Opened 7 days ago

Closed 6 days ago

#19705 closed defect (can't reproduce)

Crash + problem submitting bug report

Reported by: darshika.wickramasinghemudiyanselage@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Infrastructure Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-26.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error

Thread 0x000000030704f000 (most recent call first):
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000306043000 (most recent call first):
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000305037000 (most recent call first):
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.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/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030402b000 (most recent call first):
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030301f000 (most recent call first):
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000302013000 (most recent call first):
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000301007000 (most recent call first):
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000017fa03000 (most recent call first):
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000017e9f7000 (most recent call first):
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000017d9eb000 (most recent call first):
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000017c9df000 (most recent call first):
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000017a797000 (most recent call first):
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000001fd7ca080 (most recent call first):
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
  File "/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/235EA3F6-86A4-4EBA-B02E-2BDF1E2A0AE3/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler (total: 41)


{"app_name":"ChimeraX","timestamp":"2026-01-09 12:30:27.00 +1300","app_version":"","slice_uuid":"9cf8124a-d876-34ad-b7ee-c011183ebc15","build_version":"","platform":1,"share_with_app_devs":0,"is_first_party":1,"bug_type":"309","os_version":"macOS 26.1 (25B78)","roots_installed":0,"incident_id":"5FD1CF5D-02D8-4BDB-B9A4-90E3059FC705","name":"ChimeraX"}
{
  "uptime" : 700000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac15,12",
  "coalitionID" : 95052,
  "osVersion" : {
    "train" : "macOS 26.1",
    "build" : "25B78",
    "releaseType" : "User"
  },
  "captureTime" : "2026-01-09 12:30:21.0601 +1300",
  "codeSigningMonitor" : 2,
  "incident" : "5FD1CF5D-02D8-4BDB-B9A4-90E3059FC705",
  "pid" : 64530,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2026-01-09 12:29:09.9064 +1300",
  "procStartAbsTime" : 16929014432385,
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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: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  


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

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

Failed to send bug report. Error while sending follows:  

Traceback (most recent call last):  
File
"/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/40D37662-1ED3-4D6C-AD62-B0CBDD4848AD/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/bug_reporter/tool.py", line 253, in submit  
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields, timeout=10)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/40D37662-1ED3-4D6C-AD62-B0CBDD4848AD/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/webservices/post_form.py", line 45, in
post_multipart_formdata  
return r.status, r.msg, r.getheaders(), r.read()  
^^^^^^^^  
File
"/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/40D37662-1ED3-4D6C-AD62-B0CBDD4848AD/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 482, in read  
s = self._safe_read(self.length)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/40D37662-1ED3-4D6C-AD62-B0CBDD4848AD/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 633, in _safe_read  
raise IncompleteRead(data, amt-len(data))  
http.client.IncompleteRead: IncompleteRead(666 bytes read, 6446 more expected)  

Failed to send bug report. Error while sending follows:  

Traceback (most recent call last):  
File
"/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/40D37662-1ED3-4D6C-AD62-B0CBDD4848AD/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/bug_reporter/tool.py", line 253, in submit  
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields, timeout=10)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/40D37662-1ED3-4D6C-AD62-B0CBDD4848AD/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/webservices/post_form.py", line 45, in
post_multipart_formdata  
return r.status, r.msg, r.getheaders(), r.read()  
^^^^^^^^  
File
"/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/40D37662-1ED3-4D6C-AD62-B0CBDD4848AD/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 482, in read  
s = self._safe_read(self.length)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/private/var/folders/c2/fqh7mxmj6rj10dpz2zpqm5qh0000gn/T/AppTranslocation/40D37662-1ED3-4D6C-AD62-B0CBDD4848AD/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 633, in _safe_read  
raise IncompleteRead(data, amt-len(data))  
http.client.IncompleteRead: IncompleteRead(666 bytes read, 6446 more expected)  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M3
OpenGL vendor: Apple

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

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac15,12
      Model Number: MXCV3X/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 13822.41.1
      OS Loader Version: 13822.41.1

Software:

    System Software Overview:

      System Version: macOS 26.1 (25B78)
      Kernel Version: Darwin 25.1.0
      Time since boot: 47 days, 17 hours, 59 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 4
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

Change History (2)

comment:1 by Eric Pettersen, 6 days ago

Component: Unassigned → Infrastructure
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash + problem submitting bug report

Reported by Darshika

comment:2 by Tom Goddard, 6 days ago

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

ChimeraX crashed in the Qt window toolkit event loop, not in any ChimeraX code so I think it is a bug in Qt. Probably it was triggered by some mouse action in ChimeraX. If ChimeraX crashes often you may want to try the newer ChimeraX 1.11 version which uses a newer version of Qt (Qt 6.9 instead of Qt 6.8 in your current ChimeraX). Sorry I don't have any better suggestion.

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