Opened 3 years ago
Closed 3 years ago
#8118 closed defect (fixed)
Crash with segidChains true
Reported by: | Owned by: | Eric Pettersen | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Input/Output | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.5rc202210280053 (2022-10-28 00:53:19 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Thread 0x000070005c716000 (most recent call first): File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap Current thread 0x000000011d14d600 (most recent call first): File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/pdb/pdb.py", line 77 in open_pdb File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/pdb/__init__.py", line 34 in open File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 428 in remember_data_format File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 457 in collated_open File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 193 in provider_open File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 118 in cmd_open File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/scripting.py", line 173 in _run_commands File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/scripting.py", line 160 in open_command_script File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core_formats/__init__.py", line 37 in open File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 428 in remember_data_format File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 440 in collated_open File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 193 in provider_open File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 118 in cmd_open File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/dialog.py", line 162 in _qt_safe File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 880 in init File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1031 in File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code File "/Applications/ChimeraX-1.5-rc2022.10.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main {"app_name":"ChimeraX","timestamp":"2022-12-03 10:48:37.00 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{"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"}, "storeInfo" : {"deviceIdentifierForVendor":"69D200E6-D564-54EF-9FE4-A96E911B2460","thirdParty":true}, "parentProc" : "csh", "parentPid" : 38172, "coalitionName" : "com.apple.Terminal", "crashReporterKey" : "10C2B2CC-AEF4-F281-EA3C-3121CF12466B", "responsiblePid" : 1022, "responsibleProc" : "Terminal", "wakeTime" : 5013, "bridgeVersion" : {"build":"14Y910","train":"3.0"}, "sleepWakeUUID" : "E62411CF-9880-4222-8A58-88C2B1A1C8CB", "sip" : "enabled", "isCorpse" : 1, "exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"}, "asi" : {"libsystem_c.dylib":["abort() called"]}, "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0}, "faultingThread" : 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All rights reserved. How to cite UCSF ChimeraX > open > /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/sc_Ku_DNA_RAP1_221122/CHARMM/build_new_comp_kdr3.cxc > open 6erf 6erf title: Complex of APLF factor and Ku heterodimer bound to DNA [more info...] Chain information for 6erf #1 --- Chain | Description | UniProt A C E G | X-ray repair cross-complementing protein 6 | XRCC6_HUMAN B D F H | X-ray repair cross-complementing protein 5 | XRCC5_HUMAN I K M O | DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3') | J L N P | DNA (34-MER) | Q R S T | Aprataxin and PNK-like factor | APLF_HUMAN 6erf mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly 4| author_defined_assembly > select #1/C/E/G/D/F/H/K/M/O/L/N/P/Q/R/S/T 26720 atoms, 27404 bonds, 83 pseudobonds, 3200 residues, 3 models selected > delete atoms sel > open dna_new_kdr3_super.pdb segidChains true name dnanew ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.5rc202210280053 (2022-10-28) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-4.8.101 OpenGL renderer: AMD Radeon Pro 450 OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro13,3 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2,6 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 499.40.2.0.0 OS Loader Version: 540.120.3~22 SMC Version (system): 2.38f12 Software: System Software Overview: System Version: macOS 12.6.1 (21G217) Kernel Version: Darwin 21.6.0 Time since boot: 8 days 22:30 Graphics/Displays: Intel HD Graphics 530: Chipset Model: Intel HD Graphics 530 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x191b Revision ID: 0x0006 Automatic Graphics Switching: Supported gMux Version: 4.0.29 [3.2.8] Metal Family: Supported, Metal GPUFamily macOS 2 Radeon Pro 450: Chipset Model: AMD Radeon Pro 450 Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 2 GB Vendor: AMD (0x1002) Device ID: 0x67ef Revision ID: 0x00ef ROM Revision: 113-C980AF-908 VBIOS Version: 113-C9801AL-028 EFI Driver Version: 01.A0.908 Automatic Graphics Switching: Supported gMux Version: 4.0.29 [3.2.8] Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2880 x 1800 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.0.8 Babel: 2.10.3 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 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Change History (2)
comment:1 by , 3 years ago
Component: | Unassigned → Input/Output |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → Crash with segidChains true |
comment:2 by , 3 years ago
Resolution: | → fixed |
---|---|
Status: | accepted → closed |
Some segment IDs were blank, resulting in null chain IDs. These segment IDs didn't actually correspond to chains, so the actual desired behavior would be for them to be their own attribute (#1524).
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Reproducible with plato:/wynton/group/ferrin/usr.local/projects/chimera/staff/pett/test-data/large-PDB/syn+lig_23.pdb