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Opened 8 months ago
Closed 8 months ago
#16940 closed defect (can't reproduce)
Crash in event loop
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000000028c3f7000 (most recent call first):
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000028805b000 (most recent call first):
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000028704f000 (most recent call first):
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000286043000 (most recent call first):
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.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/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000285037000 (most recent call first):
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000028402b000 (most recent call first):
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000028301f000 (most recent call first):
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000282013000 (most recent call first):
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000281007000 (most recent call first):
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000017f427000 (most recent call first):
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000017e41b000 (most recent call first):
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000017d40f000 (most recent call first):
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x0000000100268580 (most recent call first):
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, 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, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.mlp._mlp, chimerax.coulombic._esp (total: 56)
{"app_name":"ChimeraX","timestamp":"2025-02-22 19:09:36.00 -0800","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.5 (21G72)","incident_id":"952BB2E4-8144-4156-8982-CF22BEBCF3A7","name":"ChimeraX"}
{
"uptime" : 310000,
"procLaunch" : "2025-02-22 14:53:18.4401 -0800",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"procStartAbsTime" : 7403610474927,
"coalitionID" : 40750,
"osVersion" : {
"train" : "macOS 12.5",
"build" : "21G72",
"releaseType" : "User"
},
"captureTime" : "2025-02-22 19:09:23.9552 -0800",
"incident" : "952BB2E4-8144-4156-8982-CF22BEBCF3A7",
"bug_type" : "309",
"pid" : 88511,
"procExitAbsTime" : 7647888880687,
"translated" : false,
"cpuType" : "ARM-64",
"procName" : "ChimeraX",
"procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"A2FD9D35-5E78-52CB-B508-06B5447935BE","thirdParty":true},
"parentProc" : "launchd",
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.4G resident=0K(0%) swapped_out_or_unallocated=1.4G(100%)\nWritable regions: Total=5.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=5.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 640K 5 \nActivity Tracing 256K 1 \nCG backing stores 3328K 4 \nCG image 7888K 88 \nCG raster data 288K 6 \nColorSync 640K 28 \nCoreAnimation 17.6M 114 \nCoreGraphics 32K 2 \nCoreUI image data 5408K 37 \nFoundation 16K 1 \nKernel Alloc Once 1424K 4 \nMALLOC 3.3G 169 \nMALLOC guard page 192K 11 \nMALLOC_MEDIUM (reserved) 928.0M 9 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.8M 52 \nStack 393.2M 52 \nVM_ALLOCATE 234.9M 219 \nVM_ALLOCATE (reserved) 128.0M 1 reserved VM address space (unallocated)\n__AUTH 3382K 406 \n__AUTH_CONST 24.0M 623 \n__CTF 756 1 \n__DATA 26.9M 774 \n__DATA_CONST 33.1M 780 \n__DATA_DIRTY 2187K 267 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 607.3M 161 \n__OBJC_CONST 5144K 371 \n__OBJC_RO 83.0M 1 \n__OBJC_RW 3168K 1 \n__TEXT 847.5M 798 \n__UNICODE 592K 1 \ndyld private memory 1072K 3 \nmapped file 204.6M 57 \nshared memory 3344K 29 \n=========== ======= ======= \nTOTAL 7.0G 5085 \nTOTAL, minus reserved VM space 5.8G 5085 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "6112e14f37f5d11121dcd519",
"factorPackIds" : {
"SIRI_TEXT_TO_SPEECH" : "634710168e8be655c1316aaa"
},
"deploymentId" : 240000229
},
{
"rolloutId" : "6297d96be2c9387df974efa4",
"factorPackIds" : {
},
"deploymentId" : 240000032
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
Startup Messages
---
warning | QCoreApplication::postEvent: Unexpected null receiver
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: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> help help:quickstart
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
> open /Users/nurnisajanybek/Desktop/2hyy.cif
Summary of feedback from opening /Users/nurnisajanybek/Desktop/2hyy.cif
---
note | Fetching CCD STI from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/I/STI/STI.cif
2hyy.cif title:
Human Abl kinase domain in complex with imatinib (STI571, Glivec) [more
info...]
Chain information for 2hyy.cif #1
---
Chain | Description | UniProt
A B C D | Proto-oncogene tyrosine-protein kinase ABL1 | ABL1_HUMAN 228-500
Non-standard residues in 2hyy.cif #1
---
STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-
pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571; imatinib)
2hyy.cif mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
> select ::name="HOH"
200 atoms, 200 residues, 1 model selected
> hide sel atoms
> select clear
> open /Users/nurnisajanybek/Desktop/1lpa.pdb
1lpa.pdb title:
Interfacial activation of the lipase-procolipase complex by mixed micelles
revealed by X-ray crystallography [more info...]
Chain information for 1lpa.pdb #2
---
Chain | Description | UniProt
A | colipase | COL_PIG 1-95
B | lipase | LIPP_HUMAN 1-449
Non-standard residues in 1lpa.pdb #2
---
BNG — nonyl β-D-glucopyranoside (β-nonylglucoside; nonyl β-D-glucoside; nonyl
D-glucoside; nonyl glucoside)
CA — calcium ion
PLC — diundecyl phosphatidyl choline
> select add #1
8702 atoms, 8736 bonds, 5 pseudobonds, 1258 residues, 3 models selected
> close
> open /Users/nurnisajanybek/Desktop/1lpa.pdb format pdb
1lpa.pdb title:
Interfacial activation of the lipase-procolipase complex by mixed micelles
revealed by X-ray crystallography [more info...]
Chain information for 1lpa.pdb #1
---
Chain | Description | UniProt
A | colipase | COL_PIG 1-95
B | lipase | LIPP_HUMAN 1-449
Non-standard residues in 1lpa.pdb #1
---
BNG — nonyl β-D-glucopyranoside (β-nonylglucoside; nonyl β-D-glucoside; nonyl
D-glucoside; nonyl glucoside)
CA — calcium ion
PLC — diundecyl phosphatidyl choline
> select nucleic-acid
Nothing selected
> show atoms
> hide atoms
> select nucleic-acid
Nothing selected
> set bgColor white
> lighting simple
> lighting soft
> lighting simple
> lighting full
> set bgColor black
> select /B
3554 atoms, 3648 bonds, 5 pseudobonds, 452 residues, 2 models selected
> color (#!1 & sel) purple
> color (#!1 & sel) hot pink
> ui tool show H-Bonds
> hbonds sel color #2ca3fa twoColors true reveal true
434 hydrogen bonds found
222 strict hydrogen bonds found
> save /Users/nurnisajanybek/Desktop/image1.png supersample 3
> select clear
> save /Users/nurnisajanybek/Desktop/image2.png supersample 3
> mlp
Map values for surface "1lpa.pdb_A SES surface": minimum -24.79, mean -3.881,
maximum 21.98
Map values for surface "1lpa.pdb_B SES surface": minimum -30.59, mean -5.371,
maximum 23.16
To also show corresponding color key, enter the above mlp command and add key
true
> save /Users/nurnisajanybek/Desktop/image3.png supersample 3
> hbonds reveal true
498 hydrogen bonds found
> mlp
Map values for surface "1lpa.pdb_A SES surface": minimum -24.79, mean -3.881,
maximum 21.98
Map values for surface "1lpa.pdb_B SES surface": minimum -30.59, mean -5.371,
maximum 23.16
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 1lpa.pdb_A SES surface #1.3: minimum, -14.79, mean -1.46,
maximum 9.59
Coulombic values for 1lpa.pdb_B SES surface #1.4: minimum, -18.17, mean -1.81,
maximum 15.04
To also show corresponding color key, enter the above coulombic command and
add key true
> save /Users/nurnisajanybek/Desktop/image4.png supersample 3
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 7459.141.1
OS Loader Version: 7459.141.1
Software:
System Software Overview:
System Version: macOS 12.5 (21G72)
Kernel Version: Darwin 21.6.0
Time since boot: 27 days 5:11
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
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
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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 1.18.1
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
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: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 8 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop |
comment:2 by , 8 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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