Opened 2 years ago

Closed 2 years ago

#9453 closed defect (nonchimerax)

Graphics crash, macOS 13.4.1, Intel Iris Plus Graphics 655

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics 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: Aborted

Thread 0x000070001055b000 (most recent call first):
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700021ea6000 (most recent call first):
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700020ea3000 (most recent call first):
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070001fea0000 (most recent call first):
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070001ee9d000 (most recent call first):
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070001de9a000 (most recent call first):
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070001ce97000 (most recent call first):
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070001be94000 (most recent call first):
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070001ae91000 (most recent call first):
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700019e8e000 (most recent call first):
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700018e8b000 (most recent call first):
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700017e88000 (most recent call first):
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007ff854478640 (most recent call first):
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 2730 in draw_elements
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1736 in draw
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 836 in _draw_geometry
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 771 in draw_self
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 764 in draw
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1551 in _draw_multiple
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1538 in draw_opaque
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 247 in _draw_scene
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 177 in draw
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/sideview/tool.py", line 288 in render
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/sideview/tool.py", line 113 in _redraw
  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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
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  File "/private/var/folders/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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/bn/gdbr8qjx4m329ghwwpw4ykmr0000gn/T/AppTranslocation/D4B06AFF-6829-4FB9-814A-2CF82AEE4CAD/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 =====
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 "/Volumes/TRACY/alphafold files/1-1500 vs
> actin/MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_2_seed_000.pdb"
> format pdb

No such file/path: /Volumes/TRACY/alphafold files/1-1500 vs
actin/MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_2_seed_000.pdb  

> open "/Volumes/TRACY/alphafold files/1-1500 vs
> actin/MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb"

Chain information for
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
#1  
---  
Chain | Description  
A | No description available  
B C | No description available  
  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> set bgColor white

> mlp

Map values for surface
"MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb_A
SES surface": minimum -31.54, mean -6.383, maximum 24.61  
Map values for surface
"MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb_B
SES surface": minimum -30.94, mean -5.335, maximum 21.77  
Map values for surface
"MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb_C
SES surface": minimum -30.52, mean -5.286, maximum 23.45  
To also show corresponding color key, enter the above mlp command and add key
true  

> split

Split
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
(#1) into 3 models  
Chain information for
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
C #1.3  
---  
Chain | Description  
C | No description available  
  

> mlp

Map values for surface
"MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
A_A SES surface": minimum -31.54, mean -6.383, maximum 24.61  
Map values for surface
"MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
B_B SES surface": minimum -30.94, mean -5.335, maximum 21.77  
Map values for surface
"MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
C_C SES surface": minimum -30.52, mean -5.286, maximum 23.45  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide #!1.2 models

> hide #!1.3 models

> show #!1.2 models

> hide #!1.2 models

> mlp #!1.1

Map values for surface
"MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
A_A SES surface": minimum -31.54, mean -6.383, maximum 24.61  
To also show corresponding color key, enter the above mlp command and add key
true  

> interfaces #!1.1 & ~solvent

0 buried areas:  

> ribbons

Unknown command: ribbons  

> hide #!1.1 surfaces

> show #!1.1 surfaces

> hide #!1.1 surfaces

> interfaces #!1.1 & ~solvent

0 buried areas:  
Alignment identifier is 1.1/A  
Alignment identifier is 1  

> select #1.1/A:316

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1.1/A:316-364

382 atoms, 387 bonds, 49 residues, 1 model selected  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select
> #1.1/A:37-43,87-90,98-103,107-113,134-140,185-189,211-214,261-265,272-277,280-284,306-309,356-359,409-414,418-426,448-452,458-462,470-477,485-489

838 atoms, 840 bonds, 102 residues, 1 model selected  

> color sel bynucleotide

> color sel byhetero

> color sel bychain

> view sel

> ui mousemode right distance

> ui mousemode right zoom

> ui tool show "Side View"

> view sel

> style sel stick

Changed 838 atom styles  

> style sel sphere

Changed 838 atom styles  

> show sel surfaces

> style sel sphere

Changed 838 atom styles  

> style sel stick

Changed 838 atom styles  

> hide sel surfaces

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> show sel atoms

> hide sel atoms

> show sel surfaces

> mlp sel

Map values for surface
"MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
A_A SES surface": minimum -31.54, mean -6.383, maximum 24.61  
To also show corresponding color key, enter the above mlp command and add key
true  

> mlp sel

Map values for surface
"MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
A_A SES surface": minimum -31.54, mean -6.383, maximum 24.61  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide sel surfaces

> show sel surfaces

> mlp sel

Map values for surface
"MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
A_A SES surface": minimum -31.54, mean -6.383, maximum 24.61  
To also show corresponding color key, enter the above mlp command and add key
true  

> color sel bynucleotide

> hbonds sel reveal true

105 hydrogen bonds found  

> hide sel surfaces

> hbonds sel reveal true

105 hydrogen bonds found  

> hbonds sel reveal true

105 hydrogen bonds found  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> color #1.2 #d7433dff

> show #!1.2 models

> color #1.3 #36d739ff

> show #!1.3 models

> hide #!1.3 models

> show #!1.3 models

> hide #!1.3 models

> show #!1.3 models

> hide #!1.3 models

> open "/Volumes/TRACY/alphafold files/1-1500 phosphomimetic vs
> actin/MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb"

Chain information for
MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
#2  
---  
Chain | Description  
A | No description available  
B C | No description available  
  

> hide #!1 models

> hide #!1.1 models

> hide #!1.2 models

> ribbonssplit

Unknown command: ribbonssplit  

> split

Did not split
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
A, has only one piece  
Did not split
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
B, has only one piece  
Did not split
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
C, has only one piece  
Split
MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
(#2) into 3 models  
Chain information for
MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
A #2.1  
---  
Chain | Description  
A | No description available  
  
Chain information for
MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
B #2.2  
---  
Chain | Description  
B | No description available  
  
Chain information for
MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
C #2.3  
---  
Chain | Description  
C | No description available  
  

> hide #2.2 models

> hide #2.3 models

> select
> #1.1/A:49-64,75-85,117-129,159-167,169-176,180-182,194-197,201-203,205-208,224-236,242-245,293-296,298-300,317-336,344-349,376-390,432-440,463-466,495-505,509-511,518-524,821-824,830-847

1604 atoms, 1609 bonds, 192 residues, 1 model selected  

> select
> #1.1/A:37-43,87-90,98-103,107-113,134-140,185-189,211-214,261-265,272-277,280-284,306-309,356-359,409-414,418-426,448-452,458-462,470-477,485-489

838 atoms, 840 bonds, 78 pseudobonds, 102 residues, 2 models selected  

> color #2.2 #ec1c2dff

> show #2.2 models

> show #2.1-2 surfaces

> hide #!2.1-2 surfaces

> color #!2.1-2 bynucleotide

> select add #1

17465 atoms, 17787 bonds, 105 pseudobonds, 2250 residues, 6 models selected  

> select subtract #1

3 models selected  

> select add #1.1

11617 atoms, 11813 bonds, 105 pseudobonds, 1500 residues, 2 models selected  

> select subtract #1.1

1 model selected  

> select add #2

17472 atoms, 17794 bonds, 2250 residues, 7 models selected  

> color sel & #!2.1-2 bynucleotide

> view #2 clip false

> show target m

> hide target m

> show target m

> hide #!1 models

> hide #!1.1 models

> hide #!1.2 models

> hide #!1.3 models

> hide #2.3 models

> color sel & #!2.1-2 bynucleotide

Alignment identifier is 2.1/A  
Alignment identifier is 1  

> split

Did not split
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
A, has only one piece  
Did not split
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
B, has only one piece  
Did not split
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
C, has only one piece  
Did not split
MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
A, has only one piece  
Did not split
MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
B, has only one piece  
Did not split
MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
C, has only one piece  

> select #2.1/A:233

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2.1/A:233-298

500 atoms, 514 bonds, 66 residues, 1 model selected  

> select
> #2.1/A:37-43,87-90,98-103,107-113,134-140,185-189,211-214,261-265,272-277,280-284,306-309,356-359,409-414,418-426,448-452,458-462,470-477,485-489

838 atoms, 840 bonds, 102 residues, 1 model selected  

> hbonds sel reveal true

139 hydrogen bonds found  

> show sel surfaces

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> select
> #2.2/B:8-12,16-21,29-32,35-38,65-68,103-107,132-136,150-155,160-165,176-178,238-241,247-250,297-300
> #2.3/C:8-12,16-21,29-32,35-38,65-68,103-107,132-136,150-155,160-165,176-178,238-241,247-250,297-300

918 atoms, 908 bonds, 120 residues, 2 models selected  

> select #2.2/B:1 #2.3/C:1

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #2.2/B #2.3/C

5848 atoms, 5974 bonds, 750 residues, 2 models selected  
1 [ID: 1] region chains B,C [1-375] RMSD: 53.451  
  

> show sel & #!2.2 surfaces

> show #!1.1 models

> hide #!2 models

> hide #!2.1 models

> hide #!2.2 models

> hide #!1 models

> show #!1.2 models

> ui tool show "Side View"

> view

> view orient

> hide #3 models

> show #3 models

> show #!2.1 models

> show #!2.2 models

> hide #!2.2 models

> show #!2.2 models

> hide #!1.2 models

> show #!1.2 models

> select #2.1/A:1395

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2.1/A:1395

8 atoms, 7 bonds, 1 residue, 1 model selected  

> rainbow sel

> select #2.1/A:1395

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2.1/A:1387-1395

75 atoms, 75 bonds, 9 residues, 1 model selected  

> select #2.1/A:1388-1389

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #2.1/A:1388-1484

750 atoms, 765 bonds, 97 residues, 1 model selected  

> select #2.1/A:1395

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2.1/A:1395

8 atoms, 7 bonds, 1 residue, 1 model selected  
Destroying pre-existing alignment with identifier 2.1/A  
Alignment identifier is 2.1/A  
Destroying pre-existing alignment with identifier 2.1/A  
Alignment identifier is 2.1/A  
Destroying pre-existing alignment with identifier 2.1/A  
Alignment identifier is 2.1/A  

> select add #2

17472 atoms, 17794 bonds, 106 pseudobonds, 2250 residues, 6 models selected  

> select subtract #2

2 models selected  

> select add #2.1

11624 atoms, 11820 bonds, 106 pseudobonds, 1500 residues, 2 models selected  

> select add #2

17472 atoms, 17794 bonds, 106 pseudobonds, 2250 residues, 6 models selected  

> select subtract #2.1

5848 atoms, 5974 bonds, 750 residues, 5 models selected  

> select add #2

17472 atoms, 17794 bonds, 106 pseudobonds, 2250 residues, 6 models selected  

> select subtract #2

2 models selected  

> select add #1.1

11617 atoms, 11813 bonds, 1500 residues, 1 model selected  
Alignment identifier is 1.1/A  

> hide #!1 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> select #1.1/A:442

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1.1/A:438-442

47 atoms, 48 bonds, 5 residues, 1 model selected  

> select
> #1.1/A:49-64,75-85,117-129,159-167,169-176,180-182,194-197,201-203,205-208,224-236,242-245,293-296,298-300,317-336,344-349,376-390,432-440,463-466,495-505,509-511,518-524,821-824,830-847

1604 atoms, 1609 bonds, 192 residues, 1 model selected  

> select #2.1/A:1395

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2.1/A:1395

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1.1/A:1395

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #1.1/A:1395

6 atoms, 5 bonds, 1 residue, 1 model selected  

> view sel

> view

> ui tool show "Side View"

> hide sel surfaces

> select add #2.2

2930 atoms, 2992 bonds, 376 residues, 3 models selected  

> select subtract #2.2

6 atoms, 5 bonds, 1 residue, 3 models selected  

> hide #!2 models

> hide #!2.1 models

> hide #!2.2 models

> hide #3 models

> select add #1.1

11617 atoms, 11813 bonds, 1500 residues, 2 models selected  

> select subtract #1.1

1 model selected  

> select add #1

17465 atoms, 17787 bonds, 2250 residues, 4 models selected  

> show #!1.3 models

> hide #!1.3 models

> select: .b & :.a zr select: .b & : .a zr select : .b & : .a zr select #2.2/B #2.3/C

5848 atoms, 5974 bonds, 750 residues, 2 models selected  

> select : .b & : .a zr select add #1

23313 atoms, 23761 bonds, 3000 residues, 7 models selected  

> select add #2

34937 atoms, 35581 bonds, 106 pseudobonds, 4500 residues, 13 models selected  

> select subtract #2

17465 atoms, 17787 bonds, 2250 residues, 9 models selected  

> select subtract #1.3

14541 atoms, 14800 bonds, 1875 residues, 6 models selected  

> select : .b & : .a zr select subtract #1.1

2924 atoms, 2987 bonds, 375 residues, 4 models selected  

> select add #1.1

14541 atoms, 14800 bonds, 1875 residues, 4 models selected  

> select add #1

17465 atoms, 17787 bonds, 2250 residues, 6 models selected  

> select subtract #1

3 models selected  

> hide #!1 models

> hide #!1.1 models

> hide #!1.2 models

> select add #1.1

11617 atoms, 11813 bonds, 1500 residues, 1 model selected  

> select add #1.2

14541 atoms, 14800 bonds, 1875 residues, 3 models selected  

> show #!1.1 models

> show #!1.2 models

> select : .b & : .a zr color red :.b & :.a zr view #1 clip false

> show #!1 target m

> close #1

> log metadata #2.1

No models had metadata

> log chains #2.1

Chain information for
MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
A #2.1  
---  
Chain | Description  
A | No description available  
  

> log metadata #2.2

No models had metadata

> log chains #2.2

Chain information for
MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
B #2.2  
---  
Chain | Description  
B | No description available  
  

> log metadata #2.3

The model has no metadata

> log chains #2.3

Chain information for
MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
C #2.3  
---  
Chain | Description  
C | No description available  
  

> show #!2 models

> select #2.2/B:1-375

2924 atoms, 2987 bonds, 375 residues, 1 model selected  

> select #2.1/A:1-1500

11624 atoms, 11820 bonds, 106 pseudobonds, 1500 residues, 2 models selected  

> select #2.2/B:1-375

2924 atoms, 2987 bonds, 375 residues, 1 model selected  

> select #2.1/A:1-1500

11624 atoms, 11820 bonds, 106 pseudobonds, 1500 residues, 2 models selected  

> select #2.3/C:1-375

2924 atoms, 2987 bonds, 375 residues, 1 model selected  

> select #2.3/C:1-375

2924 atoms, 2987 bonds, 375 residues, 1 model selected  

> select #2.2/B:1-375

2924 atoms, 2987 bonds, 375 residues, 1 model selected  

> select #2.1/A:1-1500

11624 atoms, 11820 bonds, 106 pseudobonds, 1500 residues, 2 models selected  

> hide #!2 models

> show #!2.1 models

> select #2.1/A:1-1500

11624 atoms, 11820 bonds, 106 pseudobonds, 1500 residues, 2 models selected  

> hide #!2.1 models

> show #!2.1 models

> hide #!2 models

> color red :.b & :.a zr select: .B & :.A zr select : .B & :.A zr hide #!2.1 models

> show #!2.1 models

Alignment identifier is 2.1/A  

> select #2.1/A:392

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #2.1/A:392-394

23 atoms, 22 bonds, 3 residues, 1 model selected  

> select
> #2.1/A:37-43,87-90,98-103,107-113,134-140,185-189,211-214,261-265,272-277,280-284,306-309,356-359,409-414,418-426,448-452,458-462,470-477,485-489

838 atoms, 840 bonds, 78 pseudobonds, 102 residues, 2 models selected  

> select : .B & :.A zr select #2.2: .B & : #2.1.A zr split

Did not split
MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
A, has only one piece  
Did not split
MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
B, has only one piece  
Did not split
MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
C, has only one piece  

> hide #2.1.1 models

> show #2.1.1 models

> hide #2.1.1 models

> show #2.1.1 models

> hide #2.1.1 models

> select: .2.2 & :.2.1 zr show #2 & ligand zr show #2

> show #2.1

> show #2.2

> show #2.1

> show #2.2

> repr bs ligand

Unknown command: repr bs ligand  

> ~modeldisplay. #1

Unknown command: ~modeldisplay. #1  

> ~m~modeldisplay. #2

Unknown command: ~m~modeldisplay. #2  

> ~modeldisplay. #2

Unknown command: ~modeldisplay. #2  

> ~modeldisplay. #2

Unknown command: ~modeldisplay. #2  

> ~modeldisplay. #2.1

Unknown command: ~modeldisplay. #2.1  

> show ligand

> show surfaces

> hide surfaces

> target r

Unknown command: target r  

> diselect

Unknown command: diselect  

> select
> #2.1/A:49-64,75-85,117-129,159-167,169-176,180-182,194-198,201-203,205-208,224-236,242-245,293-296,298-300,317-336,347-349,376-390,432-440,463-466,495-505,509-511,518-524,819-825,830-845

1590 atoms, 1593 bonds, 191 residues, 1 model selected  

> select #2.1/A:952-953

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select #2.1/A:952-1280

2497 atoms, 2536 bonds, 329 residues, 1 model selected  

> select #2.1/A:820

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2.1/A:820-821

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select
> #2.1/A:49-64,75-85,117-129,159-167,169-176,180-182,194-198,201-203,205-208,224-236,242-245,293-296,298-300,317-336,347-349,376-390,432-440,463-466,495-505,509-511,518-524,819-825,830-845

1590 atoms, 1593 bonds, 191 residues, 1 model selected  

> close session

> open "/Volumes/TRACY/alphafold files/1-1500 vs
> actin/MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb"

Chain information for
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
#1  
---  
Chain | Description  
A | No description available  
B C | No description available  
  

> set bgColor white

> select: .b& :.a zr select #1: .B & #1:.A zr select #1: .B & #1:.A za select #1: .B & #1:.A za select /B:1-375

2924 atoms, 2987 bonds, 375 residues, 1 model selected  

> select /C:1-375

2924 atoms, 2987 bonds, 375 residues, 1 model selected  

> select /A:1-1500

11617 atoms, 11813 bonds, 1500 residues, 1 model selected  

> select #1: .B & #1:.A za select /A:1-1500

11617 atoms, 11813 bonds, 1500 residues, 1 model selected  

> select /B:1-375

2924 atoms, 2987 bonds, 375 residues, 1 model selected  

> select /C:1-375

2924 atoms, 2987 bonds, 375 residues, 1 model selected  

> measure center sel mark true radius 0.3 color cyan

Center of mass of 2924 atoms = (-5.07, 0.15, 21.84)  

> ~findclash

Unknown command: ~findclash  

> ~select

Nothing selected  

> select ::name="ALA"

755 atoms, 619 bonds, 151 residues, 1 model selected  

> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"

17465 atoms, 17787 bonds, 2250 residues, 1 model selected  

> select sel : hide #1 models

> show #1 models

> split

Split
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
(#1) into 3 models  
Chain information for
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
C #1.3  
---  
Chain | Description  
C | No description available  
  

> select #1.1/A:1-1500

11617 atoms, 11813 bonds, 1500 residues, 1 model selected  

> close session

> open "/Volumes/TRACY/alphafold files/1-1500 vs
> actin/MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb"
> format pdb

Chain information for
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
#1  
---  
Chain | Description  
A | No description available  
B C | No description available  
  

> open "/Volumes/TRACY/alphafold files/1-1500 phosphomimetic vs
> actin/MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb"

Chain information for
MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
#2  
---  
Chain | Description  
A | No description available  
B C | No description available  
  

> splitsplit

Unknown command: splitsplit  

> splits

Unknown command: splits  

> split

Split
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
(#1) into 3 models  
Split
MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
(#2) into 3 models  
Chain information for
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for
MAP1B_MOUSE_1-1500_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
C #1.3  
---  
Chain | Description  
C | No description available  
  
Chain information for
MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
A #2.1  
---  
Chain | Description  
A | No description available  
  
Chain information for
MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
B #2.2  
---  
Chain | Description  
B | No description available  
  
Chain information for
MAP1B_HC_1500_phosphomimetic_actin_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
C #2.3  
---  
Chain | Description  
C | No description available  
  

> color #1.2 #d72310ff

> color #1.3 #3fd723ff

> color #2.2 #ec6067ff

> color #2.3 #76ec80ff

> ui tool show "Side View"

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #1.1 models

> show #!1 models

> show #1.1 models

> hide #!1 models

> hide #!2 models

> show #!2 models

> show #!1 models

> select add #1.1

11617 atoms, 11813 bonds, 1500 residues, 1 model selected  
Alignment identifier is 1.1/A  

> select add #2

29089 atoms, 29607 bonds, 3750 residues, 5 models selected  

> select subtract #1.1

17472 atoms, 17794 bonds, 2250 residues, 4 models selected  

> select subtract #2

Nothing selected  

> select add #2.1

11624 atoms, 11820 bonds, 1500 residues, 1 model selected  
Alignment identifier is 2.1/A  

> select add #2

17472 atoms, 17794 bonds, 2250 residues, 4 models selected  

> select subtract #2

Nothing selected  

> select add #1.2

2924 atoms, 2987 bonds, 375 residues, 1 model selected  
Alignment identifier is 1.2/B  

> show sel surfaces

> select
> #1.1/A:49-64,75-85,117-129,159-167,169-176,180-182,194-197,201-203,205-208,224-236,242-245,293-296,298-300,317-336,344-349,376-390,432-440,463-466,495-505,509-511,518-524,821-824,830-847

1604 atoms, 1609 bonds, 192 residues, 1 model selected  

> ui tool show "Selection Inspector"


===== 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 INTEL-20.6.1
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.

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: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.8 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1968.120.12.0.0 (iBridge: 20.16.5060.0.0,0)
      OS Loader Version: 577~170

Software:

    System Software Overview:

      System Version: macOS 13.4.1 (22F82)
      Kernel Version: Darwin 22.5.0
      Time since boot: 13 days, 8 hours, 59 minutes

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: On
          Mirror Status: Hardware Mirror
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        LG UltraFine:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: On
          Mirror Status: Master Mirror
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes


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 Eric Pettersen, 2 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Graphics hardware encountered an error and was reset

comment:2 by Tom Goddard, 2 years ago

Resolution: → nonchimerax
Status: assigned → closed
Summary: Graphics hardware encountered an error and was reset → Graphics crash, macOS 13.4.1, Intel Iris Plus Graphics 655

Apple Intel graphics driver crash.

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