test cctbx/regression/tst_grm_modifications.py broken

[Anthchirp]

And has been since at least March 2019.

As the test is skipped unless CCP4 is present we only notice its failure during our release process, at which point we manually disable the test every time.

Thought you might want to know.

[olegsobolev]

Works for me everywhere. Even on all Azure pipelines (e.g. here)

Any helpful debugging info?

[Anthchirp]

This is the test output:

Sorry: Fatal problems interpreting model file:
 Number of atoms with unknown nonbonded energy type symbols: 2
 Please edit the model file to resolve the problems and/or supply a
 CIF file with matching restraint definitions, along with
 apply_cif_modification and apply_cif_link parameter definitions
 if necessary.

[nwmoriarty]

Looks like the CCP4 restraints library has different ideas about the atom names compared to Phenix library. To debug, we need more output from the test. Setting the env. var. LIBTBX_DISABLE_TRACEBACKLIMIT to 1 will do the trick. Can you provide the augmented error message?

Cheers

Nigel

---

Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Thu, Aug 20, 2020 at 12:06 AM Markus Gerstel [email protected] wrote:

This is the test output:

Sorry: Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols: 2 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary.

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[Anthchirp]

This is with DIALS 3.0.4 and CCP4 7.1.0:

$ LIBTBX_DISABLE_TRACEBACKLIMIT=1 dials.python /dls_sw/apps/dials/dials-v3-0-4/modules/cctbx_project/cctbx/regression/tst_grm_modifications.py 
Traceback (most recent call last):
  File "/dls_sw/apps/dials/dials-v3-0-4/modules/cctbx_project/cctbx/regression/tst_grm_modifications.py", line 684, in <module>
    exercise()
  File "/dls_sw/apps/dials/dials-v3-0-4/modules/cctbx_project/cctbx/regression/tst_grm_modifications.py", line 680, in exercise
    exercise_bond_over_symmetry(mon_lib_srv, ener_lib)
  File "/dls_sw/apps/dials/dials-v3-0-4/modules/cctbx_project/cctbx/regression/tst_grm_modifications.py", line 526, in exercise_bond_over_symmetry
    grm = model.get_restraints_manager().geometry
  File "/dls_sw/apps/dials/dials-v3-0-4/modules/cctbx_project/mmtbx/model/model.py", line 677, in get_restraints_manager
    self.setup_restraints_manager()
  File "/dls_sw/apps/dials/dials-v3-0-4/modules/cctbx_project/mmtbx/model/model.py", line 1198, in setup_restraints_manager
    self._process_input_model()
  File "/dls_sw/apps/dials/dials-v3-0-4/modules/cctbx_project/mmtbx/model/model.py", line 1124, in _process_input_model
    allow_missing_symmetry=True)
  File "/dls_sw/apps/dials/dials-v3-0-4/modules/cctbx_project/mmtbx/utils/__init__.py", line 1007, in process_pdb_files
    allow_missing_symmetry   = allow_missing_symmetry)
  File "/dls_sw/apps/dials/dials-v3-0-4/modules/cctbx_project/mmtbx/utils/__init__.py", line 1092, in _process_pdb_file
    raise Sorry(msg)
Sorry: Fatal problems interpreting model file:
  Number of atoms with unknown nonbonded energy type symbols: 2
    Please edit the model file to resolve the problems and/or supply a
    CIF file with matching restraint definitions, along with
    apply_cif_modification and apply_cif_link parameter definitions
    if necessary.

[ndevenish]

Still finding this, bypassing for release again https://github.com/dials/cctbx/commit/f217ceb32920ff4547e1cd7b26cb94e9ae3328d0