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 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.

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On Apr 10, 2015, at 9:29 AM, Oliver Clarke wrote:

Hi all,

When I attempt to run a refinement using phenix.refine from the command

Oliver. 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

...

command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/Applications/phenix-dev-2006/modules/phenix/phenix/refinement/command_line.py",

...

master_params=customized_master_params) File "/Applications/phenix-dev-2006/modules/phenix/phenix/refinement/driver.py",

"/Applications/phenix-dev-2006/build/../modules/phenix/phenix/command_line/refine.py", line 11, in <module> line 96, in run 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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