[phenixbb] Error refining with ramachandran restraints

Oliver Clarke olibclarke at gmail.com
Fri Apr 10 06:46:24 PDT 2015

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.

> 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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