id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
17122	Crash in QWebEngine backend	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-15.3.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error

Thread 0x000000038fb3b000 (most recent call first):
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000038eb2f000 (most recent call first):
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000038db23000 (most recent call first):
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/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 ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000038cb17000 (most recent call first):
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000038bb0b000 (most recent call first):
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000038aaff000 (most recent call first):
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000389af3000 (most recent call first):
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000388ae7000 (most recent call first):
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000387adb000 (most recent call first):
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000386acf000 (most recent call first):
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000385ac3000 (most recent call first):
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000384ab7000 (most recent call first):
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000383aab000 (most recent call first):
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000382a9f000 (most recent call first):
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000381a93000 (most recent call first):
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000380a87000 (most recent call first):
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/nf/h8dr_s152_b61ts86dft7z0c0000gp/T/AppTranslocation/FEB3FAAA-8A2E-4ABF-A660-392805EE8AE8/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
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Thread 0x000000037ea6f000 (most recent call first):
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Current thread 0x00000001f7f6c840 (most recent call first):
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  File """", line 88 in _run_code
  File """", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, 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.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.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 54)


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  ""usedImages"" : [
  {
    ""size"" : 0,
    ""source"" : ""A"",
    ""base"" : 0,
    ""uuid"" : ""00000000-0000-0000-0000-000000000000""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""arm64e"",
    ""base"" : 6679912448,
    ""size"" : 532288,
    ""uuid"" : ""398a133c-9bcb-317f-a064-a40d3cea3c0f"",
    ""path"" : ""\/usr\/lib\/dyld"",
    ""name"" : ""dyld""
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],
  ""sharedCache"" : {
  ""base"" : 6679101440,
  ""size"" : 4865835008,
  ""uuid"" : ""5700d77a-6190-36e0-884d-fee6d586d62f""
},
  ""vmSummary"" : ""ReadOnly portion of Libraries: Total=606.7M resident=0K(0%) swapped_out_or_unallocated=606.7M(100%)\nWritable regions: Total=4.2G written=2051K(0%) resident=2051K(0%) swapped_out=0K(0%) unallocated=4.2G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG image                          2208K       42 \nCG raster data                     384K        8 \nColorSync                          640K       32 \nCoreAnimation                     3264K      126 \nCoreGraphics                        48K        3 \nCoreUI image data                 5232K       39 \nFoundation                          48K        2 \nKernel Alloc Once                 1424K        4 \nMALLOC                             3.1G      143 \nMALLOC guard page                  288K       18 \nMach message                        64K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                       57.0M       62 \nStack                            507.0M       62 \nVM_ALLOCATE                      269.7M      218 \nVM_ALLOCATE (reserved)           352.0M        5         reserved VM address space (unallocated)\n__DATA                              11K        1 \n__DATA_CONST                        24K        1 \n__DATA_DIRTY                         7K        1 \n__LINKEDIT                       606.2M        1 \n__TEXT                             520K        1 \n__TPRO_CONST                       272K        1 \ndyld private memory                 32K        2 \nmapped file                      632.5M      676 \nowned unmapped memory             30.2M        1 \npage table in kernel              2051K        1 \nshared memory                     5840K       46 \n===========                     =======  ======= \nTOTAL                              5.5G     1507 \nTOTAL, minus reserved VM space     5.1G     1507 \n"",
  ""legacyInfo"" : {
  ""threadTriggered"" : {
    ""name"" : ""CrBrowserMain""
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},
  ""logWritingSignature"" : ""cce115b394edb402e3011c3c18bcd9121b08464b"",
  ""trialInfo"" : {
  ""rollouts"" : [
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      ""factorPackIds"" : {

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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  

> open ""/Users/luyenhoang/Downloads/ApoE Chimp Structure.cif""

Chain information for ApoE Chimp Structure.cif #1  
---  
Chain | Description | UniProt  
A | Apolipoprotein E | APOE_PANTR 1-317  
  
Color ApoE Chimp Structure.cif by residue attribute pLDDT_score  

> color byattribute r:pLDDT_score #1 palette red:yellow:green

2536 atoms, 317 residues, atom pLDDT_score range 28.4 to 97.9  

> color byattribute r:pLDDT_score #1 palette red:yellow:green

2536 atoms, 317 residues, atom pLDDT_score range 28.4 to 97.9  

> open ""/Users/luyenhoang/Downloads/ApoE Human Structure.cif""

Chain information for ApoE Human Structure.cif #2  
---  
Chain | Description | UniProt  
A | Apolipoprotein E | APOE_HUMAN 1-317  
  
Color ApoE Human Structure.cif by residue attribute pLDDT_score  

> color byattribute r:pLDDT_score #2 palette red:yellow:green

2539 atoms, 317 residues, atom pLDDT_score range 32.5 to 98.2  

> color byattribute r:pLDDT_score #2 palette red:yellow:green

2539 atoms, 317 residues, atom pLDDT_score range 32.5 to 98.2  

> open ""/Users/luyenhoang/Downloads/ApoE Mouse Structure.cif""

Chain information for ApoE Mouse Structure.cif #3  
---  
Chain | Description | UniProt  
A | Apolipoprotein E | APOE_MOUSE 1-311  
  
Color ApoE Mouse Structure.cif by residue attribute pLDDT_score  

> hide #3 models

> hide #2 models

> select add #1

2536 atoms, 2571 bonds, 317 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select add #1

2536 atoms, 2571 bonds, 317 residues, 1 model selected  

> select subtract #1

Nothing selected  

> color #2 #0fe125ff

> color #1 #e10800ff

> color #1 #e106ceff

> show #2 models

> show #3 models

> color #1 #e10300ff

> hide #3 models

> hide #2 models

> color #1 bypolymer

> color #1 byhetero

> color #1 bynucleotide

> rainbow #1

> coulombic #1

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for ApoE Chimp Structure.cif_A SES surface #1.1: minimum,
-16.61, mean -1.28, maximum 15.95  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp #!1

Map values for surface ""ApoE Chimp Structure.cif_A SES surface"": minimum
-26.94, mean -4.254, maximum 22.58  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor #!1

2536 atoms, 317 residues, 1 surfaces, atom bfactor range 28.5 to 97.9  

> hbonds #!1 reveal true

413 hydrogen bonds found  

> color #!1 bypolymer

> color #!1 byhetero

> nucleotides #!1 atoms

> style nucleic & #!1 stick

Changed 0 atom styles  

> nucleotides #!1 fill

> style nucleic & #!1 stick

Changed 0 atom styles  

> color bfactor #!1

2536 atoms, 317 residues, 1 surfaces, atom bfactor range 28.5 to 97.9  

> mlp #!1

Map values for surface ""ApoE Chimp Structure.cif_A SES surface"": minimum
-26.94, mean -4.254, maximum 22.58  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic #!1

Coulombic values for ApoE Chimp Structure.cif_A SES surface #1.1: minimum,
-16.61, mean -1.28, maximum 15.95  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color #!1 bynucleotide

> color #!1 byhetero

Alignment identifier is 1/A  
Alignment identifier is 2/A  
Alignment identifier is 3/A  

> hide #!1 models

> show #!1 models

> show #2 models

> hide #2 models

> nucleotides #!1 atoms

> style nucleic & #!1 stick

Changed 0 atom styles  

> style #!1 sphere

Changed 2536 atom styles  

> style #!1 sphere

Changed 2536 atom styles  

> undo

> interfaces #!1 & ~solvent

0 buried areas:  

> hide #!1 atoms

> show #!1 atoms

> show #!1 cartoons

> show #!1 surfaces

> hide #!1 cartoons

> show #!1 cartoons

> color #!1 bypolymer

> color #!1 bychain

> hide #!1 target m

> hide #4 models

> show #!1 models

> show #2 models

> show #3 models

> hide #!1 models

> set bgColor white

> set bgColor black

> lighting simple

> lighting soft

> lighting full

> ui tool show ""Selection Inspector""


===== 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 M4 Max
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: Mac16,5
      Model Number: Z1FW0008BLL/A
      Chip: Apple M4 Max
      Total Number of Cores: 16 (12 performance and 4 efficiency)
      Memory: 64 GB
      System Firmware Version: 11881.81.4
      OS Loader Version: 11881.81.4

Software:

    System Software Overview:

      System Version: macOS 15.3.2 (24D81)
      Kernel Version: Darwin 24.3.0
      Time since boot: 5 days, 13 hours, 57 minutes

Graphics/Displays:

    Apple M4 Max:

      Chipset Model: Apple M4 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 40
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


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
    babel: 2.16.0
    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-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-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
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    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
    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
    packaging: 23.2
    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
    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
    tornado: 6.4.2
    traitlets: 5.14.3
    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-filename: 1.4.1
    widgetsnbextension: 4.0.13
}}}
"	defect	closed	normal		Window Toolkit		can't reproduce		Tom Goddard				all	ChimeraX