IMP systems

Modeling of the bacterial molecular chaperone GroEL using 3D EM data and cnmultifit [more...]

This system (using these input files) was tested but does not work with:

MODELLER version 9.12
IMP main branch (version 2.0.1, 2013-05-02), revision 73085ddf54 (built with all checks turned on)

Detailed test information

test.py FAILED with code 1 (took 28 minutes) and stderr:

..ETraceback (most recent call last):
  File "scripts/script4_score_templates_by_cc.py", line 44, in <module>
    sols=IMP.multifit.pca_based_rigid_fitting(rb,rb_refiner,dmap,dens_threshold)
  File "/salilab/diva1/home/imp/master/20130502-73085dd/lib/x86_64-intel8/IMP/multifit/__init__.py", line 750, in pca_based_rigid_fitting
    return _IMP_multifit.pca_based_rigid_fitting(*args)
_IMP_base.UsageException: Usage check failure: Cannot compare against anything other than the default PrincipalComponentAnalysis

E.Traceback (most recent call last):
  File "scripts/script6_model_building_and_assessment.py", line 58, in <module>
    sols=IMP.multifit.pca_based_rigid_fitting(rb,rb_refiner,dmap,0.02)
  File "/salilab/diva1/home/imp/master/20130502-73085dd/lib/x86_64-intel8/IMP/multifit/__init__.py", line 750, in pca_based_rigid_fitting
    return _IMP_multifit.pca_based_rigid_fitting(*args)
_IMP_base.UsageException: Usage check failure: Cannot compare against anything other than the default PrincipalComponentAnalysis

E...
======================================================================
ERROR: Test step 3 (density segmentation)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./test.py", line 47, in test_script3
    m = modeller.model(e, file='output/groel_segments_center.pdb')
  File "/salilab/diva1/home/modeller/9.12/modlib/modeller/model.py", line 89, in __init__
    self.read(**vars)
  File "/salilab/diva1/home/modeller/9.12/modlib/modeller/model.py", line 134, in read
    model_format, model_segment)
IOError: pdbnam_____E> Filename for PDB code not found: output/groel_segments_center.pdb
              Directories: 
              Extensions : :.atm:.pdb:.ent:.crd
              (Also tried prepending 'pdb', looking for .Z, .gz, .bz2, .7z, .xz,
              and trying PDB-style subdirectories - e.g. ab for pdb1abc.ent)


======================================================================
ERROR: Test step 4 (score templates by cc)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./test.py", line 66, in test_script4
    p = subprocess.check_call(['scripts/script4_score_templates_by_cc.py'])
  File "/usr/lib64/python2.6/subprocess.py", line 502, in check_call
    raise CalledProcessError(retcode, cmd)
CalledProcessError: Command '['scripts/script4_score_templates_by_cc.py']' returned non-zero exit status 1

======================================================================
ERROR: Test step 6 (model building and assessment)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./test.py", line 98, in test_script6
    p = subprocess.check_call(['scripts/' \
  File "/usr/lib64/python2.6/subprocess.py", line 502, in check_call
    raise CalledProcessError(retcode, cmd)
CalledProcessError: Command '['scripts/script6_model_building_and_assessment.py']' returned non-zero exit status 1

----------------------------------------------------------------------
Ran 9 tests in 1699.367s

FAILED (errors=3)

Build information