[phenixbb] Autobuild error

Pavel Afonine pafonine at lbl.gov
Sun Oct 20 11:31:55 PDT 2013


Hi Nora,

just FYI: Tom Terwilliger (who would normally reply this particular 
query) is away till October 22. So you may not get a very quick reply.

All the best,
Pavel

On 10/18/13 6:23 AM, Nora Cronin wrote:
> 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
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> London
> SW3 6JB
>
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>
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