![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 weeks ago
Closed 4 weeks ago
#18815 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| 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-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000000315a67000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000314a5b000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000313a4f000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000312a43000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000311a37000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000310a2b000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030fa1f000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030ea13000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030da07000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030c9fb000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030b9ef000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000002009020c0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, 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, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.graphics._graphics (total: 49)
{"app_name":"ChimeraX","timestamp":"2025-09-18 14:48:32.00 +0200","app_version":"1.8.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.6.1 (24G90)","roots_installed":0,"name":"ChimeraX","incident_id":"CD466744-8B4B-4D28-B5B8-79B222F3F8C7"}
{
"uptime" : 320000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 38690,
"osVersion" : {
"train" : "macOS 15.6.1",
"build" : "24G90",
"releaseType" : "User"
},
"captureTime" : "2025-09-18 14:48:23.2295 +0200",
"codeSigningMonitor" : 1,
"incident" : "CD466744-8B4B-4D28-B5B8-79B222F3F8C7",
"pid" : 93187,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-09-18 10:53:43.8096 +0200",
"procStartAbsTime" : 7604542938598,
"procExitAbsTime" : 7792712072039,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"C8D5DC0B-60ED-55CE-BACE-10C1ABEF1693","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "A032151A-3102-DB1C-CE1A-78095CA33466",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "F60DD3ED-E170-4295-B791-EB2844EFB877",
"wakeTime" : 933,
"sleepWakeUUID" : "997E40FC-801A-4A69-8C7F-BB52CF833485",
"sip" : "enabled",
"vmRegionInfo" : "0xad400068c3b is not in any region. Bytes after previous region: 11424613436476 Bytes before following region: 93647466492869\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00068ad400068c3b","rawCodes":[1,1841492998392891],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00068ad400068c3b -> 0x00000ad400068c3b (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":93187},
"vmregioninfo" : "0xad400068c3b is not in any region. Bytes after previous region: 11424613436476 Bytes before following region: 93647466492869\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"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" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":5234850456},{"value":99},{"value":95},{"value":5173420544},{"value":9223372042073756168},{"value":9138894542171563766},{"value":9138894533574280758},{"value":14757395258967641293},{"value":4294967286},{"value":5234850386},{"value":0},{"value":52},{"value":4294967280},{"value":328},{"value":8616514904},{"value":0},{"value":11},{"value":259},{"value":8599380384,"symbolLocation":224,"symbol":"_main_thread"},{"value":0},{"value":1},{"value":4362946096,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8560545792,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTouchBarInputMethodCandidateList._list"},{"value":8560545792,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTouchBarInputMethodCandidateList._list"},{"value":5},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6754334860},"cpsr":{"value":1073745920},"fp":{"value":5234850528},"sp":{"value":5234850496},"esr":{"value":1442840704,"description":" 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"name" : "libqjpeg.dylib"
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{
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqtiff.dylib",
"name" : "libqtiff.dylib"
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{
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"uuid" : "77608453-0c22-327c-909a-3e61997f035f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqsvg.dylib",
"name" : "libqsvg.dylib"
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{
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtSvg.framework\/Versions\/A\/QtSvg",
"name" : "QtSvg"
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{
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"uuid" : "2170e2a2-3e24-3e7d-889f-70bfe1445514",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqpdf.dylib",
"name" : "libqpdf.dylib"
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{
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"size" : 8011776,
"uuid" : "2297c440-bc47-3988-b508-c4f43a12de4c",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtPdf.framework\/Versions\/A\/QtPdf",
"name" : "QtPdf"
},
{
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"name" : "libqicns.dylib"
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{
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"uuid" : "97f0c601-577c-3e3d-9728-1b67a04a846f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqtga.dylib",
"name" : "libqtga.dylib"
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{
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"uuid" : "73065b31-2315-3d94-8ece-5a8b66a743b4",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqmacjp2.dylib",
"name" : "libqmacjp2.dylib"
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{
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"uuid" : "117d4c42-f31b-3051-a57f-edb1c3f20c84",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/core\/_mac_util.cpython-311-darwin.so",
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"uuid" : "c37482c0-7aab-3517-b3ef-3bd2294eab02",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_multiprocessing.cpython-311-darwin.so",
"name" : "_multiprocessing.cpython-311-darwin.so"
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{
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_posixshmem.cpython-311-darwin.so",
"name" : "_posixshmem.cpython-311-darwin.so"
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{
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"arch" : "arm64",
"base" : 5747785728,
"size" : 81920,
"uuid" : "703104dc-b212-3b8d-9c78-4f57b3c9cb18",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/numpy_formathandler.cpython-311-darwin.so",
"name" : "numpy_formathandler.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/nones_formathandler.cpython-311-darwin.so",
"name" : "nones_formathandler.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_osx.abi3.so",
"name" : "_psutil_osx.abi3.so"
},
{
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so",
"name" : "_imagingmath.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
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"queue" : "com.apple.main-thread"
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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
> artiax start
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/NPC_Spombe_Markus/npc_motl_analysis_output/IR_elliptical_rings/motl_M7_rf58_1_rings_per13n30_bin4_1.em
> format motl
Summary of feedback from opening
/Users/eunyoung/Dropbox/BeckLab/NPCinPombe/NPC_Spombe_Markus/npc_motl_analysis_output/IR_elliptical_rings/motl_M7_rf58_1_rings_per13n30_bin4_1.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list motl_M7_rf58_1_rings_per13n30_bin4_1.em with 308
particles.
> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/NPC_Spombe_Markus/npc_motl_analysis_output/IR_elliptical_centers/motl_M7_rf58_1_centers_per13n30_bin4_1_gamma_min_orientation_1.em
> format motl
Summary of feedback from opening
/Users/eunyoung/Dropbox/BeckLab/NPCinPombe/NPC_Spombe_Markus/npc_motl_analysis_output/IR_elliptical_centers/motl_M7_rf58_1_centers_per13n30_bin4_1_gamma_min_orientation_1.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list
motl_M7_rf58_1_centers_per13n30_bin4_1_gamma_min_orientation_1.em with 53
particles.
> artiax hide axes
> hide #!1.2.2 models
> hide #!1.2.1 models
> show #!1.2.1 models
> show #!1.2.2 models
> hide #!1.2.1 models
> show #!1.2.1 models
> open /Users/eunyoung/Downloads/M7_rf54_bin8_30_symmetrized.em
Opened M7_rf54_bin8_30_symmetrized.em as #2, grid size 104,104,104, pixel 1,
shown at level 0.107, step 1, values float32
> artiax attach #2 toParticleList #1.2.2
Opened M7_rf54_bin8_30_symmetrized.em as #1.2.2.1.1, grid size 104,104,104,
pixel 1, shown at level 0.107, step 1, values float32
> volume #1.2.2.1.1 capFaces false
> artiax show #1.2.2 surfaces
> artiax particles #1.2.2 surfaceLevel -0.12246
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> artiax particles #1.2.2 surfaceLevel -0.30686
> open /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/motl_M6_rf37_1.em
Opened motl_M6_rf37_1.em as #2, grid size 20,710,1, pixel 1, shown at step 1,
values float32
> artiax attach #2 toParticleList #1.2.1
Opened motl_M6_rf37_1.em as #1.2.1.1.1, grid size 20,710,1, pixel 1, shown at
level 1.33e+03, step 1, values float32
> volume #1.2.1.1.1 capFaces false
> artiax show #1.2.1 surfaces
> open /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/motl_M6_rf37_1.em
Opened motl_M6_rf37_1.em as #2, grid size 20,710,1, pixel 1, shown at step 1,
values float32
> artiax attach #2 toParticleList #1.2.1
Opened motl_M6_rf37_1.em as #1.2.1.1.1, grid size 20,710,1, pixel 1, shown at
level 1.33e+03, step 1, values float32
> volume #1.2.1.1.1 capFaces false
> artiax show #1.2.1 surfaces
> artiax particles #1.2.1 surfaceLevel 507.8736
> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/M7_rf4_IR_bin4_17.em
Opened M7_rf4_IR_bin4_17.em as #2, grid size 120,120,120, pixel 1, shown at
level 0.0905, step 1, values float32
> artiax attach #2 toParticleList #1.2.1
Opened M7_rf4_IR_bin4_17.em as #1.2.1.1.1, grid size 120,120,120, pixel 1,
shown at level 0.0905, step 1, values float32
> volume #1.2.1.1.1 capFaces false
> artiax show #1.2.1 surfaces
> artiax particles #1.2.1 surfaceLevel -0.13545
> lighting soft
> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/M7_rf18_bin4_20_symmetrized.em
Opened M7_rf18_bin4_20_symmetrized.em as #2, grid size 180,180,180, pixel 1,
shown at level 0.0656, step 1, values float32
> artiax attach #2 toParticleList #1.2.2
Opened M7_rf18_bin4_20_symmetrized.em as #1.2.2.1.1, grid size 180,180,180,
pixel 1, shown at level 0.0656, step 1, values float32
> volume #1.2.2.1.1 capFaces false
> artiax show #1.2.2 surfaces
> hide #!1.2.1 models
> artiax particles #1.2.2 surfaceLevel -0.09289
> artiax particles #1.2.2 color 37,95,95,100
> artiax particles #1.2.2 surfaceLevel -0.08607
> show #!1.2.1 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/M7_rf56_bin4_17.em
Opened M7_rf56_bin4_17.em as #2, grid size 120,120,120, pixel 1, shown at
level 0.104, step 1, values float32
> artiax attach #2 toParticleList #1.2.2
Opened M7_rf56_bin4_17.em as #1.2.2.1.1, grid size 120,120,120, pixel 1, shown
at level 0.104, step 1, values float32
> volume #1.2.2.1.1 capFaces false
> artiax show #1.2.2 surfaces
> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/M7_rf18_bin4_20_symmetrized.em
Opened M7_rf18_bin4_20_symmetrized.em as #2, grid size 180,180,180, pixel 1,
shown at level 0.0656, step 1, values float32
> artiax attach #2 toParticleList #1.2.2
Opened M7_rf18_bin4_20_symmetrized.em as #1.2.2.1.1, grid size 180,180,180,
pixel 1, shown at level 0.0656, step 1, values float32
> volume #1.2.2.1.1 capFaces false
> artiax show #1.2.2 surfaces
> artiax particles #1.2.2 surfaceLevel -0.10652
> show #!1.2.2 models
> hide #!1.2.1 models
> artiax particles #1.2.2 surfaceLevel -0.0779
> show #!1.2.1 models
> hide #!1.2.2 models
> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/M7_rf56_bin4_17.em
Opened M7_rf56_bin4_17.em as #2, grid size 120,120,120, pixel 1, shown at
level 0.104, step 1, values float32
> artiax attach #2 toParticleList #1.2.1
Opened M7_rf56_bin4_17.em as #1.2.1.1.1, grid size 120,120,120, pixel 1, shown
at level 0.104, step 1, values float32
> volume #1.2.1.1.1 capFaces false
> artiax show #1.2.1 surfaces
> artiax particles #1.2.1 surfaceLevel -0.13775
> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/M7_rf4_IR_bin4_17.em
Opened M7_rf4_IR_bin4_17.em as #2, grid size 120,120,120, pixel 1, shown at
level 0.0905, step 1, values float32
> artiax attach #2 toParticleList #1.2.1
Opened M7_rf4_IR_bin4_17.em as #1.2.1.1.1, grid size 120,120,120, pixel 1,
shown at level 0.0905, step 1, values float32
> volume #1.2.1.1.1 capFaces false
> artiax show #1.2.1 surfaces
> artiax particles #1.2.1 surfaceLevel -0.12073
> artiax particles #1.2.1 surfaceLevel -0.10969
> artiax particles #1.2.1 surfaceLevel -0.13545
> hide #1.1 models
> hide #!1 models
> hide #!1.2 models
> hide #1.3 models
> hide #!1.2.1 models
> show #!1.2.1 models
> save /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/test1.mrc
> models #1.2.1.1.1
> vop resample #1.2.1
volume resample must specify onGrid option or spacing option
> vop resample #1.2.1 onGrid #1.2
Opened M7_rf4_IR_bin4_17.em resampled as #2, grid size 120,120,120, pixel 1,
shown at step 1, values float32
Opened M7_rf4_IR_bin4_17.em resampled as #3, grid size 180,180,180, pixel 1,
shown at step 1, values float32
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> hide #!1.2.1 models
> hide #!1.2 models
> show #!2 models
> show #!3 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> view orient
> hide #!3 models
> show #!3 models
> show #1.3 models
> close #3
> close #2
> show #!1.2.2 models
> hide #!1.2.2 models
> volume combine #1.2.1 method sum
Expected a density maps specifier or a keyword
> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/M7_rf4_IR_bin4_17.em
Opened M7_rf4_IR_bin4_17.em as #2, grid size 120,120,120, pixel 1, shown at
level 0.0905, step 1, values float32
> close #2
> close #1.2.2.1.1
> close #1.2.1.1.1
> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/M7_rf4_IR_bin4_17.em
Opened M7_rf4_IR_bin4_17.em as #2, grid size 120,120,120, pixel 1, shown at
level 0.0905, step 1, values float32
> artiax attach #2 toParticleList #1.2.1
Opened M7_rf4_IR_bin4_17.em as #1.2.1.1.1, grid size 120,120,120, pixel 1,
shown at level 0.0905, step 1, values float32
> volume #1.2.1.1.1 capFaces false
> artiax particles #1.2.1 surfaceLevel -0.12441
> volume combine #2 method sum
Expected a density maps specifier or a keyword
> volume combine #1.2 method sum
Expected a density maps specifier or a keyword
> hide #!1.2.1 models
> volume #1.2.1.1.1 level -0.162
> view orient
> show #!1.2.1 models
> volume combine #1.2.1.1.1 method sum
Expected a density maps specifier or a keyword
> volume #1.2.1.1.1 level -0.09708
> volume combine #1.2.1 method sum
Expected a density maps specifier or a keyword
> export map
Unknown command: artiax export map
> volume copy #1.2.1.1.1 coordinateSystem #1.2.1
Expected a keyword
> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/M7_rf4_IR_bin4_17.em
Opened M7_rf4_IR_bin4_17.em as #2, grid size 120,120,120, pixel 1, shown at
level 0.0905, step 1, values float32
> volume copy #2 coordinateSystem #1.2.1
Expected a keyword
0.202">volume #4 level -0.202
> volume #4 color #aeafe7
> volume #4 level -0.2202
> volume #5 level -0.1815
> volume #4 level -0.2385
> volume #4 level -0.2124
> volume #18 level -0.1602
> volume #16 level -0.1474
> volume #16 level -0.1528
> volume #18 level -0.1459
> ui tool show "Map Coordinates"
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_1.em
Opened M7_rf720_bin4_1.em as #19, grid size 140,140,140, pixel 1, shown at
level 0.17, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_2.em
Opened M7_rf720_bin4_2.em as #20, grid size 140,140,140, pixel 1, shown at
level 0.174, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_3.em
Opened M7_rf720_bin4_3.em as #21, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_4.em
Opened M7_rf720_bin4_4.em as #22, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_5.em
Opened M7_rf720_bin4_5.em as #23, grid size 140,140,140, pixel 1, shown at
level 0.174, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_6.em
Opened M7_rf720_bin4_6.em as #24, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_7.em
Opened M7_rf720_bin4_7.em as #25, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_8.em
Opened M7_rf720_bin4_8.em as #26, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_9.em
Opened M7_rf720_bin4_9.em as #27, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_10.em
Opened M7_rf720_bin4_10.em as #28, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_11.em
Opened M7_rf720_bin4_11.em as #29, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32
> hide #!18 models
> hide #!18-29 target m
> volume capFaces false
> show #!19 models
> hide #!19 models
> volume #29 level -0.2036
> volume #29 level -0.2054
> volume #28 level -0.1904
> close #28
> volume #27 level -0.2042
> close #27
> close #26
> close #25
> close #24
> close #23
> close #22
> close #21
> close #20
> close #19
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_13.em
Opened M7_rf720_bin4_13.em as #19, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_15.em
Opened M7_rf720_bin4_15.em as #20, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_17.em
Opened M7_rf720_bin4_17.em as #21, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_19.em
Opened M7_rf720_bin4_19.em as #22, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_21.em
Opened M7_rf720_bin4_21.em as #23, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32
> volume capFaces false
> hide #!19-23 target m
> volume #23 level -0.1845
> surface dust #23 size 10
> volume #23 level -0.1623
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder724/M7_rf724_bin4_21.em
Opened M7_rf724_bin4_21.em as #24, grid size 140,140,140, pixel 1, shown at
level 0.189, step 1, values float32
> volume capFaces false
> volume #24 level -0.1711
> surface dust #24 size 10
> volume #24 level -0.1557
> volume #24 level -0.1711
> volume #23 level -0.1458
> volume #24 level -0.1557
> close #16-24,29
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder720/M7_rf720_bin4_21.em
Opened M7_rf720_bin4_21.em as #16, grid size 140,140,140, pixel 1, shown at
level 0.175, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder721/M7_rf721_bin4_21.em
Opened M7_rf721_bin4_21.em as #17, grid size 140,140,140, pixel 1, shown at
level 0.124, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder722/M7_rf722_bin4_21.em
Opened M7_rf722_bin4_21.em as #18, grid size 140,140,140, pixel 1, shown at
level 0.134, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder723/M7_rf723_bin4_21.em
Opened M7_rf723_bin4_21.em as #19, grid size 140,140,140, pixel 1, shown at
level 0.128, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder724/M7_rf724_bin4_21.em
Opened M7_rf724_bin4_21.em as #20, grid size 140,140,140, pixel 1, shown at
level 0.189, step 1, values float32
> volume capFaces false
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder725_new/M7_rf725_bin4_21.em
Opened M7_rf725_bin4_21.em as #21, grid size 140,140,140, pixel 1, shown at
level 0.191, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder726_new/M7_rf726_bin4_21.em
Opened M7_rf726_bin4_21.em as #22, grid size 140,140,140, pixel 1, shown at
level 0.134, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder727/M7_rf727_bin4_21.em
Opened M7_rf727_bin4_21.em as #23, grid size 140,140,140, pixel 1, shown at
level 0.159, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder728/M7_rf728_bin4_21.em
Opened M7_rf728_bin4_21.em as #24, grid size 140,140,140, pixel 1, shown at
level 0.141, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder729/M7_rf729_bin4_21.em
Opened M7_rf729_bin4_21.em as #25, grid size 140,140,140, pixel 1, shown at
level 0.204, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder730/M7_rf730_bin4_21.em
Opened M7_rf730_bin4_21.em as #26, grid size 140,140,140, pixel 1, shown at
level 0.188, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder731/M7_rf731_bin4_21.em
Opened M7_rf731_bin4_21.em as #27, grid size 140,140,140, pixel 1, shown at
level 0.124, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder732/M7_rf732_bin4_21.em
Opened M7_rf732_bin4_21.em as #28, grid size 140,140,140, pixel 1, shown at
level 0.141, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder733/M7_rf733_bin4_21.em
Opened M7_rf733_bin4_21.em as #29, grid size 140,140,140, pixel 1, shown at
level 0.129, step 1, values float32
> open /Volumes/NPC-
> Processing/M6/novaSTA_M6/tomsaSTA-M7/M7_run_folder734/M7_rf734_bin4_21.em
Opened M7_rf734_bin4_21.em as #30, grid size 140,140,140, pixel 1, shown at
level 0.198, step 1, values float32
> volume capFaces false
> surface dust #16 size 10
> surface dust #17 size 10
> surface dust #18 size 10
> surface dust #19 size 10
> surface dust #20 size 10
> surface dust #21 size 10
> surface dust #22 size 10
> surface dust #23 size 10
> surface dust #24 size 10
> surface dust #25 size 10
> surface dust #26 size 10
> surface dust #27 size 10
> surface dust #28 size 10
> surface dust #29 size 10
> surface dust #30 size 10
> hide #!16-30 target m
> show #!30 models
> volume #30 level -0.146
> volume #28 level -0.1314
> volume #28 level -0.1153
> volume #26 level -0.1508
> volume #27 level -0.1317
> volume #29 level -0.1112
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> volume #25 level -0.1678
> volume #25 level -0.1339
> volume #24 level -0.0859
> volume #24 level -0.09677
> volume #24 color #9bd2d2
> volume #23 level -0.145
> volume #23 level -0.1203
> volume #23 color #dcdba5
> volume #22 level -0.09814
> volume #23 level -0.107
> volume #21 level -0.1549
> volume #21 color #89d589
> volume #21 level -0.1233
> volume #20 level -0.1309
> volume #20 level -0.1538
> volume #20 level -0.1481
> volume #20 level -0.1423
> volume #16 level -0.1328
> open /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/Chimerax/M7_Maps/test1.mrc
Opened test1.mrc as #31, grid size 120,120,120, pixel 1, shown at level
0.0905, step 1, values float32
> close #31
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/eunyoung/Dropbox/BeckLab/NPCinPombe/NPC_Spombe_Markus/npc_motl_analysis_output/IR_elliptical_rings/motl_M7_rf58_1_rings_per13n30_bin4_1.em
Opened motl_M7_rf58_1_rings_per13n30_bin4_1.em as #1, grid size 20,308,1,
pixel 1, shown at step 1, values float32
> volume #1
> volume #1 style image
> volume #1 colorMode opaque8 showOutlineBox true orthoplanes xyz
> positionPlanes 9,153,0 imageMode orthoplanes
> volume #1 colorMode auto8 imageMode "tilted slab" tiltedSlabAxis
> -0.2485,-0.002018,0.9686 tiltedSlabOffset -3.17
> volume #1 colorMode opaque8 imageMode "box faces"
> lighting soft
> ui tool show "Side View"
> view orient
> close #1
> toolshed show
Downloading bundle ChimeraX_ArtiaX-0.6.0-py3-none-any.whl
Installed ChimeraX-ArtiaX (0.6.0)
Downloading bundle ChimeraX_ArtiaX-0.6.0-py3-none-any.whl
Installed ChimeraX-ArtiaX (0.6.0)
Replacing data format 'Artiatomi Motivelist' as defined by ChimeraX-ArtiaX
with definition from ChimeraX-ArtiaX
Replacing data format 'Generic Particle List' as defined by ChimeraX-ArtiaX
with definition from ChimeraX-ArtiaX
Replacing data format 'Dynamo Table' as defined by ChimeraX-ArtiaX with
definition from ChimeraX-ArtiaX
Replacing data format 'RELION STAR file' as defined by ChimeraX-ArtiaX with
definition from ChimeraX-ArtiaX
Replacing data format 'RELION5 STAR file' as defined by ChimeraX-ArtiaX with
definition from ChimeraX-ArtiaX
Replacing data format 'cryoET Data Portal' as defined by ChimeraX-ArtiaX with
definition from ChimeraX-ArtiaX
Replacing data format 'Coords file' as defined by ChimeraX-ArtiaX with
definition from ChimeraX-ArtiaX
Replacing data format 'Copick Picks file' as defined by ChimeraX-ArtiaX with
definition from ChimeraX-ArtiaX
Replacing data format 'PEET mod/csv' as defined by ChimeraX-ArtiaX with
definition from ChimeraX-ArtiaX
Replacing data format 'ArtiaX geometric model' as defined by ChimeraX-ArtiaX
with definition from ChimeraX-ArtiaX
Overriding existing toolbar provider for toolbar provider 'Launch' in bundle
'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'Help' in bundle
'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'XY' in bundle
'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'XZ' in bundle
'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'YZ' in bundle
'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'Clip' in bundle
'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'Invert Contrast' in
bundle 'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'Invert Selection'
in bundle 'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'Sphere' in bundle
'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'Line' in bundle
'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'Surface' in bundle
'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'Boundary' in bundle
'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'Triangles From
Links' in bundle 'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'Triangulate' in
bundle 'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'Remove Selected' in
bundle 'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'Create Mask' in
bundle 'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'Volume to Geomodel'
in bundle 'ChimeraX-ArtiaX'
Overriding existing toolbar provider for toolbar provider 'Geomodel to Volume'
in bundle 'ChimeraX-ArtiaX'
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16S000PCD/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 14 days, 29 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
EV2795:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.2.2
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-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 4 weeks ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 4 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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