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Opened 9 months ago
Closed 9 months ago
#16764 closed defect (can't reproduce)
Crash in event loop
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.2-x86_64-i386-64bit
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 0x0000700027392000 (most recent call first):
File "/private/var/folders/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070002638f000 (most recent call first):
File "/private/var/folders/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070002538c000 (most recent call first):
File "/private/var/folders/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700024389000 (most recent call first):
File "/private/var/folders/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700023386000 (most recent call first):
File "/private/var/folders/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700022383000 (most recent call first):
File "/private/var/folders/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700021380000 (most recent call first):
File "/private/var/folders/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070002037d000 (most recent call first):
File "/private/var/folders/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001f37a000 (most recent call first):
File "/private/var/folders/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001e377000 (most recent call first):
File "/private/var/folders/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001d374000 (most recent call first):
File "/private/var/folders/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001c371000 (most recent call first):
File "/private/var/folders/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001b36e000 (most recent call first):
File "/private/var/folders/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001a36b000 (most recent call first):
File "/private/var/folders/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700019368000 (most recent call first):
File "/private/var/folders/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/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/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007ff85a65c4c0 (most recent call first):
File "/private/var/folders/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/private/var/folders/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/private/var/folders/gk/xrjtzhlx1sv14gqndykws4440000gn/T/AppTranslocation/318B0109-549D-4D2E-9E77-456C7E8F9AAB/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
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===== Log before crash start =====
Startup Messages
---
warning | QCoreApplication::postEvent: Unexpected null receiver
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
> close
> open 3bse
Summary of feedback from opening 3bse fetched from pdb
---
notes | Fetching compressed mmCIF 3bse from http://files.rcsb.org/download/3bse.cif
Fetching CCD CA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif
3bse title:
Crystal structure analysis of a 16-base-pair B-DNA [more info...]
Chain information for 3bse #1
---
Chain | Description
A | DNA (5'-D(*DA*DCP*DAP*DCP*DTP*DAP*DCP*DAP*DAP*DTP*DGP*DTP*DTP*DGP*DCP*DAP*DAP*DT)-3')
B | DNA (5'-D(*DG*DTP*DAP*DTP*DTP*DGP*DCP*DAP*DAP*DCP*DAP*DTP*DTP*DGP*DTP*DAP*DGP*DT)-3')
Non-standard residues in 3bse #1
---
CA — calcium ion
Computing secondary structure
> set bgColor white
> hide
> hide cartoons
> show atoms
> hide solvent
> hide :Ca
> nucleotides atoms
> style ball
Changed 867 atom styles
===== 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
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Processor Name: 6-Core Intel Core i7
Processor Speed: 2.6 GHz
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L2 Cache (per Core): 256 KB
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Hyper-Threading Technology: Enabled
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OS Loader Version: 582~2898
Software:
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Kernel Version: Darwin 24.2.0
Time since boot: 11 hours, 48 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-020
Option ROM Version: 113-D32207P1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
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
Change History (2)
comment:1 by , 9 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop |
comment:2 by , 9 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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