Opened 6 months ago

Last modified 6 months ago

#17713 feedback defect

Crash in garbage collection

Reported by: ellen_goodall@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-15.4.1-arm64-arm-64bit
ChimeraX Version: 1.8rc202406062357 (2024-06-06 23:57:44 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Opening a previously saved session file (.cxs) while an unsaved session was already open with some of the same models in it.  The saved session was saved in Dropbox.
Fatal Python error: Segmentation fault

Thread 0x000000030d89f000 (most recent call first):
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030c893000 (most recent call first):
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030b887000 (most recent call first):
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030a87b000 (most recent call first):
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030986f000 (most recent call first):
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000308863000 (most recent call first):
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000307857000 (most recent call first):
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030684b000 (most recent call first):
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030583f000 (most recent call first):
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000304833000 (most recent call first):
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000303827000 (most recent call first):
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000001fdc48c80 (most recent call first):
  Garbage-collecting
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py", line 81 in msgpack_deserialize
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 731 in restore
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 1027 in open
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 37 in open
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 514 in collated_open
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 2075 in _open_dropped_file
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 278 in event
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
  File "/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 57)


{"app_name":"ChimeraX","timestamp":"2025-05-17 11:36:02.00 -0400","app_version":"1.8.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.4.1 (24E263)","roots_installed":0,"name":"ChimeraX","incident_id":"287BFAC6-9632-4112-B34A-4F5DE98E4686"}
{
  "uptime" : 570000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac15,12",
  "coalitionID" : 31659,
  "osVersion" : {
    "train" : "macOS 15.4.1",
    "build" : "24E263",
    "releaseType" : "User"
  },
  "captureTime" : "2025-05-17 11:35:34.0789 -0400",
  "codeSigningMonitor" : 1,
  "incident" : "287BFAC6-9632-4112-B34A-4F5DE98E4686",
  "pid" : 54982,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-05-05 10:53:19.7452 -0400",
  "procStartAbsTime" : 4838873906041,
  "procExitAbsTime" : 13753008067126,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.8-rc2024.06.06.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"42F7C1EC-CD6D-5968-9338-1A326C717D71","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "6A0D85A0-73D0-FDF6-2CF9-64F58447F9D8",
  "appleIntelligenceStatus" : {"state":"available"},
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "codeSigningAuxiliaryInfo" : 0,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "bootSessionUUID" : "75B705A4-6C92-4BD1-97D4-11D68297E5BF",
  "wakeTime" : 1539,
  "sleepWakeUUID" : "2C71A223-E793-466A-9D12-9487857885A3",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 4363206487\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      104114000-104118000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.8-rc2024.06.06.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":54982},
  "vmregioninfo" : "0xa9 is not in any region.  Bytes before following region: 4363206487\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      104114000-104118000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.8-rc2024.06.06.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" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":4832197272},{"value":80},{"value":95},{"value":0},{"value":0},{"value":6150242987246246045},{"value":6150242984221922333},{"value":14757395258967641293},{"value":4294967286},{"value":4832197202},{"value":0},{"value":53},{"value":4294967280},{"value":328},{"value":8569719488},{"value":0},{"value":11},{"value":259},{"value":8552484192,"symbolLocation":224,"symbol":"_main_thread"},{"value":0},{"value":1},{"value":4386981424,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":4385108828,"symbolLocation":0,"symbol":"visit_decref"},{"value":6103621760},{"value":0},{"value":4387916384,"symbolLocation":59712,"symbol":"_PyRuntime"}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6691444876},"cpsr":{"value":1073745920},"fp":{"value":4832197344},"sp":{"value":4832197312},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6691210120,"matchesCrashFrame":1},"far":{"value":0}},"id":2842750,"triggered":true,"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":37768,"symbol":"__pthread_kill","symbolLocation":8,"imageIndex":154},{"imageOffset":26764,"symbol":"pthread_kill","symbolLocation":296,"imageIndex":155},{"imageOffset":265476,"symbol":"raise","symbolLocation":32,"imageIndex":156},{"imageOffset":2417160,"symbol":"faulthandler_fatal_error","symbolLocation":392,"imageIndex":1},{"imageOffset":13860,"symbol":"_sigtramp","symbolLocation":56,"imageIndex":157},{"imageOffset":1120748,"symbol":"tupletraverse","symbolLocation":56,"imageIndex":1},{"imageOffset":1120748,"symbol":"tupletraverse","symbolLocation":56,"imageIndex":1},{"imageOffset":2401060,"symbol":"gc_collect_main","symbolLocation":1968,"imageIndex":1},{"imageOffset":2407432,"symbol":"_PyObject_GC_Link","symbolLocation":316,"imageIndex":1},{"imageOffset":829344,"symbol":"PyList_New","symbolLocation":364,"imageIndex":1},{"imageOffset":88960,"symbol":"int 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    "CFBundleIdentifier" : "com.apple.AE",
    "size" : 472968,
    "uuid" : "af465d64-f47f-3e27-bdfc-622fc7d39fd9",
    "path" : "\/System\/Library\/Frameworks\/CoreServices.framework\/Versions\/A\/Frameworks\/AE.framework\/Versions\/A\/AE",
    "name" : "AE",
    "CFBundleVersion" : "944"
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    "arch" : "arm64e",
    "base" : 6884225024,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 3174368,
    "uuid" : "6cc82a38-f1b5-3f2b-876b-9b3d7b278490",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
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    "source" : "P",
    "arch" : "arm64e",
    "base" : 6687621120,
    "size" : 633476,
    "uuid" : "aca43a8d-6369-3a2c-af92-3d4c458523d6",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "size" : 0,
    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
  },
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    "source" : "P",
    "arch" : "arm64e",
    "base" : 6691897344,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 5500928,
    "uuid" : "39e0f63a-3ab8-39e9-97f8-333cde9a7ba4",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "3423"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6690471936,
    "size" : 577528,
    "uuid" : "53484980-83fc-35e9-8786-e6cf5eba9471",
    "path" : "\/usr\/lib\/libc++.1.dylib",
    "name" : "libc++.1.dylib"
  }
],
  "sharedCache" : {
  "base" : 6686785536,
  "size" : 5020123136,
  "uuid" : "bb86a9b4-8362-37b8-b028-212703af6f30"
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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=2.5G written=3783K(0%) resident=1735K(0%) swapped_out=2048K(0%) unallocated=2.5G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework              2048K       16 \nActivity Tracing                   256K        1 \nCG image                           672K       33 \nColorSync                          608K       32 \nCoreAnimation                     1440K       88 \nCoreGraphics                        80K        5 \nCoreUI image data                 5232K       40 \nFoundation                          48K        2 \nKernel Alloc Once                 1424K        4 \nMALLOC                             1.8G       98 \nMALLOC guard page                  288K       18 \nMach message                        64K        4 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        704K       44 \nStack                            336.6M       45 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      286.8M      186 \nVM_ALLOCATE (reserved)            64.0M        2         reserved VM address space (unallocated)\n__AUTH                            5486K      695 \n__AUTH_CONST                      77.2M      942 \n__CTF                               824        1 \n__DATA                            34.1M     1086 \n__DATA_CONST                      36.9M     1102 \n__DATA_DIRTY                      2775K      342 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       651.4M      155 \n__OBJC_RO                         61.3M        1 \n__OBJC_RW                         2391K        1 \n__TEXT                             1.3G     1122 \n__TPRO_CONST                       128K        2 \ndyld private memory               1952K       17 \nmapped file                      286.6M       67 \npage table in kernel              1735K        1 \nshared memory                     3216K       27 \n===========                     =======  ======= \nTOTAL                              5.0G     6187 \nTOTAL, minus reserved VM space     4.9G     6187 \n",
  "legacyInfo" : {
  "threadTriggered" : {
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},
  "logWritingSignature" : "5201bd39f0c58a0cbd52f9950993cf8930df8f28",
  "trialInfo" : {
  "rollouts" : [
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      "factorPackIds" : {
        "VISUAL_INTELLIGENCE_VICTORIA" : "66d8b2f77cd4b62688efd2cf"
      },
      "deploymentId" : 240000004
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    {
      "rolloutId" : "60f8ddccefea4203d95cbeef",
      "factorPackIds" : {

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  "experiments" : [
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      "experimentId" : "67f46e2984eaf455d73c609a",
      "deploymentId" : 400000001
    }
  ]
}
}
===== Log before crash start =====
Startup Errors  
---  
errors | Bundle 'ChimeraX-ISOLDE' custom initialization failed  
Bundle 'ChimeraX-Clipper' custom initialization failed  
warnings | Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 501, in get_module  
m = importlib.import_module(self.package_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py",
line 126, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "", line 1204, in _gcd_import  
File "", line 1176, in _find_and_load  
File "", line 1147, in _find_and_load_unlocked  
File "", line 690, in _load_unlocked  
File "", line 940, in exec_module  
File "", line 241, in _call_with_frames_removed  
File "/Users/Ellen/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/__init__.py", line 51, in   
__version__ = _version()  
^^^^^^^^^^  
File "/Users/Ellen/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/__init__.py", line 49, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 937, in require  
needed = self.resolve(parse_requirements(requirements))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 798, in resolve  
dist = self._resolve_dist(  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 844, in _resolve_dist  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-Core 1.8rc202406062357
(/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages), Requirement.parse('ChimeraX-Core~=1.8.0'), {'ChimeraX-Clipper',
'ChimeraX-ISOLDE'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 375, in initialize  
api = self._get_api(session.logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 520, in _get_api  
m = self.get_module()  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 503, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-Core 1.8rc202406062357
(/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages), Requirement.parse('ChimeraX-Core~=1.8.0'), {'ChimeraX-Clipper',
'ChimeraX-ISOLDE'})  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 501, in get_module  
m = importlib.import_module(self.package_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py",
line 126, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "", line 1204, in _gcd_import  
File "", line 1176, in _find_and_load  
File "", line 1147, in _find_and_load_unlocked  
File "", line 690, in _load_unlocked  
File "", line 940, in exec_module  
File "", line 241, in _call_with_frames_removed  
File "/Users/Ellen/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/clipper/__init__.py", line 32, in   
__version__ = _version()  
^^^^^^^^^^  
File "/Users/Ellen/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/clipper/__init__.py", line 30, in _version  
return pkg_resources.require('ChimeraX-Clipper')[0].version  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 937, in require  
needed = self.resolve(parse_requirements(requirements))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 798, in resolve  
dist = self._resolve_dist(  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 844, in _resolve_dist  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-Core 1.8rc202406062357
(/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages), Requirement.parse('ChimeraX-Core~=1.8.0'), {'ChimeraX-Clipper'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 375, in initialize  
api = self._get_api(session.logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 520, in _get_api  
m = self.get_module()  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 503, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-
Clipper's module: (ChimeraX-Core 1.8rc202406062357
(/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages), Requirement.parse('ChimeraX-Core~=1.8.0'), {'ChimeraX-Clipper'})  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.8rc202406062357 (2024-06-06)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/Ellen/HMS Dropbox/Ellen
> Goodall/Ellen_shared/Chimera_sessions_forWade/AF3_FBXO7_PI31/PI31_FBXO7_Skp1_trimer/fold_2025_02_24_o7_f1_skp1_hsapiens/fold_2025_02_24_o7_f1_skp1_hsapiens_model_0.cif"

Chain information for fold_2025_02_24_o7_f1_skp1_hsapiens_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> select #0/A

Nothing selected  

> select #0:A

Nothing selected  

> select /A:1-522

4120 atoms, 4227 bonds, 522 residues, 1 model selected  

> select /B:1-271

2108 atoms, 2179 bonds, 271 residues, 1 model selected  

> color lime sel

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel lime

> select /C:1-163

1308 atoms, 1331 bonds, 163 residues, 1 model selected  

> color sel orangered

> select clear

> select /A:1-522

4120 atoms, 4227 bonds, 522 residues, 1 model selected  

> color sel gray

> select /A:1-92

731 atoms, 747 bonds, 92 residues, 1 model selected  

> select /A:1-81

654 atoms, 667 bonds, 81 residues, 1 model selected  

> color /A:1-81 magenta

> select clear

> color /A:180-326 gold

> color /A:331-375 orange

> color /A:331-378 orange

> color /A:407-510

> color /A:407-510 forestgreen

> color /A:441-444 purple

> color /A:464-466 purple

> color /A:481-483 purple

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select /B:1-271

2108 atoms, 2179 bonds, 271 residues, 1 model selected  

> ui tool show "Color Actions"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> color sel honeydew

> select clear

> color pale turquoise

> undo

> select clear

> select /B:1-271

2108 atoms, 2179 bonds, 271 residues, 1 model selected  

> color sel pale turquoise

> color sel aquamarine

> select /C:1-163

1308 atoms, 1331 bonds, 163 residues, 1 model selected  

> color sel light coral

> select clear

> set bgColor black

> set bgColor white

> lighting simple

> lighting soft

> lighting full

> graphics silhouettes true

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> ui tool show "Side View"

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/Ellen/Desktop/movie2.mp4

Movie saved to /Users/Ellen/Desktop/movie2.mp4  
  

> ~ribbon /B

> ~ribbon /A:450-522

> select /A:381

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select /C:114

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:381

11 atoms, 10 bonds, 1 residue, 1 model selected  

> color /A:381 red

> select clear

> color /A:389 orangered

> select /A:389

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> color /A:406 lime

> select clear

> select /A:406

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> save /Users/Ellen/Desktop/image5.png supersample 3

> select /A:422

8 atoms, 7 bonds, 1 residue, 1 model selected  

> open "/Users/Ellen/HMS Dropbox/Ellen
> Goodall/Ellen_shared/Chimera_sessions_forWade/AF3_FBXO7_PI31/20S_interaction/folds_2025_03_23_00_10/betaring_pi31_corb5/fold_betaring_pi31_corb5_model_0.cif"

Chain information for fold_betaring_pi31_corb5_model_0.cif #2  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
G H | .  
I J | .  
K L | .  
M N | .  
O P | .  
  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> hide #1 models

> hide #2 atoms

> show #2 cartoons

Drag select of 22 residues  

> select clear

> color #2 grey

> color #2/P orange

> color #2/O red

> ui tool show "Show Sequence Viewer"

> sequence chain #2/O #2/P

Alignment identifier is 1  

> select #2/O-P:13

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select #2/O-P:13-17

74 atoms, 78 bonds, 10 residues, 1 model selected  

> select #2/O-P:56

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #2/O-P:56-59

74 atoms, 76 bonds, 8 residues, 1 model selected  

> open "/Users/Ellen/HMS Dropbox/Ellen
> Goodall/Ellen_shared/Chimera_sessions_forWade/AF3_FBXO7_PI31/20S_interaction/Comparison_prediction_PI3120Scryo.cxs"


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

Log:
UCSF ChimeraX version: 1.8rc202406062357 (2024-06-06)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/Ellen/HMS Dropbox/Ellen
> Goodall/Ellen_shared/Chimera_sessions_forWade/AF3_FBXO7_PI31/20S_interaction/Comparison_prediction_PI3120Scryo.cxs"

Log from Wed Mar 12 21:11:45 2025 Startup Errors  
---  
errors | Bundle 'ChimeraX-Clipper' custom initialization failed  
Bundle 'ChimeraX-ISOLDE' custom initialization failed  
warnings | Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 501, in get_module  
m = importlib.import_module(self.package_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py",
line 126, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen importlib._bootstrap>", line 1204, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1176, in _find_and_load  
File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 940, in exec_module  
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed  
File "/Users/Ellen/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/clipper/__init__.py", line 32, in <module>  
__version__ = _version()  
^^^^^^^^^^  
File "/Users/Ellen/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/clipper/__init__.py", line 30, in _version  
return pkg_resources.require('ChimeraX-Clipper')[0].version  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 937, in require  
needed = self.resolve(parse_requirements(requirements))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 798, in resolve  
dist = self._resolve_dist(  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 844, in _resolve_dist  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-Core 1.8rc202406062357
(/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages), Requirement.parse('ChimeraX-Core~=1.8.0'), {'ChimeraX-Clipper'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 375, in initialize  
api = self._get_api(session.logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 520, in _get_api  
m = self.get_module()  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 503, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-
Clipper's module: (ChimeraX-Core 1.8rc202406062357
(/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages), Requirement.parse('ChimeraX-Core~=1.8.0'), {'ChimeraX-Clipper'})  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 501, in get_module  
m = importlib.import_module(self.package_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py",
line 126, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen importlib._bootstrap>", line 1204, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1176, in _find_and_load  
File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 940, in exec_module  
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed  
File "/Users/Ellen/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/__init__.py", line 51, in <module>  
__version__ = _version()  
^^^^^^^^^^  
File "/Users/Ellen/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/__init__.py", line 49, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 937, in require  
needed = self.resolve(parse_requirements(requirements))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 798, in resolve  
dist = self._resolve_dist(  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 844, in _resolve_dist  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-Core 1.8rc202406062357
(/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages), Requirement.parse('ChimeraX-Core~=1.8.0'), {'ChimeraX-Clipper',
'ChimeraX-ISOLDE'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 375, in initialize  
api = self._get_api(session.logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 520, in _get_api  
m = self.get_module()  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 503, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-Core 1.8rc202406062357
(/Applications/ChimeraX-1.8-rc2024.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages), Requirement.parse('ChimeraX-Core~=1.8.0'), {'ChimeraX-Clipper',
'ChimeraX-ISOLDE'})  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8rc202406062357 (2024-06-06)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/Ellen/Desktop/EM_CM10/output/INA_UBL/INA_TrxA_UBL_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
INA_TrxA_UBL_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/Ellen/Desktop/EM_CM10/PRKN_UBI/PRKN_TrxA_UBL_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
PRKN_TrxA_UBL_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb
#2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #1 models

> select #2.B

Expected an objects specifier or a keyword  

> select #2/B

601 atoms, 607 bonds, 76 residues, 1 model selected  

> select #2:lys/B

763 atoms, 752 bonds, 94 residues, 1 model selected  

> select #2:lys

225 atoms, 201 bonds, 25 residues, 1 model selected  

> open /Users/Ellen/Downloads/member-sequences-A0A5N5NGW7(1).fasta

Failed opening file /Users/Ellen/Downloads/member-
sequences-A0A5N5NGW7(1).fasta:  
Sequence 'A0A061IJE0 F-box only protein 7 OX=10029 OS=Cricetulus griseus
Flag=1' differs in length from preceding sequences, and it is therefore
impossible to open these sequences as an alignment. If you want to open the
sequences individually, specify 'false' as the value of the 'alignment'
keyword in the 'open' command.  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> close #1

> close

> open
> /Users/Ellen/Downloads/fold_betaring_pi31/fold_betaring_pi31_model_0.cif
> /Users/Ellen/Downloads/fold_betaring_pi31/fold_betaring_pi31_model_1.cif

Chain information for fold_betaring_pi31_model_0.cif #1  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
G H | .  
I J | .  
K L | .  
M N | .  
O P | .  
  
Chain information for fold_betaring_pi31_model_1.cif #2  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
G H | .  
I J | .  
K L | .  
M N | .  
O P | .  
  

> show cartoons

> hide atoms

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> open /Users/Ellen/Documents/Chimera/PDB/8FV6.cif

Summary of feedback from opening /Users/Ellen/Documents/Chimera/PDB/8FV6.cif  
---  
note | Fetching CCD NA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/NA/NA.cif  
  
8FV6.cif title:  
E coli. CTP synthase in complex with dF-dCTP [more info...]  
  
Chain information for 8FV6.cif #3  
---  
Chain | Description | UniProt  
AAA BBB | CTP synthase | PYRG_ECO45 1-545  
  
Non-standard residues in 8FV6.cif #3  
---  
GTF — 2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate)
(Gemcitabine-TRIPHOSPHATE)  
MLA — malonic acid (dicarboxylic acid C3; propanediolic acid;
methanedicarboxylic acid)  
NA — sodium ion  
  
8FV6.cif mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
86 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> close #3

> open /Users/Ellen/Documents/Chimera/PDB/8FV6.cif

8FV6.cif title:  
E coli. CTP synthase in complex with dF-dCTP [more info...]  
  
Chain information for 8FV6.cif #3  
---  
Chain | Description | UniProt  
AAA BBB | CTP synthase | PYRG_ECO45 1-545  
  
Non-standard residues in 8FV6.cif #3  
---  
GTF — 2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate)
(Gemcitabine-TRIPHOSPHATE)  
MLA — malonic acid (dicarboxylic acid C3; propanediolic acid;
methanedicarboxylic acid)  
NA — sodium ion  
  
8FV6.cif mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
86 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> open /Users/Ellen/Documents/Chimera/PDB/8FZ6.pdb

8FZ6.pdb title:  
The human Π31 complexed with bovine 20S proteasome [more info...]  
  
Chain information for 8FZ6.pdb #4  
---  
Chain | Description | UniProt  
A O | proteasome subunit α type-6 | PSA6_BOVIN 1-246  
B P | proteasome subunit α type-2 | PSA2_BOVIN 1-234  
C Q | proteasome subunit α type-4 | PSA4_BOVIN 1-261  
D R | proteasome subunit α type-7 | PSA7_BOVIN 1-248  
E S | proteasome subunit α type-5 | PSA5_BOVIN 1-241  
F T | proteasome subunit α type-1 | PSA1_BOVIN 1-263  
G U | proteasome subunit α type-3 | PSA3_BOVIN 1-255  
H V | proteasome subunit β type-6 | PSB6_BOVIN -33-205  
I W | proteasome subunit β type-7 | PSB7_BOVIN -42-234  
J X | proteasome subunit β type-3 | PSB3_BOVIN 1-205  
K Y | proteasome subunit β type-2 | PSB2_BOVIN 1-201  
L Z | proteasome subunit β type-5 | PSB5_BOVIN -58-204  
M a | proteasome subunit β type-1 | PSB1_BOVIN 1-241  
N b | proteasome subunit β type-4 | PSB4_BOVIN -44-219  
c d | proteasome inhibitor Π31 subunit | PSMF1_BOVIN 1-271  
  

> close #3

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #4 to #1

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 fold_betaring_pi31_model_0.cif, chain M (#1) with 8FZ6.pdb, chain I
(#4), sequence alignment score = 1155.3  
RMSD between 218 pruned atom pairs is 0.572 angstroms; (across all 220 pairs:
0.662)  
  

> hide atoms

> show cartoons

> ~ribbon #4:.A-G

> cartoon hide #4:.A-G

Expected an atoms specifier or a keyword  

> ~ribbon #4:/A-G

> cartoon hide #4:/A-G

Expected an atoms specifier or a keyword  

> ~ribbon #4:A-G

> hide cartoons

> show cartoons

> ~ribbon #4/A-G

> ~ribbon #4/O-U

> hide #2 models

> color dark grey #4

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #4 darkgrey

> select clear

> select #1/P:35

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color #1 grey

> color #1/O orange

> color #1/p redorange

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #1/P orangered

> color #4 dimgrey

> hide #4 models

> show #4 models

> hide #1 models

> color #4/c orange

> color #4/d orangered

> color #4/d lime

> color #4/c green

> show #2 models

> hide #2 models

> show #1 models

> show #2 models

> color #2 lightgrey

> color #2/o yellow

> color #2/p gold

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #2 to #1

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 fold_betaring_pi31_model_0.cif, chain M (#1) with
fold_betaring_pi31_model_1.cif, chain M (#2), sequence alignment score =
1205.4  
RMSD between 223 pruned atom pairs is 0.152 angstroms; (across all 234 pairs:
2.246)  
  

> ~ribbon #1

> ~ribbon #2

> ribbon #1/o

> ribbon #1/p

> ribbon #2/p

> ribbon #2/o

> hide #2 models

> hide #1 models

> select #4/d:198

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #4/d:197

16 atoms, 14 bonds, 2 residues, 1 model selected  

> display sel

> style sel stick

Changed 16 atom styles  

> select #4/d:208

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #4/d:209

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select add #4/d:199

24 atoms, 21 bonds, 3 residues, 1 model selected  

> select add #4/d:193

31 atoms, 27 bonds, 4 residues, 1 model selected  

> display sel

> style sel stick

Changed 31 atom styles  

> show #2 models

> select #2/O:55

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #2/O:54

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #2/O:53

7 atoms, 7 bonds, 1 residue, 1 model selected  

> hide #2 models

> show #1 models

> select #1/O:13

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #1/O:12

16 atoms, 14 bonds, 2 residues, 1 model selected  
Drag select of 2 residues  

> select #1/O:12

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #1/O:13

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select add #1/O:11

24 atoms, 21 bonds, 3 residues, 1 model selected  

> display sel

> style sel stick

Changed 24 atom styles  

> select #1/O:7

7 atoms, 6 bonds, 1 residue, 1 model selected  

> hide #1 models

> color byhetero

> select #4/d:244

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #4/d:243

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select add #4/d:242

30 atoms, 28 bonds, 3 residues, 1 model selected  

> select add #4/I:166

38 atoms, 35 bonds, 4 residues, 1 model selected  

> select subtract #4/I:166

30 atoms, 28 bonds, 3 residues, 1 model selected  

> select add #4/d:245

37 atoms, 35 bonds, 4 residues, 1 model selected  

> select add #4/I:130

41 atoms, 38 bonds, 5 residues, 1 model selected  

> select subtract #4/I:130

37 atoms, 35 bonds, 4 residues, 1 model selected  

> display sel

> style sel stick

Changed 37 atom styles  

> select #4/d:229

7 atoms, 7 bonds, 1 residue, 1 model selected  

> show #2 models

> hide #2 models

> show #1 models

> hide #1 models

> show #2 models

> hide #2 models

> show #1 models

> open
> /Users/Ellen/Downloads/fold_betaring_fbxo7_minimal/fold_betaring_fbxo7_minimal_model_0.cif
> /Users/Ellen/Downloads/fold_betaring_fbxo7_minimal/fold_betaring_fbxo7_minimal_model_1.cif

Chain information for fold_betaring_fbxo7_minimal_model_0.cif #3  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
G H | .  
I J | .  
K L | .  
M N | .  
O P | .  
  
Chain information for fold_betaring_fbxo7_minimal_model_1.cif #5  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
G H | .  
I J | .  
K L | .  
M N | .  
O P | .  
  

> ~display #5-6

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> hide #1 models

> hide #3 models

> hide #4 models

> hide #5 models

> show #5 models

> ribbon #3

> show #3 models

> ~display #3

> color #3 grey

> color #3/o blue

> color #3/p dodgerblue

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #3 to #1

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 fold_betaring_pi31_model_0.cif, chain M (#1) with
fold_betaring_fbxo7_minimal_model_0.cif, chain M (#3), sequence alignment
score = 1202.4  
RMSD between 222 pruned atom pairs is 0.144 angstroms; (across all 234 pairs:
2.566)  
  

> show #1 models

> hide #1 models

> show #4 models

> hide #3 models

> show #3 models

> hide #3 models

> hide #5 models

> show #5 models

> ~display #5

> ribbon #5

> color grey #5

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #5 grey

> color #5/o purple

> color #5/p orchid

> ~ribbon #3

> ~ribbon #5

> ribbon #5/o

> ribbon #5/p

> ribbon #3/p

> ribbon #3/o

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #3,5 to #1

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 fold_betaring_pi31_model_0.cif, chain M (#1) with
fold_betaring_fbxo7_minimal_model_0.cif, chain M (#3), sequence alignment
score = 1202.4  
RMSD between 222 pruned atom pairs is 0.144 angstroms; (across all 234 pairs:
2.566)  
  
Matchmaker fold_betaring_pi31_model_0.cif, chain M (#1) with
fold_betaring_fbxo7_minimal_model_1.cif, chain M (#5), sequence alignment
score = 1205.4  
RMSD between 222 pruned atom pairs is 0.162 angstroms; (across all 234 pairs:
2.803)  
  

> hide #4 models

> show #3 models

> show #4 models

> select #5/O:15

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #5/O:14

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select #3/O:47

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select add #3/O:46

22 atoms, 21 bonds, 2 residues, 1 model selected  

> select add #3/O:48

30 atoms, 28 bonds, 3 residues, 1 model selected  

> select #3:46-48

322 atoms, 308 bonds, 48 residues, 1 model selected  

> select #3/46-48

Nothing selected  

> select #3.46-48

Nothing selected  

> select #3/:46-48

Expected an objects specifier or a keyword  

> help help:quickstart

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select #3/o-p:46-48

60 atoms, 60 bonds, 6 residues, 1 model selected  

> hide #4 models

> select #3-4/o-p:46-48

60 atoms, 60 bonds, 6 residues, 1 model selected  

> select #4/o-p:46-48

Nothing selected  

> select #4/o:46-48

Nothing selected  

> select #3-5/o-p:46-48

120 atoms, 120 bonds, 12 residues, 2 models selected  

> show #4 models

> hide #3 models

> hide #5 models

> select #4/Z:1

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color yellow sel

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel yellow

> select clear

[Repeated 4 time(s)]

> select #4/I:1

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color yellow sel

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel yellow

> select #4/I:59

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/I:57

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

173 atoms, 173 bonds, 24 residues, 1 model selected  

> select up

1660 atoms, 1687 bonds, 220 residues, 1 model selected  

> select clear

> show #5 models

> hide #5 models

> select clear

> select #4/L:1

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color sel yellow

> select #4/W:1

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color sel yellow

> select #4/1

Nothing selected  

> select #4.1

Nothing selected  

> select #4:1

104 atoms, 90 bonds, 14 residues, 1 model selected  

> show #5 models

> hide #5 models

> show #3 models

> show #5 models

> hide #3 models

> select #5/P:13

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select add #5/P:15

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select add #5/P:14

29 atoms, 27 bonds, 3 residues, 1 model selected  

> display sel

> style sel stick

Changed 29 atom styles  

> select clear

> show #3 models

> select #3-5/o-p:13-15

116 atoms, 116 bonds, 12 residues, 2 models selected  

> hide #4 models

> open
> /Users/Ellen/Downloads/fold_betaring_fbxo7_minimal/fold_betaring_fbxo7_minimal_model_2.cif
> /Users/Ellen/Downloads/fold_betaring_fbxo7_minimal/fold_betaring_fbxo7_minimal_model_3.cif
> /Users/Ellen/Downloads/fold_betaring_fbxo7_minimal/fold_betaring_fbxo7_minimal_model_4.cif

Chain information for fold_betaring_fbxo7_minimal_model_2.cif #6  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
G H | .  
I J | .  
K L | .  
M N | .  
O P | .  
  
Chain information for fold_betaring_fbxo7_minimal_model_3.cif #7  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
G H | .  
I J | .  
K L | .  
M N | .  
O P | .  
  
Chain information for fold_betaring_fbxo7_minimal_model_4.cif #8  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
G H | .  
I J | .  
K L | .  
M N | .  
O P | .  
  

> style sel stick

Changed 116 atom styles  

> disp#6-8

Unknown command: disp#6-8  

> display #6-8

> ~display #6-8

> ribbon #6-8/o

> ribbon #6-8/p

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #5-8 to #1

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 fold_betaring_pi31_model_0.cif, chain M (#1) with
fold_betaring_fbxo7_minimal_model_1.cif, chain M (#5), sequence alignment
score = 1205.4  
RMSD between 222 pruned atom pairs is 0.162 angstroms; (across all 234 pairs:
2.803)  
  
Matchmaker fold_betaring_pi31_model_0.cif, chain M (#1) with
fold_betaring_fbxo7_minimal_model_2.cif, chain M (#6), sequence alignment
score = 1205.4  
RMSD between 222 pruned atom pairs is 0.121 angstroms; (across all 234 pairs:
2.754)  
  
Matchmaker fold_betaring_pi31_model_0.cif, chain M (#1) with
fold_betaring_fbxo7_minimal_model_3.cif, chain M (#7), sequence alignment
score = 1202.4  
RMSD between 224 pruned atom pairs is 0.200 angstroms; (across all 234 pairs:
1.150)  
  
Matchmaker fold_betaring_pi31_model_0.cif, chain M (#1) with
fold_betaring_fbxo7_minimal_model_4.cif, chain M (#8), sequence alignment
score = 1205.4  
RMSD between 219 pruned atom pairs is 0.130 angstroms; (across all 234 pairs:
3.780)  
  

> select #3-8/o-p:13-15

290 atoms, 290 bonds, 30 residues, 5 models selected  

> hide #6 models

> hide #7 models

> hide #8 models

> select #3-8/o-p:12-15

380 atoms, 380 bonds, 40 residues, 5 models selected  

> select #3-8/o-p:9-15

540 atoms, 540 bonds, 70 residues, 5 models selected  

> show #6 models

> hide #6 models

> show #4 models

> show #6 models

> hide #6 models

> hide #4 models

> show #6 models

> show #7 models

> show #8 models

> hide #6 models

> hide #7 models

> hide #8 models

> hide #5 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> show #5 models

> show #6 models

> show #7 models

> show #8 models

> select #3-8/o-p:5-15

800 atoms, 820 bonds, 110 residues, 5 models selected  

> open
> /Users/Ellen/Downloads/fold_betaring_pi31_fbxo7/fold_betaring_pi31_fbxo7_model_0.cif
> /Users/Ellen/Downloads/fold_betaring_pi31_fbxo7/fold_betaring_pi31_fbxo7_model_1.cif
> /Users/Ellen/Downloads/fold_betaring_pi31_fbxo7/fold_betaring_pi31_fbxo7_model_2.cif
> /Users/Ellen/Downloads/fold_betaring_pi31_fbxo7/fold_betaring_pi31_fbxo7_model_3.cif
> /Users/Ellen/Downloads/fold_betaring_pi31_fbxo7/fold_betaring_pi31_fbxo7_model_4.cif

Chain information for fold_betaring_pi31_fbxo7_model_0.cif #9  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
G H | .  
I J | .  
K L | .  
M N | .  
O | .  
P | .  
  
Chain information for fold_betaring_pi31_fbxo7_model_1.cif #10  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
G H | .  
I J | .  
K L | .  
M N | .  
O | .  
P | .  
  
Chain information for fold_betaring_pi31_fbxo7_model_2.cif #11  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
G H | .  
I J | .  
K L | .  
M N | .  
O | .  
P | .  
  
Chain information for fold_betaring_pi31_fbxo7_model_3.cif #12  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
G H | .  
I J | .  
K L | .  
M N | .  
O | .  
P | .  
  
Chain information for fold_betaring_pi31_fbxo7_model_4.cif #13  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
G H | .  
I J | .  
K L | .  
M N | .  
O | .  
P | .  
  

> ~display #9-13

> ribbon #9-13/o

> ribbon #9-13/p

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #9-13 to #1

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 fold_betaring_pi31_model_0.cif, chain M (#1) with
fold_betaring_pi31_fbxo7_model_0.cif, chain M (#9), sequence alignment score =
1205.4  
RMSD between 225 pruned atom pairs is 0.166 angstroms; (across all 234 pairs:
0.877)  
  
Matchmaker fold_betaring_pi31_model_0.cif, chain M (#1) with
fold_betaring_pi31_fbxo7_model_1.cif, chain M (#10), sequence alignment score
= 1205.4  
RMSD between 224 pruned atom pairs is 0.168 angstroms; (across all 234 pairs:
1.748)  
  
Matchmaker fold_betaring_pi31_model_0.cif, chain M (#1) with
fold_betaring_pi31_fbxo7_model_2.cif, chain M (#11), sequence alignment score
= 1205.4  
RMSD between 224 pruned atom pairs is 0.162 angstroms; (across all 234 pairs:
1.424)  
  
Matchmaker fold_betaring_pi31_model_0.cif, chain M (#1) with
fold_betaring_pi31_fbxo7_model_3.cif, chain M (#12), sequence alignment score
= 1205.4  
RMSD between 222 pruned atom pairs is 0.117 angstroms; (across all 234 pairs:
3.179)  
  
Matchmaker fold_betaring_pi31_model_0.cif, chain M (#1) with
fold_betaring_pi31_fbxo7_model_4.cif, chain M (#13), sequence alignment score
= 1205.4  
RMSD between 225 pruned atom pairs is 0.176 angstroms; (across all 234 pairs:
1.142)  
  

> color lightblue #9-13/o

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #9-13/o lightblue

> color #9-13/p lightgreen

> show #4 models

> hide #5 models

> hide #6 models

> hide #7 models

> hide #8 models

> hide #3 models

> hide #4 models

> hide #13 models

> hide #12 models

> hide #11 models

> hide #10 models

> hide #9 models

> show #8 models

> show #7 models

> show #6 models

> show #5 models

> show #3 models

> hide #3 models

> hide #5 models

> hide #6 models

> hide #7 models

> hide #8 models

> open
> /Users/Ellen/Downloads/fold_betaring_pi31/fold_betaring_pi31_model_2.cif
> /Users/Ellen/Downloads/fold_betaring_pi31/fold_betaring_pi31_model_3.cif
> /Users/Ellen/Downloads/fold_betaring_pi31/fold_betaring_pi31_model_4.cif

Chain information for fold_betaring_pi31_model_2.cif #14  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
G H | .  
I J | .  
K L | .  
M N | .  
O P | .  
  
Chain information for fold_betaring_pi31_model_3.cif #15  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
G H | .  
I J | .  
K L | .  
M N | .  
O P | .  
  
Chain information for fold_betaring_pi31_model_4.cif #16  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
G H | .  
I J | .  
K L | .  
M N | .  
O P | .  
  

> ~display #14-16

> ribbon #14-16/o

> ribbon #14-16/p

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #14-16 to #1

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 fold_betaring_pi31_model_0.cif, chain M (#1) with
fold_betaring_pi31_model_2.cif, chain M (#14), sequence alignment score =
1205.4  
RMSD between 224 pruned atom pairs is 0.162 angstroms; (across all 234 pairs:
1.354)  
  
Matchmaker fold_betaring_pi31_model_0.cif, chain M (#1) with
fold_betaring_pi31_model_3.cif, chain M (#15), sequence alignment score =
1205.4  
RMSD between 223 pruned atom pairs is 0.131 angstroms; (across all 234 pairs:
1.594)  
  
Matchmaker fold_betaring_pi31_model_0.cif, chain M (#1) with
fold_betaring_pi31_model_4.cif, chain M (#16), sequence alignment score =
1202.4  
RMSD between 223 pruned atom pairs is 0.187 angstroms; (across all 234 pairs:
1.393)  
  

> ribbon #14-16/a

> ribbon #14-16/b

> show #4 models

> hide #4 models

> color darkgreen #14/p

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #14/p darkgreen

> select #14/a #15/b

3286 atoms, 3346 bonds, 424 residues, 2 models selected  

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #16 & sel to #14 & sel

No molecules/chains to match specified  

> matchmaker #15 & sel to #14 & sel

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 fold_betaring_pi31_model_2.cif, chain A (#14) with
fold_betaring_pi31_model_3.cif, chain B (#15), sequence alignment score =
1098.4  
RMSD between 212 pruned atom pairs is 0.115 angstroms; (across all 212 pairs:
0.115)  
  

> color #15/p green

> color #16/p lightgreen

> select #14/a #16/b

3286 atoms, 3346 bonds, 424 residues, 2 models selected  

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #16 & sel to #14 & sel

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 fold_betaring_pi31_model_2.cif, chain A (#14) with
fold_betaring_pi31_model_4.cif, chain B (#16), sequence alignment score =
1098.4  
RMSD between 212 pruned atom pairs is 0.121 angstroms; (across all 212 pairs:
0.121)  
  

> show #1 models

> show #2 models

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #16 & sel to #1 & sel

No 'to' model specified  

> select #0/a #16/b

1643 atoms, 1673 bonds, 212 residues, 1 model selected  

> select #1/a #16/b

3286 atoms, 3346 bonds, 424 residues, 2 models selected  

> matchmaker #16 & sel to #1 & sel

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 fold_betaring_pi31_model_0.cif, chain A (#1) with
fold_betaring_pi31_model_4.cif, chain B (#16), sequence alignment score =
1095.4  
RMSD between 212 pruned atom pairs is 0.093 angstroms; (across all 212 pairs:
0.093)  
  

> select #1/b #16/b

3286 atoms, 3346 bonds, 424 residues, 2 models selected  

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #1 & sel to #16 & sel

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 fold_betaring_pi31_model_4.cif, chain B (#16) with
fold_betaring_pi31_model_0.cif, chain B (#1), sequence alignment score =
1095.4  
RMSD between 212 pruned atom pairs is 0.085 angstroms; (across all 212 pairs:
0.085)  
  

> select #1/b #16/b

3286 atoms, 3346 bonds, 424 residues, 2 models selected  

> matchmaker #1 & sel to #16 & sel

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 fold_betaring_pi31_model_4.cif, chain B (#16) with
fold_betaring_pi31_model_0.cif, chain B (#1), sequence alignment score =
1095.4  
RMSD between 212 pruned atom pairs is 0.085 angstroms; (across all 212 pairs:
0.085)  
  

> matchmaker #1 & sel to #16 & sel

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 fold_betaring_pi31_model_4.cif, chain B (#16) with
fold_betaring_pi31_model_0.cif, chain B (#1), sequence alignment score =
1095.4  
RMSD between 212 pruned atom pairs is 0.085 angstroms; (across all 212 pairs:
0.085)  
  

> select #2/b #16/b

3286 atoms, 3346 bonds, 424 residues, 2 models selected  

> matchmaker #2 & sel to #16 & sel

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 fold_betaring_pi31_model_4.cif, chain B (#16) with
fold_betaring_pi31_model_1.cif, chain B (#2), sequence alignment score =
1098.4  
RMSD between 212 pruned atom pairs is 0.070 angstroms; (across all 212 pairs:
0.070)  
  

> save "/Users/Ellen/HMS Dropbox/Ellen
> Goodall/Ellen_shared/Chimera_sessions_forWade/AF3_FBXO7_PI31/20S_interaction/Comparison_prediction_PI3120Scryo.cxs"
> includeMaps true

——— End of log from Wed Mar 12 21:11:45 2025 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac15,12
      Model Number: Z1G600070LL/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.101.1
      OS Loader Version: 11881.101.1

Software:

    System Software Overview:

      System Version: macOS 15.4.1 (24E263)
      Kernel Version: Darwin 24.4.0
      Time since boot: 18 days, 16 hours, 12 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57
    ChimeraX-AtomicLibrary: 14.0.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    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: 1.8rc202406062357
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.46
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.1
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (2)

comment:1 by Eric Pettersen, 6 months ago

Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in garbage collection

comment:2 by Eric Pettersen, 6 months ago

Status: accepted → feedback

Hi Ellen,

Thanks for reporting this problem. There have many bug fixes and improvements in ChimeraX since the 1.8 release candidate that you are using, some of them specifically related to the garbage-collection crash you're having. Please try the 1.10 release candidate and see if that works any better for you. If you still get a crash opening that session, we will go from there (and it will be much easier to debug if you are using the current code base).

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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