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Opened 3 years ago
Last modified 3 years ago
#8447 feedback defect
Crash closing tool window
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | 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-13.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000002b46e7000 (most recent call first):
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000285037000 (most recent call first):
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028402b000 (most recent call first):
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028301f000 (most recent call first):
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000282013000 (most recent call first):
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000281007000 (most recent call first):
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000017f713000 (most recent call first):
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000017e707000 (most recent call first):
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000017d6fb000 (most recent call first):
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000017c6ef000 (most recent call first):
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000017b6e3000 (most recent call first):
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000017a6d7000 (most recent call first):
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00000001f3663a80 (most recent call first):
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2301 in destroy
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2165 in _destroy
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 772 in remove_tool
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 335 in remove_tool
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py", line 154 in delete
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 639 in close_request
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2267 in
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/private/var/folders/7x/84yjjbvs1kl_7pcyhkjf6fmm0000gn/T/AppTranslocation/1CB38E58-3D00-462F-B31D-7DE1930CB7C6/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2023-02-06 20:15:35.00 +0000","app_version":"1.5.0","slice_uuid":"a5992708-d5b4-36ec-ac0a-e525f6105b56","build_version":"1.5.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.1 (22C65)","roots_installed":0,"name":"ChimeraX","incident_id":"4509CFBB-1D9E-4BBC-9DD8-A223C1692988"}
{
"uptime" : 1400000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
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"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1953.300"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4416339968,
"size" : 20709376,
"uuid" : "6b8373ed-7142-34ea-9b4b-9f502e8a6f33",
"path" : "\/private\/var\/folders\/*\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
}
],
"vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=2.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 2176K 4 \nCG image 2288K 39 \nColorSync 576K 29 \nCoreAnimation 8864K 34 \nCoreGraphics 32K 2 \nCoreUI image data 4640K 32 \nFoundation 16K 1 \nKernel Alloc Once 32K 1 \nMALLOC 817.4M 100 \nMALLOC guard page 192K 10 \nMALLOC_MEDIUM (reserved) 760.0M 8 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 736K 46 \nStack 353.1M 47 \nStack Guard 56.0M 1 \nVM_ALLOCATE 237.8M 367 \nVM_ALLOCATE (reserved) 128.0M 1 reserved VM address space (unallocated)\n__AUTH 1882K 352 \n__AUTH_CONST 24.6M 575 \n__CTF 756 1 \n__DATA 19.7M 701 \n__DATA_CONST 36.8M 711 \n__DATA_DIRTY 1977K 226 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 794.4M 135 \n__OBJC_CONST 4671K 317 \n__OBJC_RO 65.4M 1 \n__OBJC_RW 1986K 1 \n__TEXT 797.4M 732 \ndyld private memory 416K 3 \nmapped file 218.8M 59 \nshared memory 3280K 30 \n=========== ======= ======= \nTOTAL 4.4G 4579 \nTOTAL, minus reserved VM space 3.4G 4579 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "61fd92db295c182621ececc3",
"factorPackIds" : {
},
"deploymentId" : 240000309
},
{
"rolloutId" : "6347054113acce15305b7b82",
"factorPackIds" : {
"SIRI_MEMORY_SYNC_CONFIG" : "634705e78e8be655c1316a6e"
},
"deploymentId" : 240000005
}
],
"experiments" : [
]
},
"reportNotes" : [
"dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/chidamios/Desktop/epi-sbt-
> alphafold/EPI1_PHYIT_mm_NbD038072_NbSBT5_2a_dee4c.result/EPI1_PHYIT_mm_NbD038072_NbSBT5_2a_dee4c_unrelaxed_rank_001_alphafold2_multimer_v2_model_3_seed_000.pdb
Chain information for
EPI1_PHYIT_mm_NbD038072_NbSBT5_2a_dee4c_unrelaxed_rank_001_alphafold2_multimer_v2_model_3_seed_000.pdb
#1
---
Chain | Description
A | No description available
B | No description available
> color bychain
> hbonds reveal true
690 hydrogen bonds found
> ~hbonds
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
EPI1_PHYIT_mm_NbD038072_NbSBT5_2a_dee4c_unrelaxed_rank_001_alphafold2_multimer_v2_model_3_seed_000.pdb_A
SES surface #1.1: minimum, -21.21, mean -2.81, maximum 10.66
Coulombic values for
EPI1_PHYIT_mm_NbD038072_NbSBT5_2a_dee4c_unrelaxed_rank_001_alphafold2_multimer_v2_model_3_seed_000.pdb_B
SES surface #1.2: minimum, -19.55, mean -2.54, maximum 13.38
To also show corresponding color key, enter the above coulombic command and
add key true
> select /B
4882 atoms, 4985 bonds, 661 residues, 1 model selected
> select /A
1004 atoms, 1026 bonds, 133 residues, 1 model selected
> surface hidePatches (#!1 & sel)
> select ::name="LYS"
468 atoms, 421 bonds, 52 residues, 1 model selected
> show (#!1 & sel) target ab
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file /Users/chidamios/Desktop/epi-sbt-
> alphafold/EPI1_PHYIT_mm_NbD038072_NbSBT5_2a_dee4c.result/EPI1_PHYIT_mm_NbD038072_NbSBT5_2a_dee4c_scores_rank_001_alphafold2_multimer_v2_model_3_seed_000.json
> color bfactor #1 palette alphafold
5886 atoms, 794 residues, 2 surfaces, atom bfactor range 19.1 to 99
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: Z11C000JAD/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8419.60.44
OS Loader Version: 8419.60.44
Software:
System Software Overview:
System Version: macOS 13.1 (22C65)
Kernel Version: Darwin 22.2.0
Time since boot: 50 days, 7 hours, 28 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash closing tool window |
comment:2 by , 3 years ago
| Status: | accepted → feedback |
|---|
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Hi Chidam,
--Eric