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Opened 89 minutes ago
#20072 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-15.7.4-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: Bus error
Thread 0x00000003378c3000 (most recent call first):
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x00000003368b7000 (most recent call first):
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x00000003358ab000 (most recent call first):
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 948 in wait
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.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/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000033489f000 (most recent call first):
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000333893000 (most recent call first):
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000332887000 (most recent call first):
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000033187b000 (most recent call first):
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000033086f000 (most recent call first):
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000032f863000 (most recent call first):
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000032e857000 (most recent call first):
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000032d84b000 (most recent call first):
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000032c83f000 (most recent call first):
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000032b833000 (most recent call first):
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Current thread 0x0000000205a2e240 (most recent call first):
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/private/var/folders/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.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/8y/9q65ydv97sz3xjjt7_g_0qnr0000gp/T/AppTranslocation/0F067296-5C2E-459F-AECD-355EDBBB4C8A/d/ChimeraX-1.11.1.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.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, PIL._imaging, 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, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 51)
{"app_name":"ChimeraX","timestamp":"2026-03-26 15:15:46.00 +0100","app_version":"","slice_uuid":"c20e09a8-923e-3fb3-856b-3e765bcb267b","build_version":"","platform":1,"share_with_app_devs":0,"is_first_party":1,"bug_type":"309","os_version":"macOS 15.7.4 (24G517)","roots_installed":0,"incident_id":"5ECFDC7F-D044-4C6D-AF21-9F4C48A795E7","name":"ChimeraX"}
{
"uptime" : 550000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac16,1",
"coalitionID" : 270057,
"osVersion" : {
"train" : "macOS 15.7.4",
"build" : "24G517",
"releaseType" : "User"
},
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"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
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"arch" : "arm64e",
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"size" : 636284,
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Writable regions: Total=2.9G written=15.5M(1%) resident=1394K(0%) swapped_out=14.2M(0%) unallocated=2.8G(99%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 256K 2
Activity Tracing 256K 1
CG image 160K 8
ColorSync 608K 32
CoreAnimation 912K 57
CoreGraphics 48K 3
CoreUI image data 3024K 20
Foundation 32K 2
Kernel Alloc Once 1424K 4
MALLOC 2.1G 107
MALLOC guard page 288K 18
Mach message 64K 4
OpenGL GLSL 256K 3
STACK GUARD 56.8M 51
Stack 415.7M 51
VM_ALLOCATE 199.5M 106
VM_ALLOCATE (reserved) 192.0M 4 reserved VM address space (unallocated)
__DATA 11K 1
__DATA_CONST 30K 1
__DATA_DIRTY 7K 1
__LINKEDIT 616.8M 1
__TEXT 624K 1
__TPRO_CONST 128K 1
dyld private memory 3632K 31
mapped file 604.1M 589
page table in kernel 1394K 1
shared memory 5120K 41
=========== ======= =======
TOTAL 4.1G 1141
TOTAL, minus reserved VM space 3.9G 1141
",
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"name" : "CrBrowserMain"
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},
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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 "/Users/sarah.stadlmayr/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Desktop/PostDoc/Erwin Schrödinger/Functionalized
> Silk/Material Characterization/AlphaFold Prediction/His-TEV-
> YIGSR-A3IA/fold_2026_03_12_15_28_model_0.cif"
Chain information for fold_2026_03_12_15_28_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
> open "/Users/sarah.stadlmayr/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Desktop/PostDoc/Erwin Schrödinger/Functionalized
> Silk/Material Characterization/AlphaFold
> Prediction/YIGSR-A3IA/fold_2026_03_12_15_27_model_0.cif"
Chain information for fold_2026_03_12_15_27_model_0.cif #2
---
Chain | Description
A | .
Computing secondary structure
> select add #1
2523 atoms, 2560 bonds, 370 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
2523 atoms, 2560 bonds, 370 residues, 1 model selected
> select add #2
4892 atoms, 4957 bonds, 722 residues, 2 models selected
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_2026_03_12_15_27_model_0.cif, chain A (#2) with
fold_2026_03_12_15_28_model_0.cif, chain A (#1), sequence alignment score =
1690.7
RMSD between 79 pruned atom pairs is 0.675 angstroms; (across all 352 pairs:
27.585)
> select subtract #1
2369 atoms, 2397 bonds, 352 residues, 1 model selected
> select subtract #2
Nothing selected
> hide #1 models
> hide #2 models
> show #2 models
> show #1 models
===== 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 - 89.4
OpenGL renderer: Apple M4
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: Mac16,1
Model Number: MW2V3KS/A
Chip: Apple M4
Total Number of Cores: 10 (4 performance and 6 efficiency)
Memory: 16 GB
System Firmware Version: 13822.81.10
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.7.4 (24G517)
Kernel Version: Darwin 24.6.0
Time since boot: 22 days, 1 hour, 31 minutes
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
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: No
Connection Type: Internal
PHL 288P6L:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 30.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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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