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#15614 closed defect (duplicate)

Crash changing display configuration on Mac

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-14.4.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00000003202a3000 (most recent call first):
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031f297000 (most recent call first):
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031e28b000 (most recent call first):
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031d27f000 (most recent call first):
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031c273000 (most recent call first):
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031b267000 (most recent call first):
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031a25b000 (most recent call first):
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031924f000 (most recent call first):
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000318243000 (most recent call first):
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000317237000 (most recent call first):
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031622b000 (most recent call first):
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000001e8d5bac0 (most recent call first):
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
  File "/private/var/folders/v9/5rxmjwq54sxf25mvy1764_tsd4q3pk/T/AppTranslocation/C19E5B9B-31B6-4870-8EE1-5C2CBCF12387/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 58)


{"app_name":"ChimeraX","timestamp":"2024-07-15 17:17:29.00 +1000","app_version":"1.8.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.4.1 (23E224)","roots_installed":0,"name":"ChimeraX","incident_id":"7D7F2C40-96F3-4CE7-903A-F03A54CE93DF"}
{
  "uptime" : 1000000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 1514901202,
  "deployVersion" : 210,
  "modelCode" : "Mac15,3",
  "coalitionID" : 158416,
  "osVersion" : {
    "train" : "macOS 14.4.1",
    "build" : "23E224",
    "releaseType" : "User"
  },
  "captureTime" : "2024-07-15 17:11:28.6653 +1000",
  "codeSigningMonitor" : 1,
  "incident" : "7D7F2C40-96F3-4CE7-903A-F03A54CE93DF",
  "pid" : 81294,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-07-07 18:16:21.3786 +1000",
  "procStartAbsTime" : 22462570748737,
  "procExitAbsTime" : 24600994984959,
  "procName" : "ChimeraX",
  "procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"074E81E7-E027-53CF-B669-C5AFD99A2FBF","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "DA9F06BC-4B04-704A-1911-C2EF68139B51",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "wakeTime" : 6392,
  "sleepWakeUUID" : "E2AA19CD-8480-460A-8931-1F02579AE6A5",
  "sip" : "enabled",
  "vmRegionInfo" : "0x169 is not in any region.  Bytes before following region: 4297129623\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      100210000-100214000    [   16K] r-x\/r-x SM=COW  \/var\/folders\/*\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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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: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/s3000708/Desktop/Postdoc/Experimental Data/RNA-Seq/Nm
> M0579/Final Experiment/M0579 RNA-Seq Data 20240704 /LTA Synthase Family
> Protein/fold_2024_07_07_18_03_lta (1)/fold_2024_07_07_18_03_lta_model_0.cif"

Chain information for fold_2024_07_07_18_03_lta_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> open "/Users/s3000708/Desktop/Postdoc/Experimental Data/RNA-Seq/Nm
> M0579/Final Experiment/M0579 RNA-Seq Data 20240704 /LTA Synthase Family
> Protein/fold_2024_07_07_18_03_lta (1)/fold_2024_07_07_18_03_lta_model_1.cif"

Chain information for fold_2024_07_07_18_03_lta_model_1.cif #2  
---  
Chain | Description  
A | .  
  

> hide #1 models

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #2/A

Alignment identifier is 1  

> select #1/A:1 #2/A:1

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A:1-19 #2/A:1-19

318 atoms, 330 bonds, 38 residues, 2 models selected  
. [ID: 1] region 2 chains [1-19] RMSD: 104.551  
  

> select #1/A:1 #2/A:1

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A:1-12 #2/A:1-12

204 atoms, 208 bonds, 24 residues, 2 models selected  
. [ID: 1] region 2 chains [1-12] RMSD: 112.490  
  

> select #1/A:1-12 #2/A:1-12

204 atoms, 208 bonds, 24 residues, 2 models selected  
. [ID: 1] region 2 chains [1-12] RMSD: 112.490  
  

> select #1/A:1-12 #2/A:1-12

204 atoms, 208 bonds, 24 residues, 2 models selected  
. [ID: 1] region 2 chains [1-12] RMSD: 112.490  
  

> select #1/A:1-17 #2/A:1-17

286 atoms, 296 bonds, 34 residues, 2 models selected  
. [ID: 1] region 2 chains [1-12] + 1 other block RMSD: 106.831  
  

> select #1/A:471 #2/A:471

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A:464-471 #2/A:464-471

144 atoms, 150 bonds, 16 residues, 2 models selected  
. [ID: 1] region 2 chains [464-471] RMSD: 43.319  
  

> select add #1

3814 atoms, 3926 bonds, 480 residues, 2 models selected  

> select subtract #1

72 atoms, 75 bonds, 8 residues, 1 model selected  

> select add #1

3814 atoms, 3926 bonds, 480 residues, 2 models selected  

> select subtract #1

72 atoms, 75 bonds, 8 residues, 1 model selected  

> lighting full

> lighting soft

> lighting simple

> lighting full

> save /Users/s3000708/Desktop/image1.png supersample 3

> select #1/A:464-471 #2/A:464-471

144 atoms, 150 bonds, 16 residues, 2 models selected  
. [ID: 1] region 2 chains [464-471] RMSD: 43.319  
  

> select #1/A:464-471 #2/A:464-471

144 atoms, 150 bonds, 16 residues, 2 models selected  
. [ID: 1] region 2 chains [464-471] RMSD: 43.319  
  

> select #1/A:464-471 #2/A:464-471

144 atoms, 150 bonds, 16 residues, 2 models selected  
. [ID: 1] region 2 chains [464-471] RMSD: 43.319  
  

> select #1/A:472 #2/A:472

20 atoms, 18 bonds, 2 residues, 2 models selected  

> select #1/A:462-472 #2/A:462-472

192 atoms, 200 bonds, 22 residues, 2 models selected  
. [ID: 1] region 2 chains [462-472] RMSD: 43.190  
  

> color (#2 & sel) red

> select
> #1/A:3-7,18-42,51-61,65-90,96-107,111-137,140-157,168-173,183-191,194-200,214-217,240-246,248-256,271-280,290-292,295-297,302-308,323-333,341-343,352-354,358-360,362-371,390-392,400-403,410-430,432-434,452-458
> #2/A:3-7,18-42,51-61,65-90,96-107,111-137,140-157,168-173,183-191,194-200,214-217,240-246,248-256,271-280,290-292,295-297,302-308,323-333,341-343,352-354,358-360,362-371,390-392,400-403,410-430,432-434,452-458

4092 atoms, 4134 bonds, 514 residues, 2 models selected  

> select #1/A:91-92 #2/A:91-92

36 atoms, 38 bonds, 4 residues, 2 models selected  

> select #1/A:91-103 #2/A:91-103

202 atoms, 206 bonds, 26 residues, 2 models selected  
. [ID: 1] region 2 chains [91-103] RMSD: 11.692  
  

> select #1/A:17 #2/A:17

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A:1-17 #2/A:1-17

286 atoms, 296 bonds, 34 residues, 2 models selected  
. [ID: 1] region 2 chains [1-17] RMSD: 106.831  
  

> color (#2 & sel) red

> open "/Users/s3000708/Desktop/Postdoc/Experimental Data/RNA-Seq/Nm
> M0579/Final Experiment/M0579 RNA-Seq Data 20240704 /LTA Synthase Family
> Protein/Staph aureus/AF-Q6GIS3-F1-model_v4_MRSA252_Sa.pdb"

AF-Q6GIS3-F1-model_v4_MRSA252_Sa.pdb title:  
Alphafold monomer V2.0 prediction for lipoteichoic acid synthase (Q6GIS3)
[more info...]  
  
Chain information for AF-Q6GIS3-F1-model_v4_MRSA252_Sa.pdb #3  
---  
Chain | Description | UniProt  
A | lipoteichoic acid synthase | LTAS_STAAR 1-646  
  

> view #2 clip false

> hide #2 target m

> show #2 target m

> show #1 target m

> hide #1 target m

> ui tool show Matchmaker

> matchmaker #3 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_2024_07_07_18_03_lta_model_1.cif, chain A (#2) with
AF-Q6GIS3-F1-model_v4_MRSA252_Sa.pdb, chain A (#3), sequence alignment score =
374.1  
RMSD between 96 pruned atom pairs is 0.982 angstroms; (across all 428 pairs:
25.138)  
  

> ui mousemode right zoom

> ui mousemode right translate

> ui mousemode right pivot

> ui mousemode right "next docked"

> lighting simple

> lighting soft

> lighting full

> select add #2

3885 atoms, 3999 bonds, 489 residues, 2 models selected  

> select subtract #2

143 atoms, 148 bonds, 17 residues, 1 model selected  

> select add #3

5415 atoms, 5558 bonds, 663 residues, 2 models selected  

> select add #2

9157 atoms, 9409 bonds, 1135 residues, 3 models selected  

> select add #1

12756 atoms, 13112 bonds, 1590 residues, 3 models selected  

> select subtract #1

9014 atoms, 9261 bonds, 1118 residues, 2 models selected  

> select subtract #2

5272 atoms, 5410 bonds, 646 residues, 1 model selected  

> select subtract #3

Nothing selected  
Alignment identifier is 1  
Alignment identifier is 3/A  

> select #1/A:1 #2/A:1

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A:1-21 #2/A:1-21

356 atoms, 368 bonds, 42 residues, 2 models selected  
. [ID: 1] region 2 chains [1-21] RMSD: 102.191  
  

> select
> #1/A:3-7,18-42,51-61,65-90,96-107,111-137,140-157,168-173,183-191,194-200,214-217,240-246,248-256,271-280,290-292,295-297,302-308,323-333,341-343,352-354,358-360,362-371,390-392,400-403,410-430,432-434,452-458
> #2/A:3-7,18-42,51-61,65-90,96-107,111-137,140-157,168-173,183-191,194-200,214-217,240-246,248-256,271-280,290-292,295-297,302-308,323-333,341-343,352-354,358-360,362-371,390-392,400-403,410-430,432-434,452-458

4092 atoms, 4134 bonds, 514 residues, 2 models selected  

> select #1/A:1 #2/A:1

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A #2/A

7484 atoms, 7702 bonds, 944 residues, 2 models selected  
. [ID: 1] region 2 chains [1-472] RMSD: 44.666  
  

> color (#2 & sel) cornflower blue

> select #1/A:471-472 #2/A:471-472

36 atoms, 34 bonds, 4 residues, 2 models selected  

> select #1/A:471-472 #2/A:471-472

36 atoms, 34 bonds, 4 residues, 2 models selected  
. [ID: 1] region 2 chains [471-472] RMSD: 63.609  
  

> select #1/A:472 #2/A:472

20 atoms, 18 bonds, 2 residues, 2 models selected  

> select #1/A:471-472 #2/A:471-472

36 atoms, 34 bonds, 4 residues, 2 models selected  
. [ID: 1] region 2 chains [471-472] RMSD: 63.609  
  

> select #1/A:472 #2/A:472

20 atoms, 18 bonds, 2 residues, 2 models selected  

> select #1/A:471-472 #2/A:471-472

36 atoms, 34 bonds, 4 residues, 2 models selected  
. [ID: 1] region 2 chains [471-472] RMSD: 63.609  
  

> select
> #1/A:204-207,225-231,257-266,282-286,312-317,337-339,375-380,437-443,463-471
> #2/A:204-207,225-231,257-266,282-286,312-317,337-339,375-380,437-443,463-471

940 atoms, 962 bonds, 114 residues, 2 models selected  

> select #1/A:1 #2/A:1

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A #2/A

7484 atoms, 7702 bonds, 944 residues, 2 models selected  
. [ID: 1] region 2 chains [1-472] RMSD: 44.666  
  

> select #1/A:472 #2/A:472

20 atoms, 18 bonds, 2 residues, 2 models selected  

> select #1/A:472 #2/A:472

20 atoms, 18 bonds, 2 residues, 2 models selected  

> select #1/A:472 #2/A:472

20 atoms, 18 bonds, 2 residues, 2 models selected  
. [ID: 1] region 2 chains [472] RMSD: 67.200  
  

> ui tool show "Side View"

> view sel

> ui tool show "Side View"

> view

> view sel

> view

> ui tool show "Side View"

> select #1/A:410 #2/A:410

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A:410-470 #2/A:410-470

1006 atoms, 1036 bonds, 122 residues, 2 models selected  
. [ID: 1] region 2 chains [410-470] RMSD: 35.433  
  

> select #1/A:410 #2/A:410

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A:410-420 #2/A:410-420

184 atoms, 186 bonds, 22 residues, 2 models selected  
. [ID: 1] region 2 chains [410-420] RMSD: 19.587  
  

> undo

> view

> select #1/A:472 #2/A:472

20 atoms, 18 bonds, 2 residues, 2 models selected  

> select #1/A #2/A

7484 atoms, 7702 bonds, 944 residues, 2 models selected  
. [ID: 1] region 2 chains [1-472] RMSD: 44.666  
  

> select #1/A:472 #2/A:472

20 atoms, 18 bonds, 2 residues, 2 models selected  

> select #1/A:472 #2/A:472

20 atoms, 18 bonds, 2 residues, 2 models selected  
. [ID: 1] region 2 chains [472] RMSD: 67.200  
  

> select
> #1/A:3-7,18-42,51-61,65-90,96-107,111-137,140-157,168-173,183-191,194-200,214-217,240-246,248-256,271-280,290-292,295-297,302-308,323-333,341-343,352-354,358-360,362-371,390-392,400-403,410-430,432-434,452-458
> #2/A:3-7,18-42,51-61,65-90,96-107,111-137,140-157,168-173,183-191,194-200,214-217,240-246,248-256,271-280,290-292,295-297,302-308,323-333,341-343,352-354,358-360,362-371,390-392,400-403,410-430,432-434,452-458

4092 atoms, 4134 bonds, 514 residues, 2 models selected  

> select
> #3/A:10-31,39-48,51-63,66-94,100-103,106-108,113-119,124-140,142-144,152-176,187-194,196-216,219-232,259-261,273-280,300-309,319-322,331-339,353-361,371-373,378-380,388-401,423-425,436-461,481-491,497-504,526-536,595-614,617-619,631-633

2676 atoms, 2715 bonds, 324 residues, 1 model selected  

> select
> #1/A:3-7,18-42,51-61,65-90,96-107,111-137,140-157,168-173,183-191,194-200,214-217,240-246,248-256,271-280,290-292,295-297,302-308,323-333,341-343,352-354,358-360,362-371,390-392,400-403,410-430,432-434,452-458
> #2/A:3-7,18-42,51-61,65-90,96-107,111-137,140-157,168-173,183-191,194-200,214-217,240-246,248-256,271-280,290-292,295-297,302-308,323-333,341-343,352-354,358-360,362-371,390-392,400-403,410-430,432-434,452-458

4092 atoms, 4134 bonds, 514 residues, 2 models selected  

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> select ~sel & ##selected

3392 atoms, 3568 bonds, 430 residues, 2 models selected  

> select ~sel & ##selected

4092 atoms, 4134 bonds, 514 residues, 2 models selected  

> select ~sel & ##selected

3392 atoms, 3568 bonds, 430 residues, 2 models selected  

> select ~sel & ##selected

4092 atoms, 4134 bonds, 514 residues, 2 models selected  

> select ~sel & ##selected

3392 atoms, 3568 bonds, 430 residues, 2 models selected  

> select ~sel & ##selected

4092 atoms, 4134 bonds, 514 residues, 2 models selected  

> select ~sel & ##selected

3392 atoms, 3568 bonds, 430 residues, 2 models selected  

> select ~sel & ##selected

4092 atoms, 4134 bonds, 514 residues, 2 models selected  

> select ~sel & ##selected

3392 atoms, 3568 bonds, 430 residues, 2 models selected  

> select ~sel & ##selected

4092 atoms, 4134 bonds, 514 residues, 2 models selected  

> select ~sel & ##selected

3392 atoms, 3568 bonds, 430 residues, 2 models selected  

> select ~sel & ##selected

4092 atoms, 4134 bonds, 514 residues, 2 models selected  

> select ~sel & ##selected

3392 atoms, 3568 bonds, 430 residues, 2 models selected  

> select ~sel & ##selected

4092 atoms, 4134 bonds, 514 residues, 2 models selected  

> select ~sel

8664 atoms, 8870 bonds, 1076 residues, 3 models selected  

> select ~sel

4092 atoms, 4134 bonds, 514 residues, 2 models selected  

> select clear

> save /Users/s3000708/Desktop/image1.png supersample 3

> save /Users/s3000708/Desktop/image2.png supersample 3

> open "/Users/s3000708/Desktop/Postdoc/Experimental Data/RNA-Seq/Nm
> M0579/Final Experiment/M0579 RNA-Seq Data 20240704 /LTA Synthase Family
> Protein/fold_2024_07_07_18_03_lta (1)/fold_2024_07_07_18_03_lta_model_2.cif"

Chain information for fold_2024_07_07_18_03_lta_model_2.cif #4  
---  
Chain | Description  
A | .  
  

> ui tool show Matchmaker

> matchmaker #2-3 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_2024_07_07_18_03_lta_model_2.cif, chain A (#4) with
fold_2024_07_07_18_03_lta_model_1.cif, chain A (#2), sequence alignment score
= 2462.8  
RMSD between 156 pruned atom pairs is 0.502 angstroms; (across all 472 pairs:
12.064)  
  
Matchmaker fold_2024_07_07_18_03_lta_model_2.cif, chain A (#4) with
AF-Q6GIS3-F1-model_v4_MRSA252_Sa.pdb, chain A (#3), sequence alignment score =
362.1  
RMSD between 97 pruned atom pairs is 0.981 angstroms; (across all 428 pairs:
11.351)  
  

> hide #2 models

> open "/Users/s3000708/Desktop/Postdoc/Experimental Data/RNA-Seq/Nm
> M0579/Final Experiment/M0579 RNA-Seq Data 20240704 /LTA Synthase Family
> Protein/fold_2024_07_07_18_03_lta (1)/fold_2024_07_07_18_03_lta_model_3.cif"

Chain information for fold_2024_07_07_18_03_lta_model_3.cif #5  
---  
Chain | Description  
A | .  
  

> hide #4 models

> ui tool show Matchmaker

> matchmaker #3 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_2024_07_07_18_03_lta_model_3.cif, chain A (#5) with
AF-Q6GIS3-F1-model_v4_MRSA252_Sa.pdb, chain A (#3), sequence alignment score =
361.3  
RMSD between 98 pruned atom pairs is 0.997 angstroms; (across all 420 pairs:
12.099)  
  

> open "/Users/s3000708/Desktop/Postdoc/Experimental Data/RNA-Seq/Nm
> M0579/Final Experiment/M0579 RNA-Seq Data 20240704 /LTA Synthase Family
> Protein/fold_2024_07_07_18_03_lta (1)/fold_2024_07_07_18_03_lta_model_4.cif"

Chain information for fold_2024_07_07_18_03_lta_model_4.cif #6  
---  
Chain | Description  
A | .  
  

> hide #5 models

> ui tool show Matchmaker

> matchmaker #3 to #6

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_2024_07_07_18_03_lta_model_4.cif, chain A (#6) with
AF-Q6GIS3-F1-model_v4_MRSA252_Sa.pdb, chain A (#3), sequence alignment score =
362.1  
RMSD between 96 pruned atom pairs is 0.984 angstroms; (across all 428 pairs:
11.439)  
  

> show #2 models

> show #4 models

> show #5 models

> hide #5 models

> hide #3 models

> hide #4 models

> show #3 models

> hide #6 models

> hide #2 models

> show #4 models

> hide #4 models

> show #6 models

> hide #6 models

> show #5 models

> ui tool show Matchmaker

> matchmaker #3 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_2024_07_07_18_03_lta_model_3.cif, chain A (#5) with
AF-Q6GIS3-F1-model_v4_MRSA252_Sa.pdb, chain A (#3), sequence alignment score =
361.3  
RMSD between 98 pruned atom pairs is 0.997 angstroms; (across all 420 pairs:
12.099)  
  

> select #1/A:445 #2/A:445

20 atoms, 20 bonds, 2 residues, 2 models selected  

> select #1/A:437-445 #2/A:437-445

136 atoms, 136 bonds, 18 residues, 2 models selected  
. [ID: 1] region 2 chains [437-445] RMSD: 30.513  
  

> select #1/A:217 #2/A:217

20 atoms, 20 bonds, 2 residues, 2 models selected  

> select #1/A:217-469 #2/A:217-469

4060 atoms, 4180 bonds, 506 residues, 2 models selected  
. [ID: 1] region 2 chains [217-469] RMSD: 28.050  
  

> view sel

No displayed objects specified.  

> view sel

No displayed objects specified.  

> show #2 models

> hide #5 models

> select clear

> show #5 models

> hide #2 models

> hide #5 models

> show #4 models

> hide #4 models

> show #6 models

> ui tool show Matchmaker

> matchmaker #3 to #6

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_2024_07_07_18_03_lta_model_4.cif, chain A (#6) with
AF-Q6GIS3-F1-model_v4_MRSA252_Sa.pdb, chain A (#3), sequence alignment score =
362.1  
RMSD between 96 pruned atom pairs is 0.984 angstroms; (across all 428 pairs:
11.439)  
  

> save /Users/s3000708/Desktop/image3.png supersample 3

> ui tool show "Show Sequence Viewer"

> hide #6 models

> show #1 models

> ui tool show Matchmaker

> matchmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_2024_07_07_18_03_lta_model_0.cif, chain A (#1) with
AF-Q6GIS3-F1-model_v4_MRSA252_Sa.pdb, chain A (#3), sequence alignment score =
378.3  
RMSD between 89 pruned atom pairs is 0.987 angstroms; (across all 428 pairs:
25.042)  
  

> ui tool show "Modeller Comparative"

> ui tool show "Model Loops"

> select
> #3/A:10-31,39-48,51-63,66-94,100-103,106-108,113-119,124-140,142-144,152-176,187-194,196-216,219-232,259-261,273-280,300-309,319-322,331-339,353-361,371-373,378-380,388-401,423-425,436-461,481-491,497-504,526-536,595-614,617-619,631-633

2676 atoms, 2715 bonds, 324 residues, 1 model selected  

> select #3/A:245-246

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

> select #3/A:245-646

3266 atoms, 3345 bonds, 402 residues, 1 model selected  

> color sel purple

> select clear

> hide #1 models

> show #6 models

> show #1 models

> hide #6 models

> save "/Users/s3000708/Desktop/Postdoc/Experimental Data/RNA-Seq/Nm
> M0579/Final Experiment/M0579 RNA-Seq Data 20240704 /LTA Synthase Family
> Protein/LTA Synthase Modelling and Alignment.cxs"


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3
OpenGL vendor: Apple

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

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,3
      Model Number: Z1A90004RX/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.101.3
      OS Loader Version: 10151.101.3

Software:

    System Software Overview:

      System Version: macOS 14.4.1 (23E224)
      Kernel Version: Darwin 23.4.0
      Time since boot: 84 days, 21 hours, 23 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


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-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: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (2)

comment:1 by Eric Pettersen, 15 months ago

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

comment:2 by Tom Goddard, 15 months ago

Resolution:	→ duplicate
Status:	assigned → closed

Mac Qt 6.6 crash probably from unplugging or plugging in external display.

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