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Opened 5 months ago
Closed 5 months ago
#17790 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-13.5.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Thread 0x00000002a7e97000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a6e8b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a5e7f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a4e73000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a3e67000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a2e5b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a1e4f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a0e43000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029fe37000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029ee2b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029de1f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029ce13000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029be07000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001f0fca080 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, 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, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, psutil._psutil_osx, psutil._psutil_posix, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 62)
{"app_name":"ChimeraX","timestamp":"2025-05-23 21:09:10.00 -0700","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.5.1 (22G90)","roots_installed":0,"name":"ChimeraX","incident_id":"B95A62AF-F19B-4869-9677-EC027430ECAC"}
{
"uptime" : 2300000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,4",
"coalitionID" : 279338,
"osVersion" : {
"train" : "macOS 13.5.1",
"build" : "22G90",
"releaseType" : "User"
},
"captureTime" : "2025-05-23 21:09:06.3472 -0700",
"incident" : "B95A62AF-F19B-4869-9677-EC027430ECAC",
"pid" : 37216,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-23 17:48:36.3107 -0700",
"procStartAbsTime" : 57123782659593,
"procExitAbsTime" : 57412480915955,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"062E0CE8-98CE-5129-A957-D4E56B34948A","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "E5D8037D-B86B-DA73-2DAC-F4047F53C45E",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 13948,
"sleepWakeUUID" : "61A63437-7842-4F59-A607-5EC6A571825C",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4337844224\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1028e4000-1028e8000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":37216},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4337844224\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1028e4000-1028e8000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":1},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"triggered":true,"id":22716736,"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6129025288},{"value":99},{"value":101},{"value":11824067696},{"value":0},{"value":1037250056748429495},{"value":1037250062377472055},{"value":14757395258967641293},{"value":4294967286},{"value":6129025218},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8416850848},{"value":0},{"value":11},{"value":8338055296,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8338055520,"symbolLocation":224,"symbol":"_main_thread"},{"value":1},{"value":4356752944,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8295710720,"symbolLocation":0,"symbol":"OBJC_IVAR_$__NSSliderCellDataDrivenMetrics._state"},{"value":8295710720,"symbolLocation":0,"symbol":"OBJC_IVAR_$__NSSliderCellDataDrivenMetrics._state"},{"value":4},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6810795048},"cpsr":{"value":1073745920},"fp":{"value":6129025360},"sp":{"value":6129025328},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6810568548,"matchesCrashFrame":1},"far":{"value":5229838760}},"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":38756,"symbol":"__pthread_kill","symbolLocation":8,"imageIndex":188},{"imageOffset":27688,"symbol":"pthread_kill","symbolLocation":288,"imageIndex":189},{"imageOffset":259180,"symbol":"raise","symbolLocation":32,"imageIndex":190},{"imageOffset":2417160,"symbol":"faulthandler_fatal_error","symbolLocation":392,"imageIndex":1},{"imageOffset":14884,"symbol":"_sigtramp","symbolLocation":56,"imageIndex":191},{"imageOffset":349380,"imageIndex":69},{"imageOffset":349160,"imageIndex":69},{"imageOffset":381560,"symbol":"_NSViewHierarchyDidChangeBackingProperties","symbolLocation":244,"imageIndex":192},{"imageOffset":8460236,"symbol":"-[NSWindow 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"name" : "_ribbons.cpython-311-darwin.so"
},
{
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"arch" : "arm64",
"base" : 11409604608,
"size" : 16384,
"uuid" : "de871a78-14f2-3e72-9bde-e4f2c7493f1b",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
"name" : "_graphics.cpython-311-darwin.so"
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{
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
"name" : "_pdbio.cpython-311-darwin.so"
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{
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"path" : "\/Applications\/ChimeraX-1.9.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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"uuid" : "f4191524-316f-3e56-8aa1-9a441a05fd70",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atom_search\/ast.cpython-311-darwin.so",
"name" : "ast.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/chem_group\/_chem_group.cpython-311-darwin.so",
"name" : "_chem_group.cpython-311-darwin.so"
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{
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/coulombic\/_esp.cpython-311-darwin.so",
"name" : "_esp.cpython-311-darwin.so"
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{
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"base" : 11176689664,
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"uuid" : "cc06500d-d418-3365-b197-36b1304a819e",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGL.abi3.so",
"name" : "QtOpenGL.abi3.so"
},
{
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGLWidgets.abi3.so",
"name" : "QtOpenGLWidgets.abi3.so"
},
{
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtOpenGLWidgets.framework\/Versions\/A\/QtOpenGLWidgets",
"name" : "QtOpenGLWidgets"
},
{
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"size" : 32768,
"uuid" : "a55a4181-c446-3fa3-8fd6-27f845527eab",
"path" : "\/Applications\/ChimeraX-1.9.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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"arch" : "arm64",
"base" : 10945675264,
"size" : 16384,
"uuid" : "a516c5bc-1157-318a-a306-5c9b350e0c09",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_posix.abi3.so",
"name" : "_psutil_posix.abi3.so"
},
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"arch" : "arm64",
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"size" : 16384,
"uuid" : "644b1794-90c5-3838-9ffa-b772683aeb37",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/_sw.cpython-311-darwin.so",
"name" : "_sw.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/dssp\/_dssp.cpython-311-darwin.so",
"name" : "_dssp.cpython-311-darwin.so"
},
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"uuid" : "93fd54d8-5d5e-319d-94c5-2702d533d751",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/_nw.cpython-311-darwin.so",
"name" : "_nw.cpython-311-darwin.so"
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"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
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"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
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"uuid" : "6d458354-3c39-3f35-a3bb-d01a78817b4a",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
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===== Log before crash start =====
Startup Messages
---
warning | Registration file '/Users/ak/Library/Application Support/ChimeraX/registration' has expired
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/ak/Downloads/fold_wp_220577189_1_atp_1x_mg_2x
> 2/fold_wp_220577189_1_atp_1x_mg_2x_model_0.cif"
Summary of feedback from opening
/Users/ak/Downloads/fold_wp_220577189_1_atp_1x_mg_2x
2/fold_wp_220577189_1_atp_1x_mg_2x_model_0.cif
---
notes | Fetching CCD ATP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ATP/ATP.cif
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
Chain information for fold_wp_220577189_1_atp_1x_mg_2x_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Contacts
> contacts intraMol false ignoreHiddenModels true color #ff2600
78 contacts
> select protein
3894 atoms, 3967 bonds, 486 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_wp_220577189_1_atp_1x_mg_2x_model_0.cif_A SES
surface #1.2: minimum, -17.42, mean -1.68, maximum 9.15
To also show corresponding color key, enter the above coulombic command and
add key true
> select add #1
3927 atoms, 4000 bonds, 78 pseudobonds, 489 residues, 3 models selected
> select subtract #1
1 model selected
> lighting soft
> close #1
> open /Users/ak/Downloads/mohawk_0502_fixed-
> bsheets_ccID_isolde_real_space_refined_022.pdb format pdb
Chain information for mohawk_0502_fixed-
bsheets_ccID_isolde_real_space_refined_022.pdb #1
---
Chain | Description
Q T c d f | No description available
V W Z | No description available
X Y | No description available
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 92403 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> lighting soft
> color bychain
> select add /X:299
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show Contacts
> contacts sel intraMol false ignoreHiddenModels true color #ff2600
59 contacts
> select add /Y:310
40 atoms, 40 bonds, 2 residues, 1 model selected
> show sel atoms
> view orient
> select subtract /X:299@CE2
39 atoms, 37 bonds, 2 residues, 1 model selected
> select add /X:299@CE2
40 atoms, 37 bonds, 2 residues, 1 model selected
> ui tool show Contacts
> contacts sel intraMol false ignoreHiddenModels true color #ff2600
83 contacts
> select add #1
92643 atoms, 93968 bonds, 83 pseudobonds, 5643 residues, 2 models selected
> select subtract #1
Nothing selected
> open "/Users/ak/Downloads/cryosparc_P755_J51_006_volume_map_flipped (1).mrc"
> format mrc
Opened cryosparc_P755_J51_006_volume_map_flipped (1).mrc as #2, grid size
300,300,300, pixel 1.3, shown at level 0.031, step 2, values float32
> close #2
> select add /Z:299
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show Contacts
> contacts sel intraMol false ignoreHiddenModels true color #ff2600
15 contacts
> select add /Y:667
40 atoms, 40 bonds, 2 residues, 1 model selected
> show sel atoms
> ui tool show Contacts
> contacts sel intraMol false ignoreHiddenModels true color #ff2600
15 contacts
> open /Users/ak/Downloads/cryosparc_P69_J76_004_volume_map_sharp.mrc
Opened cryosparc_P69_J76_004_volume_map_sharp.mrc as #2, grid size
800,800,800, pixel 0.65, shown at step 1, values float32
> volume #2 region 0,0,0,799,799,799 step 4
> volume #2 step 2
> ui tool show "Hide Dust"
> surface dust #2 size 3.9
> surface dust #2 size 4.09
> surface dust #2 size 4.67
> surface dust #2 size 4.75
> surface dust #2 size 14.16
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule mohawk_0502_fixed-bsheets_ccID_isolde_real_space_refined_022.pdb
(#1) to map cryosparc_P69_J76_004_volume_map_sharp.mrc (#2) using 92643 atoms
average map value = 0.03889, steps = 256
shifted from previous position = 14.2
rotated from previous position = 13.1 degrees
atoms outside contour = 32736, contour level = 0.012731
Position of mohawk_0502_fixed-bsheets_ccID_isolde_real_space_refined_022.pdb
(#1) relative to cryosparc_P69_J76_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99045848 -0.00227239 0.13779270 -31.69279510
0.02723002 0.98337865 -0.17951308 42.57371435
-0.13509447 0.18155235 0.97405761 9.43191854
Axis 0.79609040 0.60167170 0.06504800
Axis point 0.00000000 -17.94595110 235.47683584
Rotation angle (degrees) 13.10722620
Shift along axis 0.99859690
> volume flip #2
Opened cryosparc_P69_J76_004_volume_map_sharp.mrc z flip as #3, grid size
800,800,800, pixel 0.65, shown at step 1, values float32
> ui tool show "Hide Dust"
> surface dust #3 size 3.9
> surface dust #3 size 4.1
> surface dust #3 size 15.07
> close #2
> fitmap #1 inMap #3
Fit molecule mohawk_0502_fixed-bsheets_ccID_isolde_real_space_refined_022.pdb
(#1) to map cryosparc_P69_J76_004_volume_map_sharp.mrc z flip (#3) using 92643
atoms
average map value = 0.07151, steps = 236
shifted from previous position = 14.2
rotated from previous position = 13.1 degrees
atoms outside contour = 1851, contour level = 0.012731
Position of mohawk_0502_fixed-bsheets_ccID_isolde_real_space_refined_022.pdb
(#1) relative to cryosparc_P69_J76_004_volume_map_sharp.mrc z flip (#3)
coordinates:
Matrix rotation and translation
0.99999996 -0.00028340 -0.00006686 0.07437942
0.00028337 0.99999983 -0.00051374 0.07442764
0.00006701 0.00051372 0.99999987 -0.15564442
Axis 0.86997172 -0.11334700 0.47989756
Axis point 0.00000000 285.80387684 140.71460724
Rotation angle (degrees) 0.03383382
Shift along axis -0.01842154
> volume #3 style mesh
> volume #3 level 0.0682
> hide #!3 models
> show #!3 models
> volume #3 style surface
> volume #3 level 0.0912
> volume #3 level 0.125
> volume #3 level 0.1043
> volume #3 level 0.08218
> ui tool show "Side View"
> volume #3 style mesh
> volume #3 level 0.06639
> volume #3 style surface
> volume #3 style mesh
> volume #3 level 0.01499
> volume #3 style surface
> volume #3 style mesh
> ui tool show "Side View"
> view sel
> ui tool show "Side View"
> view sel
> volume #3 style surface
> volume #3 style mesh
> view sel
> select add #1
92643 atoms, 93968 bonds, 15 pseudobonds, 5643 residues, 2 models selected
> select subtract #1
Nothing selected
> volume #3 level 0.05647
> view orient
> volume #3 style surface
> volume #3 level 0.08218
> volume #3 level 0.08939
> volume #3 style mesh
> volume #3 level 0.03618
> volume #3 level 0.05106
> volume #3 level 0.05602
> volume #3 level 0.0691
> volume #3 level 0.06459
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
> select /V-W,Z:288
60 atoms, 60 bonds, 3 residues, 1 model selected
> select /V-W,Z:288
60 atoms, 60 bonds, 3 residues, 1 model selected
> select add #1
92643 atoms, 93968 bonds, 15 pseudobonds, 5643 residues, 2 models selected
> select subtract #1
Nothing selected
> select /V-W,Z:288
60 atoms, 60 bonds, 3 residues, 1 model selected
> select /V-W,Z:288
60 atoms, 60 bonds, 3 residues, 1 model selected
> select /V-W,Z:288-289
132 atoms, 132 bonds, 6 residues, 1 model selected
> select /V-W,Z:288-289
132 atoms, 132 bonds, 6 residues, 1 model selected
> select /V-W,Z:288-290
204 atoms, 204 bonds, 9 residues, 1 model selected
> select /V-W,Z:284
36 atoms, 33 bonds, 3 residues, 1 model selected
> select /V-W,Z:284-289
315 atoms, 321 bonds, 18 residues, 1 model selected
> select add #1
92643 atoms, 93968 bonds, 15 pseudobonds, 5643 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!3 models
> select
> /V-W,Z:31-34,64-68,105-111,114-121,139-142,145-148,170-173,213-216,219-223,243-247,263-267,290-294,301-305,331-336,339-345,358-360,414-416,420-426,452-459,486-492,495-500,516-529,532-545,563-568,573-581,585-590,595-600,604-606,662-664,667-671,695-697,731-740,770-774,778-780,808-813,842-845,885-890,904-909,918-921,952-957,981-988,1010-1014,1017-1020,1038-1044
13155 atoms, 13230 bonds, 765 residues, 1 model selected
> select /V-W,Z:3
39 atoms, 36 bonds, 3 residues, 1 model selected
> select /V-W,Z:3-292
14190 atoms, 14397 bonds, 870 residues, 1 model selected
> select /V-W,Z:298
21 atoms, 18 bonds, 3 residues, 1 model selected
> select /V-W,Z:298-300
114 atoms, 114 bonds, 9 residues, 1 model selected
> select /V-W,Z:297
36 atoms, 33 bonds, 3 residues, 1 model selected
> select /V-W,Z:297-301
210 atoms, 213 bonds, 15 residues, 1 model selected
> select /V-W,Z:301
60 atoms, 60 bonds, 3 residues, 1 model selected
> select /V-W,Z:300-301
93 atoms, 93 bonds, 6 residues, 1 model selected
> select /V-W,Z:300
33 atoms, 30 bonds, 3 residues, 1 model selected
> select /V-W,Z:293-300
360 atoms, 363 bonds, 24 residues, 1 model selected
> select /V-W,Z:294
72 atoms, 69 bonds, 3 residues, 1 model selected
> select /V-W,Z:294-299
264 atoms, 264 bonds, 18 residues, 1 model selected
> select /V-W,Z:295
33 atoms, 30 bonds, 3 residues, 1 model selected
> select /V-W,Z:295-300
225 atoms, 225 bonds, 18 residues, 1 model selected
> select /V-W,Z:297
36 atoms, 33 bonds, 3 residues, 1 model selected
> select /V-W,Z:297
36 atoms, 33 bonds, 3 residues, 1 model selected
> show sel atoms
> ui tool show Contacts
> contacts sel intraMol false ignoreHiddenModels true color #ff2600
10 contacts
> hide #!1 models
> select add #1
92643 atoms, 93968 bonds, 10 pseudobonds, 5643 residues, 2 models selected
> select subtract #1
Nothing selected
> open /Users/ak/Downloads/rzago_apo-tet_rsr19_mg-
> added_real_space_refined_021.cif format mmcif
Summary of feedback from opening /Users/ak/Downloads/rzago_apo-tet_rsr19_mg-
added_real_space_refined_021.cif
---
warnings | Atom H1 is not in the residue template for LYS /C:161
Atom H1 is not in the residue template for LYS /A:161
Missing or incomplete sequence information. Inferred polymer connectivity.
note | Fetching CCD AGS from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/AGS/AGS.cif
Chain information for rzago_apo-tet_rsr19_mg-added_real_space_refined_021.cif
#2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Computing secondary structure
> view orient
> color #2 bychain
> show #!1 models
> ui mousemode right "move picked models"
> view matrix models #2,1,0,0,3.5852,0,1,0,-53.978,0,0,1,-63.769
> hide #!1 models
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 2/A
Alignment identifier is 2/B
> select #1/V-W,Z:287 #2/C:287
96 atoms, 100 bonds, 4 residues, 2 models selected
> select #1/V-W,Z:287-288 #2/C:287-288
176 atoms, 184 bonds, 8 residues, 2 models selected
2 [ID: 2] region chains C,V,W,Z [285-286] RMSD: 173.329
> select add #2
50524 atoms, 51178 bonds, 3114 residues, 2 models selected
> select subtract #2
132 atoms, 138 bonds, 6 residues, 1 model selected
> select add #1
92643 atoms, 93968 bonds, 10 pseudobonds, 5643 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #1
92643 atoms, 93968 bonds, 10 pseudobonds, 5643 residues, 2 models selected
> select subtract #1
Nothing selected
> rainbow #2
> select #1/V-W,Z:430 #2/C:430
60 atoms, 56 bonds, 4 residues, 2 models selected
> select #1/V-W,Z:430-431 #2/C:430-431
120 atoms, 116 bonds, 8 residues, 2 models selected
2 [ID: 2] region chains C,V,W,Z [428-429] RMSD: 179.231
> view matrix models #2,1,0,0,-3.412,0,1,0,-40.267,0,0,1,-81.673
> select #1/V-W,Z:426-427 #2/C:426-427
124 atoms, 120 bonds, 8 residues, 2 models selected
> select #1/V-W,Z:426-429 #2/C:426-429
256 atoms, 252 bonds, 16 residues, 2 models selected
2 [ID: 2] region chains C,V,W,Z [424-427] RMSD: 179.326
> select add #1
92707 atoms, 94031 bonds, 10 pseudobonds, 5647 residues, 3 models selected
> select subtract #1
64 atoms, 63 bonds, 4 residues, 1 model selected
> select add #2
50392 atoms, 51040 bonds, 3108 residues, 1 model selected
> select subtract #2
Nothing selected
> color #2 bychain
> select #1/V-W,Z:430 #2/C:430
60 atoms, 56 bonds, 4 residues, 2 models selected
> select #1/V-W,Z:430-431 #2/C:430-431
120 atoms, 116 bonds, 8 residues, 2 models selected
2 [ID: 2] region chains C,V,W,Z [428-429] RMSD: 182.955
> view matrix models #2,1,0,0,-13.298,0,1,0,-25.764,0,0,1,-90.718
> select #1/V-W,Z:426 #2/C:426
68 atoms, 64 bonds, 4 residues, 2 models selected
> select #1/V-W,Z:426 #2/C:426
68 atoms, 64 bonds, 4 residues, 2 models selected
2 [ID: 2] region chains C,V,W,Z [424] RMSD: 178.957
> select
> #1/V-W,Z:4-9,11-19,21-29,42-59,85-98,151-161,166-168,176-178,181-191,198-200,203-210,224-230,234-236,252-254,258-260,271-284,309-322,373-381,389-391,396-408,429-436,461-463,466-483,492-494,510-515,549-551,554-559,569-571,591-593,601-603,610-620,626-633,641-659,708-710,716-723,741-756,764-768,783-796,798-801,827-838,847-851,857-868,896-900,926-944,963-976,1050-1063,1076-1095,1102-1106
> #2/C:4-9,11-19,21-29,42-59,85-98,151-161,166-168,176-178,181-191,198-200,203-210,224-230,234-236,252-254,258-260,271-284,309-322,373-381,389-391,396-408,429-436,461-463,466-483,492-494,510-515,549-551,554-559,569-571,591-593,601-603,610-620,626-633,641-659,708-710,716-723,741-756,764-768,783-796,798-801,827-838,847-851,857-868,896-900,926-944,963-976,1050-1063,1076-1095,1102-1106
27608 atoms, 27668 bonds, 1656 residues, 2 models selected
> select #1/V-W,Z:423 #2/C:423
76 atoms, 72 bonds, 4 residues, 2 models selected
> select #1/V-W,Z:423 #2/C:423
76 atoms, 72 bonds, 4 residues, 2 models selected
2 [ID: 2] region chains C,V,W,Z [421] RMSD: 174.657
> select
> #1/V-W,Z:31-34,64-68,105-111,114-121,139-142,145-148,170-173,213-216,219-223,243-247,263-267,290-294,301-305,331-336,339-345,358-360,414-417,420-426,449-459,486-492,495-500,516-529,532-545,563-568,573-581,585-590,595-600,604-606,662-664,667-671,675-677,695-697,731-740,770-774,778-780,808-814,842-846,885-893,901-909,918-921,952-957,981-988,1010-1014,1017-1020,1038-1044
> #2/C:31-34,64-68,105-111,114-121,139-142,145-148,170-173,213-216,219-223,243-247,263-267,290-294,301-305,331-336,339-345,358-360,414-417,420-426,449-459,486-492,495-500,516-529,532-545,563-568,573-581,585-590,595-600,604-606,662-664,667-671,675-677,695-697,731-740,770-774,778-780,808-814,842-846,885-893,901-909,918-921,952-957,981-988,1010-1014,1017-1020,1038-1044
18508 atoms, 18616 bonds, 1080 residues, 2 models selected
> select #1/V-W,Z:427-428 #2/C:427-428
112 atoms, 108 bonds, 8 residues, 2 models selected
> select #1/V-W,Z:427-428 #2/C:427-428
112 atoms, 108 bonds, 8 residues, 2 models selected
2 [ID: 2] region chains C,V,W,Z [425-426] RMSD: 181.637
> select #1/V-W,Z:427 #2/C:427
56 atoms, 52 bonds, 4 residues, 2 models selected
> select #1/V-W,Z:427-460 #2/C:427-460
2197 atoms, 2229 bonds, 136 residues, 2 models selected
2 [ID: 2] region chains C,V,W,Z [425-458] RMSD: 192.731
> select #1/V-W,Z:449 #2/C:449
84 atoms, 84 bonds, 4 residues, 2 models selected
> select #1/V-W,Z:427-449 #2/C:427-449
1493 atoms, 1513 bonds, 92 residues, 2 models selected
2 [ID: 2] region chains C,V,W,Z [425-447] RMSD: 190.943
> select
> #1/V-W,Z:31-34,64-68,105-111,114-121,139-142,145-148,170-173,213-216,219-223,243-247,263-267,290-294,301-305,331-336,339-345,358-360,414-417,420-426,449-459,486-492,495-500,516-529,532-545,563-568,573-581,585-590,595-600,604-606,662-664,667-671,675-677,695-697,731-740,770-774,778-780,808-814,842-846,885-893,901-909,918-921,952-957,981-988,1010-1014,1017-1020,1038-1044
> #2/C:31-34,64-68,105-111,114-121,139-142,145-148,170-173,213-216,219-223,243-247,263-267,290-294,301-305,331-336,339-345,358-360,414-417,420-426,449-459,486-492,495-500,516-529,532-545,563-568,573-581,585-590,595-600,604-606,662-664,667-671,675-677,695-697,731-740,770-774,778-780,808-814,842-846,885-893,901-909,918-921,952-957,981-988,1010-1014,1017-1020,1038-1044
18508 atoms, 18616 bonds, 1080 residues, 2 models selected
> select #1/V-W,Z:449 #2/C:449
84 atoms, 84 bonds, 4 residues, 2 models selected
> select #1/V-W,Z:449 #2/C:449
84 atoms, 84 bonds, 4 residues, 2 models selected
2 [ID: 2] region chains C,V,W,Z [447] RMSD: 196.345
> show sel & #2 atoms
> ui tool show Contacts
> contacts sel intraMol false ignoreHiddenModels true color #ff2600
No contacts
> select add #1
92664 atoms, 93989 bonds, 10 pseudobonds, 5644 residues, 3 models selected
> select subtract #1
21 atoms, 21 bonds, 1 residue, 1 model selected
> select add #2
50392 atoms, 51040 bonds, 3108 residues, 1 model selected
> select subtract #2
Nothing selected
> select subtract #4
Nothing selected
> select add #4
Nothing selected
> select subtract #4
Nothing selected
> select add #4
Nothing selected
> select subtract #4
Nothing selected
> close #4
> rainbow #2
> open /Users/ak/Downloads/5xq2.cif
5xq2.cif title:
Crystal structure of T. thermophilus Argonaute protein complexed with a bulge
5A6 on the guide strand [more info...]
Chain information for 5xq2.cif #4
---
Chain | Description | UniProt
A B | TtAgo (D546N) | Q746M7_THET2 1-685
C D | DNA (5'-D(*AP*GP*T)-3') |
E X | DNA (5'-D(P*TP*GP*AP*AP*GP*AP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3') |
F Y | DNA (5'-D(*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3') |
Non-standard residues in 5xq2.cif #4
---
MG — magnesium ion
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 11721 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> ui tool show Matchmaker
> matchmaker #!4 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker mohawk_0502_fixed-bsheets_ccID_isolde_real_space_refined_022.pdb,
chain W (#1) with 5xq2.cif, chain A (#4), sequence alignment score = 407.7
RMSD between 121 pruned atom pairs is 1.260 angstroms; (across all 603 pairs:
20.413)
> ui tool show Matchmaker
> matchmaker #!4 to #2
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker rzago_apo-tet_rsr19_mg-added_real_space_refined_021.cif, chain D
(#2) with 5xq2.cif, chain A (#4), sequence alignment score = 373.4
RMSD between 124 pruned atom pairs is 1.246 angstroms; (across all 612 pairs:
26.429)
> select #4/B
5187 atoms, 5312 bonds, 1 pseudobond, 681 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
> select #4/C
59 atoms, 66 bonds, 3 residues, 1 model selected
> select #4/F
317 atoms, 354 bonds, 16 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select #4/F
317 atoms, 354 bonds, 16 residues, 1 model selected
> select #4/F#4/Y
634 atoms, 708 bonds, 32 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select #4/C#4/D
118 atoms, 132 bonds, 6 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select #4/E#4/X
720 atoms, 806 bonds, 36 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> view matrix models #2,1,0,0,-51.322,0,1,0,14.417,0,0,1,-132.39
> undo
===== Log before crash end =====
Log:
Startup Messages
---
warning | Registration file '/Users/ak/Library/Application Support/ChimeraX/registration' has expired
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/ak/Downloads/fold_wp_106257897_1_trimer/fold_wp_106257897_1_trimer_model_0.cif
Chain information for fold_wp_106257897_1_trimer_model_0.cif #1
---
Chain | Description
A B C | .
Computing secondary structure
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,4
Model Number: Z15H00108LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 8422.141.2
OS Loader Version: 8422.141.2
Software:
System Software Overview:
System Version: macOS 13.5.1 (22G90)
Kernel Version: Darwin 22.6.0
Time since boot: 42 days, 2 hours, 7 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
ChimeraX-Clipper: 0.24.0
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: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.9
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-XMAS: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
et_xmlfile: 2.0.0
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
msgpack: 1.0.8
narwhals: 1.30.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 2.2.3
numpy: 1.26.4
openpyxl: 3.1.5
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
pandas: 2.2.3
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
plotly: 6.0.0
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pyKVFinder: 0.7.3
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
QtRangeSlider: 0.1.5
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
seaborn: 0.13.2
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
toml: 0.10.2
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 5 months 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 , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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