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. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
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 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.
This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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: [email protected] [[email protected]] on behalf of Nora Cronin [[email protected]] Sent: Friday, October 18, 2013 7:23 AM To: [email protected] 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. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (3)
-
Nora Cronin -
Pavel Afonine -
Terwilliger, Thomas C