Opened 13 months ago

Closed 13 months ago

#16203 closed defect (nonchimerax)

Graphics crash, macOS 13.2.1, Intel Iris Plus Graphics

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: 1.6rc202305021906 (2023-05-02 19:06:00 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Current thread 0x00007ff85a5d6680 (most recent call first):
  File "/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 235 in swap_buffers
  File "/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 497 in swap_buffers
  File "/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 191 in draw
  File "/Applications/ChimeraX-1.6-rc2023.05.02.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 "/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 158 in update_graphics_now
  File "/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume_viewer.py", line 2003 in _planes_slider_moved_cb
  File "/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX-1.6-rc2023.05.02.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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{
  "uptime" : 120000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro16,2",
  "coalitionID" : 24069,
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    "build" : "22D68",
    "releaseType" : "User"
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  "captureTime" : "2024-10-28 18:59:33.3813 +0100",
  "incident" : "903629D5-CF91-4241-8A45-5883E3260DBC",
  "pid" : 22179,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-10-28 17:54:39.1642 +0100",
  "procStartAbsTime" : 124910873839864,
  "procExitAbsTime" : 128805078074012,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.6-rc2023.05.02.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.6.0","CFBundleVersion":"1.6.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"3A79D504-E499-5692-B687-A33EF89D56DA","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "94FF881E-17F8-24BF-E3B0-161DB4B2EC81",
  "throttleTimeout" : 2147483647,
  "wakeTime" : 23869,
  "bridgeVersion" : {"build":"20P3045","train":"7.2"},
  "sleepWakeUUID" : "FFDA9BCE-05FA-408C-90DF-9773CD20D070",
  "sip" : "enabled",
  "exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
  "asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000011\n"],
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  "faultingThread" : 0,
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    "uuid" : "04645919-7592-3a26-93b5-95663f983856",
    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    "name" : "libsystem_platform.dylib"
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  {
    "size" : 0,
    "source" : "A",
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    "uuid" : "00000000-0000-0000-0000-000000000000"
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  {
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    "size" : 45048,
    "uuid" : "9c22fd4a-d2a5-3898-a05b-fe14e5c7784c",
    "path" : "\/System\/Library\/PrivateFrameworks\/GPUSupport.framework\/Versions\/A\/Libraries\/libGPUSupportMercury.dylib",
    "name" : "libGPUSupportMercury.dylib"
  },
  {
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    "uuid" : "4d827e3a-80f4-3b8b-820e-f4360001de8a",
    "path" : "\/System\/Library\/Extensions\/AppleIntelICLGraphicsGLDriver.bundle\/Contents\/MacOS\/AppleIntelICLGraphicsGLDriver",
    "name" : "AppleIntelICLGraphicsGLDriver",
    "CFBundleVersion" : "20.0.2"
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  {
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    "uuid" : "5659457d-2e03-3826-b003-c422b503973b",
    "path" : "\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/Resources\/GLEngine.bundle\/GLEngine",
    "name" : "GLEngine"
  },
  {
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    "arch" : "x86_64",
    "base" : 140712460562432,
    "CFBundleShortVersionString" : "20.0.34",
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    "size" : 65528,
    "uuid" : "bdc969e3-dc5a-342d-81a2-dfdfb9ecc404",
    "path" : "\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/OpenGL",
    "name" : "OpenGL",
    "CFBundleVersion" : "20.0.34"
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  {
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    "base" : 140703563272192,
    "CFBundleShortVersionString" : "6.9",
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    "size" : 16814067,
    "uuid" : "540cedfd-5a35-3f35-8953-dcb7c4834eb5",
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    "name" : "AppKit",
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  {
    "source" : "P",
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    "base" : 4603723776,
    "size" : 638976,
    "uuid" : "7175bc4c-ca2f-30b6-9734-062b84bd0ae2",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.05.02.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
    "name" : "libqcocoa.dylib"
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  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4592926720,
    "size" : 7094272,
    "uuid" : "cf0b9ade-9377-380e-9a84-904983d7bb60",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.05.02.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui",
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    "path" : "\/Applications\/ChimeraX-1.6-rc2023.05.02.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" : 4319604736,
    "CFBundleShortVersionString" : "3.9.11, (c) 2001-2021 Python Software Foundation.",
    "CFBundleIdentifier" : "org.python.python",
    "size" : 2527232,
    "uuid" : "ef9cc1f4-5991-3213-9a9e-e68c578b6c1b",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.05.02.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
    "name" : "Python",
    "CFBundleVersion" : "3.9.11"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4326387712,
    "size" : 1605632,
    "uuid" : "5590e5eb-1a53-3bf0-9ffc-71d23992c730",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.05.02.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" : 4420390912,
    "size" : 5210112,
    "uuid" : "6238782e-d1aa-3245-81ef-2925bf1a4c96",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.05.02.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" : 4605284352,
    "size" : 4931584,
    "uuid" : "5bfaef33-ce47-32bf-acb3-03cbe9e68a6f",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.05.02.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" : 4408934400,
    "size" : 2834432,
    "uuid" : "951581e2-ae51-392a-82d9-fdf83e162d11",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.05.02.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" : 140703511302144,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 4825072,
    "uuid" : "c2615780-0140-315c-a455-7e03bb22d3d6",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "1953.300"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703672373248,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 3112958,
    "uuid" : "7bf47984-29cb-319e-a6da-0884d158f96a",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
  {
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    "CFBundleShortVersionString" : "1.6.0",
    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 4096,
    "uuid" : "5df621ee-554e-36a8-b448-93b2334e5480",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.05.02.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
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  {
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    "uuid" : "bba77709-6cad-3592-ab03-09d0f7b8610e",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
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    "uuid" : "9a744198-7fb3-3c4f-b935-3646fa131615",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.05.02.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numexpr\/interpreter.cpython-39-darwin.so",
    "name" : "interpreter.cpython-39-darwin.so"
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    "path" : "\/Applications\/ChimeraX-1.6-rc2023.05.02.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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  {
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    "size" : 64028672,
    "uuid" : "24c9d5c5-4854-3af4-9550-cb0204044dfa",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.05.02.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
    "name" : "libopenblas64_.0.dylib"
  },
  {
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    "uuid" : "ccf8b470-9ccf-3558-9748-04374e88d1ea",
    "path" : "\/Applications\/ChimeraX-1.6-rc2023.05.02.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/scipy\/.dylibs\/libopenblas.0.dylib",
    "name" : "libopenblas.0.dylib"
  }
],
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "62699e1ec1ff2978b47f6c3b",
      "factorPackIds" : {
        "SIRI_FIND_MY_CONFIGURATION_FILES" : "652805151bce5442b8d752e1"
      },
      "deploymentId" : 240000031
    },
    {
      "rolloutId" : "61675b89201f677a9a4cbd65",
      "factorPackIds" : {
        "HEALTH_FEATURE_AVAILABILITY" : "65a855f5f087695cfac03d1f"
      },
      "deploymentId" : 240000155
    }
  ],
  "experiments" : [
    {
      "treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
      "experimentId" : "6643969b3099cf28e049862f",
      "deploymentId" : 400000007
    }
  ]
},
  "reportNotes" : [
  "dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.6rc202305021906 (2023-05-02)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/makubanska/Desktop/204_bin4.rec

Opened 204_bin4.rec as #1, grid size 1024,1024,550, pixel 1, shown at step 1,
values float32  

> close #1

> open
> /Volumes/msdata/makubans/algae_light/arrays/tomsa_mem_cleaned_redo/ref_mem_redo_0.em

Opened ref_mem_redo_0.em as #1, grid size 84,84,84, pixel 1, shown at level
0.137, step 1, values float32  

> open
> /Volumes/msdata/makubans/algae_light/arrays/tomsa_mem_cleaned_redo/ref_mem_redo_1.em

Opened ref_mem_redo_1.em as #2, grid size 84,84,84, pixel 1, shown at level
0.177, step 1, values float32  

> open
> /Volumes/msdata/makubans/algae_light/arrays/tomsa_mem_cleaned_redo/ref_mem_redo_2.em

Opened ref_mem_redo_2.em as #3, grid size 84,84,84, pixel 1, shown at level
0.181, step 1, values float32  

> surface dust #16 size 100

No surfaces specified  

> volume capFaces false

> volume #1 level -0.07709

> volume #1 level -0.08422

> volume #2 level -0.06451

> volume #3 level 0.1809

> volume #3 level -0.05185

> close #2

> close #1

> close #3

> artiax start

Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  
Opened 204_bin4.rec as #1.1.1, grid size 1024,1024,550, pixel 1, shown at
level 7.13e+11, step 1, values float32  

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

> volume #1.1.1 region 0,0,272,1023,1023,272 step 1 showOutlineBox true
> imageMode "full region"

> volume #1.1.1 level -1.792e+12,0 level 1.402e+10,0.6317 level 1.849e+12,1

> volume #1.1.1 level -9.869e+11,0 level 1.402e+10,0.6317 level 1.849e+12,1

> volume #1.1.1 level -9.869e+11,0 level -5.558e+10,0.9385 level 1.849e+12,1

> volume #1.1.1 level -6.985e+11,0.01538 level -5.558e+10,0.9385 level
> 1.849e+12,1

> volume #1.1.1 level -6.985e+11,0.01538 level 2.129e+11,0.7231 level
> 1.849e+12,1

> close #1.1.1

Opened TS_204_AT_fSIRT_full_rec.mrc as #1.1.1, grid size 1024,1024,550, pixel
7.88,7.88,7.88, shown at level 1.06e+03, step 1, values int16  

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

> volume #1.1.1 level -1847,0 level 170.9,0.5 level 2603,1

> volume #1.1.1 level -1847,0 level -636.3,0.08462 level 2603,1

> open /Users/makubanska/Desktop/motl_rot_merged_v2_5_ARTIAXB4.em format motl

Summary of feedback from opening
/Users/makubanska/Desktop/motl_rot_merged_v2_5_ARTIAXB4.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list motl_rot_merged_v2_5_ARTIAXB4.em with 42907 particles.  

> volume #1.1.1 region 0,0,272,1023,1023,272 step 1 showOutlineBox true
> imageMode "full region"

> volume #1.1.1 level -1847,0 level -1246,0 level 2603,1

> volume #1.1.1 level -1847,0 level -1246,0 level 1007,1

> view #1.1 clip false

> hide #!1.2.1 models

> open /Users/makubanska/Desktop/motl_rot_lwr2_ARTIAXB4.em
> /Users/makubanska/Desktop/motl_rot_lwr1_ARTIAXB4.em format motl

Summary of feedback from opening
/Users/makubanska/Desktop/motl_rot_lwr2_ARTIAXB4.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
/Users/makubanska/Desktop/motl_rot_lwr1_ARTIAXB4.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list motl_rot_lwr2_ARTIAXB4.em with 7104 particles.  
Opened Particle list motl_rot_lwr1_ARTIAXB4.em with 7107 particles.  

> hide #!1.2.2 models

> hide #!1.2.3 models

> show #!1.2.3 models

> hide #!1.2.3 models

> show #!1.2.3 models

> artiax view xy

> artiax view xz

> artiax view yz

> artiax view xy

> ui mousemode right select

Drag select of axes, 1478 of 7107 instances, 1458 atoms  
Drag select of axes, 1731 of 7107 instances, 1727 atoms  
fine  

> select clear

Drag select of axes, 56 of 5299 instances, 60 atoms  
fine  

> hide #!1.2.3 models

> show #!1.2.2 models

> select clear

> open /Users/makubanska/Desktop/motl_rot_top2_ARTIAXB4.em
> /Users/makubanska/Desktop/motl_rot_top1_ARTIAXB4.em
> /Users/makubanska/Desktop/motl_rot_mid2_ARTIAXB4.em
> /Users/makubanska/Desktop/motl_rot_mid_ARTIAXB4.em format motl

Summary of feedback from opening
/Users/makubanska/Desktop/motl_rot_top2_ARTIAXB4.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
/Users/makubanska/Desktop/motl_rot_top1_ARTIAXB4.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
/Users/makubanska/Desktop/motl_rot_mid2_ARTIAXB4.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
/Users/makubanska/Desktop/motl_rot_mid_ARTIAXB4.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list motl_rot_top2_ARTIAXB4.em with 7103 particles.  
Opened Particle list motl_rot_top1_ARTIAXB4.em with 7388 particles.  
Opened Particle list motl_rot_mid2_ARTIAXB4.em with 7110 particles.  
Opened Particle list motl_rot_mid_ARTIAXB4.em with 7107 particles.  

> select clear

Drag select of axes, 1459 of 7104 instances, axes, 1370 of 7103 instances,
axes, 1387 of 7388 instances, axes, 1388 of 7110 instances, axes, 1381 of 7107
instances, 6944 atoms  
fine  
fine  
fine  
fine  
fine  
set axis size 16.00114  
16.00114  
['.arrow', '0', '0', '0', '16.00114', '0', '0', '1.0667426666666666',
'4.2669706666666665']  
set axis size 13.72955  
13.72955  
['.arrow', '0', '0', '0', '13.72955', '0', '0', '0.9153033333333334',
'3.6612133333333334']  
set axis size 12.97235  
12.97235  
['.arrow', '0', '0', '0', '12.97235', '0', '0', '0.8648233333333334',
'3.4592933333333336']  
set axis size 12.21515  
12.21515  
['.arrow', '0', '0', '0', '12.21515', '0', '0', '0.8143433333333333',
'3.2573733333333332']  
set axis size 10.70076  
10.70076  
['.arrow', '0', '0', '0', '10.70076', '0', '0', '0.713384', '2.853536']  
set axis size 8.42917  
8.42917  
['.arrow', '0', '0', '0', '8.42917', '0', '0', '0.5619446666666666',
'2.2477786666666666']  
set axis size 6.15758  
6.15758  
['.arrow', '0', '0', '0', '6.15758', '0', '0', '0.41050533333333333',
'1.6420213333333333']  
set axis size 1.61439  
1.61439  
['.arrow', '0', '0', '0', '1.61439', '0', '0', '0.107626', '0.430504']  
set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  
set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  

> artiax particles #1.2.7 axesSize 0.1

set axis size 12.97235  
12.97235  
['.arrow', '0', '0', '0', '12.97235', '0', '0', '0.8648233333333334',
'3.4592933333333336']  
set axis size 11.45795  
11.45795  
['.arrow', '0', '0', '0', '11.45795', '0', '0', '0.7638633333333333',
'3.0554533333333334']  
set axis size 10.70076  
10.70076  
['.arrow', '0', '0', '0', '10.70076', '0', '0', '0.713384', '2.853536']  
set axis size 9.94356  
9.94356  
['.arrow', '0', '0', '0', '9.94356', '0', '0', '0.6629039999999999',
'2.6516159999999998']  
set axis size 9.18636  
9.18636  
['.arrow', '0', '0', '0', '9.18636', '0', '0', '0.6124240000000001',
'2.4496960000000003']  
set axis size 6.91477  
6.91477  
['.arrow', '0', '0', '0', '6.91477', '0', '0', '0.46098466666666665',
'1.8439386666666666']  
set axis size 1.61439  
1.61439  
['.arrow', '0', '0', '0', '1.61439', '0', '0', '0.107626', '0.430504']  
set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  
set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  

> artiax particles #1.2.6 axesSize 0.1

set axis size 14.48674  
14.48674  
['.arrow', '0', '0', '0', '14.48674', '0', '0', '0.9657826666666666',
'3.8631306666666663']  
set axis size 12.97235  
12.97235  
['.arrow', '0', '0', '0', '12.97235', '0', '0', '0.8648233333333334',
'3.4592933333333336']  
set axis size 12.21515  
12.21515  
['.arrow', '0', '0', '0', '12.21515', '0', '0', '0.8143433333333333',
'3.2573733333333332']  
set axis size 11.45795  
11.45795  
['.arrow', '0', '0', '0', '11.45795', '0', '0', '0.7638633333333333',
'3.0554533333333334']  
set axis size 9.94356  
9.94356  
['.arrow', '0', '0', '0', '9.94356', '0', '0', '0.6629039999999999',
'2.6516159999999998']  
set axis size 9.18636  
9.18636  
['.arrow', '0', '0', '0', '9.18636', '0', '0', '0.6124240000000001',
'2.4496960000000003']  
set axis size 7.67197  
7.67197  
['.arrow', '0', '0', '0', '7.67197', '0', '0', '0.5114646666666667',
'2.0458586666666667']  
set axis size 6.15758  
6.15758  
['.arrow', '0', '0', '0', '6.15758', '0', '0', '0.41050533333333333',
'1.6420213333333333']  
set axis size 5.40038  
5.40038  
['.arrow', '0', '0', '0', '5.40038', '0', '0', '0.36002533333333336',
'1.4401013333333335']  
set axis size 3.88598  
3.88598  
['.arrow', '0', '0', '0', '3.88598', '0', '0', '0.2590653333333333',
'1.0362613333333333']  
set axis size 3.12879  
3.12879  
['.arrow', '0', '0', '0', '3.12879', '0', '0', '0.208586', '0.834344']  
set axis size 1.61439  
1.61439  
['.arrow', '0', '0', '0', '1.61439', '0', '0', '0.107626', '0.430504']  
set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  
set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  

> artiax particles #1.2.5 axesSize 0.1

set axis size 12.21515  
12.21515  
['.arrow', '0', '0', '0', '12.21515', '0', '0', '0.8143433333333333',
'3.2573733333333332']  
set axis size 10.70076  
10.70076  
['.arrow', '0', '0', '0', '10.70076', '0', '0', '0.713384', '2.853536']  
set axis size 9.94356  
9.94356  
['.arrow', '0', '0', '0', '9.94356', '0', '0', '0.6629039999999999',
'2.6516159999999998']  
set axis size 8.42917  
8.42917  
['.arrow', '0', '0', '0', '8.42917', '0', '0', '0.5619446666666666',
'2.2477786666666666']  
set axis size 7.67197  
7.67197  
['.arrow', '0', '0', '0', '7.67197', '0', '0', '0.5114646666666667',
'2.0458586666666667']  
set axis size 6.91477  
6.91477  
['.arrow', '0', '0', '0', '6.91477', '0', '0', '0.46098466666666665',
'1.8439386666666666']  
set axis size 6.15758  
6.15758  
['.arrow', '0', '0', '0', '6.15758', '0', '0', '0.41050533333333333',
'1.6420213333333333']  
set axis size 4.64318  
4.64318  
['.arrow', '0', '0', '0', '4.64318', '0', '0', '0.30954533333333334',
'1.2381813333333334']  
set axis size 3.88598  
3.88598  
['.arrow', '0', '0', '0', '3.88598', '0', '0', '0.2590653333333333',
'1.0362613333333333']  
set axis size 1.61439  
1.61439  
['.arrow', '0', '0', '0', '1.61439', '0', '0', '0.107626', '0.430504']  
set axis size 0.8572  
0.8572  
['.arrow', '0', '0', '0', '0.8572', '0', '0', '0.057146666666666665',
'0.22858666666666666']  
set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  
set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  

> artiax particles #1.2.4 axesSize 0.1

set axis size 12.21515  
12.21515  
['.arrow', '0', '0', '0', '12.21515', '0', '0', '0.8143433333333333',
'3.2573733333333332']  
set axis size 10.70076  
10.70076  
['.arrow', '0', '0', '0', '10.70076', '0', '0', '0.713384', '2.853536']  
set axis size 9.94356  
9.94356  
['.arrow', '0', '0', '0', '9.94356', '0', '0', '0.6629039999999999',
'2.6516159999999998']  
set axis size 8.42917  
8.42917  
['.arrow', '0', '0', '0', '8.42917', '0', '0', '0.5619446666666666',
'2.2477786666666666']  
set axis size 2.37159  
2.37159  
['.arrow', '0', '0', '0', '2.37159', '0', '0', '0.158106', '0.632424']  
set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  
set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  

> artiax particles #1.2.3 axesSize 0.1

set axis size 15.24394  
15.24394  
['.arrow', '0', '0', '0', '15.24394', '0', '0', '1.0162626666666668',
'4.065050666666667']  
set axis size 12.97235  
12.97235  
['.arrow', '0', '0', '0', '12.97235', '0', '0', '0.8648233333333334',
'3.4592933333333336']  
set axis size 12.21515  
12.21515  
['.arrow', '0', '0', '0', '12.21515', '0', '0', '0.8143433333333333',
'3.2573733333333332']  
set axis size 11.45795  
11.45795  
['.arrow', '0', '0', '0', '11.45795', '0', '0', '0.7638633333333333',
'3.0554533333333334']  
set axis size 10.70076  
10.70076  
['.arrow', '0', '0', '0', '10.70076', '0', '0', '0.713384', '2.853536']  
set axis size 8.42917  
8.42917  
['.arrow', '0', '0', '0', '8.42917', '0', '0', '0.5619446666666666',
'2.2477786666666666']  
set axis size 7.67197  
7.67197  
['.arrow', '0', '0', '0', '7.67197', '0', '0', '0.5114646666666667',
'2.0458586666666667']  
set axis size 6.15758  
6.15758  
['.arrow', '0', '0', '0', '6.15758', '0', '0', '0.41050533333333333',
'1.6420213333333333']  
set axis size 5.40038  
5.40038  
['.arrow', '0', '0', '0', '5.40038', '0', '0', '0.36002533333333336',
'1.4401013333333335']  
set axis size 4.64318  
4.64318  
['.arrow', '0', '0', '0', '4.64318', '0', '0', '0.30954533333333334',
'1.2381813333333334']  
set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  
set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  

> artiax particles #1.2.2 axesSize 0.1

> ui mousemode right select

> select #1.1.1

3 models selected  

> select #1.1.1

3 models selected  

> select add #1.1

4 models selected  

> ui mousemode right "translate selected models"

> view matrix models #1.1,1,0,0,0,0,1,0,0,0,0,1,0

> select add #1

76618 atoms, 76618 residues, 35 models selected  

> select add #1

76618 atoms, 76618 residues, 35 models selected  

> select add #1

76618 atoms, 76618 residues, 35 models selected  

> select add #1.1

76618 atoms, 76618 residues, 35 models selected  

> select subtract #1.2

6 models selected  

> select add #1.1

6 models selected  

> select add #1

76618 atoms, 76618 residues, 35 models selected  

> view matrix models #1,1,0,0,3.6069,0,1,0,0.89977,0,0,1,0.24891

> select add #1.1

76618 atoms, 76618 residues, 35 models selected  

> hide #1.3 models

> show #1.3 models

> select subtract #1.3

76618 atoms, 76618 residues, 34 models selected  

> select subtract #1.2

5 models selected  

> select add #1.1

5 models selected  

> select add #1

76618 atoms, 76618 residues, 35 models selected  

> select add #1

76618 atoms, 76618 residues, 35 models selected  

> select add #1

76618 atoms, 76618 residues, 35 models selected  

> select add #1

76618 atoms, 76618 residues, 35 models selected  

> select subtract #1.3

76618 atoms, 76618 residues, 34 models selected  

> select subtract #1.2

5 models selected  

> select add #1.1.1

5 models selected  

> select add #1.2

76618 atoms, 76618 residues, 34 models selected  

> view matrix models #1,1,0,0,9.8654,0,1,0,-0.75331,0,0,1,0.46872

> ui mousemode right translate

> ui mousemode right select

> select clear

> ui mousemode right rotate

> ui mousemode right select

Drag select of axes, axes, axes, axes, axes, 28503 atoms  

> ui mousemode right rotate

> ui mousemode right select

> select clear

> hide #!1.1.1 models

Opened 204_bin4.rec as #1.1.2, grid size 1024,1024,550, pixel 1, shown at
level 7.13e+11, step 1, values float32  

> artiax tomo #1.1.2 sliceDirection 0,0,1

> artiax view xy

> select add #1.1

7 models selected  

> volume #1.1.2 region 0,0,272,1023,1023,272 step 1 showOutlineBox true
> imageMode "full region"

> volume #1.1.2 level -1.792e+12,0 level -9.625e+11,0 level 1.849e+12,1

> volume #1.1.2 level -1.792e+12,0 level -9.625e+11,0 level 5.826e+11,1

> hide target m

> show #!1.1 models

> show #!1.1.1 models

> volume #1.1.2 style image

> hide #!1.1.1 models

> show #!1.1.1 models

> hide #!1.1.1 models

> show #!1.2.2 models

> show #!1.2.3 models

> show #!1.2.6 models

> show #!1.2.4 models

> show #!1.2.5 models

> show #!1.1.1 models

> hide #!1.1.1 models

> show #1.3 models

> hide #1.3 models

> show #!1.2.1 models

> hide #!1.2.1 models

> show #!1.2.7 models

> show #!1.2.2 target m

> close #1.2.2

> close #1.2.1

> close #1.2.3

> close #1.2.4

> close #1.2.5

> close #1.2.6

> close #1.2.7

> artiax view yz

> open /Users/makubanska/Desktop/motl_rot_merged_v2_5_ARTIAXB4.em format motl

Summary of feedback from opening
/Users/makubanska/Desktop/motl_rot_merged_v2_5_ARTIAXB4.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list motl_rot_merged_v2_5_ARTIAXB4.em with 42907 particles.  

> ui mousemode right select

Drag select of axes, 13812 of 42907 instances, 13788 atoms  
fine  
Drag select of axes, 21005 of 28516 instances, 20913 atoms  
fine  

> artiax view xy

> open /Users/makubanska/Desktop/motl_rot_merged_v2_5_ARTIAXB4.em format motl

Summary of feedback from opening
/Users/makubanska/Desktop/motl_rot_merged_v2_5_ARTIAXB4.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list motl_rot_merged_v2_5_ARTIAXB4.em with 42907 particles.  

> hide #!1.2.1 models

> show #!1.2.1 models

> artiax view yz

Drag select of axes, 22304 of 42907 instances, 22403 atoms  
fine  
Drag select of axes, 14074 of 19868 instances, 14058 atoms  
fine  
set axis size 18.27273  
18.27273  
['.arrow', '0', '0', '0', '18.27273', '0', '0', '1.2181819999999999',
'4.8727279999999995']  
set axis size 15.24394  
15.24394  
['.arrow', '0', '0', '0', '15.24394', '0', '0', '1.0162626666666668',
'4.065050666666667']  
set axis size 13.72955  
13.72955  
['.arrow', '0', '0', '0', '13.72955', '0', '0', '0.9153033333333334',
'3.6612133333333334']  
set axis size 12.21515  
12.21515  
['.arrow', '0', '0', '0', '12.21515', '0', '0', '0.8143433333333333',
'3.2573733333333332']  
set axis size 9.18636  
9.18636  
['.arrow', '0', '0', '0', '9.18636', '0', '0', '0.6124240000000001',
'2.4496960000000003']  
set axis size 5.40038  
5.40038  
['.arrow', '0', '0', '0', '5.40038', '0', '0', '0.36002533333333336',
'1.4401013333333335']  
set axis size 3.88598  
3.88598  
['.arrow', '0', '0', '0', '3.88598', '0', '0', '0.2590653333333333',
'1.0362613333333333']  
set axis size 3.12879  
3.12879  
['.arrow', '0', '0', '0', '3.12879', '0', '0', '0.208586', '0.834344']  
set axis size 2.37159  
2.37159  
['.arrow', '0', '0', '0', '2.37159', '0', '0', '0.158106', '0.632424']  
set axis size 1.61439  
1.61439  
['.arrow', '0', '0', '0', '1.61439', '0', '0', '0.107626', '0.430504']  
set axis size 0.8572  
0.8572  
['.arrow', '0', '0', '0', '0.8572', '0', '0', '0.057146666666666665',
'0.22858666666666666']  
set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  
set axis size 0.1  
0.1  
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']  

> artiax particles #1.2.1 axesSize 0.1

> artiax particles #1.2.1 radius 1.61439

> artiax view xy

> artiax particles #1.2.1 radius 3.88598

> open /Users/makubanska/Desktop/ref_0.em

Opened ref_0.em as #2, grid size 84,84,84, pixel 1, shown at level 0.386, step
1, values float32  

> volume #2 level -0.7562

> volume capFaces false

> volume #2 level -0.3426

> view #2 clip false

> surface dust #2 size 5

> volume #2 level -0.3328

> volume #2 color #009193

> view #1.1 clip false

> artiax attach #2 toParticleList #1.2.1

Opened ref_0.em as #1.2.1.1.1, grid size 84,84,84, pixel 0.5, shown at level
0.386, step 1, values float32  

> volume #1.2.1.1.1 capFaces false

> volume #1.2.1.1.1 level 0.3861

> volume #1.2.1.1.1 level 0.7308

> close #1.2.1.1.1

> open /Users/makubanska/Desktop/ref_rev_0.em

Opened ref_rev_0.em as #2, grid size 84,84,84, pixel 1, shown at level 0.45,
step 1, values float32  

> artiax attach #2 toParticleList #1.2.1

Opened ref_rev_0.em as #1.2.1.1.1, grid size 84,84,84, pixel 1, shown at level
0.45, step 1, values float32  

> volume #1.2.1.1.1 capFaces false

> open /Users/makubanska/Desktop/ref_rev_0.em

Opened ref_rev_0.em as #2, grid size 84,84,84, pixel 0.5, shown at level 0.45,
step 1, values float32  

> artiax attach #2 toParticleList #1.2.1

Opened ref_rev_0.em as #1.2.1.1.1, grid size 84,84,84, pixel 0.5, shown at
level 0.45, step 1, values float32  

> volume #1.2.1.1.1 capFaces false

> artiax show #1.2.1 surfaces

> volume #1.2.1.1.1 level 0.1846

> volume #1.2.1.1.1 level 0.8345

> volume #1.2.1.1.1 level 0.3717

> open /Users/makubanska/Desktop/ref_rev_0.em

Opened ref_rev_0.em as #2, grid size 84,84,84, pixel 0.5, shown at level 0.45,
step 1, values float32  

> artiax attach #2 toParticleList #1.2.1

Opened ref_rev_0.em as #1.2.1.1.1, grid size 84,84,84, pixel 0.5, shown at
level 0.45, step 1, values float32  

> volume #1.2.1.1.1 capFaces false

> artiax show #1.2.1 surfaces

> artiax particles #1.2.1 surfaceLevel -2.46856

> artiax particles #1.2.1 surfaceLevel 0.09189


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

Log:
UCSF ChimeraX version: 1.6rc202305021906 (2023-05-02)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 INTEL-20.2.50
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0)
      OS Loader Version: 564.40.4~66

Software:

    System Software Overview:

      System Version: macOS 13.2.1 (22D68)
      Kernel Version: Darwin 22.3.0
      Time since boot: 3 days, 9 hours, 12 minutes

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a53
      Revision ID: 0x0007
      Metal Support: Metal 3
      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
        EV2795:
          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: 50045042
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.3
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    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: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6rc202305021906
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    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: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    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-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    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: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    geomdl: 5.3.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    pandas: 2.0.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    starfile: 0.4.12
    superqt: 0.4.1
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by Eric Pettersen, 13 months 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

comment:2 by Tom Goddard, 13 months ago

Resolution: → nonchimerax
Status: assigned → closed
Summary: Graphics hardware encountered an error and was reset → Graphics crash, macOS 13.2.1, Intel Iris Plus Graphics

Apple Intel graphics driver crash.

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