[phenixbb] Autobuild error
Terwilliger, Thomas C
terwilliger at lanl.gov
Mon Oct 21 14:49:54 PDT 2013
Hi Nora,
I'm sorry for the trouble! This is a new problem I haven't seen before. It looks as though the search for NCS in the last model built failed in a strange way.
The work-around is: specify find_ncs=False because you don't need it anyhow.
However I wonder if you can help me debug it by sending me (off-list) these files:
1. your input PDB file
2. /local/ncronin/phenix/APC4/Autobuild_20131018/AutoBuild_run_2_/TEMP0/AutoBuild_run_5_/overall_best.pdb
Let me know if the work-around does not do it.
Thanks!
-Tom T
________________________________________
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Nora Cronin [Nora.Cronin at icr.ac.uk]
Sent: Friday, October 18, 2013 7:23 AM
To: phenixbb at phenix-online.org
Subject: [phenixbb] Autobuild error
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
London
SW3 6JB
The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
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