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 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]