[phenixbb] Error refining with ramachandran restraints

[Oleg Sobolev]

Dear Oliver,

Thank you for the bug report. I have fixed the issue with ramachandran
restraints and they should be working in the next available nightly build
(after dev-2009).

Regarding secondary structure: User notes for dev-1999: Parameters for
secondary structure restraints moved to pdb_interpretation scope. Old
parameter files will not be suitable for secondary structure restraints
definitions.

Therefore since dev-1999, please use the following parameter:
secondary_structure.enabled=True

If you encounter other problems, please get back to us.

Best regards,
Oleg Sobolev.

On Fri, Apr 10, 2015 at 6:46 AM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Also (possibly related?) when I add the parameter
> "main.secondary_structure_restraints=True” to the command line, I get an
> error stating that this parameter does not exist, which is weird, because
> I’m sure that worked previously.
>
> Oliver.
> > On Apr 10, 2015, at 9:29 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> >
> > Hi all,
> >
> > When I attempt to run a refinement using phenix.refine from the command
> line, using the parameter “ramachandran_restraints=true”, in the latest
> nightly build of phenix (dev-2006), I get the following error:
> >
> > ========================== Anomalous scatterer groups
> =========================
> >
> > All atoms refined with f_prime=0 and f_double_prime=0.
> > Traceback (most recent call last):
> >  File
> "/Applications/phenix-dev-2006/build/../modules/phenix/phenix/command_line/refine.py",
> line 11, in <module>
> >    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
> >  File
> "/Applications/phenix-dev-2006/modules/phenix/phenix/refinement/command_line.py",
> line 96, in run
> >    master_params=customized_master_params)
> >  File
> "/Applications/phenix-dev-2006/modules/phenix/phenix/refinement/driver.py",
> line 272, in __init__
> >    secondary_structure_manager=self.sec_str,
> > AttributeError: refine instance has no attribute 'sec_str'
> >
> >
> > This happens for two different structures, so I don’t think it is a
> structure-specific thing, and I don’t recall this happening in older builds
> of phenix. The refinement runs fine if I don’t specify ramachandran
> restraints. Is there something obvious I am doing wrong?
> >
> > Best,
> > Oliver.
> >
>
>
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