The following bug report has been submitted:
Platform: macOS-13.3.1-arm64-arm-64bit
ChimeraX Version: 1.6 (2023-03-23 07:59:11 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000002b40bb000 (most recent call first):
File "/Applications/ChimeraX-1.6.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002b30af000 (most recent call first):
File "/Applications/ChimeraX-1.6.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002b20a3000 (most recent call first):
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/Applications/ChimeraX-1.6.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002b1097000 (most recent call first):
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002b008b000 (most recent call first):
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002af07f000 (most recent call first):
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002ae073000 (most recent call first):
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002ad067000 (most recent call first):
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002ac05b000 (most recent call first):
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002ab04f000 (most recent call first):
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002aa043000 (most recent call first):
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002a9037000 (most recent call first):
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002a802b000 (most recent call first):
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002a701f000 (most recent call first):
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002a6013000 (most recent call first):
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00000001e2ffdb40 (most recent call first):
File "/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 284 in event_loop
File "/Applications/ChimeraX-1.6.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.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":"2023-05-30 09:44:39.00 -0400","app_version":"1.6.0","slice_uuid":"a5992708-d5b4-36ec-ac0a-e525f6105b56","build_version":"1.6.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.3.1 (22E261)","roots_installed":0,"name":"ChimeraX","incident_id":"0BF92235-ABA3-42C0-BF03-F35CC4213C7E"}
{
"uptime" : 720000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 1195785599,
"deployVersion" : 210,
"modelCode" : "Mac14,5",
"coalitionID" : 3746,
"osVersion" : {
"train" : "macOS 13.3.1",
"build" : "22E261",
"releaseType" : "User"
},
"captureTime" : "2023-05-30 09:44:36.4752 -0400",
"incident" : "0BF92235-ABA3-42C0-BF03-F35CC4213C7E",
"pid" : 62472,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-05-29 23:22:11.3894 -0400",
"procStartAbsTime" : 17143321933399,
"procExitAbsTime" : 17339582721924,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.0","CFBundleVersion":"1.6.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"0EC3B9EC-4136-540D-AC90-521AA6712099","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "CDC9D036-6330-4586-894A-C78543E17FE8",
"throttleTimeout" : 2147483647,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 1,
"sleepWakeUUID" : "789EC8E5-27B9-48E6-B416-53D8128D8BCA",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 105553518919656\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600018000000-600020000000 [128.0M] rw-\/rwx 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: 105553518919656\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600018000000-600020000000 [128.0M] rw-\/rwx 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":13841562,"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6572244493},{"value":5503450136},{"value":16632694883298047084},{"value":0},{"value":6097498136},{"value":11641120131354832276},{"value":11641120130866509524},{"value":78},{"value":0},{"value":49},{"value":16},{"value":4931452928},{"value":536870912},{"value":328},{"value":8182189856},{"value":0},{"value":11},{"value":8103385920,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8103386144,"symbolLocation":224,"symbol":"_main_thread"},{"value":4965202288},{"value":1},{"value":32769},{"value":32768},{"value":8103392352,"symbolLocation":0,"symbol":"_NSConcreteStackBlock"},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6572063784},"cpsr":{"value":1073745920},"fp":{"value":5503449936},"sp":{"value":5503449904},"esr":{"value":1442840704,"description":" Address size 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"path" : "\/usr\/lib\/libobjc-trampolines.dylib",
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"path" : "\/Applications\/ChimeraX-1.6.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/_posixshmem.cpython-39-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.6.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/OpenGL_accelerate\/numpy_formathandler.cpython-39-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.6.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/psutil\/_psutil_osx.abi3.so",
"name" : "_psutil_osx.abi3.so"
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"uuid" : "065bc7bc-cc26-3df8-a331-eedaf6a57935",
"path" : "\/Applications\/ChimeraX-1.6.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/psutil\/_psutil_posix.abi3.so",
"name" : "_psutil_posix.abi3.so"
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"uuid" : "997112e8-855e-344b-86ab-ceab352542fc",
"path" : "\/Applications\/ChimeraX-1.6.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/graphics\/_graphics.cpython-39-darwin.so",
"name" : "_graphics.cpython-39-darwin.so"
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{
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"base" : 6571798528,
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"uuid" : "7acbd9bc-d056-310e-858d-81b116cf6d28",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
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"uuid" : "b401cfb3-8dfe-32db-92b3-ba8af0f8ca6e",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.6 (2023-03-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/dout2/Downloads/Refine3D_job105/run_class001_lp15.mrc
Opened run_class001_lp15.mrc as #1, grid size 200,200,200, pixel 0.83, shown
at level 0.00813, step 1, values float32
> open /Users/dout2/Downloads/Refine3D_job105/run_class001.mrc
Opened run_class001.mrc as #2, grid size 200,200,200, pixel 0.83, shown at
level 0.00917, step 1, values float32
> set bgColor white
> lighting soft
> volume #1 level 0.002949
> volume #1 level 0.001671
> ui tool show "Side View"
> close #1
> open /Users/dout2/Downloads/mask.mrc
Opened mask.mrc as #1, grid size 200,200,200, pixel 0.83, shown at level 1,
step 1, values float32
> volume #1 level 0.9982
> open /Users/dout2/Downloads/mask.mrc
Opened mask.mrc as #3, grid size 200,200,200, pixel 0.83, shown at level 1,
step 1, values float32
> volume #3 level 1
> close #1
> close #3
> open /Users/dout2/Downloads/Refine3D_job105/run_class001_region_536.mrc
Opened run_class001_region_536.mrc as #1, grid size 200,200,200, pixel 0.83,
shown at level 1.92e-06, step 1, values float32
> open /Users/dout2/Downloads/mask.mrc
Opened mask.mrc as #3, grid size 200,200,200, pixel 0.83, shown at level 1,
step 1, values float32
> volume #3 level 0.9853
> view
> close session
> open /Users/dout2/Downloads/job115/run_class001_angdist.bild
> /Users/dout2/Downloads/job115/run_class001.mrc
Opened run_class001.mrc as #2, grid size 200,200,200, pixel 0.83, shown at
level 0.00913, step 1, values float32
Opened BILD data containing 3056 objects
> hide #1 models
> show #1 models
> open /Users/dout2/Downloads/job116/run_class001_angdist.bild
> /Users/dout2/Downloads/job116/run_class001.mrc
Opened run_class001.mrc as #4, grid size 200,200,200, pixel 0.83, shown at
level 0.00919, step 1, values float32
Opened BILD data containing 3068 objects
> hide #!2 models
> hide #1 models
> hide #3 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> show #!2 models
> open /Users/dout2/Downloads/job120/run_class001_angdist.bild
> /Users/dout2/Downloads/job120/run_class001.mrc
Opened run_class001.mrc as #6, grid size 200,200,200, pixel 0.83, shown at
level 0.00849, step 1, values float32
Opened BILD data containing 3070 objects
> hide #!2 models
> hide #!4 models
> hide #5 models
> volume #6 level 0.01085
> volume #6 level 0.006433
> volume #6 level 0.01177
> open /Users/dout2/Downloads/job080/run_class001_angdist.bild
> /Users/dout2/Downloads/job080/run_class001.mrc
Opened run_class001.mrc as #8, grid size 200,200,200, pixel 0.83, shown at
level 0.00899, step 1, values float32
Opened BILD data containing 3070 objects
> hide #7 models
> hide #!8 models
> show #!8 models
> volume #8 level 0.01018
> hide #!6 models
> show #!6 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!6 models
> show #!6 models
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 (2023-03-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/dout2/Downloads/run_it200_class001.mrc
Opened run_it200_class001.mrc as #1, grid size 200,200,200, pixel 0.83, shown
at level 0.00965, step 1, values float32
> open /Users/dout2/Downloads/run_it200_class004_angdist.bild
Opened BILD data containing 757 objects
> open /Users/dout2/Downloads/run_it200_class004.mrc
Opened run_it200_class004.mrc as #3, grid size 200,200,200, pixel 0.83, shown
at level 0.00989, step 1, values float32
> open /Users/dout2/Downloads/run_it200_class003_angdist.bild
Opened BILD data containing 766 objects
> open /Users/dout2/Downloads/run_it200_class003.mrc
Opened run_it200_class003.mrc as #5, grid size 200,200,200, pixel 0.83, shown
at level 0.00967, step 1, values float32
> open /Users/dout2/Downloads/run_it200_class002_angdist.bild
Opened BILD data containing 758 objects
> open /Users/dout2/Downloads/run_it200_class002.mrc
Opened run_it200_class002.mrc as #7, grid size 200,200,200, pixel 0.83, shown
at level 0.00837, step 1, values float32
> open /Users/dout2/Downloads/run_it200_class001_angdist.bild
Opened BILD data containing 757 objects
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Max
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: Mac14,5
Model Number: MPHG3LL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: 8422.100.650
OS Loader Version: 8422.100.650
Software:
System Software Overview:
System Version: macOS 13.3.1 (22E261)
Kernel Version: Darwin 22.4.0
Time since boot: 20 days, 21 hours, 41 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
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
ROG PG278QR:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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
ChimeraX-AddH: 2.2.3
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
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: 1.3.3
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
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: 1.10.2
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.1
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-ToQuest: 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
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
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