![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 13 months ago
Closed 13 months ago
#15981 closed defect (duplicate)
Crash on display change, Mac, Qt 6.6
| 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-14.6.1-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 0x0000000331c9b000 (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 0x0000000330c8f000 (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 0x000000032fc83000 (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 0x000000032ec77000 (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 0x000000032dc6b000 (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 0x000000032cc5f000 (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 0x000000032bc53000 (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 0x000000032ac47000 (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 0x0000000329c3b000 (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 0x000000031d23f000 (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 0x000000031c233000 (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 0x000000031b227000 (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 0x000000031a21b000 (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 0x0000000208034f40 (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.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.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 59)
{"app_name":"ChimeraX","timestamp":"2024-09-19 13:59:36.00 -0400","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":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.6.1 (23G93)","roots_installed":0,"name":"ChimeraX","incident_id":"20492BA3-4B1E-4A50-B7E6-4BF2E5E27B37"}
{
"uptime" : 310000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 1875666232,
"deployVersion" : 210,
"modelCode" : "Mac14,9",
"coalitionID" : 860,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2024-09-19 13:59:20.9898 -0400",
"codeSigningMonitor" : 1,
"incident" : "20492BA3-4B1E-4A50-B7E6-4BF2E5E27B37",
"pid" : 6436,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-09-09 10:03:47.6498 -0400",
"procStartAbsTime" : 2932332020,
"procExitAbsTime" : 7634775542228,
"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":"2E9AB1F0-01ED-5F30-A1D3-2C8A509CD1B1","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "4F584847-7AD6-5BCD-E501-A13CC9769292",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 13858,
"sleepWakeUUID" : "60E6BEA5-A4F2-4BC5-93CF-CFA861713858",
"sip" : "enabled",
"vmRegionInfo" : "0x48b1612a5ef8 is not in any region. Bytes after previous region: 79445640240889 Bytes before following region: 25626439688456\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, 0x0000c8b1612a5ef8","rawCodes":[1,220664164933368],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000c8b1612a5ef8 -> 0x000048b1612a5ef8 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":6436},
"vmregioninfo" : "0x48b1612a5ef8 is not in any region. Bytes after previous region: 79445640240889 Bytes before following region: 25626439688456\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":0},{"value":1701147252},{"value":1701147252},{"value":4611791571575020640},{"value":1},{"value":17543101884729694993},{"value":17543101876274189393},{"value":14757395258967641293},{"value":4294967286},{"value":5100829266},{"value":0},{"value":53},{"value":4294967280},{"value":328},{"value":8899486952},{"value":0},{"value":11},{"value":8724369216,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8724369440,"symbolLocation":224,"symbol":"_main_thread"},{"value":1},{"value":4361831984,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8729944064,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSCGSStatusItem._selectedContentFrame"},{"value":8729944064,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSCGSStatusItem._selectedContentFrame"},{"value":6},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6981311520},"cpsr":{"value":1073745920},"fp":{"value":5100829408},"sp":{"value":5100829376},"esr":{"value":1442840704,"description":" 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_postWindowDidChangeBackingPropertiesAndDisplayWindowForPreviousBackingScaleFactor:previousColorSpace:]","symbolLocation":192,"imageIndex":161},{"imageOffset":2095464,"symbol":"__67-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]_block_invoke","symbolLocation":448,"imageIndex":161},{"imageOffset":510204,"symbol":"NSPerformVisuallyAtomicChange","symbolLocation":108,"imageIndex":161},{"imageOffset":2095004,"symbol":"-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]","symbolLocation":96,"imageIndex":161},{"imageOffset":515532,"symbol":"-[NSWindow _setFrameCommon:display:fromServer:]","symbolLocation":1856,"imageIndex":161},{"imageOffset":11494832,"symbol":"-[NSWindow _windowMovedToRect:dueToMoveEvent:]","symbolLocation":184,"imageIndex":161},{"imageOffset":1469360,"symbol":"-[NSWindow _windowMoved:]","symbolLocation":832,"imageIndex":161},{"imageOffset":1468452,"symbol":"-[NSWindow _internalHandleAppKitDefinedEvent:]","symbolLocation":152,"imageIndex":161},{"imageOffset":1468140,"symbol":"-[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:]","symbolLocation":776,"imageIndex":161},{"imageOffset":1466896,"symbol":"-[NSWindow(NSEventRouting) sendEvent:]","symbolLocation":284,"imageIndex":161},{"imageOffset":416340,"imageIndex":87},{"imageOffset":8582580,"symbol":"-[NSApplication(NSEventRouting) sendEvent:]","symbolLocation":1800,"imageIndex":161},{"imageOffset":33392,"imageIndex":87},{"imageOffset":4705692,"symbol":"-[NSApplication _handleEvent:]","symbolLocation":60,"imageIndex":161},{"imageOffset":184352,"symbol":"-[NSApplication 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_object*)","symbolLocation":96,"imageIndex":105},{"imageOffset":1004504,"symbol":"cfunction_call","symbolLocation":96,"imageIndex":155},{"imageOffset":594156,"symbol":"_PyObject_MakeTpCall","symbolLocation":128,"imageIndex":155},{"imageOffset":1789244,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":54984,"imageIndex":155},{"imageOffset":1729512,"symbol":"PyEval_EvalCode","symbolLocation":276,"imageIndex":155},{"imageOffset":1707120,"symbol":"builtin_exec","symbolLocation":428,"imageIndex":155},{"imageOffset":1007044,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS","symbolLocation":80,"imageIndex":155},{"imageOffset":1788292,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":54032,"imageIndex":155},{"imageOffset":1811404,"symbol":"_PyEval_Vector","symbolLocation":156,"imageIndex":155},{"imageOffset":2389028,"symbol":"pymain_run_module","symbolLocation":256,"imageIndex":155},{"imageOffset":2387652,"symbol":"Py_RunMain","symbolLocation":1784,"imageIndex":155},{"imageOffset":2392180,"symbol":"pymain_main","symbolLocation":52,"imageIndex":155},{"imageOffset":2392116,"symbol":"Py_Main","symbolLocation":36,"imageIndex":155},{"imageOffset":15700,"symbol":"main","symbolLocation":128,"imageIndex":156},{"imageOffset":24916,"symbol":"start","symbolLocation":2476,"imageIndex":162}]},{"id":46180,"name":"ThreadPoolServiceThread","threadState":{"x":[{"value":4},{"value":0},{"value":0},{"value":105553158803392},{"value":4},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":3},{"value":25288767444738},{"value":13563349664},{"value":63747},{"value":1},{"value":1},{"value":369},{"value":13038071808},{"value":0},{"value":6152500984},{"value":6146775616},{"value":0},{"value":13038071120},{"value":12297829382473034411},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":13456693688},"cpsr":{"value":2684358656},"fp":{"value":13038071104},"sp":{"value":13038071040},"esr":{"value":1442840704,"description":" Address size 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"name" : "_posixsubprocess.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4344987648,
"size" : 16384,
"uuid" : "9e9f3dfb-1383-3420-bfcf-d996842d8e9e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/fcntl.cpython-311-darwin.so",
"name" : "fcntl.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4344872960,
"size" : 32768,
"uuid" : "167d8231-8346-37b6-9d67-149a1fe3df21",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_struct.cpython-311-darwin.so",
"name" : "_struct.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4344774656,
"size" : 32768,
"uuid" : "c4b2ad90-cc7d-3780-bee9-9f1dbc2aa560",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/binascii.cpython-311-darwin.so",
"name" : "binascii.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4344692736,
"size" : 16384,
"uuid" : "487467f0-5417-397f-8fb9-43ce116abec8",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_sha512.cpython-311-darwin.so",
"name" : "_sha512.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4342906880,
"size" : 16384,
"uuid" : "1eab426b-5d06-3a22-b7b5-6dbc112704d6",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_random.cpython-311-darwin.so",
"name" : "_random.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4342824960,
"size" : 16384,
"uuid" : "a97f3cfd-a5a7-3ce2-9eb6-5ebc0943bd1d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_bisect.cpython-311-darwin.so",
"name" : "_bisect.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4347396096,
"size" : 196608,
"uuid" : "a4b86716-73ef-3046-b7ee-1d069dfd7cd0",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_lzma.cpython-311-darwin.so",
"name" : "_lzma.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4342743040,
"size" : 16384,
"uuid" : "dc7a591b-ef8a-3b77-9396-ecee27303fdb",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_bz2.cpython-311-darwin.so",
"name" : "_bz2.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4342628352,
"size" : 32768,
"uuid" : "65172ede-2b95-337d-970f-ed6c4a217cb1",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/zlib.cpython-311-darwin.so",
"name" : "zlib.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4341137408,
"size" : 16384,
"uuid" : "39aa96c6-b691-3e20-9540-292b9dd1c861",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_typing.cpython-311-darwin.so",
"name" : "_typing.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4340957184,
"size" : 81920,
"uuid" : "3b2e1e73-f5e1-3fa3-80b3-e46009060893",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_datetime.cpython-311-darwin.so",
"name" : "_datetime.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4341219328,
"size" : 49152,
"uuid" : "51d31d0d-1dcc-31ad-b6c1-73d57e544a3a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/math.cpython-311-darwin.so",
"name" : "math.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4357554176,
"CFBundleShortVersionString" : "3.11.4, (c) 2001-2023 Python Software Foundation.",
"CFBundleIdentifier" : "org.python.python",
"size" : 3948544,
"uuid" : "88bffd37-99d8-36ab-9b95-9f54b30bd667",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python",
"name" : "Python",
"CFBundleVersion" : "3.11.4"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4338745344,
"CFBundleShortVersionString" : "1.8.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 16384,
"uuid" : "17982d98-65bc-3327-8526-577ec996453c",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.8.0.0"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6981042176,
"size" : 241660,
"uuid" : "71ff45b8-f14e-3666-9e96-6cf58315b91d",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6981283840,
"size" : 53248,
"uuid" : "e03e8478-6f5c-3d21-a79a-58408f514000",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6979829760,
"size" : 520184,
"uuid" : "d30f1830-93d0-3d0b-8cba-9544e84bfd5b",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6981492736,
"size" : 32744,
"uuid" : "b4bf9f89-31d7-3742-8ce7-ab3554f9f525",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
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"arch" : "arm64e",
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"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 20180992,
"uuid" : "7acbeef9-a453-3e4d-98ac-f9441d86e183",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2487.70.105"
},
{
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"size" : 562440,
"uuid" : "f635824e-318b-3f0c-842c-c369737f2b68",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
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"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
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"size" : 5083136,
"uuid" : "55720ee0-d8c3-33a1-9854-8e61a6f44895",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
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"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
}
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=3.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 272K 16 \nColorSync 656K 31 \nCoreAnimation 2528K 156 \nCoreGraphics 64K 4 \nCoreServices 624K 2 \nCoreUI image data 576K 9 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.6G 103 \nMALLOC guard page 192K 12 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 912K 57 \nStack 367.0M 58 \nStack Guard 56.0M 1 \nVM_ALLOCATE 250.8M 225 \nVM_ALLOCATE (reserved) 192.0M 3 reserved VM address space (unallocated)\n__AUTH 2199K 404 \n__AUTH_CONST 31.8M 622 \n__CTF 824 1 \n__DATA 22.1M 776 \n__DATA_CONST 42.5M 785 \n__DATA_DIRTY 2024K 232 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 555.4M 158 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2200K 1 \n__TEXT 941.1M 802 \ndyld private memory 592K 6 \nmapped file 530.0M 78 \nshared memory 3200K 26 \n=========== ======= ======= \nTOTAL 5.6G 4584 \nTOTAL, minus reserved VM space 5.4G 4584 \n",
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}
}
===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/sierkml/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/TAF/fold_2024_09_12_17_05_taf7_importin_alpha/fold_2024_09_12_17_05_taf7_importin_alpha_model_0.cif
> /Users/sierkml/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/TAF/fold_2024_09_12_17_05_taf7_importin_alpha/fold_2024_09_12_17_05_taf7_importin_alpha_model_1.cif
> /Users/sierkml/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/TAF/fold_2024_09_12_17_05_taf7_importin_alpha/fold_2024_09_12_17_05_taf7_importin_alpha_model_2.cif
> /Users/sierkml/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/TAF/fold_2024_09_12_17_05_taf7_importin_alpha/fold_2024_09_12_17_05_taf7_importin_alpha_model_3.cif
> /Users/sierkml/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/TAF/fold_2024_09_12_17_05_taf7_importin_alpha/fold_2024_09_12_17_05_taf7_importin_alpha_model_4.cif
Chain information for fold_2024_09_12_17_05_taf7_importin_alpha_model_0.cif #1
---
Chain | Description
A | .
B | .
Chain information for fold_2024_09_12_17_05_taf7_importin_alpha_model_1.cif #2
---
Chain | Description
A | .
B | .
Chain information for fold_2024_09_12_17_05_taf7_importin_alpha_model_2.cif #3
---
Chain | Description
A | .
B | .
Chain information for fold_2024_09_12_17_05_taf7_importin_alpha_model_3.cif #4
---
Chain | Description
A | .
B | .
Chain information for fold_2024_09_12_17_05_taf7_importin_alpha_model_4.cif #5
---
Chain | Description
A | .
B | .
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> color #1 bychain
> show #2 models
> hide #2 models
> show #3 models
> hide #3 models
> hide #1 models
> show #2 models
> color #2 bychain
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #2/A #3/A #4/A #5/A
Alignment identifier is 1
> select #1/A:142 #2/A:142 #3/A:142 #4/A:142 #5/A:142
40 atoms, 35 bonds, 5 residues, 5 models selected
> select #1/A:142-158 #2/A:142-158 #3/A:142-158 #4/A:142-158 #5/A:142-158
780 atoms, 785 bonds, 85 residues, 5 models selected
. [ID: 1] region 5 chains [142-158] RMSD: 41.287
> select #1/A:236 #2/A:236 #3/A:236 #4/A:236 #5/A:236
35 atoms, 30 bonds, 5 residues, 5 models selected
> select #1/A:236-245 #2/A:236-245 #3/A:236-245 #4/A:236-245 #5/A:236-245
425 atoms, 425 bonds, 50 residues, 5 models selected
. [ID: 1] region 5 chains [236-245] RMSD: 78.944
> select #1/A:336 #2/A:336 #3/A:336 #4/A:336 #5/A:336
40 atoms, 35 bonds, 5 residues, 5 models selected
> select #1/A:336-345 #2/A:336-345 #3/A:336-345 #4/A:336-345 #5/A:336-345
390 atoms, 385 bonds, 50 residues, 5 models selected
. [ID: 1] region 5 chains [336-345] RMSD: 81.323
> hide #2 models
> show #3 models
> color sel & #3 bychain
> select
> #1/A:22-33,37-41,116-130,138-140,143-146,152-157,160-175,186-195,214-227,248-308,312-347
> #2/A:22-33,37-41,116-130,138-140,143-146,152-157,160-175,186-195,214-227,248-308,312-347
> #3/A:22-33,37-41,116-130,138-140,143-146,152-157,160-175,186-195,214-227,248-308,312-347
> #4/A:22-33,37-41,116-130,138-140,143-146,152-157,160-175,186-195,214-227,248-308,312-347
> #5/A:22-33,37-41,116-130,138-140,143-146,152-157,160-175,186-195,214-227,248-308,312-347
7535 atoms, 7535 bonds, 910 residues, 5 models selected
> select clear
> color #3 bychain
> hide #3 models
> show #4 models
> color #4 bychain
> hide #4 models
> show #5 models
> color #5 bychain
> hide #5 models
> close
> open /Users/sierkml/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/TAF/fold_2024_09_12_17_06_taf7_crm1/fold_2024_09_12_17_06_taf7_crm1_model_0.cif
> /Users/sierkml/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/TAF/fold_2024_09_12_17_06_taf7_crm1/fold_2024_09_12_17_06_taf7_crm1_model_1.cif
> /Users/sierkml/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/TAF/fold_2024_09_12_17_06_taf7_crm1/fold_2024_09_12_17_06_taf7_crm1_model_2.cif
> /Users/sierkml/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/TAF/fold_2024_09_12_17_06_taf7_crm1/fold_2024_09_12_17_06_taf7_crm1_model_3.cif
> /Users/sierkml/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/TAF/fold_2024_09_12_17_06_taf7_crm1/fold_2024_09_12_17_06_taf7_crm1_model_4.cif
Chain information for fold_2024_09_12_17_06_taf7_crm1_model_0.cif #1
---
Chain | Description
A | .
B | .
Chain information for fold_2024_09_12_17_06_taf7_crm1_model_1.cif #2
---
Chain | Description
A | .
B | .
Chain information for fold_2024_09_12_17_06_taf7_crm1_model_2.cif #3
---
Chain | Description
A | .
B | .
Chain information for fold_2024_09_12_17_06_taf7_crm1_model_3.cif #4
---
Chain | Description
A | .
B | .
Chain information for fold_2024_09_12_17_06_taf7_crm1_model_4.cif #5
---
Chain | Description
A | .
B | .
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> color #1 bychain
> hide #1 models
> show #2 models
> color #2 bychain
> hide #2 models
> show #3 models
> color #3 bychain
> hide #3 models
> show #4 models
> color #4 bychain
> hide #4 models
> show #5 models
> color #5 bychain
> hide #5 models
> close #3
> close
> open /Users/sierkml/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/TAF/TAF_models.cxs
opened ChimeraX session
> hide #3 models
> select clear
> color #2 bychain
> show #!1 models
> hide #!1 models
> hide #1.1 models
> hide #2 models
> show #2 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> select #2/A:41
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel byhetero
> color sel byelement
> select #2/A:44
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byelement
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #2/A:45
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byelement
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #2/B:5
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
619 atoms, 690 bonds, 29 residues, 1 model selected
> style sel stick
Changed 619 atom styles
> hide sel cartoons
> show sel atoms
> color sel byelement
> hide sel atoms
> show sel atoms
> nucleotides sel atoms
> select clear
> select #2/A:46
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byelement
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #2/A:49
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byelement
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #2/A:50
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byelement
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #2/A:51
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byelement
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #2/A:41@CB
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #2/A:52
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:53
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byelement
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #2/B:9@C1'
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #2/B:8@C1'
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #2/B:7@C3'
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #2/A:54
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byelement
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #2/A:55
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byelement
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select down
2 atoms, 1 bond, 1 residue, 1 model selected
> select down
1 bond, 1 model selected
> select down
1 bond, 1 model selected
> select down
1 bond, 1 model selected
> select clear
> set bgColor white
> save /Users/sierkml/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/TAF/TAF_models.cxs
> save /Users/sierkml/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/TAF/TAR_RBD_interface_all.png width 1264 height
> 758 supersample 3
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> interfaces #!2 & ~solvent
1 buried areas: A B 658
> interfaces #!2 & ~solvent
1 buried areas: A B 658
> select #2/B:8@OP2
1 atom, 1 residue, 1 model selected
> select #2/A:50@NZ
1 atom, 1 residue, 1 model selected
> select #2/B:8@OP2
1 atom, 1 residue, 1 model selected
> select #2/A:50@NZ
1 atom, 1 residue, 1 model selected
> select add #2/B:8@OP2
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #2/A:50@NZ #2/B:8@OP2
Distance between fold_2024_08_06_16_17_taf7_rbd_tar_model_4.cif #2/A LYS 50 NZ
and /B C 8 OP2: 2.632Å
> select #2/A:44@NH1
1 atom, 1 residue, 1 model selected
> select add #2/B:8@N4
2 atoms, 2 residues, 1 model selected
> distance #2/A:44@NH1 #2/B:8@N4
Distance between fold_2024_08_06_16_17_taf7_rbd_tar_model_4.cif #2/A ARG 44
NH1 and /B C 8 N4: 4.177Å
> save /Users/sierkml/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/TAF/TAR_RBD_Hbonds_1.png width 1264 height 758
> supersample 3
> select #2/B:8@C4
1 atom, 1 residue, 1 model selected
> select add #2/A:48@CG
2 atoms, 2 residues, 1 model selected
> distance #2/B:8@C4 #2/A:48@CG
Distance between fold_2024_08_06_16_17_taf7_rbd_tar_model_4.cif #2/B C 8 C4
and /A PHE 48 CG: 9.308Å
> ~distance #2/B:8@C4 #2/A:48@CG
> select #2/B:19@OP1
1 atom, 1 residue, 1 model selected
> select add #2/A:46@NH1
2 atoms, 2 residues, 1 model selected
> distance #2/B:19@OP1 #2/A:46@NH1
Distance between fold_2024_08_06_16_17_taf7_rbd_tar_model_4.cif #2/B A 19 OP1
and /A ARG 46 NH1: 6.692Å
> ~distance #2/B:19@OP1 #2/A:46@NH1
> select clear
> select #2/A:53@NZ
1 atom, 1 residue, 1 model selected
> select add #2/B:8@O2'
2 atoms, 2 residues, 1 model selected
> distance #2/A:53@NZ #2/B:8@O2'
Distance between fold_2024_08_06_16_17_taf7_rbd_tar_model_4.cif #2/A LYS 53 NZ
and /B C 8 O2': 2.329Å
> select #2/B:9@N3
1 atom, 1 residue, 1 model selected
> view sel
> cofr sel
> ui tool show "Side View"
> select #2/A:21
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #2/A:24
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #2/A:25
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:22
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #2/A:21
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:20
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:18
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #2/A:47
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byelement
> label sel text "{0.name} {0.number}{0.insertion_code}"
> save /Users/sierkml/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/TAF/TAF_models.cxs
> select #2/B:13@P
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
619 atoms, 690 bonds, 29 residues, 1 model selected
> nucleotides sel stubs
> nucleotides sel tube/slab shape box
> nucleotides sel fill
> style nucleic & sel stick
Changed 619 atom styles
> color sel bynucleotide
> cartoon sel
> save /Users/sierkml/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/TAF/TAR_bulge_RBD.png width 1264 height 758
> supersample 3
> hide #* target a
> show sel target ab
> undo
> select #2/B
619 atoms, 690 bonds, 29 residues, 1 model selected
> show sel target ab
> cartoon hide sel
> style sel ringFill off
Changed 29 residue ring styles
> color sel byelement
> select #2/A:54
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:55
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:53
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:51
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:49
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:50
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:44
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:45
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:47
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:41
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
===== Log before crash end =====
Log:
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: 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: Mac14,9
Model Number: Z17G002HSLL/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 10 days, 3 hours, 58 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
LF24T35:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
LF24T450F:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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 , 13 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens(?) |
comment:2 by , 13 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
| Summary: | Crash moving window between screens(?) → Crash on display change, Mac, Qt 6.6 |
Note:
See TracTickets
for help on using tickets.
Crash in Mac Qt 6.6 in _NSViewHierarchyDidChangeBackingProperties probably connecting or disconnecting an external display or waking from sleep.