Opened 4 weeks ago

Closed 3 weeks ago

#20519 closed defect (limitation)

Crash running ChimeraX from .dmg and ejecting disk image?

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-13.0-arm64-arm-64bit
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error

Thread 0x00000002b075b000 (most recent call first):
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x00000002af74f000 (most recent call first):
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x00000002ae743000 (most recent call first):
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 948 in wait
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x00000002ad737000 (most recent call first):
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x00000002ac72b000 (most recent call first):
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x00000002ab71f000 (most recent call first):
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x00000002aa713000 (most recent call first):
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x00000002a9707000 (most recent call first):
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x00000002a86fb000 (most recent call first):
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x00000002a76ef000 (most recent call first):
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x00000002a66e3000 (most recent call first):
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x00000002a56d7000 (most recent call first):
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x00000002a46cb000 (most recent call first):
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x00000002a36bf000 (most recent call first):
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x00000002a26b3000 (most recent call first):
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap

Current thread 0x00000001e140e500 (most recent call first):
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 424 in event_loop
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
  File "/private/var/folders/_4/73d99g5x0bg829s4l1bk5g240000gn/T/AppTranslocation/0ED0F61B-FB52-45A8-A099-EC3CF51210D3/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, OpenGL_accelerate.nones_formathandler, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imaging, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree (total: 60)


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{
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  "incident" : "8FD4F9A4-6503-42A4-8B57-5C1C6EC0AFBA",
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  "translated" : false,
  "cpuType" : "ARM-64",
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  "exception" : {"codes":"0x000000000000000a, 0x00000001079f69b8","rawCodes":[10,4422855096],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_MEMORY_ERROR at 0x00000001079f69b8"},
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  "faultingThread" : 0,
  "threads" : [{"triggered":true,"id":136426,

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__TEXT                             556K        1 
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===========                     =======  ======= 
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",
  "legacyInfo" : {
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},
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      "factorPackIds" : {
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      },
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},
  "reportNotes" : [
  "dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.12 (2026-06-12)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/victohugofonsecadejesus/Downloads/9AX6 (1).cif"

Summary of feedback from opening /Users/victohugofonsecadejesus/Downloads/9AX6
(1).cif  
---  
notes | PDBx/mmCIF styling lost on line 4102. Rereading mmCIF file from the beginning.  
Fetching CCD A1AHB from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/A1AHB/A1AHB.cif  
Fetching CCD GNP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GNP/GNP.cif  
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif  
  
9AX6 (1).cif title:  
Tricomplex of RMC-6236, KRAS G12D, and CypA [more info...]  
  
Chain information for 9AX6 (1).cif #1  
---  
Chain | Description | UniProt  
A | GTPase KRas | RASK_HUMAN 1-169  
D | Peptidyl-prolyl cis-trans isomerase A | PPIA_HUMAN 1-165  
  
Non-standard residues in 9AX6 (1).cif #1  
---  
A1AHB —
(1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide  
GNP — phosphoaminophosphonic acid-guanylate ester  
MG — magnesium ion  
  
37 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
3008 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> save /Users/victohugofonsecadejesus/Desktop/image1.png supersample 3

> show atoms

> hide atoms

> show atoms

> style stick

Changed 3015 atom styles  

> style sphere

Changed 3015 atom styles  

> style ball

Changed 3015 atom styles  

> color bfactor

3015 atoms, 657 residues, atom bfactor range 17.2 to 80.5  

> color bfactor

3015 atoms, 657 residues, atom bfactor range 17.2 to 80.5  

> hbonds reveal true

1183 hydrogen bonds found  

> color bynucleotide

> color byhetero

> color bychain

> hbonds reveal true

1183 hydrogen bonds found  

> hbonds reveal true

1183 hydrogen bonds found  

> open "/Users/victohugofonsecadejesus/Downloads/9ax6 (2).cif"

9ax6 (2).cif title:  
Tricomplex of RMC-6236, KRAS G12D, and CypA [more info...]  
  
Chain information for 9ax6 (2).cif #2  
---  
Chain | Description | UniProt  
A B | GTPase KRas | RASK_HUMAN 1-169  
C D | Peptidyl-prolyl cis-trans isomerase A | PPIA_HUMAN 1-165  
  
Non-standard residues in 9ax6 (2).cif #2  
---  
A1AHB —
(1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide  
GNP — phosphoaminophosphonic acid-guanylate ester  
MG — magnesium ion  
  
9ax6 (2).cif mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  
49 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
5170 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> close session

> open "/Users/victohugofonsecadejesus/Downloads/9ax6 (2).cif"

9ax6 (2).cif title:  
Tricomplex of RMC-6236, KRAS G12D, and CypA [more info...]  
  
Chain information for 9ax6 (2).cif #1  
---  
Chain | Description | UniProt  
A B | GTPase KRas | RASK_HUMAN 1-169  
C D | Peptidyl-prolyl cis-trans isomerase A | PPIA_HUMAN 1-165  
  
Non-standard residues in 9ax6 (2).cif #1  
---  
A1AHB —
(1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide  
GNP — phosphoaminophosphonic acid-guanylate ester  
MG — magnesium ion  
  
9ax6 (2).cif mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  
49 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
5170 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> close session

> open "/Users/victohugofonsecadejesus/Downloads/9ax6 (2).cif"

9ax6 (2).cif title:  
Tricomplex of RMC-6236, KRAS G12D, and CypA [more info...]  
  
Chain information for 9ax6 (2).cif #1  
---  
Chain | Description | UniProt  
A B | GTPase KRas | RASK_HUMAN 1-169  
C D | Peptidyl-prolyl cis-trans isomerase A | PPIA_HUMAN 1-165  
  
Non-standard residues in 9ax6 (2).cif #1  
---  
A1AHB —
(1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide  
GNP — phosphoaminophosphonic acid-guanylate ester  
MG — magnesium ion  
  
9ax6 (2).cif mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  
49 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
5170 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> close session

> open "/Users/victohugofonsecadejesus/Downloads/9AX6 (1).cif"

Summary of feedback from opening /Users/victohugofonsecadejesus/Downloads/9AX6
(1).cif  
---  
note | PDBx/mmCIF styling lost on line 4102. Rereading mmCIF file from the beginning.  
  
9AX6 (1).cif title:  
Tricomplex of RMC-6236, KRAS G12D, and CypA [more info...]  
  
Chain information for 9AX6 (1).cif #1  
---  
Chain | Description | UniProt  
A | GTPase KRas | RASK_HUMAN 1-169  
D | Peptidyl-prolyl cis-trans isomerase A | PPIA_HUMAN 1-165  
  
Non-standard residues in 9AX6 (1).cif #1  
---  
A1AHB —
(1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide  
GNP — phosphoaminophosphonic acid-guanylate ester  
MG — magnesium ion  
  
37 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
3008 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> color #1 #d72e1fff

> color #1 #d76018ff

> color #1 #d72e5cff

> color #1 #abc2d7ff

> color #1 #51d7b9ff

> color #1 #87d722ff

> select add #1

3015 atoms, 2750 bonds, 6 pseudobonds, 657 residues, 2 models selected  

> show sel atoms

> hide sel atoms

> set bgColor white

> lighting full

> lighting simple

> lighting full

> show sel atoms

> hide sel atoms

> show sel atoms

> hide sel atoms

> style sel stick

Changed 3015 atom styles  

> style sel sphere

Changed 3015 atom styles  

> style sel ball

Changed 3015 atom styles  

> style sel stick

Changed 3015 atom styles  

> style sel sphere

Changed 3015 atom styles  

> style sel ball

Changed 3015 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> view sel

> show target m

> show #1.1 target m

> sequence chain #1/A

Alignment identifier is 1/A  

> open P01116 fromDatabase uniprot associate #1/A

Request url https://rest.uniprot.org/idmapping/run failed:   

> select /A:0-167

1344 atoms, 1365 bonds, 168 residues, 1 model selected  

> select :A1AHB

58 atoms, 65 bonds, 1 residue, 1 model selected  

> close session

> open "/Users/victohugofonsecadejesus/Downloads/9AX6 (1).cif"

Summary of feedback from opening /Users/victohugofonsecadejesus/Downloads/9AX6
(1).cif  
---  
note | PDBx/mmCIF styling lost on line 4102. Rereading mmCIF file from the beginning.  
  
9AX6 (1).cif title:  
Tricomplex of RMC-6236, KRAS G12D, and CypA [more info...]  
  
Chain information for 9AX6 (1).cif #1  
---  
Chain | Description | UniProt  
A | GTPase KRas | RASK_HUMAN 1-169  
D | Peptidyl-prolyl cis-trans isomerase A | PPIA_HUMAN 1-165  
  
Non-standard residues in 9AX6 (1).cif #1  
---  
A1AHB —
(1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide  
GNP — phosphoaminophosphonic acid-guanylate ester  
MG — magnesium ion  
  
37 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
3008 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> sequence chain #1/A

Alignment identifier is 1/A  

> open P01116 fromDatabase uniprot associate #1/A

Summary of feedback from opening P01116 fetched from uniprot  
---  
notes | Fetching compressed P01116 UniProt info from https://www.uniprot.org/uniprot/P01116.xml  
Alignment identifier is P01116  
Associated 9AX6 (1).cif chain A to P01116 with 11 mismatches and/or gaps  
  
Opened UniProt P01116  

> select /A:13-18,28-30,57,116-117,119,145-147

114 atoms, 109 bonds, 16 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> hide sel cartoons

> close session

> open "/Users/victohugofonsecadejesus/Downloads/9AX6 (1).cif"

Summary of feedback from opening /Users/victohugofonsecadejesus/Downloads/9AX6
(1).cif  
---  
note | PDBx/mmCIF styling lost on line 4102. Rereading mmCIF file from the beginning.  
  
9AX6 (1).cif title:  
Tricomplex of RMC-6236, KRAS G12D, and CypA [more info...]  
  
Chain information for 9AX6 (1).cif #1  
---  
Chain | Description | UniProt  
A | GTPase KRas | RASK_HUMAN 1-169  
D | Peptidyl-prolyl cis-trans isomerase A | PPIA_HUMAN 1-165  
  
Non-standard residues in 9AX6 (1).cif #1  
---  
A1AHB —
(1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide  
GNP — phosphoaminophosphonic acid-guanylate ester  
MG — magnesium ion  
  
37 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
3008 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> color byelement

> undo

> select protein

2602 atoms, 2651 bonds, 332 residues, 1 model selected  

> color chain

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color chain A

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> olor cornflowerblue /A

Unknown command: olor cornflowerblue /A  

> color cornflowerblue /A

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color skyblue /A

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color forestgreen /B

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color gold ligand

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> select /A:0-167

1344 atoms, 1365 bonds, 168 residues, 1 model selected  

> select /D:2-165

1258 atoms, 1286 bonds, 164 residues, 1 model selected  

> select /D:2-165

1258 atoms, 1286 bonds, 164 residues, 1 model selected  

> select /A:0-167

1344 atoms, 1365 bonds, 168 residues, 1 model selected  

> select /A:0-167

1344 atoms, 1365 bonds, 168 residues, 1 model selected  

> hide sel atoms

> show sel atoms

> hide sel atoms

Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> close session

> open "/Users/victohugofonsecadejesus/Downloads/9AX6 (1).cif"

Summary of feedback from opening /Users/victohugofonsecadejesus/Downloads/9AX6
(1).cif  
---  
note | PDBx/mmCIF styling lost on line 4102. Rereading mmCIF file from the beginning.  
  
9AX6 (1).cif title:  
Tricomplex of RMC-6236, KRAS G12D, and CypA [more info...]  
  
Chain information for 9AX6 (1).cif #1  
---  
Chain | Description | UniProt  
A | GTPase KRas | RASK_HUMAN 1-169  
D | Peptidyl-prolyl cis-trans isomerase A | PPIA_HUMAN 1-165  
  
Non-standard residues in 9AX6 (1).cif #1  
---  
A1AHB —
(1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide  
GNP — phosphoaminophosphonic acid-guanylate ester  
MG — magnesium ion  
  
37 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
3008 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> select /A:0-167

1344 atoms, 1365 bonds, 168 residues, 1 model selected  

> select /D:2-165

1258 atoms, 1286 bonds, 164 residues, 1 model selected  

> select :A1AHB

58 atoms, 65 bonds, 1 residue, 1 model selected  

> select :GNP

32 atoms, 34 bonds, 1 residue, 1 model selected  

> select :MG

1 atom, 1 residue, 1 model selected  

> select :MG

1 atom, 1 residue, 1 model selected  

> select :GNP

32 atoms, 34 bonds, 1 residue, 1 model selected  

> select :MG

1 atom, 1 residue, 1 model selected  

> select :A1AHB

58 atoms, 65 bonds, 1 residue, 1 model selected  

> select /A:0-167

1344 atoms, 1365 bonds, 168 residues, 1 model selected  

> color sel red

> select /D:2-165

1258 atoms, 1286 bonds, 164 residues, 1 model selected  

> color sel light sea green

> select :A1AHB

58 atoms, 65 bonds, 1 residue, 1 model selected  

> color sel purple

> select /A:0-167

1344 atoms, 1365 bonds, 168 residues, 1 model selected  

> color sel forest green

> select /D:2-165

1258 atoms, 1286 bonds, 164 residues, 1 model selected  

> color sel cornflower blue

> select :A1AHB

58 atoms, 65 bonds, 1 residue, 1 model selected  

> color sel red

> select :GNP

32 atoms, 34 bonds, 1 residue, 1 model selected  

> color sel orange

> select :MG

1 atom, 1 residue, 1 model selected  

> color sel cyan

> save figure.png width 6000 height 4500

> select /A:0-167

1344 atoms, 1365 bonds, 168 residues, 1 model selected  

> select /A:0-167

1344 atoms, 1365 bonds, 168 residues, 1 model selected  

> select /D:2-165

1258 atoms, 1286 bonds, 164 residues, 1 model selected  

> select :A1AHB

58 atoms, 65 bonds, 1 residue, 1 model selected  

> select :GNP

32 atoms, 34 bonds, 1 residue, 1 model selected  

> select :MG

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> show sel atoms

> hide sel atoms

> style sel stick

Changed 1 atom style  

> style sel sphere

Changed 1 atom style  

> style sel ball

Changed 1 atom style  

> cartoon hide sel

> hide solvent

> select :MG

1 atom, 1 residue, 1 model selected  

> color sel purple

> close session

> open "/Users/victohugofonsecadejesus/Downloads/9AX6 (1).cif"

Summary of feedback from opening /Users/victohugofonsecadejesus/Downloads/9AX6
(1).cif  
---  
note | PDBx/mmCIF styling lost on line 4102. Rereading mmCIF file from the beginning.  
  
9AX6 (1).cif title:  
Tricomplex of RMC-6236, KRAS G12D, and CypA [more info...]  
  
Chain information for 9AX6 (1).cif #1  
---  
Chain | Description | UniProt  
A | GTPase KRas | RASK_HUMAN 1-169  
D | Peptidyl-prolyl cis-trans isomerase A | PPIA_HUMAN 1-165  
  
Non-standard residues in 9AX6 (1).cif #1  
---  
A1AHB —
(1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide  
GNP — phosphoaminophosphonic acid-guanylate ester  
MG — magnesium ion  
  
37 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
3008 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> select /A:0-167

1344 atoms, 1365 bonds, 168 residues, 1 model selected  

> color sel forest green

> select /D:2-165

1258 atoms, 1286 bonds, 164 residues, 1 model selected  

> color sel medium blue

> color sel cornflower blue

> select :A1AHB

58 atoms, 65 bonds, 1 residue, 1 model selected  

> color sel red

> select :GNP

32 atoms, 34 bonds, 1 residue, 1 model selected  

> color sel orange

> select :MG

1 atom, 1 residue, 1 model selected  

> color sel purple

> hide solvent

> save /Users/victohugofonsecadejesus/Downloads/figure.cxs

> save figure.png width 4000 height 3000 transparentBackground true

> open /Users/victohugofonsecadejesus/Downloads/figure.cxs

> view name session-start

opened ChimeraX session  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.12 (2026-06-12)  
© 2016-2026 Regents of the University of California. All rights reserved.  

> open /Users/victohugofonsecadejesus/Downloads/figure.cxs

Log from Sat Jun 20 19:26:13 2026

> show sel atoms

[Repeated 1 time(s)]

> hide sel atoms

> hide sel cartoons

> close session

> open "/Users/victohugofonsecadejesus/Downloads/9AX6 (1).cif"

Summary of feedback from opening /Users/victohugofonsecadejesus/Downloads/9AX6
(1).cif  
---  
note | PDBx/mmCIF styling lost on line 4102. Rereading mmCIF file from the beginning.  
  
9AX6 (1).cif title:  
Tricomplex of RMC-6236, KRAS G12D, and CypA [more info...]  
  
Chain information for 9AX6 (1).cif #1  
---  
Chain | Description | UniProt  
A | GTPase KRas | RASK_HUMAN 1-169  
D | Peptidyl-prolyl cis-trans isomerase A | PPIA_HUMAN 1-165  
  
Non-standard residues in 9AX6 (1).cif #1  
---  
A1AHB —
(1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide  
GNP — phosphoaminophosphonic acid-guanylate ester  
MG — magnesium ion  
  
37 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
3008 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> color byelement

> undo

> select protein

2602 atoms, 2651 bonds, 332 residues, 1 model selected  

> color chain

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color chain A

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> olor cornflowerblue /A

Unknown command: olor cornflowerblue /A  

> color cornflowerblue /A

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color skyblue /A

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color forestgreen /B

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color gold ligand

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> select /A:0-167

1344 atoms, 1365 bonds, 168 residues, 1 model selected  

> select /D:2-165

1258 atoms, 1286 bonds, 164 residues, 1 model selected  

> select /D:2-165

1258 atoms, 1286 bonds, 164 residues, 1 model selected  

> select /A:0-167

1344 atoms, 1365 bonds, 168 residues, 1 model selected  

> select /A:0-167

1344 atoms, 1365 bonds, 168 residues, 1 model selected  

> hide sel atoms

> show sel atoms

> hide sel atoms

Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> close session

> open "/Users/victohugofonsecadejesus/Downloads/9AX6 (1).cif"

Summary of feedback from opening /Users/victohugofonsecadejesus/Downloads/9AX6
(1).cif  
---  
note | PDBx/mmCIF styling lost on line 4102. Rereading mmCIF file from the beginning.  
  
9AX6 (1).cif title:  
Tricomplex of RMC-6236, KRAS G12D, and CypA [more info...]  
  
Chain information for 9AX6 (1).cif #1  
---  
Chain | Description | UniProt  
A | GTPase KRas | RASK_HUMAN 1-169  
D | Peptidyl-prolyl cis-trans isomerase A | PPIA_HUMAN 1-165  
  
Non-standard residues in 9AX6 (1).cif #1  
---  
A1AHB —
(1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide  
GNP — phosphoaminophosphonic acid-guanylate ester  
MG — magnesium ion  
  
37 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
3008 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> select /A:0-167

1344 atoms, 1365 bonds, 168 residues, 1 model selected  

> select /D:2-165

1258 atoms, 1286 bonds, 164 residues, 1 model selected  

> select :A1AHB

58 atoms, 65 bonds, 1 residue, 1 model selected  

> select :GNP

32 atoms, 34 bonds, 1 residue, 1 model selected  

> select :MG

1 atom, 1 residue, 1 model selected  

> select :MG

1 atom, 1 residue, 1 model selected  

> select :GNP

32 atoms, 34 bonds, 1 residue, 1 model selected  

> select :MG

1 atom, 1 residue, 1 model selected  

> select :A1AHB

58 atoms, 65 bonds, 1 residue, 1 model selected  

> select /A:0-167

1344 atoms, 1365 bonds, 168 residues, 1 model selected  

> color sel red

> select /D:2-165

1258 atoms, 1286 bonds, 164 residues, 1 model selected  

> color sel light sea green

> select :A1AHB

58 atoms, 65 bonds, 1 residue, 1 model selected  

> color sel purple

> select /A:0-167

1344 atoms, 1365 bonds, 168 residues, 1 model selected  

> color sel forest green

> select /D:2-165

1258 atoms, 1286 bonds, 164 residues, 1 model selected  

> color sel cornflower blue

> select :A1AHB

58 atoms, 65 bonds, 1 residue, 1 model selected  

> color sel red

> select :GNP

32 atoms, 34 bonds, 1 residue, 1 model selected  

> color sel orange

> select :MG

1 atom, 1 residue, 1 model selected  

> color sel cyan

> save figure.png width 6000 height 4500

> select /A:0-167

1344 atoms, 1365 bonds, 168 residues, 1 model selected  

> select /A:0-167

1344 atoms, 1365 bonds, 168 residues, 1 model selected  

> select /D:2-165

1258 atoms, 1286 bonds, 164 residues, 1 model selected  

> select :A1AHB

58 atoms, 65 bonds, 1 residue, 1 model selected  

> select :GNP

32 atoms, 34 bonds, 1 residue, 1 model selected  

> select :MG

1 atom, 1 residue, 1 model selected  

> hide sel atoms

[Repeated 2 time(s)]

> show sel atoms

> hide sel atoms

> style sel stick

Changed 1 atom style  

> style sel sphere

Changed 1 atom style  

> style sel ball

Changed 1 atom style  

> cartoon hide sel

> hide solvent

> select :MG

1 atom, 1 residue, 1 model selected  

> color sel purple

> close session

> open "/Users/victohugofonsecadejesus/Downloads/9AX6 (1).cif"

Summary of feedback from opening /Users/victohugofonsecadejesus/Downloads/9AX6
(1).cif  
---  
note | PDBx/mmCIF styling lost on line 4102. Rereading mmCIF file from the beginning.  
  
9AX6 (1).cif title:  
Tricomplex of RMC-6236, KRAS G12D, and CypA [more info...]  
  
Chain information for 9AX6 (1).cif #1  
---  
Chain | Description | UniProt  
A | GTPase KRas | RASK_HUMAN 1-169  
D | Peptidyl-prolyl cis-trans isomerase A | PPIA_HUMAN 1-165  
  
Non-standard residues in 9AX6 (1).cif #1  
---  
A1AHB —
(1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide  
GNP — phosphoaminophosphonic acid-guanylate ester  
MG — magnesium ion  
  
37 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
3008 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> select /A:0-167

1344 atoms, 1365 bonds, 168 residues, 1 model selected  

> color sel forest green

> select /D:2-165

1258 atoms, 1286 bonds, 164 residues, 1 model selected  

> color sel medium blue

> color sel cornflower blue

> select :A1AHB

58 atoms, 65 bonds, 1 residue, 1 model selected  

> color sel red

> select :GNP

32 atoms, 34 bonds, 1 residue, 1 model selected  

> color sel orange

> select :MG

1 atom, 1 residue, 1 model selected  

> color sel purple

> hide solvent

> save /Users/victohugofonsecadejesus/Downloads/figure.cxs

——— End of log from Sat Jun 20 19:26:13 2026 ———

> view name session-start

opened ChimeraX session  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

Python: 3.11.9
Locale: UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,9
      Model Number: MPHF3Y/A
      Chip: Apple M2 Pro
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 8419.41.10

Software:

    System Software Overview:

      System Version: macOS 13.0 (22A8380)
      Kernel Version: Darwin 22.1.0
      Time since boot: 1 day, 8 hours, 31 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 19
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.2
    aiohttp: 3.13.4
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.13.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.4.3
    bs4: 0.0.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.7
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.67.1
    ChimeraX-AtomicLibrary: 14.4
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.4
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.12
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.2.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.8.2
    ChimeraX-Label: 1.5
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.3
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchAlign: 1.2
    ChimeraX-MatchMaker: 2.4.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.9
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.23
    ChimeraX-ModelPanel: 1.6.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.15.4
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.13
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.6
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.18
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.4
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.50.8
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.4.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.14.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.21
    decorator: 5.3.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.63.0
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.16.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.18
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.8.0
    jupyter_core: 5.9.1
    kiwisolver: 1.5.0
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.2
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.1
    narwhals: 2.22.1
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    OpenMM: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.7
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.10.0
    plotly: 6.8.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.5.2
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.13.4
    pydantic-settings: 2.14.1
    pydantic_core: 2.46.4
    pydata-sphinx-theme: 0.18.0
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.5.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.10.2
    PyQt6-Qt6: 6.10.2
    PyQt6-WebEngine-commercial: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.2
    PyQt6_sip: 13.10.3
    pytest: 9.0.3
    pytest-cov: 7.1.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.32
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    rpds-py: 2026.5.1
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.1.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.4
    Sphinx: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    sse-starlette: 3.4.4
    stack-data: 0.6.3
    starlette: 1.3.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 3.2.1
    threadpoolctl: 3.6.0
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.7
    tqdm: 4.68.2
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    Unidecode: 1.4.0
    urllib3: 2.7.0
    uvicorn: 0.49.0
    wcwidth: 0.8.1
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    yarl: 1.24.2

Change History (2)

comment:1 by Eric Pettersen, 3 weeks ago

Cc: Eric Pettersen added
Component: Unassigned → Core
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash opening session?

comment:2 by Tom Goddard, 3 weeks ago

Resolution: → limitation
Status: assigned → closed
Summary: Crash opening session? → Crash running ChimeraX from .dmg and ejecting disk image?

It looks like the user was running ChimeraX directly out of the .dmg without copying it to their local disk first. I tried that and opened a session which worked fine, and then ejected the .dmg disk image and ChimeraX crashed (ticket #20525). That may be what happened in this crash report. It may be that the disk image was ejected when logging out so the user didn't even see it.

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