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