Re: [phenixbb] Error refining with ramachandran restraints

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 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.