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Opened 3 years ago
Closed 3 years ago
#8346 closed defect (duplicate)
Crash clearing aniso_u6
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | Eric Pettersen, Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.2.1-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 0x000000028b07f000 (most recent call first):
File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028a073000 (most recent call first):
File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000289067000 (most recent call first):
File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028805b000 (most recent call first):
File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028704f000 (most recent call first):
File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000286043000 (most recent call first):
File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x000000010109c580 (most recent call first):
File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 846 in _set_aniso_u6
File "/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/sanity_check.py", line 12 in remove_invalid_anisou
File "/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 667 in _anisou_sanity_check
File "/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 636 in add_model
File "/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 594 in __init__
File "/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 170 in _get_symmetry_handler
File "/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 159 in get_symmetry_handler
File "/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py", line 814 in _change_selected_model
File "/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py", line 771 in change_selected_model
File "/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py", line 433 in selected_model
File "/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py", line 1483 in load_cryo_em_demo
File "/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/cmd/cmd.py", line 240 in _load_demo
File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134 in invoke
File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 217 in _activate
File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 186 in activate
File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 354 in activate_trigger
File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 54 in draw_new_frame
File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/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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===== 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
> isolde start
> set selectionWidth 4
Populating font family aliases took 151 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.
> isolde demo cryo_em_intro modelOnly true
6out.pdb title:
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]
Chain information for 6out.pdb #1
---
Chain | Description | UniProt
A B C | capsid protein VP1 | CAPSD_NVN68
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 51 residues in model #1 to IUPAC-IUB
standards.
===== 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 - 76.3
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: iMac
Model Identifier: iMac21,1
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 7429.81.3
OS Loader Version: 7429.81.3
Software:
System Software Overview:
System Version: macOS 12.2.1 (21D62)
Kernel Version: Darwin 21.3.0
Time since boot: 134 days 4:22
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 4.5K (4480 x 2520)
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-Clipper: 0.19.0
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-ISOLDE: 1.5
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 → Structure Editing |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash clearing aniso_u6 |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Note:
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Duplicate of #8345