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Opened 102 minutes ago
#19872 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.2-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x00000004a943b000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x00000004a842f000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x00000004a7423000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x00000004a6417000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x00000004a540b000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x00000004a43ff000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x00000004a33f3000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x00000004a23e7000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x00000004a13db000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x00000004a03cf000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000049f3c3000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000049e3b7000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000049d3ab000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000049c39f000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000049b393000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000049a387000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000049937b000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000049836f000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000497363000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000496357000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000049534b000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000049433f000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000493333000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000492327000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000049131b000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000049030f000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000048f303000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000030805b000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
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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, PIL._imaging, chimerax.surface._surface, chimerax.map._map, chimerax.pdb_lib._load_libs, 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, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 50)
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Activity Tracing 256K 1
AttributeGraph Data 1024K 1
CG image 480K 26
ColorSync 2160K 135
CoreAnimation 1632K 90
CoreGraphics 64K 4
CoreServices 144K 1
CoreUI image data 5712K 54
Foundation 32K 2
Kernel Alloc Once 96K 2
MALLOC 13.0G 1450
MALLOC guard page 3456K 4
Mach message 64K 3
OpenGL GLSL 256K 3
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STACK GUARD 1328K 83
STACK GUARD (graphics) 16K 1
Stack 883.2M 85
Stack Guard 56.0M 1
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__DATA 43.5M 1132
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__TEXT 1.4G 1120
__TEXT (graphics) 36.2M 83
__TPRO_CONST 128K 2
dyld private memory 432K 5
mapped file 644.7M 98
page table in kernel 11.3M 1
shared memory 3728K 28
=========== ======= =======
TOTAL 19.4G 9309
TOTAL, minus reserved VM space 19.1G 9309
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===== 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: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 9i05 fromDatabase pdb format mmcif
Summary of feedback from opening 9i05 fetched from pdb
---
warnings | Atom H is not in the residue template for PRO /Xo:731
Atom H1 is not in the residue template for UNK /Uf:1
notes | Fetching compressed mmCIF 9i05 from http://files.rcsb.org/download/9i05.cif
Fetching CCD FES from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/FES/FES.cif
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif
9i05 title:
Cryo-EM structure of the large subunit of the mitochondrial ribosome from
Toxoplasma gondii [more info...]
Chain information for 9i05 #1
---
Chain | Description | UniProt
AA | Putative 60S ribosomal protein L27 | A0A7J6JYF7_TOXGO 30-126
AB | Large ribosomal subunit protein mL43 | A0A7J6KC95_TOXGO 1-203
AC | Ribosomal protein L46 | A0A7J6JX23_TOXGO 1-598
AD | Large ribosomal subunit protein mL49 | A0A7J6JUD4_TOXGO 1-310
AE | mL53 | A0A7J6JX69_TOXGO -98-118
AF | Large ribosomal subunit protein mL54 | S8F6A8_TOXGM -384-130
AG | BIR protein | A0A7J6K0B0_TOXGO 1-271
AH | mL102 | A0A0F7V869_TOXGV -360-35
AI | RAP domain-containing protein | A0A7J6KFM0_TOXGO 1-656
Aa | Putative LSU ribosomal protein L2P | A0A7J6KET1_TOXGO -215-362
Ab | Large ribosomal subunit protein uL3m | A0A2G8Y818_TOXGO 1-514
Ac | Large ribosomal subunit protein uL4m | A0A151HQQ9_TOXGO 1-802
Ad | HECT-domain (Ubiquitin-transferase) domain-containing protein | A0A7J6K7T4_TOXGO -111-280
Ae | Ribosomal protein L9, N-terminal domain-containing protein | A0A086JV44_TOXGO 1-492
Af | Putative ribosomal protein L11 | A0A7J6KEF6_TOXGO 1-180
Ag | Putative 50S ribosomal protein L13 | A0A7J6K0U2_TOXGO 1-231
Ah | Putative LSU ribosomal protein L14P | A0A7J6K196_TOXGO 1-122
Ai | Ribosomal protein L15, putative | S8GIU7_TOXGM 1-638
Aj | Putative 50S ribosomal protein L16 | A0A7J6K7Z7_TOXGO 1-187
Ak | Putative 50S ribosomal protein L17 | A0A7J6KEY9_TOXGO 1-247
Al | 50S ribosomal protein L19, chloroplastic | A0A7J6JZ22_TOXGO 0-743
Am | Putative ribosomal protein L20 | B9PY19_TOXGO 1-121
An | Large ribosomal subunit protein bL21m | A0A7J6K7U7_TOXGO 1-679
Ao | Ribosomal L22p/L17e protein | S8F1I2_TOXGM -225-347
Ap | Large ribosomal subunit protein uL23m | A0A7J6K299_TOXGO 1-253
Aq | Large ribosomal subunit protein uL24c | A0A7J6JXG2_TOXGO 1-438
Ar | Ribosomal l25 family protein | S8ER88_TOXGM 1-739
As | bL27m | S8GME4_TOXGM 1-391
At | Putative ribosomal protein L28 | A0A7J6K129_TOXGO 1-282
Au | Large ribosomal subunit protein uL29m | A0A7J6K1F8_TOXGO 1-236
Av | bL32m | A0A7J6K9L3_TOXGO 1-88
Aw | Putative 50S ribosomal protein L33 | A0A7J6JWI3_TOXGO 1-126
Ax | bL35m | A0A7J6KEG8_TOXGO 1-352
Ay | bL36m | A0A3R8AVZ6_TOXGO 1-200
Az | mL40 | A0A7J6KCG7_TOXGO 1-293
RA | LSU-2 |
RB | LSU-3 |
RC | LSU-4 |
RD | LSU-5 |
RE | LSU-6 |
RF | LSU-7 |
RG | LSU-8 |
RI | LSU-9 |
RJ | LSU-10 |
RK | LSU-11 |
RL | LSU-12 |
RM | LSU-13 |
RN | LSU-14 |
RO | LSU-15 |
RP | LSU-16 |
RQ | LSU-17 |
RS | LSU-18 |
RT | LSU-19 |
RU | LSU-20 |
RV | LSU-21 |
RW | LSU-22 |
RX | LSU-23 |
RY | LSU-24 |
RZ | LSU-25 |
Ra | LSU-26 |
Rb | LSU-27 |
Rc | LSU-28 |
Rd | LSU-29 |
Rf | LSU-30 |
Rg | LSU-31 |
Rh | LSU-32 |
Ri | LSU-32 |
Ua | Ribosomal l25 family protein | A0A7J6JXW0_TOXGO 0-25
Ub | Chain Uc |
Uc | Chain Ud |
Ud | Chain Ue |
Ue | Chain Uf |
Uf | LSU-1 |
XA | mL155 | A0A7J6KDX2_TOXGO -223-86
XB | mL156 | A0A7J6K9K6_TOXGO -94-103
XC | mL157 | A0A7J6JWE1_TOXGO 1-305
XD | mL158 | S7UHA3_TOXGG -19-216
XE | mL159 | A0A7J6KA70_TOXGO 1-150
XF | mL160 | A0A7J6JZI4_TOXGO 1-141
XG | mL161 | A0A7J6K5D7_TOXGO -445-30
XH | Ribosomal protein RPL22 | A0A7J6JUA9_TOXGO -159-181
XI | Transmembrane protein | A0A7J6K730_TOXGO -166-35
XJ | Chain Ua |
Xa | mL130 | A0A7J6JZ23_TOXGO -362-181
Xb | RRM domain-containing protein | S7UYV0_TOXGG 1-664
Xc | mL132 | A0A7J6JXX9_TOXGO 1-198
Xd | RAP domain-containing protein | A0A2G8XP01_TOXGO 1-927
Xe | Large ribosomal subunit protein uL24c | A0A7J6K981_TOXGO 1-229
Xf | FAS1 domain-containing protein | A0A7J6KB94_TOXGO -9-699
Xg | DUF6832 domain-containing protein | A0A7J6KC93_TOXGO 12-486
Xh | RAP domain-containing protein | A0A7J6KAP7_TOXGO 1-632
Xi | RAP domain-containing protein | A0A7J6K2J1_TOXGO 1-445
Xj | RAP domain-containing protein | A0A7J6K4L1_TOXGO 1-955
Xk | RNA recognition motif-containing protein | A0A7J6KGH2_TOXGO 1-244
Xl Xv | RAP domain-containing protein | A0A7J6JZB1_TOXGO 1-645
Xm | Macro domain-containing protein | A0A7J6K515_TOXGO -104-506
Xn | AP2 domain transcription factor AP2VIIb-2 | A0A7J6K291_TOXGO 1-568
Xo | mL144 |
Xp | Peptidyl-prolyl cis-trans isomerase | A0A7J6K9Z8_TOXGO 1-283
Xq | mL146 | A0A7J6K1X6_TOXGO 6-1117
Xr | RAP domain-containing protein | A0A7J6KAD2_TOXGO 1-713
Xs | mL149 | A0A7J6JXX4_TOXGO 1-493
Xt | mL148 | A0A7J6JV70_TOXGO 1-123
Xw | Transmembrane protein | A0A7J6KAS3_TOXGO 1-329
Xx | mL152 | A0A7J6K0Y0_TOXGO 1-300
Xy | mL153 | Q1JTA3_TOXGO 1-424
Xz | AP2 domain transcription factor AP2IV-1 | A0A7J6KEE5_TOXGO 1-425
Non-standard residues in 9i05 #1
---
FES — FE2/S2 (inorganic) cluster
ZN — zinc ion
> sequence chain #1/Xd
Alignment identifier is 1/Xd
> sequence chain #1/Xh
Alignment identifier is 1/Xh
> sequence chain #1/Xi
Alignment identifier is 1/Xi
> sequence chain #1/Xj
Alignment identifier is 1/Xj
> sequence chain #1/Xl#1/Xv
Alignment identifier is 1
> sequence chain #1/Xr
Alignment identifier is 1/Xr
> sequence chain #1/Xr
Destroying pre-existing alignment with identifier 1/Xr
Alignment identifier is 1/Xr
> sequence chain #1/Xr
Alignment identifier is 1/Xr
> sequence chain #1/Xl#1/Xv
Alignment identifier is 1
> sequence chain #1/Xj
Alignment identifier is 1/Xj
> sequence chain #1/Xi
Alignment identifier is 1/Xi
> sequence chain #1/Xh
Alignment identifier is 1/Xh
> sequence chain #1/Xd
Alignment identifier is 1/Xd
> sequence chain #1/AI
Alignment identifier is 1/AI
> select
> /AI:296-314,319-379,382-388,395-407,409-436,443-455,461-465,469-484,499-506,525-536,540-574,605-639
3842 atoms, 3861 bonds, 1 pseudobond, 236 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> style sel stick
Changed 3842 atom styles
> style sel sphere
Changed 3842 atom styles
> show sel atoms
> hide sel atoms
> show sel atoms
> hide #!1 models
> show #!1 models
> select add #1
323886 atoms, 332064 bonds, 1281 pseudobonds, 17930 residues, 4 models
selected
> select subtract #1
Nothing selected
> select add #1
323886 atoms, 332064 bonds, 1281 pseudobonds, 17930 residues, 4 models
selected
> select subtract #1
Nothing selected
> select /AI:295-639
5401 atoms, 5458 bonds, 1 pseudobond, 329 residues, 2 models selected
> select /AH:2-35
580 atoms, 583 bonds, 34 residues, 1 model selected
> select /AH:2-35
580 atoms, 583 bonds, 34 residues, 1 model selected
> sequence chain #1/AH
Alignment identifier is 1/AH
> sequence chain #1/AH
Destroying pre-existing alignment with identifier 1/AH
Alignment identifier is 1/AH
> select /AI:295-639
5401 atoms, 5458 bonds, 1 pseudobond, 329 residues, 2 models selected
> set bgColor white
> set bgColor black
> style sel ball
Changed 5401 atom styles
> style sel ball
Changed 5401 atom styles
> style sel sphere
Changed 5401 atom styles
> style sel stick
Changed 5401 atom styles
> style sel stick
Changed 5401 atom styles
> style sel sphere
Changed 5401 atom styles
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
> hide sel atoms
> hide sel surfaces
> select add #1.2
5401 atoms, 5458 bonds, 13 pseudobonds, 329 residues, 3 models selected
> select add #1.1
5401 atoms, 5458 bonds, 1227 pseudobonds, 329 residues, 4 models selected
> hide sel surfaces
> hide sel cartoons
> hide #!1 models
> show #!1 models
> select add #1
323886 atoms, 332064 bonds, 1281 pseudobonds, 17930 residues, 4 models
selected
> select subtract #1
Nothing selected
> select add #1
323886 atoms, 332064 bonds, 1281 pseudobonds, 17930 residues, 4 models
selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> show sel atoms
> hide sel atoms
> select /AI:295-639
5401 atoms, 5458 bonds, 1 pseudobond, 329 residues, 2 models selected
> select #AI
Expected an objects specifier or a keyword
> select AI
Expected an objects specifier or a keyword
> select #1/AI
5401 atoms, 5458 bonds, 1 pseudobond, 329 residues, 2 models selected
> cartoon (#!1 & sel)
> color (#!1 & sel) red
> select clear
> select /AI:551
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
314 atoms, 313 bonds, 21 residues, 1 model selected
> select up
4564 atoms, 4611 bonds, 279 residues, 1 model selected
> select down
314 atoms, 313 bonds, 21 residues, 1 model selected
> select down
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
314 atoms, 313 bonds, 21 residues, 1 model selected
> select up
4564 atoms, 4611 bonds, 279 residues, 1 model selected
> select up
5401 atoms, 5458 bonds, 329 residues, 1 model selected
> color sel green
> show sel atoms
> hide sel atoms
> select /AI:14
Nothing selected
> select /AI:406
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /AI:cys
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /AI:lys
462 atoms, 442 bonds, 21 residues, 1 model selected
> select /AI:K
Nothing selected
> select /AI:K
Nothing selected
> select /AI
5401 atoms, 5458 bonds, 1 pseudobond, 329 residues, 2 models selected
> name frozen AI sel
> select clear
> select AI
5401 atoms, 5458 bonds, 1 pseudobond, 329 residues, 2 models selected
> show #1
> show #1 cartoons
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> show #1 cartoons
> ~hbonds
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 5401 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> show #1 cartoons
> hide sel surfaces
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel ball
Changed 5401 atom styles
> style sel ball
Changed 5401 atom styles
> style sel cartoons
Expected a keyword
> style sel off
Expected a keyword
> style sel stick
Changed 5401 atom styles
> style #1 stick
Changed 323886 atom styles
> hide sel atoms
> style #1 cartoons
Expected a keyword
> hide sel atoms
> hide #1
> color #1 grey
> select clear
> name frozen AI sel
Nothing is selected by specifier
> select AI
5401 atoms, 5458 bonds, 1 pseudobond, 329 residues, 2 models selected
> color (#!1 & sel) red
> select clear
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> show surfaces
> lighting simple
> lighting soft
> lighting full
> open 9hqv fromDatabase pdb format mmcif
Summary of feedback from opening 9hqv fetched from pdb
---
warnings | Atom H is not in the residue template for PRO /Ba:87
Atom H1 is not in the residue template for UNK /Ua:1
Atom H1 is not in the residue template for UNK /Uc:1
Atom H1 is not in the residue template for UNK /Ud:1
Atom H3 is not in the residue template for UNK /Ui:1
Atom H1 is not in the residue template for UNK /Uj:1
Atom H3 is not in the residue template for UNK /Uk:1
Atom H1 is not in the residue template for UNK /Uo:1
Atom H1 is not in the residue template for UNK /Up:1
Too many hydrogens missing from residue template(s) to warn about
notes | Fetching compressed mmCIF 9hqv from http://files.rcsb.org/download/9hqv.cif
Fetching CCD ATP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ATP/ATP.cif
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
9hqv title:
Cryo-EM structure of the small subunit of the mitochondrial ribosome from
Toxoplasma gondii [more info...]
Chain information for 9hqv #2
---
Chain | Description | UniProt
BA | Enoyl-CoA hydratase/isomerase family protein | A0A7J6KGS2_TOXGO 1-716
BB | mS75 |
BC | Pentatricopeptide repeat domain-containing protein | A0A7J6KDF6_TOXGO 1-686
BD | mS92 | A0A7J6KCE0_TOXGO 1-147
Ba | Ribosomal protein, uS2m | A0A7J6K4L0_TOXGO 1-190
Bb | Putative 30S ribosomal protein S5 | A0A7J6KBH4_TOXGO 34-1141
Bc | Putative mitochondrial ribosomal protein s6-2 | A0A7J6K9W0_TOXGO 1-163
Bd | Putative ribosomal protein S8 | A0A7J6K132_TOXGO 1-129
Be | Putative ribosomal protein S9 | A0A7J6KFS1_TOXGO 1-530
Bf | uS10m | A0A7J6K2E1_TOXGO 1-243
Bg | Putative ribosomal protein S11 | A0A7J6K2Q1_TOXGO 1-393
Bh | Putative 30S ribosomal protein S12 | A0A7J6JTW0_TOXGO 1-594
Bi | us13m | A0A7J6KC71_TOXGO -6-103
Bj | Putative ribosomal protein S14 | A0A7J6JW76_TOXGO 1-112
Bk | Putative 30S ribosomal protein S15 | A0A7J6JZR0_TOXGO 1-395
Bl | Putative 30S ribosomal protein S16 | A0A7J6KCY1_TOXGO 1-167
Bm | Putative ribosomal protein S17 | A0A125YU94_TOXGG 1-116
Bn | Putative ribosomal protein S18 | S7VTU6_TOXGG 1-738
Bo | Ribosomal protein, bS21m | S8G0I7_TOXGM 1-243
Bp | mS23 | A0A7J6K2Y2_TOXGO 1-377
Bq | Mitochondrial ribosomal protein, mS26 | A0A086KM95_TOXGO 1-447
Br | Small ribosomal subunit protein mS29 | A0A7J6JWV4_TOXGO 1-545
Bs | DNA double-strand break repair rad50 ATPase | A0A7J6K0I6_TOXGO 1-616
Bt | mS34 | A0A7J6JYF4_TOXGO 1-303
Bu | Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein | A0A7J6K5S5_TOXGO 2-584
Bv | CHCH domain-containing protein | A0A7J6JX47_TOXGO 1-138
Bx | Mitochondrial mRNA-processing protein COX24 C-terminal domain-containing protein | A0A0F7UNZ9_TOXGV -190-76
By | Homeodomain-like containing protein | A0A7J6KAD0_TOXGO -323-273
Bz | mS45 | A0A7J6JZ68_TOXGO 1-531
SA | SSU-1 |
SB | SSU-2 |
SC | SSU-3 |
SD | SSU-4 |
SE | SSU-5 |
SF | SSU-6 |
SG | SSU-7 |
SH | SSU-8 |
SI | SSU-9 |
SJ | SSU-10 |
SK | SSU-11 |
SL | SSU-12 |
SM | SSU-13 |
SN | SSU-14 |
SO | SSU-15 |
SP | SSU-16 |
SQ | SSU-17 |
SR | SSU-18 |
SS | SSU-19 |
ST | SSU-20 |
SU | SSU-21 |
TP | tRNA E-site |
UC | Chain UC |
Ua | UNK1 |
Ub | UNK2 |
Uc | UNK3 |
Ud | UNK4 |
Uh | Chain Uh |
Ui Uk | Unknown peptide |
Uj | Chain Uj |
Ul | GLY-ARG-SER-LYS-VAL-LEU-ILE-ARG-ARG-LEU-LYS-GLU-ARG-ALA-LYS-LYS-GLU-ALA-GLU-LYS-LYS-ALA |
Um | ARG-ALA-GLU-LEU-VAL-ALA-ALA-GLN-VAL-ARG-GLU-LYS-LEU-ALA-ILE-LYS-MET-ALA-ASN-ALA-LEU-ALA |
Un | Chain Un |
Uo | chain Uo |
Up | chain Up |
Uq | chain Uq |
Ya | mS117 | S7V2J1_TOXGG 1-551
Yb | ATP-dependent Clp protease proteolytic subunit,related protein | A0A7J6K1B3_TOXGO 0-1159
Yc | mS119 | A0A7J6KFI1_TOXGO 0-267
Yd | mS120 | A0A7J6K8Y5_TOXGO 1-680
Ye | mS121 | A0A7J6JZ58_TOXGO 1-314
Yf | Macro domain-containing protein | A0A7J6K475_TOXGO 1-698
Yg | Thioredoxin domain-containing protein | A0A7J6K257_TOXGO -17-1038
Yh | mS124 |
Yi | mS125 | A0A7J6JYP0_TOXGO 1-931
Yj | DnaJ domain-containing protein | A0A7J6KC34_TOXGO -168-64
Yk | RAP domain-containing protein | A0A7J6KGV4_TOXGO 1-1553
Yl | mS128 | A0A7J6KEX1_TOXGO 1-316
Ym | RAP domain-containing protein | A0A7J6K7K5_TOXGO 1-801
Yn | AP2 domain transcription factor AP2IX-6 | A0A7J6KDC3_TOXGO 1-432
Yo | mS131 | A0A7J6KFW2_TOXGO 1-421
Yp | mS132 | A0A7J6K2N1_TOXGO 1-180
Yq | mS133 | B9PYD6_TOXGO -2-302
Yr | Acylphosphatase-like domain-containing protein | A0A125YXT0_TOXGG 1-235
Ys | mS135 | A0A7J6K0G8_TOXGO 1-181
Yt | mS136 | A0A7J6K0Z5_TOXGO 1-475
Yu | mS137 |
Yv | mS138 | A0A7J6K328_TOXGO 1-419
Non-standard residues in 9hqv #2
---
ATP — adenosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
> hide #!1 models
> show #!1 models
> hide #1
> hide #1 surfaces
> hide #1 cartoons
> select add #1.4
3132 atoms, 188 residues, 1 model selected
> select subtract #1.4
1 model selected
> ui mousemode right "translate selected models"
> unhide #1 cartoons
Unknown command: unhide #1 cartoons
> show #1 cartoons
> color #1/ RE green
> lighting simple
> hide #!2 models
> ui mousemode right "translate selected models"
> select clear
> color #1/ Xh cyan
> color #1/ RA pink
> color #1/ RG cyan
> color #1/ Xh grey
> ui mousemode right "move picked models"
> view matrix models #1,1,0,0,6.3129,0,1,0,-6.2262,0,0,1,-0.79302
> ui mousemode right "translate selected models"
> color #1/ RA rose
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/ RA violet
> lighting simple
> lighting soft
> lighting full
> lighting simple
> color #1/ Aq Blue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/ Aq blue
> save /Users/dhanyshanmugam/Desktop/image1.png supersample 3
> save /Users/dhanyshanmugam/Desktop/image2.png supersample 3
> save /Users/dhanyshanmugam/Desktop/image3.png supersample 3
> save /Users/dhanyshanmugam/Desktop/image4.png supersample 3
> save /Users/dhanyshanmugam/Desktop/image5.png supersample 3
> save /Users/dhanyshanmugam/Desktop/image6.png supersample 3
> save /Users/dhanyshanmugam/Desktop/image7.png supersample 3
> save /Users/dhanyshanmugam/Desktop/image8.png supersample 3
> show #!2 models
> save /Users/dhanyshanmugam/Desktop/image9.png supersample 3
> hide #!2 models
> color #1/ AG yellow
> color #1/ AG grey
> color #1/ RB yellow
> color #1/ Rc brown
> color #1/ Rd brown
> color #1/ Rc grey
> color #1/ Rd grey
> color #1/ Rf brown
> color #1/ Rf grey
> color #1/ RC brown
> ui tool show "Selection Inspector"
> color #1/ RC grey
> color #1/ RD brown
> color #1/ RD grey
> color #1/ RF brown
> color #1/ RF grey
> color #1/ RI brown
> color #1/ RI grey
> color #1/ RJ brown
> color #1/ RJ grey
> color #1/ RK brown
> color #1/ RK grey
> color #1/ RL brown
> color #1/ RL grey
> color #1/ RM brown
> color #1/ RM grey
> color #1/ RN brown
> color #1/ RN grey
> color #1/ RO brown
> color #1/ RO grey
> color #1/ RP brown
> color #1/ RP grey
> color #1/ RQ brown
> color #1/ RQ grey
> color #1/ RR brown
> color #1/ RS brown
> color #1/ RS grey
> color #1/ RT brown
> color #1/ RT grey
> color #1/ RU brown
> color #1/ RU grey
> color #1/ RV brown
> color #1/ RV grey
> color #1/ RW brown
> color #1/ RW grey
> color #1/ RX brown
> color #1/ RX grey
> color #1/ RY brown
> select ~sel & ##selected
Nothing selected
> color #1/ RY grey
> color #1/ RZ brown
> color #1/ RZ grey
> color #1/ Ra brown
> color #1/ Ra grey
> color #1/ Rb brown
> color #1/ Rb grey
> color #1/ Rc brown
> color #1/ Rc grey
> color #1/ Rd brown
> color #1/ Rd grey
> color #1/ Rf brown
> color #1/ Rf grey
> color #1/ Rg brown
> color #1/ Rg grey
> color #1/ Rh brown
> color #1/ Rh grey
> color #1/ Ri brown
> color #1/ Ri grey
> save /Users/dhanyshanmugam/Desktop/image10.png supersample 3
> save /Users/dhanyshanmugam/Desktop/image11.png supersample 3
> save /Users/dhanyshanmugam/Desktop/image12.png supersample 3
> save /Users/dhanyshanmugam/Desktop/image13.png supersample 3
> save /Users/dhanyshanmugam/Desktop/image14.png supersample 3
> save /Users/dhanyshanmugam/Desktop/image15.png supersample 3
> save /Users/dhanyshanmugam/Desktop/image16.png supersample 3
> save /Users/dhanyshanmugam/Desktop/image17.png supersample 3
> color #1/ Rb brown
> color #1/ Rb grey
> color #1/ Rd brown
> color #1/ Rd grey
> color #1/ Rh brown
> color #1/ Rh grey
> color #1/ Xb brown
> color #1/ Xb grey
> color #1/ Xd brown
> show #!2 models
> hide #!2 models
> color #1/ Xd grey
> color #1/ Xh brown
> color #1/ Xh grey
> color #1/ Xi brown
> show #!2 models
> hide #!2 models
> color #1/ Xi grey
> color #1/ Xj brown
> color #1/ Xj grey
> color #1/ Xk brown
> color #1/ Xk yellow
> color #1/ Xk grey
> color #1/ XI yellow
> color #1/ XI goldenrod
> color #1/ XI gold
> color #1/ XI grey
> color #1/ X1 yellow
> color #1/ X1 grey
> color #1/ Xv brown
> color #1/ Xv grey
> color #1/ Xr brown
> show #!2 models
> hide #!2 models
> color #1/ Xr goldenrod
> color #1/ Xd goldenrod
> color #1/ Xh goldenrod
> color #1/ Xi goldenrod
> color #1/ Xj goldenrod
> color #1/ X1 goldenrod
> color #1/ Xv goldenrod
> color #1/ Xr goldenrod
> color #1/ Xr blue
> color #1/ Xr goldenrod
> color #1/ Xr blue
> color #1/ Xr goldenrod
> color #1/ Xv blue
> color #1/ Xv goldenrod
> color #1/ Xj blue
> color #1/ Xi blue
> color #1/ Xh blue
> color #1/ Xd blue
> color #1/ Xv blue
> color #1/ Xv goldenrod
> color #1/ Xd goldenrod
> color #1/ Xh goldenrod
> color #1/ Xi goldenrod
> color #1/ Xj goldenrod
> color #1/ Xv goldenrod
> color #1/ Xk blue
> color #1/ Xb blue
> color #1/ Xb grey
> color #1/ Xk grey
> save /Users/dhanyshanmugam/Desktop/image18.png supersample 3
> save /Users/dhanyshanmugam/Desktop/image19.png supersample 3
> save /Users/dhanyshanmugam/Desktop/image20.png supersample 3
> show #!2 models
> style stick
Changed 570134 atom styles
> style ball
Changed 570134 atom styles
> style stick
Changed 570134 atom styles
> style sphere
Changed 570134 atom styles
> style sphere
Changed 570134 atom styles
> style ball
Changed 570134 atom styles
> color bychain
> nucleotides atoms
> style nucleic stick
Changed 98216 atom styles
> show surfaces
> hide surfaces
> show surfaces
> hide #!1 models
> select add #2
246248 atoms, 251434 bonds, 773 pseudobonds, 14185 residues, 4 models selected
> color #2 grey
> select subtract #2
88 models selected
> show #!1 models
> select add #1
323886 atoms, 332064 bonds, 67 pseudobonds, 17930 residues, 3 models selected
> color #1 grey
> select subtract #1
108 models selected
> lighting simple
> lighting soft
> save /Users/dhanyshanmugam/Desktop/image21.png supersample 3
> color #1 pink
> save /Users/dhanyshanmugam/Desktop/image22.png supersample 3
> color #1 grey
> color #2 pink
> save /Users/dhanyshanmugam/Desktop/image23.png supersample 3
> color #2 skyblue
> color #1/ AI red
> save /Users/dhanyshanmugam/Desktop/image24.png supersample 3
> color #1/ AI grey
> save /Users/dhanyshanmugam/Desktop/image25.png supersample 3
> color #1/ AI red
> color #1/ RE green
> color #1/ RE grey
> color #1/ Aq blue
> color #1/ Xd goldenrod
> color #1/ Xh goldenrod
> color #1/ Xi goldenrod
> color #1/ Xj goldenrod
> color #1/ Xv goldenrod
> color #1/ Xr goldenrod
> color #1/ Xr blue
> color #1/ Xr goldenrod
> save /Users/dhanyshanmugam/Desktop/image26.png supersample 3
> select add #1.89
7539 atoms, 492 residues, 1 model selected
> view #1 clip false
> sequence chain #1/Xd
Alignment identifier is 1/Xd
> select subtract #1.89
1 model selected
> select add #1.93
6863 atoms, 421 residues, 1 model selected
> sequence chain #1/Xh
Alignment identifier is 1/Xh
> select subtract #1.93
1 model selected
> select add #1.94
7329 atoms, 444 residues, 1 model selected
> sequence chain #1/Xi
Alignment identifier is 1/Xi
> select subtract #1.94
1 model selected
> select add #1.95
9609 atoms, 585 residues, 1 model selected
> sequence chain #1/Xj
Alignment identifier is 1/Xj
> select subtract #1.95
1 model selected
> select add #1.103
7423 atoms, 451 residues, 1 model selected
> sequence chain #1/Xr
Alignment identifier is 1/Xr
> select subtract #1.103
1 model selected
> select add #1.106
6386 atoms, 394 residues, 1 model selected
> sequence chain #1/Xv
Alignment identifier is 1/Xv
> select subtract #1.106
1 model selected
> color #1/ Xl goldenrod
> color #1/ Xl blue
> color #1/ Xv blue
> color #1/ Xv pink
> color #1/ Xl pink
> color #1/ Xr pink
> color #1/ Xr goldenrod
> hide #!2 models
> show #!2 models
> hide surfaces
> sequence chain #1/Aa
Alignment identifier is 1/Aa
> sequence chain #1/Ab
Alignment identifier is 1/Ab
> sequence chain #1/Ac
Alignment identifier is 1/Ac
> sequence chain #1/Ad
Alignment identifier is 1/Ad
> sequence chain #1/Ae
Alignment identifier is 1/Ae
> sequence chain #1/Af
Alignment identifier is 1/Af
> sequence chain #1/Ag
Alignment identifier is 1/Ag
> sequence chain #1/Ah
Alignment identifier is 1/Ah
> sequence chain #1/Ai
Alignment identifier is 1/Ai
> sequence chain #1/Aj
Alignment identifier is 1/Aj
> sequence chain #1/Ak
Alignment identifier is 1/Ak
> sequence chain #1/Al
Alignment identifier is 1/Al
> sequence chain #1/Am
Alignment identifier is 1/Am
> sequence chain #1/An
Alignment identifier is 1/An
> sequence chain #1/Ao
Alignment identifier is 1/Ao
> sequence chain #1/Ap
Alignment identifier is 1/Ap
> sequence chain #1/Aq
Alignment identifier is 1/Aq
> sequence chain #1/Ar
Alignment identifier is 1/Ar
> sequence chain #1/As
Alignment identifier is 1/As
> sequence chain #1/At
Alignment identifier is 1/At
> sequence chain #1/Au
Alignment identifier is 1/Au
> sequence chain #1/Av
Alignment identifier is 1/Av
> sequence chain #1/Aw
Alignment identifier is 1/Aw
> sequence chain #1/Ax
Alignment identifier is 1/Ax
> sequence chain #1/Ay
Alignment identifier is 1/Ay
> sequence chain #1/Az
Alignment identifier is 1/Az
> sequence chain #1/AA
Alignment identifier is 1/AA
> sequence chain #1/AB
Alignment identifier is 1/AB
> sequence chain #1/AC
Alignment identifier is 1/AC
> sequence chain #1/AD
Alignment identifier is 1/AD
> sequence chain #1/AE
Alignment identifier is 1/AE
> sequence chain #1/AF
Alignment identifier is 1/AF
> sequence chain #1/AG
Alignment identifier is 1/AG
> sequence chain #1/AH
Alignment identifier is 1/AH
> sequence chain #1/AI
Alignment identifier is 1/AI
> sequence chain #1/Xa
Alignment identifier is 1/Xa
> sequence chain #1/Xb
Alignment identifier is 1/Xb
> sequence chain #1/Xc
Alignment identifier is 1/Xc
> sequence chain #1/Xd
Alignment identifier is 1/Xd
> sequence chain #1/Xe
Alignment identifier is 1/Xe
> sequence chain #1/Xf
Alignment identifier is 1/Xf
> sequence chain #1/Xg
Alignment identifier is 1/Xg
> sequence chain #1/Xh
Alignment identifier is 1/Xh
> sequence chain #1/Xi
Alignment identifier is 1/Xi
> sequence chain #1/Xj
Alignment identifier is 1/Xj
> sequence chain #1/Xk
Alignment identifier is 1/Xk
> sequence chain #1/Xl,Xv
Alignment identifier is 1
> sequence chain #1/Xm
Alignment identifier is 1/Xm
> sequence chain #1/Xn
Alignment identifier is 1/Xn
> sequence chain #1/Xo
Alignment identifier is 1/Xo
> sequence chain #1/Xp
Alignment identifier is 1/Xp
> sequence chain #1/Xq
Alignment identifier is 1/Xq
> sequence chain #1/Xr
Alignment identifier is 1/Xr
> sequence chain #1/Xs
Alignment identifier is 1/Xs
> sequence chain #1/Xt
Alignment identifier is 1/Xt
> sequence chain #1/Xw
Alignment identifier is 1/Xw
> sequence chain #1/Xx
Alignment identifier is 1/Xx
> sequence chain #1/Xy
Alignment identifier is 1/Xy
> sequence chain #1/Xz
Alignment identifier is 1/Xz
> sequence chain #1/XA
Alignment identifier is 1/XA
> sequence chain #1/XB
Alignment identifier is 1/XB
> sequence chain #1/XC
Alignment identifier is 1/XC
> sequence chain #1/XD
Alignment identifier is 1/XD
> sequence chain #1/XE
Alignment identifier is 1/XE
> sequence chain #1/XF
Alignment identifier is 1/XF
> sequence chain #1/XG
Alignment identifier is 1/XG
> sequence chain #1/XH
Alignment identifier is 1/XH
> sequence chain #1/XI
Alignment identifier is 1/XI
> sequence chain #1/XJ
Alignment identifier is 1/XJ
> sequence chain #1/Ua
Alignment identifier is 1/Ua
> sequence chain #1/Ub
Alignment identifier is 1/Ub
> sequence chain #1/Uc
Alignment identifier is 1/Uc
> sequence chain #1/Ud
Alignment identifier is 1/Ud
> sequence chain #1/Ue
Alignment identifier is 1/Ue
> sequence chain #1/Uf
Alignment identifier is 1/Uf
> sequence chain #1/RA
Alignment identifier is 1/RA
> sequence chain #1/RB
Alignment identifier is 1/RB
> sequence chain #1/RC
Alignment identifier is 1/RC
> sequence chain #1/RD
Alignment identifier is 1/RD
> sequence chain #1/RE
Alignment identifier is 1/RE
> sequence chain #1/RF
Alignment identifier is 1/RF
> sequence chain #1/RG
Alignment identifier is 1/RG
> sequence chain #1/RI
Alignment identifier is 1/RI
> sequence chain #1/RJ
Alignment identifier is 1/RJ
> sequence chain #1/RK
Alignment identifier is 1/RK
> sequence chain #1/RL
Alignment identifier is 1/RL
> sequence chain #1/RM
Alignment identifier is 1/RM
> sequence chain #1/RN
Alignment identifier is 1/RN
> sequence chain #1/RO
Alignment identifier is 1/RO
> sequence chain #1/RP
Alignment identifier is 1/RP
> sequence chain #1/RQ
Alignment identifier is 1/RQ
> sequence chain #1/RS
Alignment identifier is 1/RS
> sequence chain #1/RT
Alignment identifier is 1/RT
> sequence chain #1/RU
Alignment identifier is 1/RU
> sequence chain #1/RV
Alignment identifier is 1/RV
> sequence chain #1/RW
Alignment identifier is 1/RW
> sequence chain #1/RX
Alignment identifier is 1/RX
> sequence chain #1/RY
Alignment identifier is 1/RY
> sequence chain #1/RZ
Alignment identifier is 1/RZ
> sequence chain #1/Ra
Alignment identifier is 1/Ra
> sequence chain #1/Rb
Alignment identifier is 1/Rb
> sequence chain #1/Rc
Alignment identifier is 1/Rc
> sequence chain #1/Rd
Alignment identifier is 1/Rd
> sequence chain #1/Rf
Alignment identifier is 1/Rf
> sequence chain #1/Rg
Alignment identifier is 1/Rg
> sequence chain #1/Rh
Alignment identifier is 1/Rh
> sequence chain #1/Ri
Alignment identifier is 1/Ri
> sequence chain #2/BA
Alignment identifier is 2/BA
> sequence chain #2/BB
Alignment identifier is 2/BB
> sequence chain #2/BC
Alignment identifier is 2/BC
> sequence chain #2/BD
Alignment identifier is 2/BD
> sequence chain #2/Ba
Alignment identifier is 2/Ba
> sequence chain #2/Bb
Alignment identifier is 2/Bb
> sequence chain #2/Bc
Alignment identifier is 2/Bc
> sequence chain #2/Bd
Alignment identifier is 2/Bd
> sequence chain #2/Be
Alignment identifier is 2/Be
> sequence chain #2/Bf
Alignment identifier is 2/Bf
> sequence chain #2/Bg
Alignment identifier is 2/Bg
> sequence chain #2/Bh
Alignment identifier is 2/Bh
> sequence chain #2/Bi
Alignment identifier is 2/Bi
> sequence chain #2/Bj
Alignment identifier is 2/Bj
> sequence chain #2/Bk
Alignment identifier is 2/Bk
> sequence chain #2/Bl
Alignment identifier is 2/Bl
> sequence chain #2/Bm
Alignment identifier is 2/Bm
> sequence chain #2/Bn
Alignment identifier is 2/Bn
> sequence chain #2/Bo
Alignment identifier is 2/Bo
> sequence chain #2/Bp
Alignment identifier is 2/Bp
> sequence chain #2/Bq
Alignment identifier is 2/Bq
> sequence chain #2/Br
Alignment identifier is 2/Br
> sequence chain #2/Bs
Alignment identifier is 2/Bs
> sequence chain #2/Bt
Alignment identifier is 2/Bt
> sequence chain #2/Bu
Alignment identifier is 2/Bu
> sequence chain #2/Bv
Alignment identifier is 2/Bv
> sequence chain #2/Bx
Alignment identifier is 2/Bx
> sequence chain #2/By
Alignment identifier is 2/By
> sequence chain #2/Bz
Alignment identifier is 2/Bz
> sequence chain #2/Ua
Alignment identifier is 2/Ua
> sequence chain #2/Ub
Alignment identifier is 2/Ub
> sequence chain #2/Uc
Alignment identifier is 2/Uc
> sequence chain #2/Ud
Alignment identifier is 2/Ud
> sequence chain #2/Uh
Alignment identifier is 2/Uh
> sequence chain #2/Ui,Uk
Alignment identifier is 2
> sequence chain #2/Uj
Alignment identifier is 2/Uj
> sequence chain #2/Ul
Alignment identifier is 2/Ul
> sequence chain #2/Um
Alignment identifier is 2/Um
> sequence chain #2/Un
Alignment identifier is 2/Un
> sequence chain #2/Uo
Alignment identifier is 2/Uo
> sequence chain #2/Up
Alignment identifier is 2/Up
> sequence chain #2/Uq
Alignment identifier is 2/Uq
> sequence chain #2/Ya
Alignment identifier is 2/Ya
> sequence chain #2/Yb
Alignment identifier is 2/Yb
> sequence chain #2/Yc
Alignment identifier is 2/Yc
> sequence chain #2/Yd
Alignment identifier is 2/Yd
> sequence chain #2/Ye
Alignment identifier is 2/Ye
> sequence chain #2/Yf
Alignment identifier is 2/Yf
> sequence chain #2/Yg
Alignment identifier is 2/Yg
> sequence chain #2/Yh
Alignment identifier is 2/Yh
> sequence chain #2/Yi
Alignment identifier is 2/Yi
> sequence chain #2/Yj
Alignment identifier is 2/Yj
> sequence chain #2/Yk
Alignment identifier is 2/Yk
> sequence chain #2/Yl
Alignment identifier is 2/Yl
> sequence chain #2/Ym
Alignment identifier is 2/Ym
> sequence chain #2/Yn
Alignment identifier is 2/Yn
> sequence chain #2/Yo
Alignment identifier is 2/Yo
> sequence chain #2/Yp
Alignment identifier is 2/Yp
> sequence chain #2/Yr
Alignment identifier is 2/Yr
> sequence chain #2/Ys
Alignment identifier is 2/Ys
> sequence chain #2/Yt
Alignment identifier is 2/Yt
> sequence chain #2/Yu
Alignment identifier is 2/Yu
> sequence chain #2/Yq
Alignment identifier is 2/Yq
> sequence chain #2/SA
Alignment identifier is 2/SA
> sequence chain #2/SB
Alignment identifier is 2/SB
> sequence chain #2/SC
Alignment identifier is 2/SC
> sequence chain #2/SD
Alignment identifier is 2/SD
> sequence chain #2/SE
Alignment identifier is 2/SE
> sequence chain #2/SF
Alignment identifier is 2/SF
> sequence chain #2/SG
Alignment identifier is 2/SG
> sequence chain #2/SH
Alignment identifier is 2/SH
> sequence chain #2/SI
Alignment identifier is 2/SI
> sequence chain #2/SJ
Alignment identifier is 2/SJ
> sequence chain #2/SK
Alignment identifier is 2/SK
> sequence chain #2/SL
Alignment identifier is 2/SL
> sequence chain #2/SM
Alignment identifier is 2/SM
> sequence chain #2/SN
Alignment identifier is 2/SN
> sequence chain #2/SO
Alignment identifier is 2/SO
> sequence chain #2/SP
Alignment identifier is 2/SP
> sequence chain #2/SQ
Alignment identifier is 2/SQ
> sequence chain #2/SR
Alignment identifier is 2/SR
> sequence chain #2/SS
Alignment identifier is 2/SS
> sequence chain #2/ST
Alignment identifier is 2/ST
> sequence chain #2/SU
Alignment identifier is 2/SU
> sequence chain #2/TP
Alignment identifier is 2/TP
> sequence chain #2/UC
Alignment identifier is 2/UC
> sequence chain #2/Yv
Alignment identifier is 2/Yv
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: MRX43HN/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 13822.61.10
OS Loader Version: 13822.61.10
Software:
System Software Overview:
System Version: macOS 26.2 (25C56)
Kernel Version: Darwin 25.2.0
Time since boot: 12 days, 14 hours, 35 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 4
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: No
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
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: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
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
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
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: 1.1.4
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: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
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: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
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: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
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-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
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: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
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: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
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: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
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: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
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: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
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: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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