Opened 3 years ago

Closed 3 years ago

#8759 closed defect (can't reproduce)

Crash in QMainWindow::removeDockWidget

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: UI Version:
Keywords: Cc: Tom Goddard
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: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000070001a55f000 (most recent call first):
  File "/private/var/folders/xw/qnsy1ktj7yb3hcflq04bz_k40000gn/T/AppTranslocation/368B44F6-C194-4391-B820-8A21CFAA1411/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
  File "/private/var/folders/xw/qnsy1ktj7yb3hcflq04bz_k40000gn/T/AppTranslocation/368B44F6-C194-4391-B820-8A21CFAA1411/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
  File "/private/var/folders/xw/qnsy1ktj7yb3hcflq04bz_k40000gn/T/AppTranslocation/368B44F6-C194-4391-B820-8A21CFAA1411/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
  File "/private/var/folders/xw/qnsy1ktj7yb3hcflq04bz_k40000gn/T/AppTranslocation/368B44F6-C194-4391-B820-8A21CFAA1411/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/private/var/folders/xw/qnsy1ktj7yb3hcflq04bz_k40000gn/T/AppTranslocation/368B44F6-C194-4391-B820-8A21CFAA1411/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x000000010e046600 (most recent call first):
  File "/private/var/folders/xw/qnsy1ktj7yb3hcflq04bz_k40000gn/T/AppTranslocation/368B44F6-C194-4391-B820-8A21CFAA1411/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2301 in destroy
  File "/private/var/folders/xw/qnsy1ktj7yb3hcflq04bz_k40000gn/T/AppTranslocation/368B44F6-C194-4391-B820-8A21CFAA1411/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2165 in _destroy
  File "/private/var/folders/xw/qnsy1ktj7yb3hcflq04bz_k40000gn/T/AppTranslocation/368B44F6-C194-4391-B820-8A21CFAA1411/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 772 in remove_tool
  File "/private/var/folders/xw/qnsy1ktj7yb3hcflq04bz_k40000gn/T/AppTranslocation/368B44F6-C194-4391-B820-8A21CFAA1411/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 335 in remove_tool
  File "/private/var/folders/xw/qnsy1ktj7yb3hcflq04bz_k40000gn/T/AppTranslocation/368B44F6-C194-4391-B820-8A21CFAA1411/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py", line 154 in delete
  File "/private/var/folders/xw/qnsy1ktj7yb3hcflq04bz_k40000gn/T/AppTranslocation/368B44F6-C194-4391-B820-8A21CFAA1411/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/tool.py", line 510 in delete
  File "/private/var/folders/xw/qnsy1ktj7yb3hcflq04bz_k40000gn/T/AppTranslocation/368B44F6-C194-4391-B820-8A21CFAA1411/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 639 in close_request
  File "/private/var/folders/xw/qnsy1ktj7yb3hcflq04bz_k40000gn/T/AppTranslocation/368B44F6-C194-4391-B820-8A21CFAA1411/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2267 in 
  File "/private/var/folders/xw/qnsy1ktj7yb3hcflq04bz_k40000gn/T/AppTranslocation/368B44F6-C194-4391-B820-8A21CFAA1411/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
  File "/private/var/folders/xw/qnsy1ktj7yb3hcflq04bz_k40000gn/T/AppTranslocation/368B44F6-C194-4391-B820-8A21CFAA1411/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
  File "/private/var/folders/xw/qnsy1ktj7yb3hcflq04bz_k40000gn/T/AppTranslocation/368B44F6-C194-4391-B820-8A21CFAA1411/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in 
  File "/private/var/folders/xw/qnsy1ktj7yb3hcflq04bz_k40000gn/T/AppTranslocation/368B44F6-C194-4391-B820-8A21CFAA1411/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/private/var/folders/xw/qnsy1ktj7yb3hcflq04bz_k40000gn/T/AppTranslocation/368B44F6-C194-4391-B820-8A21CFAA1411/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


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{
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  "procLaunch" : "2023-04-01 16:40:27.8193 +0100",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookAir8,2",
  "procStartAbsTime" : 237573095986785,
  "coalitionID" : 12596,
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  "captureTime" : "2023-04-01 20:13:12.3715 +0100",
  "incident" : "5CFA45A1-0D4C-4081-AC00-7D25CAEF3B8A",
  "bug_type" : "309",
  "pid" : 23219,
  "procExitAbsTime" : 248395359194858,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "783A3E68-C79B-6DC9-F811-3935FEA55CE3",
  "wakeTime" : 10577,
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  "sleepWakeUUID" : "54ACFA0E-936D-4A8E-89F7-0DC7F29A9DA4",
  "sip" : "enabled",
  "vmRegionInfo" : "0x2e574b09d3c8 is not in any region.  Bytes after previous region: 50947054228425  Bytes before following region: 54600660298808\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      VM_ALLOCATE                 141e10000-141f80000    [ 1472K] rw-\/rwx SM=PRV  \n--->  GAP OF 0x5ffebe080000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x00002e574b09d3c8","rawCodes":[1,50952455967688],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00002e574b09d3c8"},
  "vmregioninfo" : "0x2e574b09d3c8 is not in any region.  Bytes after previous region: 50947054228425  Bytes before following region: 54600660298808\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      VM_ALLOCATE                 141e10000-141f80000    [ 1472K] rw-\/rwx SM=PRV  \n--->  GAP OF 0x5ffebe080000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",
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  "faultingThread" : 0,
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    "base" : 140703647195136,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 5255168,
    "uuid" : "3002b545-6841-3fc8-91a2-bcfbe5872465",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "1855.105"
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    "arch" : "x86_64",
    "base" : 140703794442240,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 3112960,
    "uuid" : "4163a93f-bf71-3219-80ed-6f65e9266b81",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
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    "arch" : "x86_64",
    "base" : 140703691673600,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 15257600,
    "uuid" : "dd0028a3-78e3-3a8a-a51b-ddd68123adef",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2113"
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    "arch" : "x86_64",
    "base" : 4466049024,
    "CFBundleShortVersionString" : "1.5.0",
    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 4096,
    "uuid" : "5df621ee-554e-36a8-b448-93b2334e5480",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
    "CFBundleVersion" : "1.5.0.0"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4529643520,
    "size" : 442368,
    "uuid" : "1a6ae033-9438-33c0-8077-988fd885250a",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5034811392,
    "size" : 165052416,
    "uuid" : "4aa1de3e-464c-340c-ab61-bcd39bfc7658",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
  },
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    "source" : "P",
    "arch" : "x86_64",
    "base" : 4619898880,
    "size" : 64028672,
    "uuid" : "24c9d5c5-4854-3af4-9550-cb0204044dfa",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
    "name" : "libopenblas64_.0.dylib"
  }
],
  "sharedCache" : {
  "base" : 140703643652096,
  "size" : 15213641728,
  "uuid" : "3d05845f-3f65-358f-9ebf-2236e772ac01"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.4G resident=0K(0%) swapped_out_or_unallocated=1.4G(100%)\nWritable regions: Total=1.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.0G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               640K        5 \nActivity Tracing                   256K        1 \nCG backing stores                 2160K        4 \nCG image                           376K       37 \nColorSync                          240K       28 \nCoreAnimation                      272K       26 \nCoreGraphics                        12K        2 \nCoreUI image data                 4772K       35 \nFoundation                          32K        2 \nKernel Alloc Once                    8K        1 \nMALLOC                           371.4M      699 \nMALLOC guard page                   32K        8 \nMALLOC_LARGE (reserved)            384K        1         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)\nMach message                        16K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        104K       26 \nStack                            179.2M       27 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                       82.6M      119 \n__DATA                            43.5M      652 \n__DATA_CONST                      31.3M      338 \n__DATA_DIRTY                      1620K      212 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       665.4M      138 \n__OBJC_RO                         81.5M        1 \n__OBJC_RW                         3120K        2 \n__TEXT                           778.3M      656 \n__UNICODE                          588K        1 \ndyld private memory               1184K        3 \nmapped file                      181.1M       46 \nshared memory                     2984K       26 \n===========                     =======  ======= \nTOTAL                              2.8G     3106 \nTOTAL, minus reserved VM space     2.4G     3106 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
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},
  "trialInfo" : {
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 2I3C format mmcif fromDatabase pdb

2i3c title:  
Crystal Structure of an Aspartoacylase from Homo Sapiens [more info...]  
  
Chain information for 2i3c #1  
---  
Chain | Description | UniProt  
A B | Aspartoacylase | ACY2_HUMAN  
  
Non-standard residues in 2i3c #1  
---  
PO4 — phosphate ion  
ZN — zinc ion  
  

> turn y 1 90

> set bgColor white

> select /A

2465 atoms, 2507 bonds, 5 pseudobonds, 321 residues, 2 models selected  

> select /B:9-310

2430 atoms, 2491 bonds, 302 residues, 1 model selected  

> select /A:9-310

2430 atoms, 2491 bonds, 302 residues, 1 model selected  

> select :PO4

40 atoms, 32 bonds, 8 residues, 1 model selected  

> select :PO4

40 atoms, 32 bonds, 8 residues, 1 model selected  

> select :PO4

40 atoms, 32 bonds, 8 residues, 1 model selected  

> select :ZN

2 atoms, 2 residues, 1 model selected  

> select :PO4

40 atoms, 32 bonds, 8 residues, 1 model selected  

> select /A:9-310

2430 atoms, 2491 bonds, 302 residues, 1 model selected  

> color sel red

> select /B:9-310

2430 atoms, 2491 bonds, 302 residues, 1 model selected  

> color sel yellow

> turn y 1 90

> 2dlabels text ’Monomer 1’ color red size 26 x .03 y .92

Expected a keyword  

> 2dlabels text ’monomer 1’ color red size 26 x .03 y .92

Expected a keyword  

> 2dlabels text ’monomerA’ color red size 26 xpos .03 ypos .92

> 2dlabels text ’monomerA’ color red size 26 xpos .03 ypos .82

> 2dlabels text ’monomerA’ color red size 26 xpos .03 ypos .72

> 2dlabels text monomer A color red size 26 x .03 y .72

Expected a keyword  

> 2dlabels text "monomer A" color red size 26 xpos .03 ypos .72

> close labels

Expected a models specifier or a keyword  

> select add #2

2430 atoms, 2491 bonds, 302 residues, 6 models selected  

> hide #!2 models

> 2dlabels text "monomer A" color red size 26 xpos .03 ypos .72

> show #!2 models

> turn y 1 90

> delete labels

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete label

Missing or invalid "atoms" argument: invalid atoms specifier  

> close

> open 2I3C format mmcif fromDatabase pdb

2i3c title:  
Crystal Structure of an Aspartoacylase from Homo Sapiens [more info...]  
  
Chain information for 2i3c #1  
---  
Chain | Description | UniProt  
A B | Aspartoacylase | ACY2_HUMAN  
  
Non-standard residues in 2i3c #1  
---  
PO4 — phosphate ion  
ZN — zinc ion  
  

> turn y 1 90

> select /A:9-310

2430 atoms, 2491 bonds, 302 residues, 1 model selected  

> 2dlabels text "monomer A" color red size 26 xpos .03 ypos .72

> 2dlabels text "monomer A" color red size 26 xpos .08 ypos .72

> 2dlabels text "monomer A" color red size 26 xpos .20 ypos .72

> 2dlabels text "monomer A" color red size 26 xpos .90 ypos .72

> 2dlabels text "monomer A" color red size 26 xpos .70 ypos .72

> 2dlabels text "monomer A" color red size 26 xpos .60 ypos .72

> 2dlabels text "monomer A" color red size 26 xpos .75 ypos .72

> close

> open 2I3C format mmcif fromDatabase pdb

2i3c title:  
Crystal Structure of an Aspartoacylase from Homo Sapiens [more info...]  
  
Chain information for 2i3c #1  
---  
Chain | Description | UniProt  
A B | Aspartoacylase | ACY2_HUMAN  
  
Non-standard residues in 2i3c #1  
---  
PO4 — phosphate ion  
ZN — zinc ion  
  

> turn y 1 90

> select /A:9-310

2430 atoms, 2491 bonds, 302 residues, 1 model selected  

> color sel red

> select /B:9-310

2430 atoms, 2491 bonds, 302 residues, 1 model selected  

> color sel blue

> 2dlabels text "monomer A" color red size 26 xpos .03 ypos .72

> 2dlabels text 'monomer B’ color blue size 26 x .75 y .72

Invalid "text" argument: incomplete quoted text  

> 2dlabels text monomer B color blue size 26 x .75 y .72

Expected a keyword  

> 2dlabels text "monomer B" color blue size 26 xpos .75 ypos .72

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/zahirahkargbo/Desktop/movie3.mp4

Movie saved to /Users/zahirahkargbo/Desktop/movie3.mp4  
  

> close

> open 2I3C format mmcif fromDatabase pdb

2i3c title:  
Crystal Structure of an Aspartoacylase from Homo Sapiens [more info...]  
  
Chain information for 2i3c #1  
---  
Chain | Description | UniProt  
A B | Aspartoacylase | ACY2_HUMAN  
  
Non-standard residues in 2i3c #1  
---  
PO4 — phosphate ion  
ZN — zinc ion  
  

> turn y 1 90

> label #1 attribute name

> ave my_transparent_image.png trans

Unknown command: ave my_transparent_image.png trans  

> save my_transparent_image.png transparentBackground

Missing "transparentBackground" keyword's argument  

> save /Users/zahirahkargbo/Desktop/image1.png supersample 3

> turn y 1 90

> movie record

> turn y 1 90

> movie encode

Movie encoding failed because no images were recorded.  

> movie record

> turn y 1 90

> movie encode

Movie encoding failed because no images were recorded.  

> movie record

> turn y 1 90

> movie stop

> rock y 2 180 cycle 30

> label #1 text "{0.name} {0.number}{0.insertion_code}"

> label #1 attribute name

> oll y 2 720 rock 12

Unknown command: oll y 2 720 rock 12  

> oll y 2 720 rock 12

Unknown command: oll y 2 720 rock 12  

> roll y 2 720 rock 120

> movie record

> rock y 2 180 cycle 30

> movie encode

Movie saved to /Users/zahirahkargbo/Desktop/movie.mp4  
  

> movie record

> rock y 2 180 cycle 30

> movie encode

Movie encoding failed because no images were recorded.  

> rock y 2 180 cycle 30

> close

> open 2I3C format mmcif fromDatabase pdb

2i3c title:  
Crystal Structure of an Aspartoacylase from Homo Sapiens [more info...]  
  
Chain information for 2i3c #1  
---  
Chain | Description | UniProt  
A B | Aspartoacylase | ACY2_HUMAN  
  
Non-standard residues in 2i3c #1  
---  
PO4 — phosphate ion  
ZN — zinc ion  
  

> rock y 2 180 cycle 30

> turn y 1 90

> turn z 1 90

> label #1 attribute name

> rock y 2 180 cycle 30

> movie record

> rock y 2 180 cycle 30

> wait 180

> movie encode

Movie saved to /Users/zahirahkargbo/Desktop/movie.mp4  
  

> select /A:9-310

2430 atoms, 2491 bonds, 302 residues, 1 model selected  

> color sel red

> select /B:9-310

2430 atoms, 2491 bonds, 302 residues, 1 model selected  

> color sel blue

> movie record

> rock y 2 180 cycle 30

> wait 180

> movie encode

Movie saved to /Users/zahirahkargbo/Desktop/movie.mp4  
  

> close

> open 2I3C format mmcif fromDatabase pdb

2i3c title:  
Crystal Structure of an Aspartoacylase from Homo Sapiens [more info...]  
  
Chain information for 2i3c #1  
---  
Chain | Description | UniProt  
A B | Aspartoacylase | ACY2_HUMAN  
  
Non-standard residues in 2i3c #1  
---  
PO4 — phosphate ion  
ZN — zinc ion  
  

> turn y 1 90

> ui tool show "Side View"

> select protein

4860 atoms, 4982 bonds, 604 residues, 1 model selected  

> select /A

2465 atoms, 2507 bonds, 5 pseudobonds, 321 residues, 2 models selected  

> select main

4860 atoms, 4982 bonds, 604 residues, 1 model selected  

> select coil

1981 atoms, 1984 bonds, 252 residues, 1 model selected  

> select helix

1682 atoms, 1702 bonds, 202 residues, 1 model selected  

> select sideonly

2444 atoms, 1962 bonds, 568 residues, 1 model selected  

> open P45381 fromDatabase uniprot

Summary of feedback from opening P45381 fetched from uniprot  
---  
notes | Fetching compressed P45381 UniProt info from
https://www.uniprot.org/uniprot/P45381.xml  
Alignment identifier is P45381  
Associated 2i3c chain A to P45381 with 1 mismatch  
Associated 2i3c chain B to P45381 with 1 mismatch  
  
Opened UniProt P45381  

> select /A-B:178

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A-B:9-310

4860 atoms, 4982 bonds, 604 residues, 1 model selected  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 INTEL-18.2.10
OpenGL renderer: Intel(R) UHD Graphics 617
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
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 Air
      Model Identifier: MacBookAir8,2
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 1.6 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 1715.40.15.0.0 (iBridge: 19.16.10548.0.0,0)
      OS Loader Version: 540.40.4~45

Software:

    System Software Overview:

      System Version: macOS 12.0.1 (21A559)
      Kernel Version: Darwin 21.1.0
      Time since boot: 9 days 11:11

Graphics/Displays:

    Intel UHD Graphics 617:

      Chipset Model: Intel UHD Graphics 617
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x87c0
      Revision ID: 0x0002
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    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
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → UI
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in QMainWindow::removeDockWidget

comment:2 by Eric Pettersen, 3 years ago

Resolution: → can't reproduce
Status: accepted → closed
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