[phenixbb] phenix.model_idealization

[Oleg Sobolev]

Hi Manoj,

Thank you for reporting the issue and I'm sorry for the late reply.
I believe this issue is fixed now, so can you please try the latest nightly
build (release candidate) from here:
https://phenix-online.org/download/nightly_builds.cgi

So I was wondering if I can do this fix
> in Phenix.  Is this model idealization tool the best approach?

You are welcome to try it out, it is designed to produce a good secondary
structure with minimal deviation from the starting model and/or
experimental density. Crucial part here would be to provide correct
secondary structure annotations.


>   or I have to go in and fix things manually.

If everything else fails, this might be the last option.

Please let me know if you have any questions or issues. If you can share
the data (off-list) I'm happy to look at it.

Best regards,
Oleg Sobolev.

On Tue, Jun 13, 2023 at 2:39 AM Manoj saxena <mks131 at gmail.com> wrote:

> 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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