Crash on Mac waking from sleep

[hrishikesh.das@…]

The following bug report has been submitted:
Platform:        macOS-15.7.1-x86_64-i386-64bit
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 0x0000700023210000 (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 0x000070002220d000 (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 0x000070002120a000 (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 0x0000700020207000 (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 0x000070001f204000 (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 0x000070001e201000 (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 0x000070001d1fe000 (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 0x000070001c1fb000 (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 0x000070001b1f8000 (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 0x000070001a1f5000 (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 0x00007000191f2000 (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 0x00007000181ef000 (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 0x00007000171ec000 (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 0x00007000161e9000 (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 0x00007000151e6000 (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 0x00007ff85d1f1000 (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, chimerax.surface._surface, chimerax.pdb_lib._load_libs, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, PIL._imagingmath, chimerax.core._mac_util, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group, psutil._psutil_osx, psutil._psutil_posix (total: 62)


{"app_name":"ChimeraX","timestamp":"2025-11-05 18:01:06.00 +0100","app_version":"1.9.0","slice_uuid":"079d39d3-a489-3e56-92d8-c781f5a4bb98","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 15.7.1 (24G231)","roots_installed":0,"name":"ChimeraX","incident_id":"F468CA97-935F-4251-8AE2-D38C7802D5DE"}
{
  "uptime" : 670000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro16,1",
  "coalitionID" : 39348,
  "osVersion" : {
    "train" : "macOS 15.7.1",
    "build" : "24G231",
    "releaseType" : "User"
  },
  "captureTime" : "2025-11-05 17:59:46.2946 +0100",
  "codeSigningMonitor" : 0,
  "incident" : "F468CA97-935F-4251-8AE2-D38C7802D5DE",
  "pid" : 61487,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-11-03 10:27:38.9798 +0100",
  "procStartAbsTime" : 611135423694003,
  "procExitAbsTime" : 677325648200232,
  "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":"2EF1C7E5-CB47-546C-881F-28C6D02FF09B","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "250318AF-B0C7-4CAC-6AA5-6AB535BC3FE0",
  "lowPowerMode" : 1,
  "appleIntelligenceStatus" : {"state":"unavailable","reasons":["deviceNotCapable"]},
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "codeSigningAuxiliaryInfo" : 0,
  "bootSessionUUID" : "C0ACF215-B0BA-495B-A962-DA0E275280C0",
  "wakeTime" : 4916,
  "bridgeVersion" : {"build":"23P350","train":"10.0"},
  "sleepWakeUUID" : "7EF1AF01-0AFB-4B5D-8828-2B8EC73023AF",
  "sip" : "enabled",
  "vmRegionInfo" : "0x169 is not in any region.  Bytes before following region: 4553969303\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10f701000-10f705000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":61487},
  "ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
  "vmregioninfo" : "0x169 is not in any region.  Bytes before following region: 4553969303\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10f701000-10f705000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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    "uuid" : "de5992f0-475b-3932-a605-e12ddd03c36c",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
    "name" : "_ribbons.cpython-311-darwin.so"
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  {
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    "size" : 32768,
    "uuid" : "65c46829-28f8-3e3d-8cdc-c208915d68a9",
    "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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    "size" : 524288,
    "uuid" : "f5bf81ec-04b0-36b7-8c92-173b6e72e831",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
    "name" : "mmcif.cpython-311-darwin.so"
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  {
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    "size" : 442368,
    "uuid" : "ea5ec760-6814-334e-9fb6-f03df20f8ddd",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
    "name" : "_mmcif.cpython-311-darwin.so"
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  {
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    "size" : 180224,
    "uuid" : "af5af6cd-8200-3b53-b58e-822a20f01893",
    "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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    "base" : 6112563200,
    "size" : 3915776,
    "uuid" : "bfecdf7d-82ca-36af-86fb-90f272cdc263",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
    "name" : "etree.cpython-311-darwin.so"
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  {
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    "uuid" : "21fc90fd-fbf7-3c7d-8a75-746218b81cb2",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
    "name" : "_elementpath.cpython-311-darwin.so"
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  {
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    "base" : 6030405632,
    "size" : 49152,
    "uuid" : "edded33d-79ac-3fdf-8248-6fbe46ac7aaa",
    "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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  {
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    "size" : 81920,
    "uuid" : "ca78c6b8-d415-37ba-bad4-9d335d9ff978",
    "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\/psutil\/_psutil_osx.abi3.so",
    "name" : "_psutil_osx.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\/psutil\/_psutil_posix.abi3.so",
    "name" : "_psutil_posix.abi3.so"
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    "arch" : "x86_64",
    "base" : 140703589695488,
    "size" : 248688,
    "uuid" : "031ffbbd-67f0-3987-b4a5-ecf01645bbc2",
    "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
    "name" : "libsystem_kernel.dylib"
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    "size" : 49112,
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    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
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    "size" : 559912,
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    "name" : "libsystem_c.dylib"
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    "size" : 39232,
    "uuid" : "78c9dcc0-2fba-3be4-a1dd-da618362ae68",
    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    "name" : "libsystem_platform.dylib"
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    "uuid" : "00000000-0000-0000-0000-000000000000"
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    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 22352652,
    "uuid" : "ca8a558a-fd15-3e61-b0f4-7a22e8e635fd",
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    "size" : 5036280,
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    "path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
    "name" : "SkyLight"
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    "path" : "\/usr\/lib\/system\/libdispatch.dylib",
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}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> ui tool hide "command line interface"

> ui tool show clix

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/hrishikeshdas/Documents/Projects/FASTKD/FASTKD5/Structures_FAST5/FAST5-trimer/F5_ATP6Cox3_RNA_trimer/F5_ATP6cox3_trimer_RNA_41/ATP6Cox3_41NtTrimer1.cxs

opened ChimeraX session  

> hide #!2 models

> show #!3 models

> show #!2 models

> hide #!2 models

> hide #!3 models

> show #!4 models

> show #!4 cartoons

> ~label #4 residues

> hide #!4 atoms

> select #4/G:30

23 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #!3 models

> hide #!4 models

> select #3/G:31

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #3/G:31

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #3/G:30

22 atoms, 24 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #!4 models

> hide #!3 models

> show #!3 models

> hide #!4 models

> hide #!3 models

> show #!3 models

> show #!4 models

> select clear

> view

> hide #!3-4 atoms

> hide #!4 models

> hide #!3 models

> show #!2 models

> hide #!2 surfaces

> hide #!2 atoms

> ui tool show CliX

> select #2/g:13-24

253 atoms, 282 bonds, 12 residues, 1 model selected  

> show sel atoms

> view sel

> select #2/G

862 atoms, 962 bonds, 41 residues, 1 model selected  

> color (#!2 & sel) cornflower blue

> color sel byhetero

> color (#!2 & sel) medium blue

> color (#!2 & sel) blue

> color (#!2 & sel) cyan

> color sel byhetero

> select clear

> select #2/g:13-24

253 atoms, 282 bonds, 12 residues, 1 model selected  

> hbonds sel reveal true

191 hydrogen bonds found  

> show #1 models

> color #1 #0032ffff models

> color #1 #000dffff models

> color #1 #0098ffff models

> color #1 #009856ff models

> color #1 #009878ff models

> color #1 #e29878ff models

> color #1 #fb9878ff models

> color #1 #e5f378ff models

> color #1 #e5d278ff models

> color #1 #e57c78ff models

> color #1 #e54b78ff models

> color #1 #e55b78ff models

> color #1 #e58d78ff models

> color #1 #e5a278ff models

> color #1 #e5a2ffff models

> color #1 #e545ffff models

> color #1 #e523ffff models

> color #1 #e507ffff models

> select clear

> select #2/g:13-24

253 atoms, 282 bonds, 11 pseudobonds, 12 residues, 2 models selected  

> ui tool show Contacts

> contacts sel restrict cross overlapCutoff -0.3 resSeparation 5 intraRes true
> ignoreHiddenModels true select true color #220422 showDist true reveal true

81 contacts  

> show #!5 models

> select clear

> label #1-2#!5 text "{0.name} {0.number}{0.insertion_code}"

> save
> /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD5/Structures_FAST5/FAST5-trimer/F5_ATP6Cox3_RNA_trimer/F5_ATP6cox3_trimer_RNA_41/human_ATP6Cox3_41.cxs

> hide #!5 models

> show #!5 models

> hide #1 models

> hide #!2 models

> show #1 models

> show #!4 models

> hide #!4 atoms

> view

> hide #!4 cartoons

> select #4/g:13-24

254 atoms, 283 bonds, 12 residues, 1 model selected  

> show sel atoms

> label sel text "{0.name} {0.number}{0.insertion_code}"

> hbonds sel reveal true

187 hydrogen bonds found  

> view sel

> select #4/g:13-24

254 atoms, 283 bonds, 8 pseudobonds, 12 residues, 2 models selected  

> ui tool show Contacts

> contacts sel restrict cross overlapCutoff -0.3 resSeparation 5 intraRes true
> ignoreHiddenModels true select true color #220422 showDist true reveal true

75 contacts  

> contacts sel restrict cross overlapCutoff -0.3 resSeparation 5 intraRes true
> ignoreHiddenModels true select true color #220422 showDist true reveal true

18 contacts  

> select #4/g:13-24

254 atoms, 283 bonds, 9 pseudobonds, 12 residues, 3 models selected  

> label (#!4 & sel) text "{0.name} {0.number}{0.insertion_code}"

> show #5.1 models

> hbonds sel reveal true

187 hydrogen bonds found  

> color sel byhetero

> select #4/g:13-24

254 atoms, 283 bonds, 9 pseudobonds, 12 residues, 3 models selected  

> ui tool show Contacts

> contacts sel restrict cross overlapCutoff -0.3 resSeparation 5 intraRes true
> ignoreHiddenModels true select true color #220422 showDist true reveal true

75 contacts  

> select clear

> color #!4 byhetero

> hide #5.1 models

> label #1,4#!5 text "{0.name} {0.number}{0.insertion_code}"

> hide #!5 models

> show #!5 models

> show #5.1 models

> hide #5.1 models

> hide #!5 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 atoms

> select #4/g:13-24

254 atoms, 283 bonds, 8 pseudobonds, 12 residues, 2 models selected  

> show sel atoms

> select clear

> select #2/g:13-24

253 atoms, 282 bonds, 12 residues, 1 model selected  

> show #!4 atoms

> show #!2 models

> hide sel atoms

> undo

> ~label (#!2 & sel) residues

> hide sel atoms

> hide #!2 models

> show #!2 models

> select clear

> hide #!2,4 atoms

> select #2/g:13-24

253 atoms, 282 bonds, 12 residues, 1 model selected  

> show sel atoms

> hbonds sel reveal true

191 hydrogen bonds found  

> select clear

> label #1-2,4 text "{0.name} {0.number}{0.insertion_code}"

> show #!5 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select #4/g:13-24

254 atoms, 283 bonds, 12 residues, 1 model selected  

> show sel atoms

> select clear

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!4 models

> show #!4 models

> select #4/g:20

23 atoms, 25 bonds, 1 residue, 1 model selected  

> view sel

> hide #!2 models

> select #4/g:13-24

254 atoms, 283 bonds, 12 residues, 1 model selected  

> hbonds sel reveal true

187 hydrogen bonds found  

> select clear

> select #4/g:20

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #4/g:20

23 atoms, 25 bonds, 1 residue, 1 model selected  

> view sel

> view

> view sel

> select clear

> ui tool show "Side View"

> save
> "/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD5/Structures_FAST5/FAST5-trimer/F5_ATP6Cox3_RNA_trimer/F5_ATP6cox3_trimer_RNA_41/New
> Folder With Items/Ch_G20_region.png" width 1161 height 847 supersample 3

> show #!2 models

> hide #!4 models

> hide #!5 models

> show #!5 models

> hide #!2 models

> show #!4 models

> save
> "/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD5/Structures_FAST5/FAST5-trimer/F5_ATP6Cox3_RNA_trimer/F5_ATP6cox3_trimer_RNA_41/New
> Folder With Items/Ch_A23_region.png" width 1161 height 847 supersample 3

> hide #!4 models

> show #!2 models

> select #2/g:23

20 atoms, 21 bonds, 1 residue, 1 model selected  

> view sel

> select #2/g:13-24

253 atoms, 282 bonds, 12 residues, 1 model selected  

> hbonds sel reveal true

191 hydrogen bonds found  

> select #2/g:13-24

253 atoms, 282 bonds, 11 pseudobonds, 12 residues, 2 models selected  

> ui tool show Contacts

> contacts sel restrict cross overlapCutoff -0.3 resSeparation 5 intraRes true
> ignoreHiddenModels true select true color #220422 showDist true reveal true

81 contacts  

> select clear

> select #2/g:23

20 atoms, 21 bonds, 1 residue, 1 model selected  

> view sel

> select clear

> save
> "/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD5/Structures_FAST5/FAST5-trimer/F5_ATP6Cox3_RNA_trimer/F5_ATP6cox3_trimer_RNA_41/New
> Folder With Items/Hu_C23_region.png" width 1161 height 847 supersample 3

> hide #!2 models

> hide #1 models

> show #1 models

> show #!3 models

> hide #!3 atoms

> hide #!3 cartoons

> select #3/g:13-24

249 atoms, 276 bonds, 12 residues, 1 model selected  

> show sel atoms

> label sel text "{0.name} {0.number}{0.insertion_code}"

> show #!2 models

> hide #1 models

> show #1 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!5 models

> view

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!2 models

> hide #1 models

> show #!2 models

> hide #!2 atoms

> show #!2 cartoons

> ~label #2 residues

> view sel

> select clear

> view

> open /Users/hrishikeshdas/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/FASTKD5/cryosparc_P34_J388_class_01_00142_volume_sharp_fliped.mrc

Opened cryosparc_P34_J388_class_01_00142_volume_sharp_fliped.mrc as #8, grid
size 128,128,128, pixel 2.03, shown at level 0.0754, step 1, values float32  

> volume #8 level 0.2911

> close #8

> view

> select #2/B#3/B#4/B#6/B#7/B#9/B

28482 atoms, 29130 bonds, 6 pseudobonds, 3504 residues, 12 models selected  

> color (#!2 & sel) #c7eae5ff

> select clear

> select #2/G#3/G#4/G#6/G#7/G#9/G

5182 atoms, 5786 bonds, 124 pseudobonds, 246 residues, 7 models selected  

> color (#!2 & sel) #e6f5d0ff

> select clear

> color #2 #a1d76aff

> undo

> select #2/G#3/G#4/G#6/G#7/G#9/G

5182 atoms, 5786 bonds, 124 pseudobonds, 246 residues, 7 models selected  

> select clear

> select #2/G#3/G#4/G#6/G#7/G#9/G

5182 atoms, 5786 bonds, 124 pseudobonds, 246 residues, 7 models selected  

> color (#!2 & sel) #a1d76aff

> select clear

> open /Users/hrishikeshdas/Downloads/cryosparc_P102_J452_009_volume_map.mrc

Opened cryosparc_P102_J452_009_volume_map.mrc as #8, grid size 256,256,256,
pixel 1.02, shown at level 0.0431, step 1, values float32  

> hide #!8 models

> hide #!2 models

> show #!8 models

> view

> volume #8 level 0.05443

> volume #8 level 0.1434

> open
> /Users/hrishikeshdas/Documents/Projects/PAP_SUV3-PNPase/hSUV3/SUV3_alphafold.pdb

SUV3_alphafold.pdb title:  
Alphafold monomer V2.0 prediction for atp-dependent RNA helicase SUPV3L1,
mitochondrial (Q8IYB8) [more info...]  
  
Chain information for SUV3_alphafold.pdb #10  
---  
Chain | Description | UniProt  
A | atp-dependent RNA helicase SUPV3L1, mitochondrial | SUV3_HUMAN 1-786  
  

> select add #10

6190 atoms, 6329 bonds, 786 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #10,1,0,0,3.6477,0,1,0,9.1054,0,0,1,225.41

> view matrix models #10,1,0,0,57.692,0,1,0,140.75,0,0,1,195.77

> view matrix models #10,1,0,0,97.718,0,1,0,124.03,0,0,1,159.75

> ui mousemode right "rotate selected models"

> view matrix models
> #10,0.612,0.2858,0.73741,106.79,-0.67244,0.67882,0.29499,123.92,-0.41626,-0.6764,0.60763,150.42

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.612,0.2858,0.73741,119.49,-0.67244,0.67882,0.29499,127.65,-0.41626,-0.6764,0.60763,162.83

> view matrix models
> #10,0.612,0.2858,0.73741,122,-0.67244,0.67882,0.29499,133.45,-0.41626,-0.6764,0.60763,164.03

> ui mousemode right "rotate selected models"

> view matrix models
> #10,0.34987,0.68881,0.63492,115.56,-0.84264,0.52753,-0.10797,124.4,-0.40932,-0.49724,0.76499,166.44

> ui tool show "Fit in Map"

> fitmap #10 inMap #8

Fit molecule SUV3_alphafold.pdb (#10) to map
cryosparc_P102_J452_009_volume_map.mrc (#8) using 6190 atoms  
average map value = 0.05432, steps = 84  
shifted from previous position = 2.86  
rotated from previous position = 3.83 degrees  
atoms outside contour = 5260, contour level = 0.14339  
  
Position of SUV3_alphafold.pdb (#10) relative to
cryosparc_P102_J452_009_volume_map.mrc (#8) coordinates:  
Matrix rotation and translation  
0.40704602 0.65440396 0.63723543 118.73414367  
-0.81680934 0.57303626 -0.06672292 125.40368243  
-0.40882275 -0.49334055 0.76777540 165.75977715  
Axis -0.22999311 0.56393867 -0.79314333  
Axis point 198.82141921 29.66186707 0.00000000  
Rotation angle (degrees) 68.04187599  
Shift along axis -88.05931111  
  

> vop flip #8

Opened cryosparc_P102_J452_009_volume_map.mrc z flip as #11, grid size
256,256,256, pixel 1.02, shown at step 1, values float32  

> view matrix models
> #10,0.20212,0.78026,0.5919,115.15,-0.91943,0.35935,-0.15974,123.37,-0.33734,-0.51192,0.79002,167.03

> view matrix models
> #10,0.046828,0.35652,0.93311,121.88,-0.86027,0.48916,-0.14373,123.78,-0.50768,-0.796,0.32961,157.4

> fitmap #10 inMap #11

Fit molecule SUV3_alphafold.pdb (#10) to map
cryosparc_P102_J452_009_volume_map.mrc z flip (#11) using 6190 atoms  
average map value = 0.07074, steps = 88  
shifted from previous position = 4.22  
rotated from previous position = 3.64 degrees  
atoms outside contour = 4968, contour level = 0.14339  
  
Position of SUV3_alphafold.pdb (#10) relative to
cryosparc_P102_J452_009_volume_map.mrc z flip (#11) coordinates:  
Matrix rotation and translation  
0.06263843 0.32236966 0.94453916 126.13564132  
-0.88284533 0.45928194 -0.09820506 122.40607542  
-0.46546811 -0.82773057 0.31337125 157.98356204  
Axis -0.36600604 0.70740661 -0.60466145  
Axis point 175.86716568 0.00000000 62.34065104  
Rotation angle (degrees) 94.72389760  
Shift along axis -55.10211011  
  

> view sel

> view matrix models
> #10,-0.10907,0.29831,0.94822,124.47,-0.94096,0.27654,-0.19523,120.64,-0.32046,-0.91353,0.25054,158.66

> view matrix models
> #10,0.46593,-0.80847,0.35956,123.65,0.46304,0.56907,0.67952,151.47,-0.75399,-0.15012,0.63951,158.5

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.46593,-0.80847,0.35956,157.55,0.46304,0.56907,0.67952,139.62,-0.75399,-0.15012,0.63951,147.85

> view matrix models
> #10,0.46593,-0.80847,0.35956,145.93,0.46304,0.56907,0.67952,128.29,-0.75399,-0.15012,0.63951,152.96

> view matrix models
> #10,0.46593,-0.80847,0.35956,144.95,0.46304,0.56907,0.67952,122.15,-0.75399,-0.15012,0.63951,152.23

> fitmap #10 inMap #11

Fit molecule SUV3_alphafold.pdb (#10) to map
cryosparc_P102_J452_009_volume_map.mrc z flip (#11) using 6190 atoms  
average map value = 0.06887, steps = 104  
shifted from previous position = 4.55  
rotated from previous position = 4.1 degrees  
atoms outside contour = 5007, contour level = 0.14339  
  
Position of SUV3_alphafold.pdb (#10) relative to
cryosparc_P102_J452_009_volume_map.mrc z flip (#11) coordinates:  
Matrix rotation and translation  
0.46839522 -0.82097326 0.32651009 148.16847030  
0.52158902 0.55522912 0.64781598 122.68317428  
-0.71312750 -0.13312984 0.68827730 149.46991463  
Axis -0.41783943 0.55625059 0.71832826  
Axis point 57.52632082 201.09756683 0.00000000  
Rotation angle (degrees) 69.14827117  
Shift along axis 113.70042366  
  

> view matrix models
> #10,0.4684,-0.82097,0.32651,149.61,0.52159,0.55523,0.64782,124.52,-0.71313,-0.13313,0.68828,153.07

> ui mousemode right "rotate selected models"

> view matrix models
> #10,-0.80544,0.58411,-0.10039,121.96,-0.54093,-0.65528,0.52726,115.78,0.2422,0.47898,0.84375,163.79

> ui mousemode right "translate selected models"

> view matrix models
> #10,-0.80544,0.58411,-0.10039,121.58,-0.54093,-0.65528,0.52726,126.74,0.2422,0.47898,0.84375,158.82

> ui mousemode right "rotate selected models"

> view matrix models
> #10,-0.71216,0.6882,-0.1386,121.41,-0.66062,-0.59017,0.46398,123.96,0.23751,0.42198,0.87494,159.61

> ui mousemode right "translate selected models"

> view matrix models
> #10,-0.71216,0.6882,-0.1386,121.4,-0.66062,-0.59017,0.46398,130.63,0.23751,0.42198,0.87494,157.26

> fitmap #10 inMap #11

Fit molecule SUV3_alphafold.pdb (#10) to map
cryosparc_P102_J452_009_volume_map.mrc z flip (#11) using 6190 atoms  
average map value = 0.07775, steps = 192  
shifted from previous position = 11.2  
rotated from previous position = 16.5 degrees  
atoms outside contour = 4794, contour level = 0.14339  
  
Position of SUV3_alphafold.pdb (#10) relative to
cryosparc_P102_J452_009_volume_map.mrc z flip (#11) coordinates:  
Matrix rotation and translation  
-0.52897305 0.77826941 -0.33835522 123.84394212  
-0.83530274 -0.40708256 0.36953098 129.89484165  
0.14985615 0.47810097 0.86542627 146.32351797  
Axis 0.06426901 -0.28900124 -0.95516898  
Axis point 90.15832259 4.01162330 0.00000000  
Rotation angle (degrees) 122.36525401  
Shift along axis -169.34412840  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #10,-0.30809,0.85687,-0.41336,124.42,-0.93449,-0.19112,0.30033,126.61,0.17834,0.47881,0.85962,146.51

> fitmap #10 inMap #11

Fit molecule SUV3_alphafold.pdb (#10) to map
cryosparc_P102_J452_009_volume_map.mrc z flip (#11) using 6190 atoms  
average map value = 0.07968, steps = 56  
shifted from previous position = 2.8  
rotated from previous position = 1.95 degrees  
atoms outside contour = 4743, contour level = 0.14339  
  
Position of SUV3_alphafold.pdb (#10) relative to
cryosparc_P102_J452_009_volume_map.mrc z flip (#11) coordinates:  
Matrix rotation and translation  
-0.29579411 0.86579191 -0.40362141 121.71129708  
-0.94248617 -0.19566450 0.27098940 126.93794586  
0.15564605 0.46056465 0.87387329 147.14695860  
Axis 0.09965797 -0.29400177 -0.95059521  
Axis point 98.53996828 -12.09770737 0.00000000  
Rotation angle (degrees) 107.98648529  
Shift along axis -165.06767354  
  

> select clear

> fitmap #10 inMap #11

Fit molecule SUV3_alphafold.pdb (#10) to map
cryosparc_P102_J452_009_volume_map.mrc z flip (#11) using 6190 atoms  
average map value = 0.07968, steps = 44  
shifted from previous position = 0.00763  
rotated from previous position = 0.0111 degrees  
atoms outside contour = 4741, contour level = 0.14339  
  
Position of SUV3_alphafold.pdb (#10) relative to
cryosparc_P102_J452_009_volume_map.mrc z flip (#11) coordinates:  
Matrix rotation and translation  
-0.29584858 0.86581440 -0.40353323 121.70961571  
-0.94243990 -0.19565097 0.27116004 126.93391951  
0.15582260 0.46052812 0.87386108 147.14283521  
Axis 0.09954997 -0.29405090 -0.95059133  
Axis point 98.52362778 -12.09471199 0.00000000  
Rotation angle (degrees) 107.98808636  
Shift along axis -165.08154763  
  

> rainbow #10

> select clear

> select #10:691-786

742 atoms, 753 bonds, 96 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select add #10

5448 atoms, 5575 bonds, 690 residues, 1 model selected  

> view matrix models
> #10,-0.85854,0.11702,-0.49921,122.29,-0.48252,-0.51373,0.70941,133.48,-0.17344,0.84994,0.49752,141.24

> view matrix models
> #10,0.13727,0.98091,-0.13777,124.94,-0.98863,0.14429,0.042268,122.98,0.06134,0.1304,0.98956,149.57

> view matrix models
> #10,-0.32729,-0.93001,0.16724,133.46,0.67445,-0.10596,0.73068,131.71,-0.66182,0.35194,0.66192,145.14

> view matrix models
> #10,0.33394,0.65122,0.68146,137.48,-0.60512,0.70243,-0.37473,115.33,-0.72271,-0.28723,0.62864,145.87

> view matrix models
> #10,0.45178,-0.89151,-0.033329,129.5,0.23869,0.084795,0.96739,135.39,-0.8596,-0.445,0.25111,140.71

> view matrix models
> #10,0.28787,-0.95634,-0.05052,129.55,0.09031,-0.025409,0.99559,136.18,-0.9534,-0.29116,0.079052,137.98

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.28787,-0.95634,-0.05052,142.18,0.09031,-0.025409,0.99559,128.28,-0.9534,-0.29116,0.079052,148.4

> view matrix models
> #10,0.28787,-0.95634,-0.05052,135.95,0.09031,-0.025409,0.99559,131.85,-0.9534,-0.29116,0.079052,141.93

> ui mousemode right "rotate selected models"

> view matrix models
> #10,0.63532,-0.76234,0.1233,137.78,0.43161,0.48293,0.7619,127.06,-0.64038,-0.43083,0.63585,150.09

> fitmap #10 inMap #11

Fit molecule SUV3_alphafold.pdb (#10) to map
cryosparc_P102_J452_009_volume_map.mrc z flip (#11) using 5448 atoms  
average map value = 0.07307, steps = 156  
shifted from previous position = 3.39  
rotated from previous position = 7.28 degrees  
atoms outside contour = 4308, contour level = 0.14339  
  
Position of SUV3_alphafold.pdb (#10) relative to
cryosparc_P102_J452_009_volume_map.mrc z flip (#11) coordinates:  
Matrix rotation and translation  
0.68411349 -0.72890993 0.02605898 140.42389874  
0.48741729 0.48345695 0.72711332 127.46618466  
-0.54259851 -0.48472644 0.68602272 150.00358016  
Axis -0.67000767 0.31440203 0.67248872  
Axis point 12.69902113 230.22488041 0.00000000  
Rotation angle (degrees) 64.73556626  
Shift along axis 46.86625356  
  

> view matrix models
> #10,0.5984,-0.60946,0.52008,147.65,0.55837,0.78275,0.27482,120.13,-0.57458,0.12594,0.8087,150.76

> fitmap #10 inMap #11

Fit molecule SUV3_alphafold.pdb (#10) to map
cryosparc_P102_J452_009_volume_map.mrc z flip (#11) using 5448 atoms  
average map value = 0.07477, steps = 120  
shifted from previous position = 3.41  
rotated from previous position = 12 degrees  
atoms outside contour = 4307, contour level = 0.14339  
  
Position of SUV3_alphafold.pdb (#10) relative to
cryosparc_P102_J452_009_volume_map.mrc z flip (#11) coordinates:  
Matrix rotation and translation  
0.68137099 -0.62831984 0.37543015 145.53679807  
0.50163979 0.77438953 0.38558838 120.51852373  
-0.53300200 -0.07439804 0.84283678 149.88395797  
Axis -0.30241034 0.59723343 0.74287295  
Axis point 48.80688919 273.92812562 0.00000000  
Rotation angle (degrees) 49.51125728  
Shift along axis 139.31059687  
  

> view matrix models
> #10,-0.72436,-0.65635,-0.21096,138.52,0.089167,-0.39262,0.91537,130.97,-0.68363,0.64425,0.34292,141.34

> fitmap #10 inMap #11

Fit molecule SUV3_alphafold.pdb (#10) to map
cryosparc_P102_J452_009_volume_map.mrc z flip (#11) using 5448 atoms  
average map value = 0.08795, steps = 124  
shifted from previous position = 4.14  
rotated from previous position = 13.6 degrees  
atoms outside contour = 4055, contour level = 0.14339  
  
Position of SUV3_alphafold.pdb (#10) relative to
cryosparc_P102_J452_009_volume_map.mrc z flip (#11) coordinates:  
Matrix rotation and translation  
-0.77405891 -0.54864142 -0.31595165 137.24004233  
0.09315772 -0.59231247 0.80030470 136.29387952  
-0.62622239 0.59004963 0.50959492 141.72708850  
Axis -0.28289613 0.41746624 0.86353444  
Axis point 83.17018573 53.63562102 0.00000000  
Rotation angle (degrees) 158.18494596  
Shift along axis 140.45963808  
  

> view matrix models
> #10,-0.29091,0.76451,-0.57523,130.46,-0.95361,-0.28035,0.10967,126.7,-0.077426,0.58045,0.8106,145.58

> view matrix models
> #10,0.34783,-0.68454,0.64064,150.38,0.4823,0.7166,0.50386,129.08,-0.80399,0.13372,0.57941,143.79

> ui mousemode right zoom

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.34783,-0.68454,0.64064,149.97,0.4823,0.7166,0.50386,138.29,-0.80399,0.13372,0.57941,143.01

> view matrix models
> #10,0.34783,-0.68454,0.64064,142.7,0.4823,0.7166,0.50386,144.28,-0.80399,0.13372,0.57941,144.25

> fitmap #10 inMap #8

Fit molecule SUV3_alphafold.pdb (#10) to map
cryosparc_P102_J452_009_volume_map.mrc (#8) using 5448 atoms  
average map value = 0.07237, steps = 100  
shifted from previous position = 8.92  
rotated from previous position = 6.69 degrees  
atoms outside contour = 4283, contour level = 0.14339  
  
Position of SUV3_alphafold.pdb (#10) relative to
cryosparc_P102_J452_009_volume_map.mrc (#8) coordinates:  
Matrix rotation and translation  
0.43614312 -0.61124021 0.66042760 145.46605914  
0.43437206 0.78574610 0.44036805 135.06497621  
-0.78809906 0.09480779 0.60820341 146.03973804  
Axis -0.18990995 0.79606846 0.57463833  
Axis point 139.54891256 0.00000000 -148.22313504  
Rotation angle (degrees) 65.47776729  
Shift along axis 163.81554746  
  

> view matrix models
> #10,0.43614,-0.61124,0.66043,142.34,0.43437,0.78575,0.44037,133.07,-0.7881,0.094808,0.6082,151.65

> view matrix models
> #10,0.43614,-0.61124,0.66043,130.24,0.43437,0.78575,0.44037,124.04,-0.7881,0.094808,0.6082,155.18

> ui mousemode right "rotate selected models"

> view matrix models
> #10,0.3073,-0.36966,0.87688,133.17,0.38096,0.8922,0.24261,120.97,-0.87203,0.2595,0.41499,152.11

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.3073,-0.36966,0.87688,137.16,0.38096,0.8922,0.24261,124.14,-0.87203,0.2595,0.41499,151.6

> view matrix models
> #10,0.3073,-0.36966,0.87688,132.03,0.38096,0.8922,0.24261,122.02,-0.87203,0.2595,0.41499,158.52

> ui mousemode right "rotate selected models"

> view matrix models
> #10,0.078111,-0.64077,0.76375,131.1,0.2474,0.75459,0.60778,127.84,-0.96576,0.14148,0.21747,155.91

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.078111,-0.64077,0.76375,138.1,0.2474,0.75459,0.60778,132.11,-0.96576,0.14148,0.21747,150.82

> fitmap #10 inMap #8

Fit molecule SUV3_alphafold.pdb (#10) to map
cryosparc_P102_J452_009_volume_map.mrc (#8) using 5448 atoms  
average map value = 0.2012, steps = 224  
shifted from previous position = 7.91  
rotated from previous position = 38.9 degrees  
atoms outside contour = 1970, contour level = 0.14339  
  
Position of SUV3_alphafold.pdb (#10) relative to
cryosparc_P102_J452_009_volume_map.mrc (#8) coordinates:  
Matrix rotation and translation  
0.37453509 -0.08115610 0.92365426 129.86010587  
-0.02718999 0.99477246 0.09843019 126.62706393  
-0.92681401 -0.06197972 0.37037055 146.95730251  
Axis -0.08632581 0.99584356 0.02904227  
Axis point 176.64418900 0.00000000 -32.11354661  
Rotation angle (degrees) 68.29430904  
Shift along axis 119.15844182  
  

> select clear

> volume #8 style mesh

> volume #8 level 0.1327

> close #11

> show #10 atoms

> color #10 byhetero

> open
> /Users/hrishikeshdas/Documents/Projects/PAP_SUV3-PNPase/hSUV3/SUV3_alphafold_dIDP_684.pdb

SUV3_alphafold_dIDP_684.pdb title:  
Alphafold monomer V2.0 prediction for atp-dependent RNA helicase SUPV3L1,
mitochondrial (Q8IYB8) [more info...]  
  
Chain information for SUV3_alphafold_dIDP_684.pdb #11  
---  
Chain | Description | UniProt  
A | atp-dependent RNA helicase SUPV3L1, mitochondrial | SUV3_HUMAN 1-786  
  

> hide #!8 models

> show #!8 models

Error processing trigger "graphics update":  
  
You deleted or moved a volume file that is still open in ChimeraX.  
  
/Users/hrishikeshdas/Downloads/cryosparc_P102_J452_009_volume_map.mrc  
  
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.  

> hide #10-11 atoms

> hide #!8 models

> show #!8 models

> hide #10 models

> show #10 models

> hide #!8 models

> show #!8 models

> hide #11 models

> show #11 models

> select add #11

6190 atoms, 6329 bonds, 786 residues, 1 model selected  

> view matrix models #11,1,0,0,63.85,0,1,0,159.69,0,0,1,126.23

> view matrix models #11,1,0,0,103.36,0,1,0,120.45,0,0,1,140.39

> ui mousemode right "rotate selected models"

> view matrix models
> #11,-0.96375,-0.26623,0.017402,83.842,-0.11442,0.47137,0.87448,138.44,-0.24102,0.84079,-0.48474,105.44

> ui mousemode right "translate selected models"

> view matrix models
> #11,-0.96375,-0.26623,0.017402,162.85,-0.11442,0.47137,0.87448,137.76,-0.24102,0.84079,-0.48474,120.84

> view matrix models
> #11,-0.96375,-0.26623,0.017402,119.39,-0.11442,0.47137,0.87448,122.56,-0.24102,0.84079,-0.48474,99.193

> ui mousemode right "rotate selected models"

> view matrix models
> #11,-0.42042,-0.87145,-0.25264,122.4,-0.88223,0.32758,0.33819,104.5,-0.21196,0.36506,-0.90653,93.224

> ui mousemode right "translate selected models"

> view matrix models
> #11,-0.42042,-0.87145,-0.25264,146.34,-0.88223,0.32758,0.33819,116.24,-0.21196,0.36506,-0.90653,95.876

> view matrix models
> #11,-0.42042,-0.87145,-0.25264,136.74,-0.88223,0.32758,0.33819,120.13,-0.21196,0.36506,-0.90653,103.54

> fitmap #11 inMap #8

  
You deleted or moved a volume file that is still open in ChimeraX.  
  
/Users/hrishikeshdas/Downloads/cryosparc_P102_J452_009_volume_map.mrc  
  
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.  

> fitmap #11 inMap #8

  
You deleted or moved a volume file that is still open in ChimeraX.  
  
/Users/hrishikeshdas/Downloads/cryosparc_P102_J452_009_volume_map.mrc  
  
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.  

> close #8

> open
> /Users/hrishikeshdas/Documents/Projects/PAP_SUV3-PNPase/hSUV3/cryosparc_P102_J452_009_volume_map.mrc

Opened cryosparc_P102_J452_009_volume_map.mrc as #8, grid size 256,256,256,
pixel 1.02, shown at level 0.0431, step 1, values float32  

> open
> /Users/hrishikeshdas/Documents/Projects/PAP_SUV3-PNPase/hSUV3/cryosparc_P102_J452_009_volume_map.mrc

Opened cryosparc_P102_J452_009_volume_map.mrc as #12, grid size 256,256,256,
pixel 1.02, shown at level 0.0431, step 1, values float32  

> volume #12 level 0.06798

> close #8

> volume #12 level 0.1142

> volume #12 style mesh

> volume #12 color #ffb2b2

> volume #12 color #b2b2b2

> volume #12 level 0.1249

> volume #12 level 0.164

> select clear

> volume #12 level 0.2127

> volume #12 style surface

> volume #12 level 0.3312

> fitmap #11 inMap #12

Fit molecule SUV3_alphafold_dIDP_684.pdb (#11) to map
cryosparc_P102_J452_009_volume_map.mrc (#12) using 6190 atoms  
average map value = 0.1883, steps = 96  
shifted from previous position = 5.23  
rotated from previous position = 7.31 degrees  
atoms outside contour = 5111, contour level = 0.33124  
  
Position of SUV3_alphafold_dIDP_684.pdb (#11) relative to
cryosparc_P102_J452_009_volume_map.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.46318807 -0.87322017 -0.15147058 142.13344203  
-0.86496383 0.40816518 0.29195678 121.03459743  
-0.19311754 0.26624748 -0.94436111 104.00057249  
Axis -0.51797034 0.83906913 0.16634220  
Axis point 109.13846857 0.00000000 38.77854707  
Rotation angle (degrees) 178.57792433  
Shift along axis 45.23517059  
  

> volume #12 style mesh

> volume #12 level 0.3585

> volume #12 style surface

> volume #12 level 0.1427


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> ui tool hide "command line interface"

> ui tool show clix

UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 ATI-7.0.24
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: en_US.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: MacBookPro16,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 2,6 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 2092.0.0.0.0 (iBridge: 23.16.10350.0.0,0)
      OS Loader Version: 583~2317

Software:

    System Software Overview:

      System Version: macOS 15.7.1 (24G231)
      Kernel Version: Darwin 24.6.0
      Time since boot: 22 days, 11 hours, 31 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5300M:

      Chipset Model: AMD Radeon Pro 5300M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0043
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32207P1-019
      Option ROM Version: 113-D32207P1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    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-clix: 0.2.0
    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-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-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
    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
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    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: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    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: 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: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    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
    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
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    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
    tornado: 6.4.2
    traitlets: 5.14.3
    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-filename: 1.4.1
    widgetsnbextension: 4.0.13

[Tom Goddard]

The ChimeraX bug report panel said what we know about this crash:
"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."

The ChimeraX daily builds use a newer Qt version (6.9) and we have not seen these Mac wake-up crashes with the newer Qt.