Opened 7 months ago

Closed 7 months ago

#17370 closed defect (duplicate)

Crash on Mac waking from sleep

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

Description 

The following bug report has been submitted:
Platform:        macOS-15.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Thread 0x000000033f367000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000033e35b000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000033d34f000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000033c343000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000033b337000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000033a32b000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000033931f000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000338313000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000337307000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003362fb000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003352ef000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003342e3000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003332d7000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003322cb000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003312bf000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000001ee4cc240 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, openmm._openmm, openmm.app.internal.compiled, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio (total: 62)


{"app_name":"ChimeraX","timestamp":"2025-04-14 07:34:35.00 -0700","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.2 (24C101)","roots_installed":0,"name":"ChimeraX","incident_id":"DA4EBFD6-E3B9-44C5-92E5-760B604E83B2"}
{
  "uptime" : 630000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac15,6",
  "coalitionID" : 122688,
  "osVersion" : {
    "train" : "macOS 15.2",
    "build" : "24C101",
    "releaseType" : "User"
  },
  "captureTime" : "2025-04-14 07:34:23.8793 -0700",
  "codeSigningMonitor" : 1,
  "incident" : "DA4EBFD6-E3B9-44C5-92E5-760B604E83B2",
  "pid" : 38940,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-04-10 14:46:21.3001 -0700",
  "procStartAbsTime" : 13009049118096,
  "procExitAbsTime" : 15122000892208,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"178D90C6-A022-506E-B8D9-2A6945B9D0D5","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "C038A309-F6F7-ECF2-F1A8-A6B7199AF386",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "bootSessionUUID" : "6E4CC1FC-6FBD-4640-A155-D883AD89C154",
  "wakeTime" : 4,
  "sleepWakeUUID" : "969BD3DD-27DD-4F2B-951A-AC0B527FAAA1",
  "sip" : "enabled",
  "vmRegionInfo" : "0x169 is not in any region.  Bytes before following region: 4344266391\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      102f04000-102f08000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":38940},
  "vmregioninfo" : "0x169 is not in any region.  Bytes before following region: 4344266391\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      102f04000-102f08000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":4698438296},{"value":99},{"value":117},{"value":3458870066943010144},{"value":0},{"value":870026073688825924},{"value":870026076275876356},{"value":14757395258967641293},{"value":4294967286},{"value":4698438226},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8433691824},{"value":0},{"value":11},{"value":259},{"value":8292975392,"symbolLocation":224,"symbol":"_main_thread"},{"value":0},{"value":1},{"value":4365600304,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8256081920,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTableViewCellMockElement._tableColumn"},{"value":8256081920,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTableViewCellMockElement._tableColumn"},{"value":5},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6522060656},"cpsr":{"value":1073745920},"fp":{"value":4698438368},"sp":{"value":4698438336},"esr":{"value":1442840704,"description":" Address size 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    "size" : 49152,
    "uuid" : "cd4f396b-89fe-36fd-a488-6f5b3d4b0282",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtOpenGLWidgets.framework\/Versions\/A\/QtOpenGLWidgets",
    "name" : "QtOpenGLWidgets"
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  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 13557858304,
    "size" : 3817472,
    "uuid" : "579ef19c-6e85-36be-a566-c980f789fbc0",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
    "name" : "etree.cpython-311-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 6384205824,
    "size" : 131072,
    "uuid" : "c8b24269-c8a2-3244-b044-b85c3449800d",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
    "name" : "_elementpath.cpython-311-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 6391365632,
    "size" : 32768,
    "uuid" : "a55a4181-c446-3fa3-8fd6-27f845527eab",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_osx.abi3.so",
    "name" : "_psutil_osx.abi3.so"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 6392922112,
    "size" : 16384,
    "uuid" : "a516c5bc-1157-318a-a306-5c9b350e0c09",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_posix.abi3.so",
    "name" : "_psutil_posix.abi3.so"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 6389366784,
    "size" : 81920,
    "uuid" : "3133c77c-8bf7-32a3-b5db-cbfe2e50ce9d",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
    "name" : "_ribbons.cpython-311-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 13334102016,
    "size" : 16384,
    "uuid" : "de871a78-14f2-3e72-9bde-e4f2c7493f1b",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
    "name" : "_graphics.cpython-311-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 13341016064,
    "size" : 475136,
    "uuid" : "0c6e9a11-e483-3d7d-a88f-8ad0507af167",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
    "name" : "mmcif.cpython-311-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 13427752960,
    "size" : 409600,
    "uuid" : "1ab8e5e2-c699-3efb-8f77-d375e3793c8f",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
    "name" : "_mmcif.cpython-311-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 13339000832,
    "size" : 147456,
    "uuid" : "1e310bc7-5f96-396b-816d-5b40a3dde12c",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
    "name" : "_pdbio.cpython-311-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6521790464,
    "size" : 241656,
    "uuid" : "dfc9530c-e75b-3d1c-a9a6-85c8a709d6a7",
    "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
    "name" : "libsystem_kernel.dylib"
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  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6522032128,
    "size" : 53248,
    "uuid" : "f1661613-b1c8-320d-b69d-97f174130e29",
    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    "name" : "libsystem_pthread.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6520565760,
    "size" : 532476,
    "uuid" : "67989e50-e562-3062-9ff9-44bd90648e66",
    "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    "name" : "libsystem_c.dylib"
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  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6522269696,
    "size" : 32764,
    "uuid" : "d215e3b2-fa4f-328a-a080-7650c0991858",
    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    "name" : "libsystem_platform.dylib"
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    "arch" : "arm64e",
    "base" : 6585065472,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 21204992,
    "uuid" : "4251ee1c-062c-3b9a-b6e2-751f77ef9f4a",
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    "name" : "AppKit",
    "CFBundleVersion" : "2575.30.19"
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    "arch" : "arm64e",
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    "CFBundleIdentifier" : "com.apple.SkyLight",
    "size" : 5427200,
    "uuid" : "122276c2-e3a9-3406-ace8-a2c2a4756ca0",
    "path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
    "name" : "SkyLight"
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  {
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    "arch" : "arm64e",
    "base" : 6520262656,
    "size" : 290816,
    "uuid" : "9c7ff4a8-9d78-3aed-b64d-979574a26d8f",
    "path" : "\/usr\/lib\/system\/libdispatch.dylib",
    "name" : "libdispatch.dylib"
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    "arch" : "arm64e",
    "base" : 6522499072,
    "CFBundleShortVersionString" : "6.9",
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    "size" : 5197824,
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    "name" : "CoreFoundation",
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    "arch" : "arm64e",
    "base" : 6712061952,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 3178496,
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    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
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    "arch" : "arm64e",
    "base" : 6518366208,
    "size" : 532288,
    "uuid" : "4ce86d18-f3fa-3d2a-a1b8-e7cd8a52fb0d",
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    "name" : "dyld"
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    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.Foundation",
    "size" : 14979072,
    "uuid" : "b39c1e42-f15f-3671-b63e-6be7bdad0fcd",
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    "name" : "Foundation",
    "CFBundleVersion" : "3208"
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],
  "sharedCache" : {
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  "size" : 4861722624,
  "uuid" : "e36100c7-89e7-3970-8938-8483ccd7019a"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=12.4G written=7324K(0%) resident=7324K(0%) swapped_out=0K(0%) unallocated=12.4G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               256K        2 \nActivity Tracing                   256K        1 \nCG image                           944K       49 \nColorSync                          688K       33 \nCoreAnimation                     2704K      146 \nCoreGraphics                       112K        7 \nCoreServices                       624K        2 \nCoreUI image data                 5568K       42 \nFoundation                          32K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                            11.2G      296 \nMALLOC guard page                  288K       18 \nMach message                        64K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        864K       54 \nStack                            433.8M       55 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      405.9M      285 \nVM_ALLOCATE (reserved)           224.0M        1         reserved VM address space (unallocated)\n__AUTH                            5285K      672 \n__AUTH_CONST                      70.8M      920 \n__CTF                               824        1 \n__DATA                            34.4M     1100 \n__DATA_CONST                      34.8M     1115 \n__DATA_DIRTY                      2763K      342 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       644.2M      189 \n__OBJC_RW                         2373K        1 \n__TEXT                             1.3G     1135 \n__TPRO_CONST                       272K        2 \ndyld private memory                 48K        2 \nmapped file                      299.2M       74 \nowned unmapped memory            155.2M        1 \npage table in kernel              7324K        1 \nshared memory                     3152K       23 \n===========                     =======  ======= \nTOTAL                             14.8G     6582 \nTOTAL, minus reserved VM space    14.6G     6582 \n",
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},
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}
===== 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: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> save
> /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/924_chimera4-S2merged.cxs

> open
> /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/924_chimera4-S2merged.cxs

opened ChimeraX session  

> open
> /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/cryosparc_P130_J745_006_volume_map.mrc

Opened cryosparc_P130_J745_006_volume_map.mrc as #1, grid size 480,480,480,
pixel 0.647, shown at level 0.0077, step 2, values float32  

> set bgColor white

> volume #1 step 1

> volume #1 level 0.0122

> volume #1 level 0.01027

> close

> open
> /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/cryosparc_P130_J727_008_volume_map.mrc

Opened cryosparc_P130_J727_008_volume_map.mrc as #1, grid size 480,480,480,
pixel 0.647, shown at level 0.019, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.02695

> volume #1 level 0.0329

> volume #1 level 0.04017

> open
> /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/924_chimera3.cxs

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Opened MBD-CRBN_fitToJ547.pdb map 15 thresholded as #21, grid size
480,480,480, pixel 0.647, shown at level 0.005, step 2, values float32  
Opened cryosparc_P130_J616_006_volume_map.mrc as #2, grid size 480,480,480,
pixel 0.647, shown at level 0.0118, step 1, values float32  
Opened cryosparc_P130_J618_007_volume_map.mrc as #8, grid size 480,480,480,
pixel 0.647, shown at level 0.0133, step 1, values float32  
Opened cryosparc_P130_J618_007_volume_mask_refine.mrc as #9, grid size
480,480,480, pixel 0.647, shown at level 1, step 2, values float32  
Opened cryosparc_P130_J617_003_volume_map.mrc as #7.1, grid size 480,480,480,
pixel 0.647, shown at level 0.0126, step 1, values float32  
Opened cryosparc_P130_J617_003_volume_mask_refine.mrc as #7.2, grid size
480,480,480, pixel 0.647, shown at level 0.99, step 1, values float32  
Opened MBD-CRBN_fitToJ547.pdb map 20 as #5, grid size 480,480,480, pixel
0.647, shown at level 0.001, step 1, values float32  
Opened FocusMask_J617_1pt8_0pt001.mrc as #10, grid size 480,480,480, pixel
0.647, shown at level 0.001, step 1, values float32  
Opened FocusMask_J617_1pt8_0pt001-Binary.mrc as #11, grid size 480,480,480,
pixel 0.647, shown at level 0.001, step 1, values float32  
Opened SubtractionMask_to_J617Binary.mrc as #12, grid size 480,480,480, pixel
0.647, shown at level 0.9, step 1, values float32  
Opened volume difference as #14, grid size 480,480,480, pixel 0.647, shown at
level 0.99, step 1, values float32  
Opened volume difference as #15, grid size 480,480,480, pixel 0.647, shown at
level 0.99, step 1, values float32  

Could not restore coloring on surface because surface does not exist.  

restore_snapshot for "VolumeColor" returned None  

opened ChimeraX session  

> show #!2 models

> hide #!2 models

> close #2

> hide #!3 models

> show #!3 models

> hide #!7 models

> hide #!7.1 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> hide #!12 models

> select subtract #3

Nothing selected  

> open
> /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/cryosparc_P130_J727_008_volume_map.mrc

Opened cryosparc_P130_J727_008_volume_map.mrc as #1, grid size 480,480,480,
pixel 0.647, shown at level 0.019, step 2, values float32  

> volume #1 step 1

> transparency #1.1 50

> volume #1 level 0.03535

> open
> /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/cryosparc_P130_J728_006_volume_map.mrc

Opened cryosparc_P130_J728_006_volume_map.mrc as #2, grid size 480,480,480,
pixel 0.647, shown at level 0.0205, step 2, values float32  

> transparency #1.1#2.1 0

> transparency #1.1#2.1 50

> volume #2 step 1

> volume #2 level 0.05348

> volume #1 level 0.02855

> volume #1 level 0.05169

> open
> /Users/zmotiwal@amgen.com/Downloads/cryosparc_P130_J762_013_volume_map.mrc

Opened cryosparc_P130_J762_013_volume_map.mrc as #6, grid size 480,480,480,
pixel 0.647, shown at level 0.0147, step 2, values float32  

> transparency #1.1#2.1#6.1 0

> transparency #1.1#2.1#6.1 50

> volume #6 step 1

> volume #6 level 0.02334

> volume #6 level 0.03321

> volume #6 level 0.04555

> open
> "/Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/cryosparc_P130_J440_mask
> (1).mrc"

Opened cryosparc_P130_J440_mask (1).mrc as #16, grid size 512,512,512, pixel
0.647, shown at level 1, step 2, values float32  

> hide #!16 models

> show #!16 models

> volume #16 step 1

> volume #16 level 1

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> fitmap #3 inMap #1

Fit molecule MBD-CRBN_fitToJ547.pdb (#3) to map
cryosparc_P130_J727_008_volume_map.mrc (#1) using 3904 atoms  
average map value = 0.06366, steps = 108  
shifted from previous position = 1.88  
rotated from previous position = 10.4 degrees  
atoms outside contour = 1621, contour level = 0.051689  
  
Position of MBD-CRBN_fitToJ547.pdb (#3) relative to
cryosparc_P130_J727_008_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.97971915 0.19754391 -0.03356770 -22.45445972  
-0.19850374 0.97969574 -0.02815171 38.00667615  
0.02732493 0.03424408 0.99903988 -7.61051151  
Axis 0.15386219 -0.15015554 -0.97661648  
Axis point 176.81201202 130.47372722 0.00000000  
Rotation angle (degrees) 11.69870689  
Shift along axis -1.72925450  
  

> show #!16 models

> hide #!16 models

> hide #!3 models

> show #!3 models

> show #!21 models

> hide #!21 models

> show #!21 models

> close #16

> hide #!21 models

> show #!21 models

> volume #21 level 0.0623

> volume #21 level 0.4246

> volume #21 level 0.05915

> volume #1 level 0.03059

> transparency #1.1#21.1 0

> transparency #1.1#21.1 50

> hide #!21 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> volume #1 level 0.04829

> volume #1 level 0.05509

> show #!2 models

> ui tool show "Side View"

> view

> select ::name="MSH"

80 atoms, 90 bonds, 2 residues, 2 models selected  

> view sel

> select add #3

3944 atoms, 4044 bonds, 6 pseudobonds, 480 residues, 4 models selected  

> select subtract #3

40 atoms, 45 bonds, 1 residue, 1 model selected  

> select add #4

36811 atoms, 37154 bonds, 19 pseudobonds, 2307 residues, 3 models selected  

> select subtract #4

Nothing selected  

> hide #!2 models

> volume #1 level 0.08981

> volume #2 level 0.08839

> volume #1 level 0.06462

> volume #2 level 0.06995

> view

> show #!21 models

> open
> "/Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/cryosparc_P130_J444_mask
> (1).mrc"

Opened cryosparc_P130_J444_mask (1).mrc as #16, grid size 512,512,512, pixel
0.647, shown at level 5e-05, step 2, values float32  

> hide #!21 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!21 models

> volume #1 level 0.03195

> volume #2 level 0.04624

> volume #2 level 0.04558

> volume #2 level 0.04294

> volume #2 level 0.04228

> volume #2 level 0.03372

> volume #2 level 0.03306

> volume #2 level 0.0324

> volume #1 level 0.02242

> volume #2 level 0.01791

> volume #2 level 0.02977

> hide #!21 models

> show #!21 models

> hide #!21 models

> show #!21 models

> hide #!21 models

> show #!21 models

> open
> /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/cryosparc_P130_J727_008_volume_mask_refine.mrc

Opened cryosparc_P130_J727_008_volume_mask_refine.mrc as #17, grid size
480,480,480, pixel 0.647, shown at level 1, step 2, values float32  

> volume #17 step 1

> volume #17 level 1

> hide #!21 models

> show #!21 models

> hide #!21 models

> show #!21 models

> volume #17 level 1

> hide #!21 models

> show #!21 models

> volume subtract #17 #21 onGrid #17

Opened volume difference as #18, grid size 480,480,480, pixel 0.647, shown at
step 1, values float32  

> volume #18 level 1

> volume #17 level 1

> show #!21 models

> volume #21 level 0.08872

> volume #21 level 0.1756

> volume #21 level 0.2957

> hide #!17 models

> volume #21 step 1

> hide #!18 models

> show #!17 models

> volume #21 level 0.464

> volume #21 level 0.6728

> volume #21 level 0.8688

> volume #21 level 0.04621

> volume #21 level 0.03697

> hide #!17 models

> hide #!21 models

> hide #!2 models

> select add #3

3904 atoms, 3999 bonds, 6 pseudobonds, 479 residues, 3 models selected  

> Molmap sel 20 onGrid #1

Unknown command: Molmap sel 20 onGrid #1  

> molmap sel 20 onGrid #1

Opened MBD-CRBN_fitToJ547.pdb map 20 as #19, grid size 480,480,480, pixel
0.647, shown at level 0.0305, step 1, values float32  

> volume #9 step 1

> select subtract #3

Nothing selected  

> volume #19 level 0.0123

> volume #19 level 0.001

> volume #19 level 0.005

> volume #19 level 0.008

> molmap sel 18 onGrid #1

No atoms specified  

> select add #3

3904 atoms, 3999 bonds, 6 pseudobonds, 479 residues, 3 models selected  

> molmap sel 18 onGrid #1

Opened MBD-CRBN_fitToJ547.pdb map 18 as #19, grid size 480,480,480, pixel
0.647, shown at level 0.0345, step 1, values float32  

> volume #19 level 0.005848

> volume #19 level 0.005

No map chosen to save  

> save
> /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/FocusMask_J727_1pt8_0pt005.mrc
> models #19

> show #!17 models

> hide #!17 models

> show #!17 models

> close #21

> volume subtract #17 #19 onGrid #19

Opened volume difference as #20, grid size 480,480,480, pixel 0.647, shown at
step 1, values float32  

> show #!17 models

> hide #!17 models

> show #!19 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> save
> /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/SubtractionMask_to_J727.mrc
> models #20

> save
> /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/924_chimera4-S2merged.cxs

> volume #20 level 1

> volume #20 level 0.999

> volume #20 level 0.9

> volume #20 level 0.9999

> hide #!19 models

> show #!19 models

> hide #!19 models

> show #!19 models

> hide #!19 models

> hide #!20 models

> select subtract #3

Nothing selected  

> open
> /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/cryosparc_P130_J780_volume_map.mrc

Opened cryosparc_P130_J780_volume_map.mrc as #21, grid size 480,480,480, pixel
0.647, shown at level 0.00884, step 2, values float32  

> surface dust #1 size 6.47

> surface dust #21 size 6.47

> hide #!1 models

> volume #21 step 1

> volume #21 level 0.01688

> hide #!20 models

> volume #21 level 0.02369

> volume #21 level 0.02864

> transparency #21.1 50

> volume #21 level 0.04905

> volume #21 level 0.05524

> select ::name="MSH"

80 atoms, 90 bonds, 2 residues, 2 models selected  

> view sel

> select add #3

3944 atoms, 4044 bonds, 6 pseudobonds, 480 residues, 4 models selected  

> select subtract #3

40 atoms, 45 bonds, 1 residue, 1 model selected  

> select add #4

36811 atoms, 37154 bonds, 19 pseudobonds, 2307 residues, 3 models selected  

> select subtract #4

Nothing selected  

> volume #21 level 0.07132

> volume #21 level 0.09236

> volume #21 level 0.07318

> volume #21 level 0.06266

> volume #21 level 0.07504

> view

> hide #!21 models

> show #!21 models

> show #!1 models

> hide #!21 models

> show #!19 models

> hide #!19 models

> show #!19 models

> hide #!19 models

> show #!20 models

> hide #!20 models

> close #8

> close #9

> close #7.1

> close #7.2

> close #5

> close #10

> close #11

> close #12

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!19 models

> hide #!19 models

> close #14

> close #15

> close #6

> close #16

> volume #17 level 0.9667

> volume #17 level 0.9

> volume #17 level 0.999

> volume #17 level 0.9

> close #18

> volume #1 level 0.04352

> volume #1 level 0.005

> volume #1 level 0.001

> volume #1 level 0.0001

> volume #1 level 0.01439

> volume #1 level 0.0212

> hide #!19 models

> volume #1 level 0.02324

> volume #1 level 0.04026

> show #!19 models

> hide #!19 models

> show #!19 models

> volume #1 level 0.02256

> volume #19 level 0.0001

> volume #19 level 0.001

> volume #19 level 0.005

> volume #19 level 0.008

> volume #19 level 0.009

> volume #19 level 0.01

> volume #19 level 0.001

> volume #19 level 0.005

> volume #19 level 0.001

> volume #19 level 0.0001

> volume #19 level 0.00015

> volume #19 level 0.00018

> volume #19 level 0.0001

> hide #!19 models

> hide #!17 models

> open
> /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/cryosparc_P130_J781_005_volume_map.mrc

Opened cryosparc_P130_J781_005_volume_map.mrc as #5, grid size 480,480,480,
pixel 0.647, shown at level 0.0039, step 2, values float32  

> volume #5 step 1

> volume #5 level 0.01444

> volume #5 color #0433ff

> transparency #5.1 50

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> volume #5 color #00fdff

> volume #5 color #73fdff

> transparency #5.1 50

> volume #5 level 0.04682

> volume #5 level 0.07092

> volume #5 level 0.05058

> volume #5 level 0.05209

> fitmap #3 inMap #5

Fit molecule MBD-CRBN_fitToJ547.pdb (#3) to map
cryosparc_P130_J781_005_volume_map.mrc (#5) using 3904 atoms  
average map value = 0.07471, steps = 48  
shifted from previous position = 0.229  
rotated from previous position = 0.403 degrees  
atoms outside contour = 1270, contour level = 0.052091  
  
Position of MBD-CRBN_fitToJ547.pdb (#3) relative to
cryosparc_P130_J781_005_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
0.97856834 0.20280037 -0.03572136 -22.71274225  
-0.20394417 0.97846130 -0.03194156 39.65488282  
0.02847420 0.03854216 0.99885119 -8.28539272  
Axis 0.16871494 -0.15366317 -0.97361332  
Axis point 179.37286301 129.40513553 0.00000000  
Rotation angle (degrees) 12.05696130  
Shift along axis -1.85870508  
  

> fitmap #3 inMap #5

Fit molecule MBD-CRBN_fitToJ547.pdb (#3) to map
cryosparc_P130_J781_005_volume_map.mrc (#5) using 3904 atoms  
average map value = 0.07471, steps = 40  
shifted from previous position = 0.0126  
rotated from previous position = 0.0141 degrees  
atoms outside contour = 1269, contour level = 0.052091  
  
Position of MBD-CRBN_fitToJ547.pdb (#3) relative to
cryosparc_P130_J781_005_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
0.97856552 0.20278494 -0.03588565 -22.69365915  
-0.20392989 0.97847017 -0.03176052 39.62183801  
0.02867248 0.03839790 0.99885108 -8.30324920  
Axis 0.16794748 -0.15454132 -0.97360702  
Axis point 179.23595677 129.32276315 0.00000000  
Rotation angle (degrees) 12.05614671  
Shift along axis -1.85045239  
  

> volume #5 level 0.06188

> fitmap #3 inMap #5

Fit molecule MBD-CRBN_fitToJ547.pdb (#3) to map
cryosparc_P130_J781_005_volume_map.mrc (#5) using 3904 atoms  
average map value = 0.07471, steps = 44  
shifted from previous position = 0.00785  
rotated from previous position = 0.00726 degrees  
atoms outside contour = 1628, contour level = 0.06188  
  
Position of MBD-CRBN_fitToJ547.pdb (#3) relative to
cryosparc_P130_J781_005_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
0.97857725 0.20272151 -0.03592429 -22.67795136  
-0.20387094 0.97847906 -0.03186474 39.62981845  
0.02869150 0.03850603 0.99884637 -8.31720436  
Axis 0.16848584 -0.15470695 -0.97348769  
Axis point 179.33230739 129.27667864 0.00000000  
Rotation angle (degrees) 12.05396407  
Shift along axis -1.85522583  
  

> open
> /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/cryosparc_P130_J782_map_locres.mrc

Opened cryosparc_P130_J782_map_locres.mrc as #6, grid size 480,480,480, pixel
0.647, shown at level 0.00227, step 2, values float32  

> hide #!5 models

> show #!5 models

> hide #!6 models

> volume #6 step 1

> show #!6 models

> hide #!6 models

> ui tool show "Color Zone"

> ui tool show "Surface Color"

> key red-white-blue :0.0 :0.5 :1.0 showTool true

> ui mousemode right "color key"

> color sample #5.1 map #6 palette #ff0000:#ffffff:#0000ff

Map values for surface "surface": minimum 2.588, mean 3.414, maximum 32.3  

> color sample #5.1 map #6 palette #ff0000:#ffffff:#0000ff

Map values for surface "surface": minimum 2.588, mean 3.414, maximum 32.3  

> color sample #5.1 map #6 palette 2.588,#0000ff:17.44,#00aaff:32.3,#00ffa9

Map values for surface "surface": minimum 2.588, mean 3.414, maximum 32.3  

> color sample #5.1 map #6 palette
> 2.588,#0000ff:3,#00aaff:3.5,#00ffa9:4,#00ff00:4.5,#aaff00:5,#ffaa00:5.5,#ff0000

Map values for surface "surface": minimum 2.588, mean 3.414, maximum 32.3  

> color sample #5.1 map #6 palette
> 2.588,#0000ff:3.2,#00aaff:3.6,#00ffa9:4.2,#00ff00:4.8,#aaff00:5.2,#ffaa00:6,#ff0000

Map values for surface "surface": minimum 2.588, mean 3.414, maximum 32.3  

> color sample #5.1 map #6 palette
> 2.588,#0000ff:3.2,#0091ff:3.6,#00ffda:4.2,#00ff48:4.8,#48ff00:5.2,#daff00:6,#ff9100:6.5,#ff0000

Map values for surface "surface": minimum 2.588, mean 3.414, maximum 32.3  

> color sample #5.1 map #6 palette
> 2.588,#0000ff:3.2,#0091ff:3.6,#00ffda:4.2,#00ff48:4.8,#48ff00:5.2,#daff00:6,#ff9100:6.5,#ff0000

Map values for surface "surface": minimum 2.588, mean 3.414, maximum 32.3  

> save
> /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/924_chimera4-S2merged.cxs

> key blue:2.59 #0091ff:3.20 #00ffda:3.60 #00ff48:4.20 #48ff00:4.80
> #daff00:5.20 #ff9100:6.00 red:6.50 showTool true

> ui mousemode right translate

> show #13 models

> key blue:2.59 #0091ff:3.20 #00ffda:3.60 #00ff48:4.20 #48ff00:4.80
> #daff00:5.20 #ff9100:6.00 red:6.50 showTool true

> ui mousemode right "color key"

> key numericLabelSpacing equal

> key fontSize 11

> key fontSize 10

> ui mousemode right translate

> volume #5 level 0.0461


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,6
      Model Number: Z1AY001HWLL/A
      Chip: Apple M3 Pro
      Total Number of Cores: 12 (6 performance and 6 efficiency)
      Memory: 36 GB
      System Firmware Version: 11881.81.4
      OS Loader Version: 11881.61.3

Software:

    System Software Overview:

      System Version: macOS 15.2 (24C101)
      Kernel Version: Darwin 24.2.0
      Time since boot: 13 days, 22 hours, 30 minutes

Graphics/Displays:

    Apple M3 Pro:

      Chipset Model: Apple M3 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 18
      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 P2419H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
        DELL U3223QE:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.24.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.9
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2

Change History (2)

comment:1 by Eric Pettersen, 7 months ago

Component: Unassigned → Window Toolkit
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on Mac waking from sleep

comment:2 by Eric Pettersen, 7 months ago

Resolution: → duplicate
Status: assigned → closed
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