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Opened 2 years ago
Last modified 2 years ago
#9141 feedback defect
Crash hiding tool
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
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 0x000000031dce4000 (most recent call first):
File "/private/var/folders/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031cce1000 (most recent call first):
File "/private/var/folders/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031bcde000 (most recent call first):
File "/private/var/folders/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031acdb000 (most recent call first):
File "/private/var/folders/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000319cd8000 (most recent call first):
File "/private/var/folders/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000318cd5000 (most recent call first):
File "/private/var/folders/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000317cd2000 (most recent call first):
File "/private/var/folders/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000316ccf000 (most recent call first):
File "/private/var/folders/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000315ccc000 (most recent call first):
File "/private/var/folders/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000314cc9000 (most recent call first):
File "/private/var/folders/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000313cc6000 (most recent call first):
File "/private/var/folders/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000312cc3000 (most recent call first):
File "/private/var/folders/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000311cc0000 (most recent call first):
File "/private/var/folders/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x0000000200a7a280 (most recent call first):
File "/private/var/folders/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2435 in shown
File "/private/var/folders/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2201 in _mw_set_shown
File "/private/var/folders/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 771 in remove_tool
File "/private/var/folders/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/help_viewer/tool.py", line 514 in delete
File "/private/var/folders/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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/7b/bv396syd7cn5tt03_fgbql540000gn/T/AppTranslocation/381F1119-4E1A-4312-8849-E7CDFA1DF818/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
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"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "1971"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703505350656,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 16809969,
"uuid" : "af96f40f-d333-3647-9da4-eddc52df4753",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2299.50.120"
}
],
"sharedCache" : {
"base" : 140703450284032,
"size" : 21474836480,
"uuid" : "b81581ae-ff6f-3644-8c21-c969ac66f1fa"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=2.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.9G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 4992K 8 \nCG image 600K 63 \nColorSync 264K 29 \nCoreAnimation 180K 23 \nCoreGraphics 16K 3 \nCoreGraphics (reserved) 40K 5 reserved VM address space (unallocated)\nCoreUI image data 5148K 38 \nFoundation 32K 2 \nKernel Alloc Once 1364K 4 \nMALLOC 1.0G 278 \nMALLOC guard page 192K 9 \nMALLOC_MEDIUM (reserved) 984.0M 10 reserved VM address space (unallocated)\nMach message 24K 6 \nOpenGL GLSL 384K 4 \nRosetta Arena 4096K 2 \nRosetta Generic 1816K 451 \nRosetta IndirectBranch 2048K 1 \nRosetta JIT 128.0M 1 \nRosetta Return Stack 1180K 118 \nRosetta Thread Context 1180K 118 \nSTACK GUARD 56K 14 \nStack 396.3M 59 \nStack Guard 56.2M 45 \nVM_ALLOCATE 168.9M 304 \nVM_ALLOCATE (reserved) 192.0M 11 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 46.4M 756 \n__DATA_CONST 39.9M 394 \n__DATA_DIRTY 1814K 228 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 200.8M 143 \n__OBJC_RO 66.2M 1 \n__OBJC_RW 2009K 2 \n__TEXT 921.1M 761 \ndyld private memory 680K 7 \nmapped file 4.9G 1767 \nshared memory 3532K 25 \nunshared pmap 14.2M 11 \n=========== ======= ======= \nTOTAL 9.1G 5709 \nTOTAL, minus reserved VM space 7.9G 5709 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "9d06c8145dbb49dd3334d7a89bf985ec322ad663",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "63508950b3714d3622fc77f7",
"factorPackIds" : {
"SIRI_MEMORY_SYNC_CONFIG" : "63508beab3714d3622fc7808"
},
"deploymentId" : 240000004
},
{
"rolloutId" : "60f8ddccefea4203d95cbeef",
"factorPackIds" : {
},
"deploymentId" : 240000025
}
],
"experiments" : [
{
"treatmentId" : "c28e4ee6-1b08-4f90-8e05-2809e78310a3",
"experimentId" : "6317d2003d24842ff850182a",
"deploymentId" : 400000013
},
{
"treatmentId" : "d28d100b-301c-49ae-b6c9-57930102d4d4",
"experimentId" : "64466b09a3b9440a82a18c34",
"deploymentId" : 400000002
}
]
}
}
===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields
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/mariakrasilnikov/Library/CloudStorage/Box-Box/PyMol and
> Chimera/prot.pdb"
Chain information for prot.pdb #1
---
Chain | Description
A B C | No description available
D E F | No description available
> hide atoms
> show cartoons
> molmap #1, 20
Missing or invalid "resolution" argument: Expected a number
> molmap #1 20
Opened prot.pdb map 20 as #2, grid size 34,35,34, pixel 6.67, shown at level
0.0425, step 1, values float32
> molmap #1 15
Opened prot.pdb map 15 as #2, grid size 39,41,39, pixel 5, shown at level
0.0553, step 1, values float32
> molmap #1 10
Opened prot.pdb map 10 as #2, grid size 49,52,49, pixel 3.33, shown at level
0.073, step 1, values float32
> molmap #1 20
Opened prot.pdb map 20 as #2, grid size 34,35,34, pixel 6.67, shown at level
0.0425, step 1, values float32
> molmap #1 15
Opened prot.pdb map 15 as #2, grid size 39,41,39, pixel 5, shown at level
0.0553, step 1, values float32
> save /Users/mariakrasilnikov/Desktop/pEW62_molmap15.mrc models #2
> open /Users/mariakrasilnikov/Desktop/cryosparc_P14_pEW62_molmap15.mrc
Opened cryosparc_P14_pEW62_molmap15.mrc as #3, grid size 39,41,39, pixel 15,
shown at level 0.297, step 1, values float32
> volume #3 level 0.05954
> open "/Users/mariakrasilnikov/Desktop/cryosparc_P14_pEW62_molmap15 copy.mrc"
Opened cryosparc_P14_pEW62_molmap15 copy.mrc as #4, grid size 39,41,39, pixel
5, shown at level 0.297, step 1, values float32
> hide #!3 models
> volume #4 level 0.2869
> hide #!2 models
> hide #!1 models
> volume #4 level 0.09465
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!2 models
> volume #4 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"
> volume #4 style surface
> view #4 clip false
> marker #4
Missing required "position" argument
> close #4
> undo
> open "/Users/mariakrasilnikov/Desktop/cryosparc_P14_pEW62_molmap15 copy.mrc"
Opened cryosparc_P14_pEW62_molmap15 copy.mrc as #4, grid size 39,41,39, pixel
5, shown at level 0.297, step 1, values float32
> open "/Users/mariakrasilnikov/Desktop/cryosparc_P14_pEW62_molmap15 copy.mrc"
Opened cryosparc_P14_pEW62_molmap15 copy.mrc as #5, grid size 39,41,39, pixel
5, shown at level 0.297, step 1, values float32
> hide #!4 models
> close #4
> volume #5 level 0.1157
> view clip false
> view #5 clip false
> ui mousemode right "mark center"
> view #5 clip false
> ui mousemode right "mark surface"
> ui tool show "Map Coordinates"
> view #5 clip false
> marker #4 position 19, 20, 19
> marker #5 position 19, 20, 19
Cannot create a marker set #5 with same model id as another model
> marker delete #4
Deleted 1 markers
> view #5 clip false
> marker #5 20.454,-43.997
Expected a keyword
> marker #5 position 20.454,-43.997
Invalid "position" argument: Expected 3 floats or object specifier
> marker #5 position 19, 20, 19
Cannot create a marker set #5 with same model id as another model
> marker #4 position 19, 20, 19
> hide #!5 models
> hide #!2 models
> hide #!1 models
> show #4 target m
> view #4 clip false
> show #!5 models
> view #5 clip false
> transparency #5.1 50
> volume #!5 showOutlineBox true
> hide #!5 models
> show #!5 models
> show #4 target m
> view #4 clip false
> view #5 clip false
> marker #6 position -42.31,-20.454,-43.997
> hide #4 models
> view #6 clip false
> hide #6 models
> view #5 clip false
> marker #7 position 0, 0, 0
> view #7 clip false
> show #!1 models
> centerIndex #5
Unknown command: centerIndex #5
> marker #8 position 19.5, 20.5, 19.5
> hide #7 models
> view #8 clip false
> hide #!1 models
> volume #!5 region all imageMode "full region"
> volume unzone #!5
> mousemode rightMode "crop volume"
> volume #!5 showOutlineBox false
> volume #!5 showOutlineBox true
> volume #2 orthoplanes xyz positionPlanes 19,20,19 style image region all
> mousemode rightMode "move planes"
> volume #3 orthoplanes xyz positionPlanes 19,20,19 style image region all
> mousemode rightMode "move planes"
> volume #5 orthoplanes xyz positionPlanes 19,20,19 style image region all
> mousemode rightMode "move planes"
> ui mousemode right "mark point"
> ui mousemode right "move markers"
> ui mousemode right select
> select #8/M:1@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "move markers"
> marker change #8:1 position 18.56,27.66,22.06
> marker change #8:1 position 4.606,92.6,59.91
> marker change #8:1 position 74.73,57.33,62.08
> view #5 clip false
> marker change #8:1 position 71.54,79.72,53.64
> ui mousemode right "mark center"
> marker #4 position 71.18,79.4,53.51 color yellow radius 1
> marker #4 position 71.4,79.29,53.43 color yellow radius 1
> ui mousemode right "resize markers"
> volume #!5 style surface
> ui tool show "Volume Viewer"
> volume #2 style image imageMode "box faces"
> volume #2 style surface
> volume #2 change image level 0,0 level 0.2974,0.8 level 0.4889,1
> hide #!2 models
> show #!2 models
> hide #!5 models
> transparency #2.1 50
> hide #8 models
> ui tool show "Map Coordinates"
> ui tool show "Measure Volume and Area"
> show #!1 models
> hide #!2 models
> view #1 clip false
> show #!2 models
> hide #!1 models
> view #2 clip false
> open /Users/mariakrasilnikov/Downloads/7kdp.pdb
7kdp.pdb title:
HCMV prefusion GB In complex with fusion inhibitor way-174865 [more info...]
Chain information for 7kdp.pdb #9
---
Chain | Description | UniProt
A B C | GB | GB_HCMVT
Non-standard residues in 7kdp.pdb #9
---
CA — calcium ion
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
WCY —
N-{4-[({(1S)-1-[3,5-bis(trifluoromethyl)phenyl]ethyl}carbamothioyl)amino]phenyl}-1,3-thiazole-4-carboxamide
> hide #!2 models
> view #9 clip false
> hide #9.1 models
> molmap #9 15
Opened 7kdp.pdb map 15 as #10, grid size 41,41,47, pixel 5, shown at level
0.0514, step 1, values float32
> volume #!10 showOutlineBox true
> volume #!10 showOutlineBox false
> volume #!10 showOutlineBox true
> volume #!10 showOutlineBox false
> volume #!10 showOutlineBox true
> ui tool show "Volume Viewer"
> ui tool show "Show Volume Menu"
> ui tool show "Volume Viewer"
> toolshed show
===== 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
Failed to send bug report. Possibly no internet connection.
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Max
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: MacBookPro18,2
Model Number: Z14Z0010BLL/A
Chip: Unknown
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 8422.100.650
OS Loader Version: 8422.100.650
Software:
System Software Overview:
System Version: macOS 13.3.1 (a) (22E772610a)
Kernel Version: Darwin 22.4.0
Time since boot: 16 days, 14 hours, 44 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
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: Yes
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 , 2 years ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash hiding tool |
comment:2 by , 2 years ago
| Status: | accepted → feedback |
|---|
Note:
See TracTickets
for help on using tickets.
Hi Maria,
--Eric