file, and didn't notice which file it was in.
42:    rosetta_LHOC = rosetta_path + '/main/source/bin/packing_angle.macosclangrelease'

Sun, 2017-08-13 19:16

Hello smlewis,

I have replaced the "macosclangrelease" with "linuxgccrelease" in Line 42 in the However, when I ran the script again, the expected plot wasn't produced and the output log information ended with the following lines:

Executing /app/rosetta_src_2017.08.59291_bundle/main/source/bin/packing_angle.linuxgccrelease -database /app/rosetta_src_2017.08.59291_bundle/main/database/ -s model-9.relaxed.pdb -pack_missing_sidechains false -out:file:score_only model-9.relaxe_LHOCs.score... ...done!
/app/anaconda2/lib/python2.7/site-packages/matplotlib/ UserWarning: findfont: Font family [u'arial'] not found. Falling back to DejaVu Sans
  (prop.get_family(), self.defaultFamily[fontext]))

Is there still something with it? 

Best regards.




Tue, 2017-08-15 23:30

Dunno, I'll send it along to the author.

Wed, 2017-08-16 08:30