Opened 7 weeks ago

Closed 7 weeks ago

Last modified 7 weeks ago

#18662 closed defect (can't reproduce)

Kernel memory error

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.7.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
{"app_name":"ChimeraX","timestamp":"2025-08-28 17:34:41.00 +0200","app_version":"","slice_uuid":"9cf8124a-d876-34ad-b7ee-c011183ebc15","build_version":"","platform":1,"share_with_app_devs":0,"is_first_party":1,"bug_type":"309","os_version":"macOS 14.7.1 (23H222)","roots_installed":0,"incident_id":"E72D0DC3-4E49-47B3-BEEB-763279878063","name":"ChimeraX"}
{
  "uptime" : 80000,
  "procRole" : "Unspecified",
  "version" : 2,
  "userID" : 503,
  "deployVersion" : 210,
  "modelCode" : "Mac15,3",
  "coalitionID" : 15634,
  "osVersion" : {
    "train" : "macOS 14.7.1",
    "build" : "23H222",
    "releaseType" : "User"
  },
  "captureTime" : "2025-08-28 17:34:34.1113 +0200",
  "codeSigningMonitor" : 1,
  "incident" : "E72D0DC3-4E49-47B3-BEEB-763279878063",
  "pid" : 98577,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-08-28 13:56:11.6580 +0200",
  "procStartAbsTime" : 1615696213869,
  "procExitAbsTime" : 1929188195360,
  "procName" : "ChimeraX",
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "D7FE9C74-C44A-CB50-D9A2-510BF5E79A75",
  "responsiblePid" : 98258,
  "codeSigningID" : "",
  "codeSigningTeamID" : "",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 0,
  "codeSigningTrustLevel" : 4294967295,
  "wakeTime" : 7245,
  "sleepWakeUUID" : "4ADE5EE7-E2A8-4562-A0D4-C6AA13CBDDB6",
  "sip" : "enabled",
  "vmRegionInfo" : "0x1038aa080 is in 0x10365c000-0x103a20000;  bytes after start: 2416768  bytes before end: 1531775\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      mapped file                 103654000-10365c000    [   32K] r--\/rwx SM=COW  Object_id=dc8ba316\n--->  mapped file                 10365c000-103a20000    [ 3856K] r-x\/rwx SM=COW  Object_id=bc22080e\n      mapped file                 103a20000-103a50000    [  192K] r--\/rwx SM=COW  Object_id=ef7f21d1",
  "exception" : {"codes":"0x000000000000000a, 0x00000001038aa080","rawCodes":[10,4354384000],"type":"EXC_BAD_ACCESS","signal":"SIGILL","subtype":"KERN_MEMORY_ERROR at 0x00000001038aa080"},
  "termination" : {"flags":0,"code":4,"namespace":"SIGNAL","indicator":"Illegal instruction: 4","byProc":"ChimeraX","byPid":98577},
  "ktriageinfo" : "VM - (arg = 0x0) Object has no pager because the backing vnode was force unmounted\nVM - (arg = 0x0) Object has no pager because the backing vnode was force unmounted\nVM - (arg = 0x0) Object has no pager because the backing vnode was force unmounted\nVM - (arg = 0x0) Object has no pager because the backing vnode was force unmounted\nVM - (arg = 0x0) Object has no pager because the backing vnode was force unmounted\n",
  "vmregioninfo" : "0x1038aa080 is in 0x10365c000-0x103a20000;  bytes after start: 2416768  bytes before end: 1531775\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      mapped file                 103654000-10365c000    [   32K] r--\/rwx SM=COW  Object_id=dc8ba316\n--->  mapped file                 10365c000-103a20000    [ 3856K] r-x\/rwx SM=COW  Object_id=bc22080e\n      mapped file                 103a20000-103a50000    [  192K] r--\/rwx SM=COW  Object_id=ef7f21d1",
  "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" : [{"triggered":true,"id":2300551,"threadState":{"x":[{"value":10},{"value":4966056880},{"value":4966056984},{"value":4966056880},{"value":4966056984},{"value":15068474451137618853},{"value":101},{"value":0},{"value":4354384000},{"value":8520578576},{"value":0},{"value":2},{"value":0},{"value":0},{"value":0},{"value":4422786344},{"value":3},{"value":1},{"value":0},{"value":15068474451137618853},{"value":4966056984},{"value":8520601600},{"value":4357120640},{"value":4357286672},{"value":105553116398976},{"value":4357120000},{"value":265},{"value":4334290320},{"value":4379200166}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6777644420},"cpsr":{"value":6144},"fp":{"value":4966056864},"sp":{"value":4966056832},"esr":{"value":2181038087,"description":"(Instruction Abort) Translation fault"},"pc":{"value":4354384000,"matchesCrashFrame":1},"far":{"value":4354384000}},"frames":[{"imageOffset":4354384000,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":6777644420,"imageIndex":0},{"imageOffset":4354346792,"imageIndex":0},{"imageOffset":4354583552,"imageIndex":0},{"imageOffset":4352633856,"imageIndex":0},{"imageOffset":4352571428,"imageIndex":0},{"imageOffset":4354621028,"imageIndex":0},{"imageOffset":4354619820,"imageIndex":0},{"imageOffset":4354600596,"imageIndex":0},{"imageOffset":4353750076,"imageIndex":0},{"imageOffset":4353696744,"imageIndex":0},{"imageOffset":4354211116,"imageIndex":0},{"imageOffset":4353674568,"imageIndex":0},{"imageOffset":4352974276,"imageIndex":0},{"imageOffset":4353755524,"imageIndex":0},{"imageOffset":4353696744,"imageIndex":0},{"imageOffset":4353674352,"imageIndex":0},{"imageOffset":4352974276,"imageIndex":0},{"imageOffset":4353755524,"imageIndex":0},{"imageOffset":4353778636,"imageIndex":0},{"imageOffset":4354356260,"imageIndex":0},{"imageOffset":4354354884,"imageIndex":0},{"imageOffset":4354359412,"imageIndex":0},{"imageOffset":4354359348,"imageIndex":0},{"imageOffset":4333190548,"imageIndex":0},{"imageOffset":24916,"symbol":"start","symbolLocation":2476,"imageIndex":1}]},{"id":2300639,"frames":[{"imageOffset":6777193932,"imageIndex":0},{"imageOffset":4800195416,"imageIndex":0},{"imageOffset":6777446292,"imageIndex":0},{"imageOffset":6777425204,"imageIndex":0}],"threadState":{"x":[{"value":260},{"value":0},{"value":256},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6134263496},{"value":0},{"value":4820115496},{"value":2},{"value":0},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8695655184},{"value":0},{"value":4820115472},{"value":4820115536},{"value":6134264032},{"value":0},{"value":0},{"value":256},{"value":257},{"value":512},{"value":4820029440},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6777447772},"cpsr":{"value":1610616832},"fp":{"value":6134263616},"sp":{"value":6134263472},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6777193932},"far":{"value":0}}},{"id":2300640,"frames":[{"imageOffset":6777193932,"imageIndex":0},{"imageOffset":4800195416,"imageIndex":0},{"imageOffset":6777446292,"imageIndex":0},{"imageOffset":6777425204,"imageIndex":0}],"threadState":{"x":[{"value":260},{"value":0},{"value":256},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6134836936},{"value":0},{"value":4820115624},{"value":2},{"value":0},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8695655184},{"value":0},{"value":4820115600},{"value":4820115664},{"value":6134837472},{"value":0},{"value":0},{"value":256},{"value":257},{"value":512},{"value":4820029440},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6777447772},"cpsr":{"value":1610616832},"fp":{"value":6134837056},"sp":{"value":6134836912},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6777193932},"far":{"value":0}}},{"id":2300641,"frames":[{"imageOffset":6777193932,"imageIndex":0},{"imageOffset":4800195416,"imageIndex":0},{"imageOffset":6777446292,"imageIndex":0},{"imageOffset":6777425204,"imageIndex":0}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6135410376},{"value":0},{"value":4820115752},{"value":2},{"value":0},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8695655184},{"value":0},{"value":4820115728},{"value":4820115792},{"value":6135410912},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4820029440},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6777447772},"cpsr":{"value":1610616832},"fp":{"value":6135410496},"sp":{"value":6135410352},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6777193932},"far":{"value":0}}},{"id":2300642,"frames":[{"imageOffset":6777193932,"imageIndex":0},{"imageOffset":4800195416,"imageIndex":0},{"imageOffset":6777446292,"imageIndex":0},{"imageOffset":6777425204,"imageIndex":0}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6135983816},{"value":0},{"value":4820115880},{"value":2},{"value":0},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8695655184},{"value":0},{"value":4820115856},{"value":4820115920},{"value":6135984352},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4820029440},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6777447772},"cpsr":{"value":1610616832},"fp":{"value":6135983936},"sp":{"value":6135983792},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6777193932},"far":{"value":0}}},{"id":2300643,"frames":[{"imageOffset":6777193932,"imageIndex":0},{"imageOffset":4800195416,"imageIndex":0},{"imageOffset":6777446292,"imageIndex":0},{"imageOffset":6777425204,"imageIndex":0}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6136557256},{"value":0},{"value":4820116008},{"value":2},{"value":0},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8695655184},{"value":0},{"value":4820115984},{"value":4820116048},{"value":6136557792},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4820029440},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6777447772},"cpsr":{"value":1610616832},"fp":{"value":6136557376},"sp":{"value":6136557232},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6777193932},"far":{"value":0}}},{"id":2300644,"frames":[{"imageOffset":6777193932,"imageIndex":0},{"imageOffset":4800195416,"imageIndex":0},{"imageOffset":6777446292,"imageIndex":0},{"imageOffset":6777425204,"imageIndex":0}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6137130696},{"value":0},{"value":4820116136},{"value":2},{"value":0},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8695655184},{"value":0},{"value":4820116112},{"value":4820116176},{"value":6137131232},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4820029440},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6777447772},"cpsr":{"value":1610616832},"fp":{"value":6137130816},"sp":{"value":6137130672},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6777193932},"far":{"value":0}}},{"id":2300645,"frames":[{"imageOffset":6777193932,"imageIndex":0},{"imageOffset":4800195416,"imageIndex":0},{"imageOffset":6777446292,"imageIndex":0},{"imageOffset":6777425204,"imageIndex":0}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6137704136},{"value":0},{"value":4820116264},{"value":2},{"value":0},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8695655184},{"value":0},{"value":4820116240},{"value":4820116304},{"value":6137704672},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4820029440},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6777447772},"cpsr":{"value":1610616832},"fp":{"value":6137704256},"sp":{"value":6137704112},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6777193932},"far":{"value":0}}}],
  "usedImages" : [
  {
    "size" : 0,
    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6773706752,
    "size" : 562444,
    "uuid" : "88b1da61-4519-33f6-9297-ac4de0cd940c",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  }
],
  "sharedCache" : {
  "base" : 6772948992,
  "size" : 4214374400,
  "uuid" : "8047f785-c408-34e1-a0a8-38ee34ab89f4"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=525.7M resident=0K(0%) swapped_out_or_unallocated=525.7M(100%)\nWritable regions: Total=1.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.9G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nKernel Alloc Once                   32K        1 \nMALLOC                             1.6G       34 \nMALLOC guard page                   96K        6 \nSTACK GUARD                        112K        7 \nStack                             11.7M        8 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      113.5M       25 \nVM_ALLOCATE (reserved)           160.0M        2         reserved VM address space (unallocated)\n__DATA                              11K        1 \n__DATA_CONST                        23K        1 \n__DATA_DIRTY                         7K        1 \n__LINKEDIT                       525.2M        1 \n__TEXT                             552K        1 \ndyld private memory                272K        2 \nmapped file                       46.6M      199 \nshared memory                       32K        2 \n===========                     =======  ======= \nTOTAL                              2.5G      292 \nTOTAL, minus reserved VM space     2.3G      292 \n",
  "legacyInfo" : {
  "threadTriggered" : {

  }
},
  "logWritingSignature" : "a35729e2b4098f749e251fb8816555e611b120ed",
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "5f72dc58705eff005a46b3a9",
      "factorPackIds" : {

      },
      "deploymentId" : 240000015
    },
    {
      "rolloutId" : "5fb4245a1bbfe8005e33a1e1",
      "factorPackIds" : {

      },
      "deploymentId" : 240000021
    }
  ],
  "experiments" : [

  ]
}
}
===== Log before crash start =====
Startup Messages  
---  
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: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/chavesvargas/Documents/01_CF-T6SS-Berlin/Anti-Hcp1
> antibodies/Hcp1 prediction.cxs" format session

> view name session-start

opened ChimeraX session  

> style sphere

Changed 2632 atom styles  

> set bgColor white

> set bgColor #ffffff00

> hide atoms

> show atoms

> hide atoms

> style sphere

Changed 2632 atom styles  

> style stick

Changed 2632 atom styles  

> show atoms

> style ball

Changed 2632 atom styles  

> style sphere

Changed 2632 atom styles  

> style sphere

Changed 2632 atom styles  

> style ball

Changed 2632 atom styles  

> style stick

Changed 2632 atom styles  

> hide atoms

> hide #1 models

> show #1 models

> open "/Users/chavesvargas/Documents/12_T6SS Abs Manuscript/Epitope
> prediction/MHCI/Hcp1/AF-Q9I747-F1-model_v4.pdb"

AF-Q9I747-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for protein HCP1 (Q9I747) [more info...]  
  
Chain information for AF-Q9I747-F1-model_v4.pdb #2  
---  
Chain | Description | UniProt  
A | protein HCP1 | HCP1_PSEAE 1-162  
  
Computing secondary structure  

> hide #1 models

> ui tool show "Show Sequence Viewer"

> hide #1 target m

> select #1/A:40

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #1/A:40-130

1444 atoms, 1460 bonds, 91 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> select #2/A:61

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

> select #2/A:61-69

73 atoms, 74 bonds, 9 residues, 1 model selected  

> select :61-69

222 atoms, 224 bonds, 18 residues, 2 models selected  

> color red sel

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

> select :61-69

222 atoms, 224 bonds, 18 residues, 2 models selected  

> color red sel

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

> show sel & #2 atoms

> color red sel

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

> select /A:61-69

222 atoms, 224 bonds, 18 residues, 2 models selected  

> color red sel

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

> show #1 models

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> select #1/A:61

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

> select #1/A:61-69

149 atoms, 150 bonds, 9 residues, 1 model selected  

> select #1/A:61

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

> select #1/A:61-67

117 atoms, 118 bonds, 7 residues, 1 model selected  

> select #1/A:66-67

36 atoms, 36 bonds, 2 residues, 1 model selected  

> select #1/A:60-67

131 atoms, 132 bonds, 8 residues, 1 model selected  

> select add #1

2632 atoms, 2666 bonds, 172 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select add #2

1220 atoms, 1240 bonds, 162 residues, 1 model selected  

> select subtract #2

Nothing selected  

> select #2/A:61

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

> select #2/A:61-69

73 atoms, 74 bonds, 9 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> show sel atoms

> hide sel atoms

> show sel atoms

> hide sel atoms

> style sel sphere

Changed 73 atom styles  

> show sel atoms

> style sel ball

Changed 73 atom styles  

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> lighting soft

> lighting full

> lighting simple

> lighting soft

> lighting full

> style sel stick

Changed 73 atom styles  

> style sel ball

Changed 73 atom styles  

> color sel byhetero

> color sel bychain

> hide #1 models


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

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,3
      Model Number: Z1GM0005LD/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.41.5
      OS Loader Version: 10151.140.19.700.2

Software:

    System Software Overview:

      System Version: macOS 14.7.1 (23H222)
      Kernel Version: Darwin 23.6.0
      Time since boot: 3 days, 40 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 XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL S2722DC:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 75.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 2.5.1
    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: 1.6.2
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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: 1.19.1
    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: 2.5.2
    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: 1.45.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

Change History (3)

comment:1 by pett, 7 weeks ago

Cc: Tom Goddard added
Component: Unassigned → Core
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Kernel memory error

comment:2 by pett, 7 weeks ago

Resolution: → can't reproduce
Status: accepted → closed

comment:3 by Tom Goddard, 7 weeks ago

Maybe the crash info ""ktriageinfo" : "VM - (arg = 0x0) Object has no pager because the backing vnode was force unmounted" means the disk volume that ChimeraX was mounted on disappeared, for instance, the user ran ChimeraX from the dmg then unmounted the dmg.

Note: See TracTickets for help on using tickets.