[phenixbb] phenix.refine crashes

Jianghai Zhu jzhu at idi.harvard.edu
Tue May 8 06:55:36 PDT 2012


Hi,

I am using phenix.refine dev-1051.  When I was trying flip_peptide, it crashes with the following error messages.

Validate:
                |--------START--------|  |--------FINAL--------|
     residue    map_cc 2mFo-DFc mFo-DFc  map_cc 2mFo-DFc mFo-DFc
Traceback (most recent call last):
  File "/home/jzhu/phenix/phenix-dev-1051/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/refine.py", line 11, in <module>
    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
  File "/home/jzhu/phenix/phenix-dev-1051/phenix/phenix/refinement/command_line.py", line 146, in run
    call_back_handler=call_back_handler)
  File "/home/jzhu/phenix/phenix-dev-1051/phenix/phenix/refinement/driver.py", line 1499, in run
    ncs_manager             = self.ncs_manager)
  File "/home/jzhu/phenix/phenix-dev-1051/phenix/phenix/refinement/strategies.py", line 928, in refinement_machine
    params                      = params.flip_peptides)
  File "/home/jzhu/phenix/phenix-dev-1051/cctbx_project/mmtbx/refinement/flip_peptides.py", line 445, in run
    log=log)
  File "/home/jzhu/phenix/phenix-dev-1051/cctbx_project/mmtbx/refinement/fit_rotamers.py", line 749, in validate_changes
    sites_cart=sites_cart)
  File "/home/jzhu/phenix/phenix-dev-1051/cctbx_project/mmtbx/refinement/flip_peptides.py", line 152, in __call__
    return (self.rama_lookup.evaluate_sites(res_type,i_seqs,sites_cart)<0.002)
  File "/home/jzhu/phenix/phenix-dev-1051/cctbx_project/mmtbx/rotamer/ramachandran_eval.py", line 76, in evaluate_sites
    "isoleucine or valine"])
AssertionError

-- Jianghai






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