id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
9864	Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-13.2.1-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x0000000286043000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap

Thread 0x0000000285037000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 528 in _handle_tasks
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap

Thread 0x000000028402b000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py"", line 416 in select
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py"", line 936 in wait
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 499 in _wait_for_updates
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 519 in _handle_workers
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap

Thread 0x000000028301f000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap

Thread 0x0000000282013000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap

Thread 0x0000000281007000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap

Thread 0x000000017fd7b000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap

Thread 0x000000017ed6f000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap

Thread 0x000000017dd63000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap

Thread 0x000000017cd57000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap

Thread 0x000000017bd4b000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap

Thread 0x000000017ad3f000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap

Thread 0x0000000179d33000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap

Current thread 0x00000001f65e4140 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.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-1.6.1.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-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in 
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code
  File ""/Applications/ChimeraX-1.6.1.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"":""2023-09-25 13:51:55.00 -0400"",""app_version"":""1.6.1"",""slice_uuid"":""a5992708-d5b4-36ec-ac0a-e525f6105b56"",""build_version"":""1.6.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.2.1 (22D68)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""E4F69B96-A170-43AE-B6A4-586CF5451A1C""}
{
  ""uptime"" : 1000000,
  ""procRole"" : ""Background"",
  ""version"" : 2,
  ""userID"" : 501,
  ""deployVersion"" : 210,
  ""modelCode"" : ""Mac14,9"",
  ""coalitionID"" : 87629,
  ""osVersion"" : {
    ""train"" : ""macOS 13.2.1"",
    ""build"" : ""22D68"",
    ""releaseType"" : ""User""
  },
  ""captureTime"" : ""2023-09-25 13:51:51.3913 -0400"",
  ""incident"" : ""E4F69B96-A170-43AE-B6A4-586CF5451A1C"",
  ""pid"" : 2766,
  ""translated"" : false,
  ""cpuType"" : ""ARM-64"",
  ""roots_installed"" : 0,
  ""bug_type"" : ""309"",
  ""procLaunch"" : ""2023-09-19 09:17:22.2196 -0400"",
  ""procStartAbsTime"" : 21228358284824,
  ""procExitAbsTime"" : 24667869770895,
  ""procName"" : ""ChimeraX"",
  ""procPath"" : ""\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX"",
  ""bundleInfo"" : {""CFBundleShortVersionString"":""1.6.1"",""CFBundleVersion"":""1.6.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""},
  ""storeInfo"" : {""deviceIdentifierForVendor"":""45799F82-EE9B-546C-B8FC-01A1F386BDB7"",""thirdParty"":true},
  ""parentProc"" : ""launchd"",
  ""parentPid"" : 1,
  ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"",
  ""crashReporterKey"" : ""6E77FEC5-96A4-E500-0E0D-525B1375ABBE"",
  ""throttleTimeout"" : 2147483647,
  ""wakeTime"" : 11998,
  ""sleepWakeUUID"" : ""4CCC9B0E-A6DF-43ED-9F83-5922F8B94165"",
  ""sip"" : ""enabled"",
  ""vmRegionInfo"" : ""0x18 is not in any region.  Bytes before following region: 68719476712\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  ...(unallocated)"",
  ""exception"" : {""codes"":""0x0000000000000001, 0x0000000000000018"",""rawCodes"":[1,24],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000000000018""},
  ""vmregioninfo"" : ""0x18 is not in any region.  Bytes before following region: 68719476712\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  ...(unallocated)"",
  ""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"" : [{""triggered"":true,""id"":10847842,""threadState"":{""x"":[{""value"":0},{""value"":0},{""value"":1},{""value"":6895982157},{""value"":5772016664},{""value"":5964653982034489514},{""value"":22},{""value"":6125879480},{""value"":13437458078039672948},{""value"":13437458074648201524},{""value"":78},{""value"":0},{""value"":49},{""value"":4341691080},{""value"":0},{""value"":0},{""value"":328},{""value"":8510535384},{""value"":0},{""value"":11},{""value"":8428339520,""symbolLocation"":0,""symbol"":""_main_thread""},{""value"":259},{""value"":8428339744,""symbolLocation"":224,""symbol"":""_main_thread""},{""value"":5727016080},{""value"":1},{""value"":32769},{""value"":32768},{""value"":8428345952,""symbolLocation"":0,""symbol"":""_NSConcreteStackBlock""},{""value"":1}],""flavor"":""ARM_THREAD_STATE64"",""lr"":{""value"":6895803628},""cpsr"":{""value"":1073745920},""fp"":{""value"":5772016464},""sp"":{""value"":5772016432},""esr"":{""value"":1442840704,""description"":"" Address size fault""},""pc"":{""value"":6895577192,""matchesCrashFrame"":1},""far"":{""value"":17186516672}},""name"":""CrBrowserMain"",""queue"":""com.apple.main-thread"",""frames"":[{""imageOffset"":39016,""symbol"":""__pthread_kill"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":27884,""symbol"":""pthread_kill"",""symbolLocation"":288,""imageIndex"":1},{""imageOffset"":268748,""symbol"":""raise"",""symbolLocation"":32,""imageIndex"":2},{""imageOffset"":17060,""symbol"":""_sigtramp"",""symbolLocation"":56,""imageIndex"":3},{""imageOffset"":3459388,""symbol"":""QMacCGContext::QMacCGContext(QPainter*)"",""symbolLocation"":40,""imageIndex"":4},{""imageOffset"":43052,""imageIndex"":5},{""imageOffset"":73708,""imageIndex"":5},{""imageOffset"":464432,""symbol"":""QCommonStyle::drawControl(QStyle::ControlElement, QStyleOption const*, QPainter*, QWidget const*) 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    ""base"" : 4960976896,
    ""size"" : 16384,
    ""uuid"" : ""cfed1505-cef2-372b-abff-2a9183ec018e"",
    ""path"" : ""\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/_queue.cpython-39-darwin.so"",
    ""name"" : ""_queue.cpython-39-darwin.so""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""arm64"",
    ""base"" : 4355358720,
    ""size"" : 32768,
    ""uuid"" : ""ff7d40db-95e6-320a-b57f-faed8f2333d9"",
    ""path"" : ""\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/select.cpython-39-darwin.so"",
    ""name"" : ""select.cpython-39-darwin.so""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""arm64"",
    ""base"" : 4456906752,
    ""size"" : 20709376,
    ""uuid"" : ""6b8373ed-7142-34ea-9b4b-9f502e8a6f33"",
    ""path"" : ""\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib"",
    ""name"" : ""libopenblas64_.0.dylib""
  },
  {
    ""size"" : 0,
    ""source"" : ""A"",
    ""base"" : 0,
    ""uuid"" : ""00000000-0000-0000-0000-000000000000""
  }
],
  ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=13.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=13.9G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG backing stores                  960K        4 \nCG image                           608K       29 \nColorSync                          592K       29 \nCoreAnimation                      304K       19 \nCoreGraphics                        96K        6 \nCoreUI image data                 4784K       41 \nDispatch continuations            80.0M        1 \nFoundation                          32K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                            12.9G      270 \nMALLOC guard page                  192K       10 \nMALLOC_MEDIUM (reserved)         152.0M        2         reserved VM address space (unallocated)\nMach message                        96K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        800K       50 \nStack                            393.2M       51 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      212.7M      419 \nVM_ALLOCATE (reserved)           192.0M        1         reserved VM address space (unallocated)\n__AUTH                            1938K      361 \n__AUTH_CONST                      24.9M      589 \n__CTF                               756        1 \n__DATA                            20.1M      727 \n__DATA_CONST                      37.8M      734 \n__DATA_DIRTY                      1984K      229 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__LINKEDIT                       796.5M      144 \n__OBJC_CONST                      4759K      325 \n__OBJC_RO                         65.5M        1 \n__OBJC_RW                         1988K        1 \n__TEXT                           825.7M      755 \ndyld private memory                256K        1 \nmapped file                      222.2M       67 \nshared memory                     3136K       21 \n===========                     =======  ======= \nTOTAL                             15.9G     4905 \nTOTAL, minus reserved VM space    15.6G     4905 \n"",
  ""legacyInfo"" : {
  ""threadTriggered"" : {
    ""name"" : ""CrBrowserMain"",
    ""queue"" : ""com.apple.main-thread""
  }
},
  ""trialInfo"" : {
  ""rollouts"" : [
    {
      ""rolloutId"" : ""6112e3d2fc54bc3389840661"",
      ""factorPackIds"" : {
        ""SIRI_TEXT_TO_SPEECH"" : ""648b9b0febdf9e3e398fa6b5""
      },
      ""deploymentId"" : 240000478
    },
    {
      ""rolloutId"" : ""62cdf63ddb3b7109d6d765cc"",
      ""factorPackIds"" : {
        ""SIRI_UNDERSTANDING_TMDC"" : ""62cdf6dddb3b7109d6d765cd""
      },
      ""deploymentId"" : 240000007
    }
  ],
  ""experiments"" : [
    {
      ""treatmentId"" : ""3a3cf641-8471-4e4e-9ad4-81d0ede970fd"",
      ""experimentId"" : ""64a84dae90d82611a0bd7d3d"",
      ""deploymentId"" : 400000010
    },
    {
      ""treatmentId"" : ""6dd670af-0633-45e4-ae5f-122ae4df02be"",
      ""experimentId"" : ""64406ba83deb637ac8a04419"",
      ""deploymentId"" : 900000017
    }
  ]
},
  ""reportNotes"" : [
  ""dyld_process_snapshot_create_for_process failed with 5""
]
}
===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

Unsupported scale factor (0.000000) detected on Display2  

Unsupported scale factor (0.000000) detected on Display3  

Unsupported scale factor (0.000000) detected on Display2  

Unsupported scale factor (0.000000) detected on Display3  

Unsupported scale factor (0.000000) detected on Display1  

Unsupported scale factor (0.000000) detected on Display2  

Unsupported scale factor (0.000000) detected on Display1  

Unsupported scale factor (0.000000) detected on Display2  

> ui tool show AlphaFold

> alphafold predict NPKKYIPGTKMAFGGLKKEK

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  
AlphaFold prediction finished  
Results in /Users/josh/Downloads/ChimeraX/AlphaFold/prediction_3  

> open /Users/josh/Downloads/ChimeraX/AlphaFold/prediction_3/best_model.pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  

> alphafold predict IALKLREDDEYDNYIGYGPV

Running AlphaFold prediction  

> open 1u74

Summary of feedback from opening 1u74 fetched from pdb  
---  
notes | Fetching compressed mmCIF 1u74 from
http://files.rcsb.org/download/1u74.cif  
Fetching CCD PO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PO4/PO4.cif  
Fetching CCD ZNH from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/H/ZNH/ZNH.cif  
Fetching CCD HEM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/HEM/HEM.cif  
  
1u74 title:  
Electron Transfer Complex between cytochrome C and cytochrome C peroxidase
[more info...]  
  
Chain information for 1u74 #2  
---  
Chain | Description | UniProt  
A C | cytochrome c peroxidase | CCPR_YEAST 1-294  
B D | Cytochrome c iso-1 | CYC1_YEAST 1-108  
  
Non-standard residues in 1u74 #2  
---  
HEM — protoporphyrin IX containing Fe (HEME)  
PO4 — phosphate ion  
ZNH — protoporphyrin IX containing Zn  
  
1u74 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> hide #1 models

> color #!2 bychain

AlphaFold prediction finished  
Results in /Users/josh/Downloads/ChimeraX/AlphaFold/prediction_4  

> open /Users/josh/Downloads/ChimeraX/AlphaFold/prediction_4/best_model.pdb

Chain information for best_model.pdb #3  
---  
Chain | Description  
A | No description available  
  

> hide #!2 models

Drag select of 20 residues  

> show sel cartoons

> show sel atoms

> color sel byhetero

> select clear

> show #!2 models

Drag select of 3 atoms, 8 residues, 3 bonds  

> select clear

> hide #3 models

> color #!2 byhetero

Unsupported scale factor (0.000000) detected on Display0  

QPainter::begin: Paint device returned engine == 0, type: 3  


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

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/josh/Downloads/complex.pdb-
> job#112924-Cytochrome_c_peroxidase.pdb

complex.pdb-job#112924-Cytochrome_c_peroxidase.pdb title:  
Electron transfer complex between cytochrome C and cytochrome C peroxidase
[more info...]  
  
Chain information for complex.pdb-job#112924-Cytochrome_c_peroxidase.pdb #1  
---  
Chain | Description | UniProt  
A C | cytochrome C peroxidase | CCPR_YEAST 1-294  
B D | cytochrome C iso-1 | CYC1_YEAST 1-108  
  
Non-standard residues in complex.pdb-job#112924-Cytochrome_c_peroxidase.pdb #1  
---  
HEM — protoporphyrin IX containing Fe (HEME)  
PO4 — phosphate ion  
ZNH — protoporphyrin IX containing Zn  
  

> open /Users/josh/Downloads/complex.pdb-
> job#112924-Cytochrome_c_peroxidase.pdb

complex.pdb-job#112924-Cytochrome_c_peroxidase.pdb title:  
Electron transfer complex between cytochrome C and cytochrome C peroxidase
[more info...]  
  
Chain information for complex.pdb-job#112924-Cytochrome_c_peroxidase.pdb #2  
---  
Chain | Description | UniProt  
A C | cytochrome C peroxidase | CCPR_YEAST 1-294  
B D | cytochrome C iso-1 | CYC1_YEAST 1-108  
  
Non-standard residues in complex.pdb-job#112924-Cytochrome_c_peroxidase.pdb #2  
---  
HEM — protoporphyrin IX containing Fe (HEME)  
PO4 — phosphate ion  
ZNH — protoporphyrin IX containing Zn  
  

> hide #!1 models

> hide #!2 models

> show #!1 models




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

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: Mac14,9
      Model Number: FPHH3LL/A
      Chip: Apple M2 Pro
      Total Number of Cores: 10 (6 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 8419.80.7
      OS Loader Version: 8419.80.7

Software:

    System Software Overview:

      System Version: macOS 13.2.1 (22D68)
      Kernel Version: Darwin 22.3.0
      Time since boot: 42 days, 4 hours, 50 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        XG270HU:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 144.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
        DELL P2417H:
          Resolution: 1080 x 1920
          UI Looks like: 1080 x 1920 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: 90


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-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: 1.6.1
    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
    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
    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
    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

}}}
"	defect	closed	normal		Window Toolkit		duplicate		Tom Goddard				all	ChimeraX