[phenixbb] Error refining with ramachandran restraints

Oliver Clarke olibclarke at gmail.com
Fri Apr 10 06:29:17 PDT 2015

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
  File "/Applications/phenix-dev-2006/modules/phenix/phenix/refinement/driver.py", line 272, in __init__
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?


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