![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 weeks ago
Closed 5 weeks ago
#19032 closed defect (duplicate)
mshMIGPerform crash in NSAccessiblity native Mac APIs
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Platform | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.4.1-x86_64-i386-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000700019e12000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007ff85b949bc0 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, psutil._psutil_osx, psutil._psutil_posix, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imaging, PIL._imagingmath, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio (total: 48)
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{
"uptime" : 370000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,1",
"coalitionID" : 7477,
"osVersion" : {
"train" : "macOS 15.4.1",
"build" : "24E263",
"releaseType" : "User"
},
"captureTime" : "2025-10-05 10:53:00.6886 +0900",
"codeSigningMonitor" : 0,
"incident" : "83D696AA-E5B9-4AC7-AA7B-E04ED47E7D58",
"pid" : 38357,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-10-05 10:51:12.9433 +0900",
"procStartAbsTime" : 373538818663542,
"procExitAbsTime" : 373646502525973,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"EB99F02C-3C59-5C4E-A06B-8BF23C5A4B7E","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "4E3F2DAB-5637-A48C-C338-81835BD62874",
"lowPowerMode" : 1,
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["siriAssetIsNotReady","unableToFetchAvailability","notOptedIn","deviceNotCapable"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"bootSessionUUID" : "D6A95589-1F0F-4B6C-8C74-7550F565EEA9",
"wakeTime" : 1744,
"bridgeVersion" : {"build":"22P4248","train":"9.4"},
"sleepWakeUUID" : "D12F4320-D8F8-40EF-A3F8-FFC99FB688B9",
"sip" : "enabled",
"vmRegionInfo" : "0x10000001e is not in any region. Bytes before following region: 64688098\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 103db1000-103db5000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x000000010000001e","rawCodes":[1,4294967326],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000010000001e"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":38357},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x10000001e is not in any region. Bytes before following region: 64688098\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 103db1000-103db5000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
"threads" : 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"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703562420224,
"size" : 560296,
"uuid" : "8fc0db40-599b-3cd2-991c-1faf1534c667",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703564087296,
"size" : 38264,
"uuid" : "581c60e7-fabf-3017-9cde-23cf85d2a0c4",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703625052160,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 22352472,
"uuid" : "a6b6d3fd-bba9-37b7-909e-e88dbdce2050",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2575.50.27"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703676252160,
"CFBundleShortVersionString" : "1.22",
"CFBundleIdentifier" : "com.apple.HIServices",
"size" : 416491,
"uuid" : "73f69def-ca31-3ed6-929c-5c64e4af02a3",
"path" : "\/System\/Library\/Frameworks\/ApplicationServices.framework\/Versions\/A\/Frameworks\/HIServices.framework\/Versions\/A\/HIServices",
"name" : "HIServices"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 140703564316672,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 4935651,
"uuid" : "52038a90-4140-3132-93c2-e08624a409af",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "3423"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703759278080,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3020526,
"uuid" : "c65d0254-38e8-3d84-89ed-a8b8504c6f57",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703560024064,
"size" : 631872,
"uuid" : "d90f985a-73b7-32a6-9f7a-a79a936bf75f",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703581687808,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 14746924,
"uuid" : "4f701cf3-5228-3b3e-b455-aa7b137f76e7",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "3423"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703623802880,
"CFBundleShortVersionString" : "2.0.2",
"CFBundleIdentifier" : "com.apple.framework.IOKit",
"size" : 807247,
"uuid" : "307a165d-ced6-34cc-8149-b93421112905",
"path" : "\/System\/Library\/Frameworks\/IOKit.framework\/Versions\/A\/IOKit",
"name" : "IOKit"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703752183808,
"CFBundleShortVersionString" : "485",
"CFBundleIdentifier" : "com.apple.IOAccelerator",
"size" : 36064,
"uuid" : "5b8943b0-5a1a-36db-8509-5e011ab62d04",
"path" : "\/System\/Library\/PrivateFrameworks\/IOAccelerator.framework\/Versions\/A\/IOAccelerator",
"name" : "IOAccelerator",
"CFBundleVersion" : "485"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703752220672,
"CFBundleShortVersionString" : "368.11.4",
"CFBundleIdentifier" : "com.apple.Metal",
"size" : 2632177,
"uuid" : "d175c5c1-c05c-35f7-85c1-6b5fd751d11e",
"path" : "\/System\/Library\/Frameworks\/Metal.framework\/Versions\/A\/Metal",
"name" : "Metal",
"CFBundleVersion" : "368.11.4"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 140716547297280,
"CFBundleShortVersionString" : "7.0.3",
"CFBundleIdentifier" : "com.apple.AMDMTLBronzeDriver",
"size" : 2410356,
"uuid" : "c580590c-8625-379c-8f68-e60fec68a6a8",
"path" : "\/System\/Library\/Extensions\/AMDMTLBronzeDriver.bundle\/Contents\/MacOS\/AMDMTLBronzeDriver",
"name" : "AMDMTLBronzeDriver",
"CFBundleVersion" : "7.0.0"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703562113024,
"size" : 291450,
"uuid" : "322735be-882c-3d00-8533-022051e5ed63",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
}
],
"sharedCache" : {
"base" : 140703531814912,
"size" : 30064771072,
"uuid" : "5182416c-b0ce-39a0-8348-5b0b287e48c6"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=1.6G written=140K(0%) resident=0K(0%) swapped_out=140K(0%) unallocated=1.6G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 48K 5 \nColorSync 260K 32 \nCoreAnimation 436K 48 \nCoreGraphics 12K 2 \nCoreUI image data 3408K 25 \nFoundation 16K 1 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 1.1G 605 \nMALLOC guard page 48K 12 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 140K 35 \nStack 213.8M 36 \nStack Guard 56.0M 1 \nVM_ALLOCATE 169.7M 257 \nVM_ALLOCATE (reserved) 96.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 44.4M 1087 \n__DATA_CONST 122.4M 1024 \n__DATA_DIRTY 2594K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 191.7M 138 \n__OBJC_RO 61.2M 1 \n__OBJC_RW 2391K 2 \n__TEXT 1.4G 1102 \n__TPRO_CONST 16 2 \ndyld private memory 1192K 12 \nmapped file 254.7M 56 \nshared memory 3004K 29 \n=========== ======= ======= \nTOTAL 3.7G 4871 \nTOTAL, minus reserved VM space 3.6G 4871 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "004dcdc55d9fa6b61781ff8fdfb4064d931cf1d8",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "63f9578e238e7b23a1f3030a",
"factorPackIds" : {
},
"deploymentId" : 240000005
},
{
"rolloutId" : "661464ecda55e5192b100804",
"factorPackIds" : {
},
"deploymentId" : 240000005
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/zhuyinan/Desktop/20250916/job042/run_it025_class001.mrc
Opened run_it025_class001.mrc as #1, grid size 128,128,128, pixel 2.12, shown
at level 0.0472, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job042/run_it025_class002.mrc
Opened run_it025_class002.mrc as #2, grid size 128,128,128, pixel 2.12, shown
at level 0.0221, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job042/run_it025_class003.mrc
Opened run_it025_class003.mrc as #3, grid size 128,128,128, pixel 2.12, shown
at level 0.0193, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job042/run_it025_class004.mrc
Opened run_it025_class004.mrc as #4, grid size 128,128,128, pixel 2.12, shown
at level 0.031, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job042/run_it025_class005.mrc
Opened run_it025_class005.mrc as #5, grid size 128,128,128, pixel 2.12, shown
at level 0.0219, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job042/run_it025_class006.mrc
Opened run_it025_class006.mrc as #6, grid size 128,128,128, pixel 2.12, shown
at level 0.0333, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job043/run_it025_class001.mrc
Opened run_it025_class001.mrc as #7, grid size 128,128,128, pixel 2.12, shown
at level 0.0344, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job043/run_it025_class002.mrc
Opened run_it025_class002.mrc as #8, grid size 128,128,128, pixel 2.12, shown
at level 0.029, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job043/run_it025_class003.mrc
Opened run_it025_class003.mrc as #9, grid size 128,128,128, pixel 2.12, shown
at level 0.0482, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job043/run_it025_class004.mrc
Opened run_it025_class004.mrc as #10, grid size 128,128,128, pixel 2.12, shown
at level 0.0195, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job043/run_it025_class005.mrc
Opened run_it025_class005.mrc as #11, grid size 128,128,128, pixel 2.12, shown
at level 0.0291, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job043/run_it025_class006.mrc
Opened run_it025_class006.mrc as #12, grid size 128,128,128, pixel 2.12, shown
at level 0.0199, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job044/run_it025_class001.mrc
Opened run_it025_class001.mrc as #13, grid size 128,128,128, pixel 2.12, shown
at level 0.0232, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job044/run_it025_class002.mrc
Opened run_it025_class002.mrc as #14, grid size 128,128,128, pixel 2.12, shown
at level 0.0494, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job044/run_it025_class003.mrc
Opened run_it025_class003.mrc as #15, grid size 128,128,128, pixel 2.12, shown
at level 0.0207, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job044/run_it025_class004.mrc
Opened run_it025_class004.mrc as #16, grid size 128,128,128, pixel 2.12, shown
at level 0.0324, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job044/run_it025_class005.mrc
Opened run_it025_class005.mrc as #17, grid size 128,128,128, pixel 2.12, shown
at level 0.0313, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job044/run_it025_class006.mrc
Opened run_it025_class006.mrc as #18, grid size 128,128,128, pixel 2.12, shown
at level 0.0189, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job045/run_it025_class001.mrc
Opened run_it025_class001.mrc as #19, grid size 128,128,128, pixel 2.12, shown
at level 0.0533, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job045/run_it025_class002.mrc
Opened run_it025_class002.mrc as #20, grid size 128,128,128, pixel 2.12, shown
at level 0.0258, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job045/run_it025_class003.mrc
Opened run_it025_class003.mrc as #21, grid size 128,128,128, pixel 2.12, shown
at level 0.0314, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job045/run_it025_class004.mrc
Opened run_it025_class004.mrc as #22, grid size 128,128,128, pixel 2.12, shown
at level 0.0232, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job045/run_it025_class005.mrc
Opened run_it025_class005.mrc as #23, grid size 128,128,128, pixel 2.12, shown
at level 0.0168, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job045/run_it025_class006.mrc
Opened run_it025_class006.mrc as #24, grid size 128,128,128, pixel 2.12, shown
at level 0.0369, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job046/run_it025_class001.mrc
Opened run_it025_class001.mrc as #25, grid size 128,128,128, pixel 2.12, shown
at level 0.0306, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job046/run_it025_class002.mrc
Opened run_it025_class002.mrc as #26, grid size 128,128,128, pixel 2.12, shown
at level 0.031, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job046/run_it025_class003.mrc
Opened run_it025_class003.mrc as #27, grid size 128,128,128, pixel 2.12, shown
at level 0.0191, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job046/run_it025_class004.mrc
Opened run_it025_class004.mrc as #28, grid size 128,128,128, pixel 2.12, shown
at level 0.0211, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job046/run_it025_class005.mrc
Opened run_it025_class005.mrc as #29, grid size 128,128,128, pixel 2.12, shown
at level 0.0464, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job046/run_it025_class006.mrc
Opened run_it025_class006.mrc as #30, grid size 128,128,128, pixel 2.12, shown
at level 0.0356, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job047/run_it025_class001.mrc
Opened run_it025_class001.mrc as #31, grid size 128,128,128, pixel 2.12, shown
at level 0.046, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job047/run_it025_class002.mrc
Opened run_it025_class002.mrc as #32, grid size 128,128,128, pixel 2.12, shown
at level 0.0161, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job047/run_it025_class003.mrc
Opened run_it025_class003.mrc as #33, grid size 128,128,128, pixel 2.12, shown
at level 0.025, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job047/run_it025_class004.mrc
Opened run_it025_class004.mrc as #34, grid size 128,128,128, pixel 2.12, shown
at level 0.0313, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job047/run_it025_class005.mrc
Opened run_it025_class005.mrc as #35, grid size 128,128,128, pixel 2.12, shown
at level 0.0334, step 1, values float32
> open /Users/zhuyinan/Desktop/20250916/job047/run_it025_class006.mrc
Opened run_it025_class006.mrc as #36, grid size 128,128,128, pixel 2.12, shown
at level 0.0242, step 1, values float32
> open /Users/zhuyinan/Downloads/7TVE.cif
Summary of feedback from opening /Users/zhuyinan/Downloads/7TVE.cif
---
note | Fetching CCD ATP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ATP/ATP.cif
7TVE.cif title:
ATP and DNA bound SMC5/6 core complex [more info...]
Chain information for 7TVE.cif #37
---
Chain | Description | UniProt
A | DNA (68-MER) |
B | DNA (78-MER) |
C | Non-structural maintenance of chromosomes element 1 | A0A7I9FFW3_YEASX 1-336
D | Structural maintenance of chromosomes protein 6 | SMC6_YEAST 1-1114
E | Structural maintenance of chromosomes protein 5 | SMC5_YEAST 1-1093
F | Non-structural maintenance of chromosome element 3 | NSE3_YEAST 1-303
G | Non-structural maintenance of chromosome element 4 | NSE4_YEAST 1-402
Non-standard residues in 7TVE.cif #37
---
ATP — adenosine-5'-triphosphate
> tile
37 models tiled
> select add #36
2 models selected
> select subtract #36
Nothing selected
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-7.0.3
OpenGL renderer: AMD Radeon Pro 555X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.2 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 9 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2075.101.2.0.0 (iBridge: 22.16.14248.0.0,0)
OS Loader Version: 583~900
Software:
System Software Overview:
System Version: macOS 15.4.1 (24E263)
Kernel Version: Darwin 24.4.0
Time since boot: 17 days, 19 hours, 38 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Radeon Pro 555X:
Chipset Model: Radeon Pro 555X
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00e3
ROM Revision: 113-C980AL-075
VBIOS Version: 113-C97501P-005
EFI Driver Version: 01.A1.075
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 5 weeks ago
| Component: | Unassigned → Platform |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → mshMIGPerform crash in NSAccessiblity native Mac APIs |
comment:2 by , 5 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #18238