[phenixbb] Autobuild error

[Nora Cronin]

Whilst running Autobuild SA omit map using 40 segments one OMIT region fail  and the program quits.

Error as follow:  Can you help?


Summary of output files for Solution 1 from rebuild cycle 2

---  Model (PDB file)  ---
pdb_file: /local/ncronin/phenix/APC4/Autobuild_20131018/AutoBuild_run_2_/TEMP0/AutoBuild_run_5_/overall_best.pdb

---  Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag ---
refine_data: /local/ncronin/phenix/APC4/Autobuild_20131018/AutoBuild_run_2_/TEMP0/AutoBuild_run_5_/overall_best_refine_data.mtz

AutoBuild_build_cycle  AutoBuild  Run 5 Fri Oct 18 13:30:32 2013


Ending these rebuild cycles as the limit is reached
All done with build cycles in this region

AutoBuild_set_up_build  AutoBuild  Run 5 Fri Oct 18 13:30:32 2013

Traceback (most recent call last):
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 989, in DoNextMethod
    self.CarryOutBest()     # to be obtained after it is finished
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 2146, in CarryOutBest
    getattr(self,str(self.application_method))()  # call this fn
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 1832, in AutoBuild_set_up_build
    self.AutoBuild_finish_current_region()
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 1909, in AutoBuild_finish_current_region
    self.AutoBuild_update_ncs()
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 5567, in AutoBuild_update_ncs
    ],quiet=True,out=f)
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/find_ncs.py", line 324, in __init__
    self.read_ncs_as_file(params,out=out)
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/find_ncs.py", line 511, in read_ncs_as_file
    quiet=self.quiet,log=null_out())
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/simple_ncs_from_pdb.py", line 546, in __init__
    starting_residue_numbers)
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/simple_ncs_from_pdb.py", line 1326, in find_invariant_groups
    minimum_size=min_size)
  File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 35, in __init__
    minimum_size=minimum_size)
  File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 70, in process
    size, index = self.find_largest( matches, used )
  File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 168, in find_largest
    max_size = flex.max( sizes )
RuntimeError: unidentifiable C++ exception
Traceback (most recent call last):
  File "/common/app/phenix/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/autobuild.py", line 230, in <module>
    run_autobuild=run_autobuild(args=sys.argv[1:])
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/wizard_command_line.py", line 564, in __init__
    self.RunWizard()
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/wizard_command_line.py", line 1000, in RunWizard
    self.runWizard.run()
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/wizard_command_line.py", line 137, in run
    self.Wizard.Run(info='script')
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 838, in Run
    self.DoNextMethod()
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 1003, in DoNextMethod
    raise AssertionError, line
AssertionError: Traceback (most recent call last):
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 989, in DoNextMethod
    self.CarryOutBest()     # to be obtained after it is finished
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 2146, in CarryOutBest
    getattr(self,str(self.application_method))()  # call this fn
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 1832, in AutoBuild_set_up_build
    self.AutoBuild_finish_current_region()
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 1909, in AutoBuild_finish_current_region
    self.AutoBuild_update_ncs()
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 5567, in AutoBuild_update_ncs
    ],quiet=True,out=f)
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/find_ncs.py", line 324, in __init__
    self.read_ncs_as_file(params,out=out)
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/find_ncs.py", line 511, in read_ncs_as_file
    quiet=self.quiet,log=null_out())
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/simple_ncs_from_pdb.py", line 546, in __init__
    starting_residue_numbers)
  File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/simple_ncs_from_pdb.py", line 1326, in find_invariant_groups
    minimum_size=min_size)
  File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 35, in __init__
    minimum_size=minimum_size)
  File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 70, in process
    size, index = self.find_largest( matches, used )
  File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 168, in find_largest
    max_size = flex.max( sizes )
RuntimeError: unidentifiable C++ exception


Best regards


Nora



Dr N B Cronin
X-Ray Laboratory Manager               Tel. (+44) 020 7153 5445
Section of Structural Biology             Fax. (+44) 020 7153 5456
Chester Beatty Laboratories		mobile: (+44) 07787554059
The Institute of Cancer Research     
237 Fulham Road                               
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