[phenixbb] phenix.model_idealization

[Manoj saxena]

Hi ,
I am trying to fix a  pdb file that was obtained from Rosetta and has some
distorted helices
so I trier to fix that with

> phenix.model_idealization model.pdb use_ss_restraints = True

I am attaching the log file ,  here is the end of the log file. Any
suggestions on what's going on ?

" NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Traceback (most recent call last):
  File
"/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py",
line 1118, in <module>
    run(sys.argv[1:])
  File
"/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py",
line 1106, in run
    mi_object.run()
  File
"/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py",
line 548, in run
    self._setup_model_h()
  File
"/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py",
line 478, in _setup_model_h
    params_h.pdb_interpretation =
self.model._pdb_interpretation_params.pdb_interpretation
AttributeError: 'NoneType' object has no attribute 'pdb_interpretation'"


My aim is to idealize the secondary structure. I first tried it in Isolde
but the
EM density is not great and always leads to some distortion. So I was
wondering if I can do this fix
in Phenix.  Is this model idealization tool the best approach?  or I have
to go in and fix things manually.

Thanks
Manoj
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