![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16880 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.3.1-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 0x000000031fe4f000 (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 0x000000031404f000 (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 0x0000000313043000 (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 0x0000000312037000 (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 0x000000031102b000 (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 0x000000031001f000 (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 0x000000030f013000 (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 0x000000030e007000 (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 0x000000030cffb000 (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 0x000000030bfef000 (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 0x000000030afe3000 (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 0x00000001fd8d4840 (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":"2025-02-17 16:58:22.00 +0000","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 15.3.1 (24D70)","roots_installed":0,"name":"ChimeraX","incident_id":"5CE4A8B5-BEA6-4120-A1F5-39C1BAA3FA7F"}
{
"uptime" : 290000,
"procRole" : "Background",
"version" : 2,
"userID" : 1128299610,
"deployVersion" : 210,
"modelCode" : "MacBookAir10,1",
"coalitionID" : 41190,
"osVersion" : {
"train" : "macOS 15.3.1",
"build" : "24D70",
"releaseType" : "User"
},
"captureTime" : "2025-02-17 16:54:48.5587 +0000",
"codeSigningMonitor" : 1,
"incident" : "5CE4A8B5-BEA6-4120-A1F5-39C1BAA3FA7F",
"pid" : 77658,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-15 16:03:32.3158 +0000",
"procStartAbsTime" : 4562310812957,
"procExitAbsTime" : 7046555274013,
"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":"7BBB5E92-E526-5619-833F-8FDD7629ACA5","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "F529BBB9-F848-F08F-ECC4-74A7C4B08CF8",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "21029A0C-84E5-4834-8918-4C95A278BEDF",
"wakeTime" : 23720,
"sleepWakeUUID" : "009E1979-84C8-4E26-B3F1-AA1AF6765222",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 4341661672\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102c88000-102c8c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":77658},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 4341661672\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102c88000-102c8c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"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":13580375,"name":"CrBrowserMain","threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6777569453},{"value":5503482904},{"value":36956514349710956},{"value":0},{"value":6125188040},{"value":1274087521964126242},{"value":1274087515042658402},{"value":78},{"value":0},{"value":49},{"value":16},{"value":6053429248},{"value":83951615},{"value":328},{"value":8689640128},{"value":0},{"value":11},{"value":259},{"value":8548862240},{"value":4686360208},{"value":4686360208},{"value":1},{"value":32769},{"value":32768},{"value":8548868488},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6777356144},"cpsr":{"value":1073745920},"fp":{"value":5503482704},"sp":{"value":5503482672},"esr":{"value":1442840704,"description":" Address size 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"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "3302.1.400"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6840414208,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 21221376,
"uuid" : "b88a44c1-d617-33dc-90ed-b6ab417c428e",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2575.40.6"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6967451648,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3178496,
"uuid" : "950f1236-acaf-379d-819f-6c6b0b5deabd",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6888730624,
"CFBundleShortVersionString" : "1.22",
"CFBundleIdentifier" : "com.apple.HIServices",
"size" : 446464,
"uuid" : "5af090d7-4d2e-3263-9bec-687bc2058651",
"path" : "\/System\/Library\/Frameworks\/ApplicationServices.framework\/Versions\/A\/Frameworks\/HIServices.framework\/Versions\/A\/HIServices",
"name" : "HIServices"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6874034176,
"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 5427200,
"uuid" : "f66e0c94-99b5-3fcd-b726-3e3cbca668a3",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6775558144,
"size" : 290816,
"uuid" : "5576e4fd-aad2-3608-8c8f-4eec421236f9",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6773661696,
"size" : 532288,
"uuid" : "398a133c-9bcb-317f-a064-a40d3cea3c0f",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6777327616,
"size" : 53248,
"uuid" : "642faf7a-874e-37e6-8aba-2b0cc09a3025",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
}
],
"sharedCache" : {
"base" : 6772850688,
"size" : 4865835008,
"uuid" : "d272b91e-f9f0-3854-b5b9-508b21c25dcc"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=14.8G written=3919K(0%) resident=3919K(0%) swapped_out=0K(0%) unallocated=14.8G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG image 224K 13 \nColorSync 688K 32 \nCoreAnimation 912K 57 \nCoreGraphics 32K 2 \nCoreGraphics (reserved) 32K 1 reserved VM address space (unallocated)\nCoreUI image data 3056K 24 \nFoundation 48K 2 \nKernel Alloc Once 1456K 5 \nMALLOC 14.0G 227 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 832K 52 \nStack 348.3M 53 \nStack Guard 56.0M 1 \nVM_ALLOCATE 311.8M 625 \nVM_ALLOCATE (reserved) 128.0M 1 reserved VM address space (unallocated)\n__AUTH 5288K 672 \n__AUTH_CONST 70.9M 920 \n__CTF 824 1 \n__DATA 32.8M 1055 \n__DATA_CONST 33.7M 1075 \n__DATA_DIRTY 2763K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 636.2M 149 \n__OBJC_RW 2374K 1 \n__TEXT 1.2G 1095 \n__TPRO_CONST 272K 2 \nmapped file 270.0M 53 \nowned unmapped memory 107.9M 1 \npage table in kernel 3919K 1 \nshared memory 3200K 25 \n=========== ======= ======= \nTOTAL 17.2G 6520 \nTOTAL, minus reserved VM space 17.0G 6520 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain"
}
},
"logWritingSignature" : "95e762d8ecb8b961d72c8c875df3ed3e56c1e3c1",
"trialInfo" : {
"rollouts" : [
{
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"factorPackIds" : {
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},
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{
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}
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
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/bgreber/Downloads/cryosparc_P20_J90_008_volume_map (1).mrc"
Opened cryosparc_P20_J90_008_volume_map (1).mrc as #1, grid size 128,128,128,
pixel 1.4, shown at level 0.103, step 1, values float32
> volume #1 level 0.1853
> volume #1 level 0.2
> open /Users/bgreber/Downloads/run_it013_class002.mrc
Opened run_it013_class002.mrc as #2, grid size 128,128,128, pixel 1.4, shown
at level 0.00464, step 1, values float32
> open /Users/bgreber/Downloads/run_it013_class003.mrc
Opened run_it013_class003.mrc as #3, grid size 128,128,128, pixel 1.4, shown
at level 0.00552, step 1, values float32
> open /Users/bgreber/Downloads/run_it013_class004.mrc
Opened run_it013_class004.mrc as #4, grid size 128,128,128, pixel 1.4, shown
at level 0.00431, step 1, values float32
> open /Users/bgreber/Downloads/run_it013_class001.mrc
Opened run_it013_class001.mrc as #5, grid size 128,128,128, pixel 1.4, shown
at level 0.00415, step 1, values float32
> close #1
> volume #4 level 0.006129
> volume #4 level 0.006828
> volume #5 level 0.006911
> volume #2 level 0.004234
> volume #4 level 0.007
> volume #2 level 0.007
> volume #5 level 0.007
> open /Users/bgreber/Downloads/run_it019_class003.mrc
Opened run_it019_class003.mrc as #1, grid size 128,128,128, pixel 1.4, shown
at level 0.0053, step 1, values float32
> open /Users/bgreber/Downloads/run_it019_class004.mrc
Opened run_it019_class004.mrc as #6, grid size 128,128,128, pixel 1.4, shown
at level 0.00443, step 1, values float32
> open /Users/bgreber/Downloads/run_it019_class001.mrc
Opened run_it019_class001.mrc as #7, grid size 128,128,128, pixel 1.4, shown
at level 0.00422, step 1, values float32
> open /Users/bgreber/Downloads/run_it019_class002.mrc
Opened run_it019_class002.mrc as #8, grid size 128,128,128, pixel 1.4, shown
at level 0.00453, step 1, values float32
> volume #1 level 0.00509
> volume #6 level 0.007088
> volume #7 level 0.007173
> volume #8 level 0.007069
> open /Users/bgreber/Downloads/run_class001.mrc
Opened run_class001.mrc as #9, grid size 128,128,128, pixel 1.4, shown at
level 0.00419, step 1, values float32
> volume #9 level 0.009623
> open "/Users/bgreber/Library/CloudStorage/OneDrive-
> TheInstituteofCancerResearch/Research/Projects/WEE1/2025 CDK2-cyclin A-WEE1
> QXLp modelling/alphafold_fitted-coot-0_real_space_refined_000.pdb"
Chain information for alphafold_fitted-coot-0_real_space_refined_000.pdb #10
---
Chain | Description
A | No description available
B | No description available
C | No description available
> show atoms
> volume #9 level 0.006144
> transparency 50 target s
> volume #9 level 0.006144
> open "/Users/bgreber/Library/CloudStorage/OneDrive-
> TheInstituteofCancerResearch/Research/Projects/WEE1/2025 CDK2-cyclin A-WEE1
> QXLp modelling/alphafold_fitted-coot-0.pdb"
Summary of feedback from opening /Users/bgreber/Library/CloudStorage/OneDrive-
TheInstituteofCancerResearch/Research/Projects/WEE1/2025 CDK2-cyclin A-WEE1
QXLp modelling/alphafold_fitted-coot-0.pdb
---
warnings | Start residue of secondary structure not found: HELIX 18 18 VAL B
172 GLU B 174 1 3
Start residue of secondary structure not found: HELIX 43 43 ALA C 5 CYS C 7 1
3
Start residue of secondary structure not found: HELIX 44 44 SER C 19 CYS C 21
1 3
Start residue of secondary structure not found: SHEET 9 9 9 ILE B 101 ASP B
104 0
Chain information for alphafold_fitted-coot-0.pdb #11
---
Chain | Description
A | No description available
B | No description available
C | No description available
> show atoms
> close #11
> open "/Users/bgreber/Library/CloudStorage/OneDrive-
> TheInstituteofCancerResearch/Research/Projects/WEE1/2025 CDK2-cyclin A-WEE1
> QXLp modelling/fold_wee1qxl_ps1_cdk2_cyclina_model_0.cif"
Chain information for fold_wee1qxl_ps1_cdk2_cyclina_model_0.cif #11
---
Chain | Description
A | .
B | .
C | .
> hide #10 models
> show #10 models
> hide #11 models
> show #11 models
> ui tool show Matchmaker
> matchmaker #11 to #10
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker alphafold_fitted-coot-0_real_space_refined_000.pdb, chain A (#10)
with fold_wee1qxl_ps1_cdk2_cyclina_model_0.cif, chain A (#11), sequence
alignment score = 1493.9
RMSD between 298 pruned atom pairs is 0.455 angstroms; (across all 298 pairs:
0.455)
> ui tool show Matchmaker
> matchmaker #11 to #10/A pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker alphafold_fitted-coot-0_real_space_refined_000.pdb, chain A (#10)
with fold_wee1qxl_ps1_cdk2_cyclina_model_0.cif, chain A (#11), sequence
alignment score = 1493.9
RMSD between 298 pruned atom pairs is 0.455 angstroms; (across all 298 pairs:
0.455)
> matchmaker #11 to #10/B pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker alphafold_fitted-coot-0_real_space_refined_000.pdb, chain B (#10)
with fold_wee1qxl_ps1_cdk2_cyclina_model_0.cif, chain B (#11), sequence
alignment score = 1343.5
RMSD between 259 pruned atom pairs is 0.383 angstroms; (across all 259 pairs:
0.383)
> show atoms
> hide #11 models
> graphics silhouettes true
> set bgColor white
> hide #10 cartoons
> show #10 cartoons
> open "/Users/bgreber/Library/CloudStorage/OneDrive-
> TheInstituteofCancerResearch/Research/Projects/CDK2/2024 CyclinA-
> RxLpeptides/Structures/SAMHD1/cyca_cdk2_refined_SAMDH1_pp26-coot-2_real_space_refined_005.pdb"
Chain information for
cyca_cdk2_refined_SAMDH1_pp26-coot-2_real_space_refined_005.pdb #12
---
Chain | Description
A | No description available
B | No description available
C | No description available
> show #10#!12 atoms
> ui tool show Matchmaker
> matchmaker #!12 to #10/B pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker alphafold_fitted-coot-0_real_space_refined_000.pdb, chain B (#10)
with cyca_cdk2_refined_SAMDH1_pp26-coot-2_real_space_refined_005.pdb, chain A
(#12), sequence alignment score = 1265.7
RMSD between 255 pruned atom pairs is 0.506 angstroms; (across all 255 pairs:
0.506)
> open "/Users/bgreber/Library/CloudStorage/OneDrive-
> TheInstituteofCancerResearch/Research/Projects/CDK2/2024 CyclinA-
> RxLpeptides/Structures/GMNC/CDK2_CyclinA_GMNC_model-
> coot-9_real_space_refined_017.pdb"
Chain information for CDK2_CyclinA_GMNC_model-
coot-9_real_space_refined_017.pdb #13
---
Chain | Description
A | No description available
B | No description available
C | No description available
> show #10#!12-13 atoms
> ui tool show Matchmaker
> matchmaker #!13 to #10/B pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker alphafold_fitted-coot-0_real_space_refined_000.pdb, chain B (#10)
with CDK2_CyclinA_GMNC_model-coot-9_real_space_refined_017.pdb, chain A (#13),
sequence alignment score = 1262.1
RMSD between 255 pruned atom pairs is 0.538 angstroms; (across all 255 pairs:
0.538)
> hide #!12 models
> open "/Users/bgreber/Library/CloudStorage/OneDrive-
> TheInstituteofCancerResearch/Research/Projects/CDK2/2024 CyclinA-
> RxLpeptides/Structures/SCAPER/CycA_cdk2_refined_SCAPER_pp42-coot-1_real_space_refined_003.pdb"
Chain information for
CycA_cdk2_refined_SCAPER_pp42-coot-1_real_space_refined_003.pdb #14
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!13 models
> show #10#!14 atoms
> matchmaker #!14 to #10/B pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker alphafold_fitted-coot-0_real_space_refined_000.pdb, chain B (#10)
with CycA_cdk2_refined_SCAPER_pp42-coot-1_real_space_refined_003.pdb, chain A
(#14), sequence alignment score = 1290.9
RMSD between 255 pruned atom pairs is 0.518 angstroms; (across all 255 pairs:
0.518)
> transparency 0 target s
> open /Users/bgreber/Downloads/postprocess.mrc
Opened postprocess.mrc as #15, grid size 128,128,128, pixel 1.4, shown at
level 0.00411, step 1, values float32
> volume #15 level 0.007978
> volume #15 level 0.01001
> transparency 50 target s
> hide #!14 models
> volume #15 level 0.004843
> open /Users/bgreber/Downloads/run17_class001.mrc
Opened run17_class001.mrc as #16, grid size 128,128,128, pixel 1.4, shown at
level 0.00406, step 1, values float32
> close #15
> volume #16 level 0.007577
> transparency 50 target s
> volume #16 level 0.004802
> open /Users/bgreber/Downloads/run30_class001.mrc
Opened run30_class001.mrc as #15, grid size 128,128,128, pixel 1.4, shown at
level 0.0043, step 1, values float32
> volume #15 level 0.006224
> transparency 50 target s
> volume #15 level 0.00601
> volume #15 level 0.005155
> volume #15 level 0.004728
> volume #15 level 0.007506
> volume #15 level 0.006865
> open /Users/bgreber/Downloads/run19_class001.mrc
Opened run19_class001.mrc as #17, grid size 128,128,128, pixel 1.4, shown at
level 0.00359, step 1, values float32
> volume #17 level 0.006907
> transparency 50 target s
> volume #17 level 0.009053
> volume #17 level 0.007883
> volume #9 level 0.008101
> volume #9 level 0.008
> ui mousemode right zoom
> volume #9 level 0.005391
> show #!13 models
> hide #!13 models
> show #!12 models
> open /Users/bgreber/Downloads/run35_class001.mrc
Opened run35_class001.mrc as #18, grid size 128,128,128, pixel 1.4, shown at
level 0.00389, step 1, values float32
> volume #18 level 0.007053
> transparency 50 target s
> volume #18 level 0.005865
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #!13 models
> show #!14 models
> open /Users/bgreber/Downloads/pp32.mrc
Opened pp32.mrc as #19, grid size 128,128,128, pixel 1.4, shown at level
0.0161, step 1, values float32
> volume #19 level 0.02401
> hide #!13 models
> hide #!14 models
> hide #!12 models
> transparency 50 target s
> volume #19 level 0.01683
> volume #19 level 0.02545
> open "/Users/bgreber/Library/CloudStorage/OneDrive-
> TheInstituteofCancerResearch/Research/Projects/CDK2/2024
> CDK1-cyclinB1-MAD1/Krios/cdk1_pp36.mrc"
Opened cdk1_pp36.mrc as #20, grid size 180,180,180, pixel 1.02, shown at level
0.00452, step 1, values float32
> open "/Users/bgreber/Library/CloudStorage/OneDrive-
> TheInstituteofCancerResearch/Research/Projects/CDK2/2024
> CDK1-cyclinB1-MAD1/Krios/pp36_MAD1.mrc"
Opened pp36_MAD1.mrc as #21, grid size 180,180,180, pixel 1.02, shown at level
0.00452, step 1, values float32
> volume #20 level 0.004516
> close #21
> close #20
> open /Users/bgreber/Downloads/run_it015_class003.mrc
Opened run_it015_class003.mrc as #20, grid size 128,128,128, pixel 1.4, shown
at level 0.00526, step 1, values float32
> open /Users/bgreber/Downloads/run_it015_class002.mrc
Opened run_it015_class002.mrc as #21, grid size 128,128,128, pixel 1.4, shown
at level 0.00531, step 1, values float32
> open /Users/bgreber/Downloads/run_it015_class001.mrc
Opened run_it015_class001.mrc as #22, grid size 128,128,128, pixel 1.4, shown
at level 0.00493, step 1, values float32
> open /Users/bgreber/Downloads/run_it015_class004.mrc
Opened run_it015_class004.mrc as #23, grid size 128,128,128, pixel 1.4, shown
at level 0.00525, step 1, values float32
> hide #!19 models
> hide #!20 models
> hide #!21 models
> hide #!22 models
> hide #!23 models
> volume #23 level 0.01206
> volume #23 level 0.01135
> volume #22 level 0.01002
> volume #21 level 0.01678
> volume #20 level 0.007946
> show #11 models
> transparency 50 target s
> transparency 0 target s
> volume #20 level 0.008
> volume #21 level 0.008
> volume #22 level 0.008
> volume #23 level 0.008
> open /Users/bgreber/Downloads/run_it020_class003.mrc
Opened run_it020_class003.mrc as #24, grid size 128,128,128, pixel 1.4, shown
at level 0.00551, step 1, values float32
> open /Users/bgreber/Downloads/run_it020_class002.mrc
Opened run_it020_class002.mrc as #25, grid size 128,128,128, pixel 1.4, shown
at level 0.00551, step 1, values float32
> open /Users/bgreber/Downloads/run_it020_class001.mrc
Opened run_it020_class001.mrc as #26, grid size 128,128,128, pixel 1.4, shown
at level 0.00499, step 1, values float32
> open /Users/bgreber/Downloads/run_it020_class004.mrc
Opened run_it020_class004.mrc as #27, grid size 128,128,128, pixel 1.4, shown
at level 0.00542, step 1, values float32
> hide #!25 models
> hide #!26 models
> hide #!27 models
> volume #24 level 0.009916
> volume #25 level 0.01243
> volume #25 level 0.008
> volume #26 level 0.008
> volume #26 level 0.01016
> volume #26 level 0.008
> volume #26 level 0.01145
> volume #25 level 0.01446
> volume #24 level 0.01726
> volume #24 level 0.02
> volume #25 level 0.02
> volume #26 level 0.02
> volume #23 level 0.02
> volume #27 level 0.02
> close #20-27
> close #1-8
> open /Users/bgreber/Downloads/cryosparc_P20_peptide_volume_mask.mrc
Opened cryosparc_P20_peptide_volume_mask.mrc as #1, grid size 128,128,128,
pixel 1.4, shown at level 0.5, step 1, values float32
> volume #1 level 1
> transparency 50 target s
> volume #1 level 1
> volume #1 level 0.5878
> volume #1 level 1
> open /Users/bgreber/Downloads/run_it012_class002.mrc
Opened run_it012_class002.mrc as #2, grid size 128,128,128, pixel 1.4, shown
at level 0.00448, step 1, values float32
> open /Users/bgreber/Downloads/run_it012_class001.mrc
Opened run_it012_class001.mrc as #3, grid size 128,128,128, pixel 1.4, shown
at level 0.00436, step 1, values float32
> hide #!1 models
> volume #2 level 0.01228
> volume #3 level 0.01174
> volume #2 level 0.01
> volume #3 level 0.01
> open /Users/bgreber/Downloads/run_it018_class002.mrc
Opened run_it018_class002.mrc as #4, grid size 128,128,128, pixel 1.4, shown
at level 0.00438, step 1, values float32
> open /Users/bgreber/Downloads/run_it018_class001.mrc
Opened run_it018_class001.mrc as #5, grid size 128,128,128, pixel 1.4, shown
at level 0.00445, step 1, values float32
> volume #4 level 0.01096
> volume #5 level 0.01182
> close #2-5
> close #15-19
> close #9
> open /Users/bgreber/Downloads/run_it010_class002.mrc
Opened run_it010_class002.mrc as #2, grid size 128,128,128, pixel 1.4, shown
at level 0.00445, step 1, values float32
> open /Users/bgreber/Downloads/run_it010_class001.mrc
Opened run_it010_class001.mrc as #3, grid size 128,128,128, pixel 1.4, shown
at level 0.00436, step 1, values float32
> volume #3 level 0.01212
> volume #2 level 0.01127
> volume #2 level 0.01
> volume #3 level 0.01
> close #2
> close #3
> open /Users/bgreber/Downloads/run_it010_class002.mrc
Opened run_it010_class002.mrc as #2, grid size 128,128,128, pixel 1.4, shown
at level 4.93e-08, step 1, values float32
> open /Users/bgreber/Downloads/run_it010_class001.mrc
Opened run_it010_class001.mrc as #3, grid size 128,128,128, pixel 1.4, shown
at level 6.47e-06, step 1, values float32
> volume #3 level 0.006134
> volume #2 level 0.005943
> volume #2 level 0.01
> volume #3 level 0.01
> transparency 50 target s
> open /Users/bgreber/Downloads/run_it015_class001.mrc
Opened run_it015_class001.mrc as #4, grid size 128,128,128, pixel 1.4, shown
at level 8.88e-07, step 1, values float32
> open /Users/bgreber/Downloads/run_it015_class002.mrc
Opened run_it015_class002.mrc as #5, grid size 128,128,128, pixel 1.4, shown
at level 8.31e-06, step 1, values float32
> volume #4 level 0.007059
> volume #5 level 0.009763
> volume #4 level 0.01
> volume #5 level 0.01
> volume #5 level 0.007561
> volume #4 level 0.076
> volume #4 level 0.0076
> volume #5 level 0.02
> volume #4 level 0.02
> open /Users/bgreber/Downloads/run_it023_class001.mrc
Opened run_it023_class001.mrc as #6, grid size 128,128,128, pixel 1.4, shown
at level 1.09e-05, step 1, values float32
> open /Users/bgreber/Downloads/run_it023_class002.mrc
Opened run_it023_class002.mrc as #7, grid size 128,128,128, pixel 1.4, shown
at level 1.26e-06, step 1, values float32
> volume #6 level 0.003187
> volume #7 level 0.00503
> hide #!4 models
> hide #!5 models
> volume #7 level 0.02
> volume #6 level 0.02
> volume #6 level 0.01
> volume #7 level 0.01
> transparency 50 target s
> volume #7 level 0.007276
> show #!13 models
> hide #11 models
> hide #10 models
> hide #!13 models
> show #11 models
> transparency 0 target s
> volume #7 level 0.001
> volume #7 level 0.01
> volume #7 level 0.007
> volume #6 level 0.007
> transparency 50 target s
> open /Users/bgreber/Downloads/run_it025_class001.mrc
Opened run_it025_class001.mrc as #8, grid size 128,128,128, pixel 1.4, shown
at level 1.07e-05, step 1, values float32
> open /Users/bgreber/Downloads/run_it025_class002.mrc
Opened run_it025_class002.mrc as #9, grid size 128,128,128, pixel 1.4, shown
at level 1.44e-06, step 1, values float32
> volume #8 level 0.006926
> volume #9 level 0.006582
> volume #8 level 0.007
> volume #9 level 0.007
> volume #8 level 0.02
> volume #9 level 0.02
> volume #8 level 0.009831
> volume #9 level 0.00666
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
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/bgreber/Downloads/run_it025_class002.mrc
Opened run_it025_class002.mrc as #1, grid size 128,128,128, pixel 1.4, shown
at level 7.54e-06, step 1, values float32
> open /Users/bgreber/Downloads/run_it025_class001.mrc
Opened run_it025_class001.mrc as #2, grid size 128,128,128, pixel 1.4, shown
at level 2.63e-06, step 1, values float32
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1
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 Air
Model Identifier: MacBookAir10,1
Model Number: Z1250001QB/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 6 days, 19 hours, 29 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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
Change History (1)
comment:1 by , 9 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Platform: | → all |
| Project: | → ChimeraX |
| Resolution: | → duplicate |
| Status: | new → closed |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
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