Opened 3 years ago

Closed 3 years ago

#7877 closed defect (nonchimerax)

Graphics crash, macOS 12.4, Intel Iris Plus Graphics 645

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics 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: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Thread 0x000070000449c000 (most recent call first):
  File "/private/var/folders/xh/mgmqjzc13xg2rqp8t8dvfyhr0000gn/T/AppTranslocation/945AAEF9-9590-4676-83C7-9F3B32B4A7D1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
  File "/private/var/folders/xh/mgmqjzc13xg2rqp8t8dvfyhr0000gn/T/AppTranslocation/945AAEF9-9590-4676-83C7-9F3B32B4A7D1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
  File "/private/var/folders/xh/mgmqjzc13xg2rqp8t8dvfyhr0000gn/T/AppTranslocation/945AAEF9-9590-4676-83C7-9F3B32B4A7D1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
  File "/private/var/folders/xh/mgmqjzc13xg2rqp8t8dvfyhr0000gn/T/AppTranslocation/945AAEF9-9590-4676-83C7-9F3B32B4A7D1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/private/var/folders/xh/mgmqjzc13xg2rqp8t8dvfyhr0000gn/T/AppTranslocation/945AAEF9-9590-4676-83C7-9F3B32B4A7D1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x0000000118d89600 (most recent call first):
  File "/private/var/folders/xh/mgmqjzc13xg2rqp8t8dvfyhr0000gn/T/AppTranslocation/945AAEF9-9590-4676-83C7-9F3B32B4A7D1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 235 in swap_buffers
  File "/private/var/folders/xh/mgmqjzc13xg2rqp8t8dvfyhr0000gn/T/AppTranslocation/945AAEF9-9590-4676-83C7-9F3B32B4A7D1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 496 in swap_buffers
  File "/private/var/folders/xh/mgmqjzc13xg2rqp8t8dvfyhr0000gn/T/AppTranslocation/945AAEF9-9590-4676-83C7-9F3B32B4A7D1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 179 in draw
  File "/private/var/folders/xh/mgmqjzc13xg2rqp8t8dvfyhr0000gn/T/AppTranslocation/945AAEF9-9590-4676-83C7-9F3B32B4A7D1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
  File "/private/var/folders/xh/mgmqjzc13xg2rqp8t8dvfyhr0000gn/T/AppTranslocation/945AAEF9-9590-4676-83C7-9F3B32B4A7D1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
  File "/private/var/folders/xh/mgmqjzc13xg2rqp8t8dvfyhr0000gn/T/AppTranslocation/945AAEF9-9590-4676-83C7-9F3B32B4A7D1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
  File "/private/var/folders/xh/mgmqjzc13xg2rqp8t8dvfyhr0000gn/T/AppTranslocation/945AAEF9-9590-4676-83C7-9F3B32B4A7D1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init
  File "/private/var/folders/xh/mgmqjzc13xg2rqp8t8dvfyhr0000gn/T/AppTranslocation/945AAEF9-9590-4676-83C7-9F3B32B4A7D1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in 
  File "/private/var/folders/xh/mgmqjzc13xg2rqp8t8dvfyhr0000gn/T/AppTranslocation/945AAEF9-9590-4676-83C7-9F3B32B4A7D1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/private/var/folders/xh/mgmqjzc13xg2rqp8t8dvfyhr0000gn/T/AppTranslocation/945AAEF9-9590-4676-83C7-9F3B32B4A7D1/d/ChimeraX-1.4.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":"2022-10-25 15:30:08.00 -0700","app_version":"1.4.0","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"1.4.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.4 (21F79)","incident_id":"8B782644-3AAE-4970-A9EE-08AEA6A2D9E5","name":"ChimeraX"}
{
  "uptime" : 170000,
  "procLaunch" : "2022-10-14 13:43:43.9564 -0700",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro15,4",
  "procStartAbsTime" : 5272635642527,
  "coalitionID" : 1791,
  "osVersion" : {
    "train" : "macOS 12.4",
    "build" : "21F79",
    "releaseType" : "User"
  },
  "captureTime" : "2022-10-25 15:29:45.1470 -0700",
  "incident" : "8B782644-3AAE-4970-A9EE-08AEA6A2D9E5",
  "bug_type" : "309",
  "pid" : 4745,
  "procExitAbsTime" : 172262741673463,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"FE8593A6-1515-525E-BBE3-7E5F38F75251","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "CA3597E7-7DF9-8A23-33FE-0342FDD4E3EF",
  "wakeTime" : 704,
  "bridgeVersion" : {"build":"19P5071","train":"6.5"},
  "sleepWakeUUID" : "FA1473F5-DBB6-4D60-B3EC-D8514C68D826",
  "sip" : "enabled",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
  "ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
  "asi" : {"libsystem_c.dylib":["abort() called"]},
  "asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000002\n"],
  "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" : 0,
  "threads" : 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    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtGui.abi3.so",
    "name" : "QtGui.abi3.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4563755008,
    "CFBundleShortVersionString" : "3.9.11, (c) 2001-2021 Python Software Foundation.",
    "CFBundleIdentifier" : "org.python.python",
    "size" : 2527232,
    "uuid" : "ef9cc1f4-5991-3213-9a9e-e68c578b6c1b",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
    "name" : "Python",
    "CFBundleVersion" : "3.9.11"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4625395712,
    "size" : 1589248,
    "uuid" : "e1eca899-9707-3319-ac6c-d8028378fb9a",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtCore.abi3.so",
    "name" : "QtCore.abi3.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4629102592,
    "size" : 5226496,
    "uuid" : "97d356c9-7652-3ff7-be10-198e30670243",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
    "name" : "QtCore"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4843106304,
    "size" : 4997120,
    "uuid" : "4969d1ff-28d9-3632-9358-784c5dec38c8",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWidgets.framework\/Versions\/A\/QtWidgets",
    "name" : "QtWidgets"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4617904128,
    "size" : 2818048,
    "uuid" : "0a164d84-8b44-3f10-9065-1d0486c25a4b",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtWidgets.abi3.so",
    "name" : "QtWidgets.abi3.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64h",
    "base" : 140703595339776,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 5255168,
    "uuid" : "f8e45ef9-9fd2-3331-bb1b-703d5dacdaf1",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "1863"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703743152128,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 3096576,
    "uuid" : "04544f53-a387-3ac3-a85d-f8adfc0bc69e",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4558934016,
    "CFBundleShortVersionString" : "1.4.0",
    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 4096,
    "uuid" : "9596eff5-d2be-396c-9c4e-6177235c3dae",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
    "CFBundleVersion" : "1.4.0.0"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4711288832,
    "size" : 442368,
    "uuid" : "b70ce1ec-b902-3852-8268-05de00bfa8d5",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4644384768,
    "size" : 63488000,
    "uuid" : "10431d8f-5e3b-3bbc-abd5-81f6a73a5269",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
    "name" : "libopenblas64_.0.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5035929600,
    "size" : 165068800,
    "uuid" : "c9795830-14cd-3b40-983d-a3143cd9cbd9",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
  }
],
  "sharedCache" : {
  "base" : 140703591768064,
  "size" : 15220686848,
  "uuid" : "398acfb4-57f6-31e0-bc82-e9959e5c92ce"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.4G resident=0K(0%) swapped_out_or_unallocated=1.4G(100%)\nWritable regions: Total=5.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=5.4G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG backing stores                 14.5M       27 \nCG image                          2852K       96 \nColorSync                          236K       28 \nCoreAnimation                     5756K      191 \nCoreGraphics                        24K        5 \nCoreServices                       108K        1 \nCoreUI image data                 3380K       38 \nFoundation                          36K        2 \nKernel Alloc Once                    8K        1 \nMALLOC                             4.5G      978 \nMALLOC guard page                   32K        8 \nMALLOC_LARGE (reserved)            384K        1         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           256.0M        1         reserved VM address space (unallocated)\nMach message                        16K        2 \nObjC additional data                15K        1 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        108K       27 \nStack                            172.2M       28 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      360.2M      194 \nVM_ALLOCATE (reserved)            32.0M        1         reserved VM address space (unallocated)\n__CTF                               756        1 \n__DATA                            44.5M      671 \n__DATA_CONST                      32.8M      351 \n__DATA_DIRTY                      1659K      218 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       677.0M      138 \n__TEXT                           806.1M      671 \n__UNICODE                          592K        1 \ndyld private memory               1184K        3 \nmapped file                      221.4M       62 \nshared memory                     3160K       40 \n===========                     =======  ======= \nTOTAL                              7.2G     3797 \nTOTAL, minus reserved VM space     6.9G     3797 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "5ffde50ce2aacd000d47a95f",
      "factorPackIds" : {

      },
      "deploymentId" : 240000211
    },
    {
      "rolloutId" : "5fc94383418129005b4e9ae0",
      "factorPackIds" : {

      },
      "deploymentId" : 240000513
    }
  ],
  "experiments" : [

  ]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/julianaabramovich/Desktop/20200602_VLP_old_3_square_04_stack_full_rec_sirtl16_zshort16_bin4__Membrane_good_seg.hdf
> format emanhdf

No such file/path:
/Users/julianaabramovich/Desktop/20200602_VLP_old_3_square_04_stack_full_rec_sirtl16_zshort16_bin4__Membrane_good_seg.hdf  

> open /Users/julianaabramovich/Downloads/output_volume(7).mrc format mrc

No such file/path: /Users/julianaabramovich/Downloads/output_volume(7).mrc  

> open /Users/julianaabramovich/Downloads/cryosparc_P3_J272_004_volume_map.mrc
> format mrc

Opened cryosparc_P3_J272_004_volume_map.mrc as #1, grid size 320,320,320,
pixel 1.66, shown at level 0.427, step 2, values float32  

> open /Users/julianaabramovich/Downloads/cryosparc_P3_J373_002_volume_map.mrc

Opened cryosparc_P3_J373_002_volume_map.mrc as #2, grid size 320,320,320,
pixel 1.66, shown at level 0.196, step 2, values float32  

> hide #!1 models

> volume #2 level 0.204

> open /Users/julianaabramovich/Downloads/J201_bigSU_vol.mrc format mrc

Opened J201_bigSU_vol.mrc as #3, grid size 205,196,215, pixel 1.33,1.33,1.33,
shown at level 0.643, step 1, values float32  

> volume #3 level 0.5575

> hide #!2 models

> open /Users/julianaabramovich/Downloads/J272_largeSU_onGrid.mrc format mrc

Opened J272_largeSU_onGrid.mrc as #4, grid size 320,320,320, pixel 1.66, shown
at level 0.358, step 2, values float32  

> hide #!3 models

> surface dust #4 size 16.6

> open /Users/julianaabramovich/Downloads/cryosparc_P3_J386_007_volume_map.mrc
> /Users/julianaabramovich/Downloads/output_volume(9).mrc

Opened cryosparc_P3_J386_007_volume_map.mrc as #5.1, grid size 320,320,320,
pixel 1.66, shown at level 0.401, step 2, values float32  
Opened output_volume(9).mrc as #5.2, grid size 320,320,320, pixel 0.83, shown
at level 1, step 2, values float32  

> hide #!5 models

> hide #!4 models

> show #!5 models

> hide #!5.2 models

> volume #5.2 level 0.9908

> surface dust #5.1 size 16.6

> surface dust #5.2 size 8.3

> volume #5.2 level 1

> volume #5.1 level 0.3638

> open /Users/julianaabramovich/Downloads/J274_largeSU_onGrid.mrc format mrc

Opened J274_largeSU_onGrid.mrc as #6, grid size 160,160,160, pixel 3.32, shown
at level 0.15, step 1, values float32  

> hide #!6 models

> open /Users/julianaabramovich/Downloads/cryosparc_P3_J274_002_volume_map.mrc
> format mrc

Opened cryosparc_P3_J274_002_volume_map.mrc as #7, grid size 320,320,320,
pixel 1.66, shown at level 0.612, step 2, values float32  

> hide #!7 models

> hide #!5.1 models

> surface dust #5.1 size 16.6

> surface dust #7 size 16.6

> volume #7 level 0.5734

> volume #5.1 level 0.3301

> hide #!5 models

> hide #!5.1 models

> hide #!7 models

> hide #!2 models

> show #!5.1 models

> close #7

> close #5.1

> open
> /Users/julianaabramovich/Downloads/cryosparc_P3_J338_class_00_01700_volume.mrc
> format mrc

No such file/path:
/Users/julianaabramovich/Downloads/cryosparc_P3_J338_class_00_01700_volume.mrc  

> open
> /Users/julianaabramovich/Downloads/cryosparc_P3_J338_class_00_01700_volume.mrc

Opened cryosparc_P3_J338_class_00_01700_volume.mrc as #7, grid size
256,256,256, pixel 3.89, shown at level 0.835, step 1, values float32  

> surface dust #7 size 38.9

> ui tool show "Map Eraser"

> volume erase #7 center 591.31,392.54,556.74 radius 127.52

Opened cryosparc_P3_J338_class_00_01700_volume.mrc copy as #9, grid size
256,256,256, pixel 3.89, shown at step 1, values float32  

> surface dust #9 size 38.9

> volume erase #9 center 632.15,460.18,596.47 radius 127.49

> molmap #9 5

No atoms specified  

> molmap #1 15

No atoms specified  

> molmap #9 15

No atoms specified  

> volume #9 step 2

> volume #9 level 0.7664

> volume #9 color #d7ea84

> volume #9 level 0.4429

> surface dust #7 size 38.9

> surface dust #9 size 38.9

> surface dust #7 size 38.9

> surface dust #9 size 38.9

> volume #9 step 1

> volume #9 level 0.584

> volume #9 level 0.6849

> volume #9 level 0.7151

> volume erase #7 center 466.21,520.16,377.56 radius 127.49

Opened cryosparc_P3_J338_class_00_01700_volume.mrc copy as #10, grid size
256,256,256, pixel 3.89, shown at step 1, values float32  

> surface dust #10 size 38.9

> volume erase #10 center 414.51,604.53,485.81 radius 159.36

> volume erase #10 center 368.03,542.23,471.89 radius 159.36

> volume #10 color #bbea81

> volume #10 color #e3eadf

> volume #10 color #eae7c7

> volume #9 color #d3ecce

> volume #9 color #bcecb7

> volume #10 level 0.733

> volume #10 level 0.682

> volume #10 level 0.6757

> save /Users/julianaabramovich/Downloads/Ribo1_J338_vol.mrc models #9

> save /Users/julianaabramovich/Downloads/Ribo2_J338_vol.mrc models #10

> open /Users/julianaabramovich/Downloads/Ribo2_J338_vol.mrc format mrc

Opened Ribo2_J338_vol.mrc as #11, grid size 256,256,256, pixel 3.89, shown at
level 0.604, step 1, values float32  

> volume #11 level 0.802

> surface dust #7 size 38.9

> surface dust #9 size 38.9

> surface dust #11 size 38.9

> volume #11 level 0.6554

> volume #11 level 0.6809

> volume #11 level 0.7638

> open /Users/julianaabramovich/Downloads/output_volume(10).mrc
> /Users/julianaabramovich/Downloads/output_volume(11).mrc

Opened output_volume(10).mrc as #12.1, grid size 256,256,256, pixel 0.83,
shown at level 1, step 1, values float32  
Opened output_volume(11).mrc as #12.2, grid size 256,256,256, pixel 0.83,
shown at level 1, step 1, values float32  

> volume #12.1 level 0.9982

> volume #12.1 level 0.9963

> volume #12.2 level 0.9834

> volume #11 step 2

> volume #11 level 0.585

> volume #9 level 0.8059

> volume #9 level 0.7857

> volume #7 step 2

> volume #7 level 0.7566

> volume #7 level 0.7664

> save /Users/julianaabramovich/Downloads/J338_it1700_poly.mrc models #7

> volume #7 level 0.7174

> volume #7 level 0.8057

> volume #12.1 level 0.9649

> volume #12.1 level 0.9834

> volume #12.1 level 0

> volume #12.2 level 0.9612

> volume #12.2 level 0.9649

> close #12.2

> close #12.1

> volume #11 level 0.6684

> open /Users/julianaabramovich/Downloads/Ribo2_J338_vol.mrc format mrc

Opened Ribo2_J338_vol.mrc as #13, grid size 256,256,256, pixel 3.89, shown at
level 0.604, step 1, values float32  

> volume #13 level 0.6363

> surface dust #13 size 38.9

> volume #13 level 0.6681

> volume #13 level 0.7319

> open /Users/julianaabramovich/Downloads/output_volume(9).mrc
> /Users/julianaabramovich/Downloads/output_volume(10).mrc

Opened output_volume(9).mrc as #14.1, grid size 320,320,320, pixel 0.83, shown
at level 1, step 2, values float32  
Opened output_volume(10).mrc as #14.2, grid size 256,256,256, pixel 0.83,
shown at level 1, step 1, values float32  

> volume #14.1 level 0.9908

> volume #14.1 level 0.009242

> volume #14.2 level 0.8854

> volume #14.2 level 0.1312

> volume #14.2 level 0.01109

> volume #5.2 level 0

> volume #5.2 level 0.01664

> surface dust #5.2 size 8.3

> surface dust #14.1 size 8.3

> surface dust #14.2 size 8.3

> surface dust #5.2 size 8.3

> surface dust #14.1 size 8.3

> surface dust #14.2 size 8.3

> volume #5.2 level 0.03327

> volume #14.1 level 0.007394

> volume #14.2 level 0.02773

> volume #14.2 level 0

> volume #14.2 level 0.0573

> open
> "/Users/julianaabramovich/Library/Containers/com.apple.mail/Data/Library/Mail
> Downloads/C1617ACE-9D2F-4894-B4BA-AE79A3E5760C/6olg_noMVM.cif" format mmcif

6olg_noMVM.cif title:  
Human ribosome nascent chain complex stalled by a drug-like small molecule
(CDH1_RNC with PP tRNA) [more info...]  
  
Chain information for 6olg_noMVM.cif #15  
---  
Chain | Description | UniProt  
A | Cadherin-1 | CADH1_HUMAN  
A2 | 28S ribosomal RNA |  
A3 | 5.8S ribosomal RNA |  
A4 | 5S ribosomal RNA |  
AA | 60S ribosomal protein L8 | RL8_HUMAN  
AB | 60S ribosomal protein L3 | RL3_HUMAN  
AC | 60S ribosomal protein L4 | RL4_HUMAN  
AD | 60S ribosomal protein L5 | RL5_HUMAN  
AE | 60S ribosomal protein L6 | RL6_HUMAN  
AF | 60S ribosomal protein L7 | RL7_HUMAN  
AG | 60S ribosomal protein L7a | RL7A_HUMAN  
AH | 60S ribosomal protein L9 | RL9_HUMAN  
AI | 60S ribosomal protein L10 | RL10_HUMAN  
AJ | 60S ribosomal protein L11 | RL11_HUMAN  
AK | 60S acidic ribosomal protein P0 | RLA0_HUMAN  
AL | 60S ribosomal protein L13 | RL13_HUMAN  
AM | 60S ribosomal protein L14 | RL14_HUMAN  
AN | 60S ribosomal protein L15 | RL15_HUMAN  
AO | 60S ribosomal protein L13a | RL13A_HUMAN  
AP | 60S ribosomal protein L17 | RL17_HUMAN  
AQ | 60S ribosomal protein L18 | RL18_HUMAN  
AR | 60S ribosomal protein L19 | RL19_HUMAN  
AS | 60S ribosomal protein L18a | RL18A_HUMAN  
AT | 60S ribosomal protein L21 | RL21_HUMAN  
AU | 60S ribosomal protein L22 | RL22_HUMAN  
AV | 60S ribosomal protein L23 | Q9BTQ7_HUMAN  
AW | 60S ribosomal protein L24 | RL24_HUMAN  
AX | 60S ribosomal protein L23a | RL23A_HUMAN  
AY | 60S ribosomal protein L26 | RL26_HUMAN  
AZ | 60S ribosomal protein L27 | RL27_HUMAN  
Aa | 60S ribosomal protein L27a | RL27A_HUMAN  
Ab | 60S ribosomal protein L29 | RL29_HUMAN  
Ac | 60S ribosomal protein L30 | RL30_HUMAN  
Ad | 60S ribosomal protein L31 | RL31_HUMAN  
Ae | 60S ribosomal protein L32 | RL32_HUMAN  
Af | 60S ribosomal protein L35a | RL35A_HUMAN  
Ag | 60S ribosomal protein L34 | RL34_HUMAN  
Ah | 60S ribosomal protein L35 | RL35_HUMAN  
Ai | 60S ribosomal protein L36 | RL36_HUMAN  
Aj | 60S ribosomal protein L37 | RL37_HUMAN  
Ak | 60S ribosomal protein L38 | RL38_HUMAN  
Al | 60S ribosomal protein L39 | RL39_HUMAN  
Am | 60S ribosomal protein L40 | RL40_HUMAN  
An | 60S ribosomal protein L41 | RL41_HUMAN  
Ao | 60S ribosomal protein L36a | RL36A_HUMAN  
Ap | 60S ribosomal protein L37a | RL37A_HUMAN  
Aq | 60S ribosomal protein L12 | RL12_HUMAN  
At | 60S ribosomal protein L28 | RL28_HUMAN  
Au | 60S ribosomal protein L10a | RL10A_HUMAN  
B1 | 18S ribosomal RNA |  
BA | 40S ribosomal protein SA | RSSA_HUMAN  
BB | 40S ribosomal protein S3a | RS3A_HUMAN  
BC | 40S ribosomal protein S2 | RS2_HUMAN  
BD | 40S ribosomal protein S3 | RS3_HUMAN  
BE | 40S ribosomal protein S4, Y isoform 1 | RS4Y1_HUMAN  
BF | 40S ribosomal protein S5 | RS5_HUMAN  
BG | 40S ribosomal protein S6 | RS6_HUMAN  
BH | 40S ribosomal protein S7 | RS7_HUMAN  
BI | 40S ribosomal protein S8 | RS8_HUMAN  
BJ | 40S ribosomal protein S9 | RS9_HUMAN  
BK | 40S ribosomal protein S10 | RS10_HUMAN  
BL | 40S ribosomal protein S11 | RS11_HUMAN  
BM | 40S ribosomal protein S12 | RS12_HUMAN  
BN | 40S ribosomal protein S13 | RS13_HUMAN  
BO | 40S ribosomal protein S14 | RS14_HUMAN  
BP | 40S ribosomal protein S15 | RS15_HUMAN  
BQ | 40S ribosomal protein S16 | RS16_HUMAN  
BR | 40S ribosomal protein S17 | RS17_HUMAN  
BS | 40S ribosomal protein S18 | RS18_HUMAN  
BT | 40S ribosomal protein S19 | RS19_HUMAN  
BU | 40S ribosomal protein S20 | RS20_HUMAN  
BV | 40S ribosomal protein S21 | RS21_HUMAN  
BW | 40S ribosomal protein S15a | RS15A_HUMAN  
BX | 40S ribosomal protein S23 | RS23_HUMAN  
BY | 40S ribosomal protein S24 | RS24_HUMAN  
BZ | 40S ribosomal protein S25 | RS25_HUMAN  
Ba | 40S ribosomal protein S26 | RS26_HUMAN  
Bb | 40S ribosomal protein S27 | RS27_HUMAN  
Bc | 40S ribosomal protein S28 | RS28_HUMAN  
Bd | 40S ribosomal protein S29 | RS29_HUMAN  
Be | 40S ribosomal protein S30 | E9PR30_HUMAN  
Bf | 40S ribosomal protein S27a | RS27A_HUMAN  
Bg | Receptor of activated protein C kinase 1 | RACK1_HUMAN  
Bv | tRNA |  
Bx | mRNA |  
  
Non-standard residues in 6olg_noMVM.cif #15  
---  
MG — magnesium ion  
ZN — zinc ion  
  

> hide atoms

> show cartoons

> select /Bv

1625 atoms, 1813 bonds, 80 pseudobonds, 78 residues, 3 models selected  

> select /Bv

1625 atoms, 1813 bonds, 80 pseudobonds, 78 residues, 3 models selected  

> delete atoms (#!15 & sel)

> delete bonds (#!15 & sel)

> select /Bx

320 atoms, 351 bonds, 16 residues, 1 model selected  


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

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 INTEL-18.7.4
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,4
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 1.4 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: 8 GB
      System Firmware Version: 1731.120.10.0.0 (iBridge: 19.16.15071.0.0,0)
      OS Loader Version: 540.120.3~6

Software:

    System Software Overview:

      System Version: macOS 12.4 (21F79)
      Kernel Version: Darwin 21.5.0
      Time since boot: 11 days 4:12

Graphics/Displays:

    Intel Iris Plus Graphics 645:

      Chipset Model: Intel Iris Plus Graphics 645
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea6
      Revision ID: 0x0001
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        MX279:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: G6LMRS046299
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.55


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    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
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Graphics hardware encountered an error and was reset after selection

comment:2 by Tom Goddard, 3 years ago

Resolution: → nonchimerax
Status: assigned → closed
Summary: Graphics hardware encountered an error and was reset after selection → Graphics crash, macOS 12.4, Intel Iris Plus Graphics 645

Apple Intel graphics driver crash.

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