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Opened 20 months ago
Closed 20 months ago
#14637 closed defect (can't reproduce)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | 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-12.4-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000070000582c000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001fb1b000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001eb18000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001db15000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001cb12000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001bb0f000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001ab0c000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700019b09000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700018b06000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700017b03000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700016b00000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700015afd000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700014afa000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700013af7000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700012af4000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700011af1000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700010aee000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070000faeb000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070000eae8000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070000dae5000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x000000010c9b8600 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 157 in asArray
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 146 in
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 145 in asArray
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 146 in
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 145 in asArray
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2828 in set_matrix
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 817 in set_projection_matrix
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 725 in _use_shader
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 801 in _opengl_shader
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 698 in shader
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 818 in _draw_geometry
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 787 in draw_self
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 780 in draw
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1567 in _draw_multiple
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1554 in draw_opaque
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 258 in _draw_scene
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio (total: 53)
{"app_name":"ChimeraX","timestamp":"2024-02-26 16:35:19.00 +0100","app_version":"1.7.1","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.7.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.4 (21F79)","incident_id":"B05F31FE-61AB-4DE4-A163-330E3F6125BC","name":"ChimeraX"}
{
"uptime" : 17000,
"procLaunch" : "2024-02-26 15:17:07.2171 +0100",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"procStartAbsTime" : 13049639584287,
"coalitionID" : 3144,
"osVersion" : {
"train" : "macOS 12.4",
"build" : "21F79",
"releaseType" : "User"
},
"captureTime" : "2024-02-26 16:35:14.1935 +0100",
"incident" : "B05F31FE-61AB-4DE4-A163-330E3F6125BC",
"bug_type" : "309",
"pid" : 5216,
"procExitAbsTime" : 17736525277596,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"E3B9F6FA-07B7-50C5-901E-8C238F0DB314","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "76DEA63D-78F4-1FF2-694D-692C59832C7F",
"wakeTime" : 4817,
"bridgeVersion" : {"build":"19P5071","train":"6.5"},
"sleepWakeUUID" : "5D57BAFA-6471-4CB3-A8D0-4CEED84D3222",
"sip" : "enabled",
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"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
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"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWidgets.framework\/Versions\/A\/QtWidgets",
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"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so",
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"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
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"base" : 140703530450944,
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"uuid" : "f8e45ef9-9fd2-3331-bb1b-703d5dacdaf1",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1863"
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"arch" : "x86_64",
"base" : 140703678263296,
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"CFBundleIdentifier" : "com.apple.HIToolbox",
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"uuid" : "04544f53-a387-3ac3-a85d-f8adfc0bc69e",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
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"size" : 15265792,
"uuid" : "832ad371-d3b8-3061-b4e2-1c4e0cffce0b",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
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"path" : "\/usr\/lib\/dyld",
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=5.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=5.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 2688K 4 \nCG image 400K 29 \nColorSync 236K 28 \nCoreAnimation 160K 14 \nCoreGraphics 12K 2 \nCoreUI image data 3484K 26 \nFoundation 64K 2 \nKernel Alloc Once 8K 1 \nMALLOC 3.1G 304 \nMALLOC guard page 48K 10 \nMALLOC_MEDIUM (reserved) 1.5G 14 reserved VM address space (unallocated)\nMach message 16K 2 \nObjC additional data 15K 1 \nOpenGL GLSL 384K 4 \nSTACK GUARD 192K 48 \nStack 477.4M 49 \nStack Guard 56.0M 1 \nVM_ALLOCATE 235.1M 247 \nVM_ALLOCATE (reserved) 128.0M 2 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 59.4M 682 \n__DATA_CONST 32.7M 343 \n__DATA_DIRTY 1641K 212 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 680.2M 155 \n__TEXT 832.0M 683 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 185.8M 48 \nshared memory 2984K 26 \n=========== ======= ======= \nTOTAL 7.2G 2948 \nTOTAL, minus reserved VM space 5.6G 2948 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
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},
"trialInfo" : {
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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: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> help help:quickstart
> open 4DIC fromDatabase pdbe_bio format mmcif
No biogical assemblies available for 4DIC
> open 4DIC format mmcif fromDatabase pdbe_bio
No biogical assemblies available for 4DIC
> open 4DIC format mmcif fromDatabase pdbe_bio
No biogical assemblies available for 4DIC
> open 4DJC
Summary of feedback from opening 4DJC fetched from pdb
---
notes | Fetching compressed mmCIF 4djc from
http://files.rcsb.org/download/4djc.cif
Fetching CCD CA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif
Fetching CCD IPA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/IPA/IPA.cif
4djc title:
1.35 A crystal structure of the NaV1.5 DIII-IV-Ca/CaM complex [more info...]
Chain information for 4djc #1
---
Chain | Description | UniProt
A | Calmodulin | CALM_HUMAN 1-149
B | Sodium channel protein type 5 subunit alpha | SCN5A_HUMAN 1491-1522
Non-standard residues in 4djc #1
---
CA — calcium ion
IPA — isopropyl alcohol (2-propanol)
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting full
> lighting soft
> lighting simple
> hide atoms
> select Ca
4 atoms, 4 residues, 1 model selected
> show sel atoms
> select clear
> select /A:55
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
103 atoms, 102 bonds, 13 residues, 1 model selected
> select up
1145 atoms, 1157 bonds, 151 residues, 1 model selected
> select up
1339 atoms, 1184 bonds, 318 residues, 1 model selected
> select up
1457 atoms, 1296 bonds, 338 residues, 1 model selected
> select up
1457 atoms, 1296 bonds, 338 residues, 1 model selected
> select down
1339 atoms, 1184 bonds, 318 residues, 1 model selected
> select down
1145 atoms, 1157 bonds, 151 residues, 1 model selected
> select up
1339 atoms, 1184 bonds, 318 residues, 1 model selected
> select up
1457 atoms, 1296 bonds, 338 residues, 1 model selected
> select #1/A
1339 atoms, 1184 bonds, 28 pseudobonds, 318 residues, 2 models selected
> surface sel
> surface #1/A
> color (#!1 & sel) light sea green
> select clear
> hide surfaces
> show surfaces
> undo
> hide sel surfaces
> select /B:1496@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
103 atoms, 104 bonds, 12 residues, 2 models selected
> select up
111 atoms, 112 bonds, 13 residues, 2 models selected
> hide sel surfaces
> surface Ca
> select clear
> select Ca
4 atoms, 4 residues, 1 model selected
> color sel byhetero atoms
> select clear
> hide cartoons
> show atoms
> select #1/A
1339 atoms, 1184 bonds, 28 pseudobonds, 318 residues, 2 models selected
> color sel byhetero atoms
> select clear
> select ::name="CA"
4 atoms, 4 residues, 1 model selected
> select ::name="HOH"
161 atoms, 161 residues, 1 model selected
> select water
Expected an objects specifier or a keyword
> select clear
> select water
Expected an objects specifier or a keyword
> select HOH
Expected an objects specifier or a keyword
> select ::name="HOH"
161 atoms, 161 residues, 1 model selected
> hide sel atoms
> show sel surfaces
> undo
> hide sel surfaces
> select clear
> surface #1/A
> save /Users/pitt/Desktop/image1.png supersample 3
> lighting soft
> lighting simple
> lighting soft
> hide surfaces
> select zone #1/B 3
Selected 12 atoms
> select zone #1/B 3 residues true
Selected 59 atoms
> color sel red
> select zone #1/B 5 residues true
Selected 196 atoms
> color sel red
> select #1/A
1339 atoms, 1184 bonds, 28 pseudobonds, 318 residues, 2 models selected
> show sel cartoons
> color #1/A green
> color byhetero
> select zone #1/B 3 residues true
Selected 59 atoms
> color sel red
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> close
> open 7A5K
Summary of feedback from opening 7A5K fetched from pdb
---
notes | Fetching compressed mmCIF 7a5k from
http://files.rcsb.org/download/7a5k.cif
Fetching CCD GCP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GCP/GCP.cif
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
Fetching CCD SPD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/SPD/SPD.cif
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif
Fetching CCD GDP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GDP/GDP.cif
7a5k title:
Structure of the human mitoribosome in the post translocation state bound to
mtEF-G1 [more info...]
Chain information for 7a5k #1
---
Chain | Description | UniProt
03 | 39S ribosomal protein L32, mitochondrial | RM32_HUMAN 1-188
13 | 39S ribosomal protein L33, mitochondrial | RM33_HUMAN 1-65
23 | 39S ribosomal protein L34, mitochondrial | RM34_HUMAN 1-92
24 FE | mt-tRNA |
33 | 39S ribosomal protein L35, mitochondrial | RM35_HUMAN 1-188
43 | 39S ribosomal protein L36, mitochondrial | RM36_HUMAN 1-103
53 | 39S ribosomal protein L37, mitochondrial | RM37_HUMAN 1-423
63 | 39S ribosomal protein L38, mitochondrial | RM38_HUMAN 1-380
73 | 39S ribosomal protein L39, mitochondrial | RM39_HUMAN 1-338
8 A3 | 16S rRNA |
93 | 39S ribosomal protein L41, mitochondrial | RM41_HUMAN 1-137
A | 39S ribosomal protein L40, mitochondrial | RM40_HUMAN 1-206
A5 | Mitochondrial inner membrane protein OXA1L | OXA1L_HUMAN 1-435
A6 | 12S rRNA |
B | Unknown protein |
B3 | mt-tRNAVal |
B6 | 28S ribosomal protein S2, mitochondrial | RT02_HUMAN 1-296
C6 | 28S ribosomal protein S24, mitochondrial | RT24_HUMAN 1-167
D H3 | 39S ribosomal protein L9, mitochondrial | RM09_HUMAN 1-267
D3 | 39S ribosomal protein L2, mitochondrial | RM02_HUMAN 1-305
D6 | 28S ribosomal protein S5, mitochondrial | RT05_HUMAN 1-430
E3 | 39S ribosomal protein L3, mitochondrial | RM03_HUMAN 1-348
E6 | 28S ribosomal protein S6, mitochondrial | RT06_HUMAN 1-125
F3 | 39S ribosomal protein L4, mitochondrial | RM04_HUMAN 1-311
F6 | 28S ribosomal protein S7, mitochondrial | RT07_HUMAN 1-242
G6 | 28S ribosomal protein S9, mitochondrial | RT09_HUMAN 1-396
H6 | 28S ribosomal protein S10, mitochondrial | RT10_HUMAN 1-201
I3 | 39S ribosomal protein L10, mitochondrial | RM10_HUMAN 1-261
I6 | 28S ribosomal protein S11, mitochondrial | RT11_HUMAN 1-194
J3 | 39S ribosomal protein L11, mitochondrial | RM11_HUMAN 1-192
J6 | 28S ribosomal protein S12, mitochondrial | RT12_HUMAN 1-138
K3 | 39S ribosomal protein L13, mitochondrial | RM13_HUMAN 1-178
K6 | 28S ribosomal protein S14, mitochondrial | RT14_HUMAN 1-128
L3 | 39S ribosomal protein L14, mitochondrial | RM14_HUMAN 1-145
L6 | 28S ribosomal protein S15, mitochondrial | RT15_HUMAN 1-257
M3 | 39S ribosomal protein L15, mitochondrial | RM15_HUMAN 1-296
M6 | 28S ribosomal protein S16, mitochondrial | RT16_HUMAN 1-137
N3 | 39S ribosomal protein L16, mitochondrial | RM16_HUMAN 1-251
N6 | 28S ribosomal protein S17, mitochondrial | RT17_HUMAN 1-130
O3 | 39S ribosomal protein L17, mitochondrial | RM17_HUMAN 1-175
O6 | 28S ribosomal protein S18b, mitochondrial | RT18B_HUMAN 1-258
P3 | Mitochondrial ribosomal protein L18, isoform CRA_b | A8K9D2_HUMAN 1-179
P6 | 28S ribosomal protein S18c, mitochondrial | RT18C_HUMAN 1-142
Q3 | 39S ribosomal protein L19, mitochondrial | RM19_HUMAN 1-292
Q6 | 28S ribosomal protein S21, mitochondrial | RT21_HUMAN 1-87
R3 | 39S ribosomal protein L20, mitochondrial | RM20_HUMAN 1-149
R6 | 28S ribosomal protein S22, mitochondrial | RT22_HUMAN 1-360
S3 | 39S ribosomal protein L21, mitochondrial | RM21_HUMAN 1-205
S6 | 28S ribosomal protein S23, mitochondrial | RT23_HUMAN 1-190
T3 | 39S ribosomal protein L22, mitochondrial | E7ESL0_HUMAN 1-212
T6 | 28S ribosomal protein S25, mitochondrial | RT25_HUMAN 1-173
U3 | 39S ribosomal protein L23, mitochondrial | RM23_HUMAN 1-153
U6 | 28S ribosomal protein S26, mitochondrial | RT26_HUMAN 1-205
V3 | 39S ribosomal protein L24, mitochondrial | RM24_HUMAN 1-216
V6 | 28S ribosomal protein S27, mitochondrial | RT27_HUMAN 1-414
W3 | 39S ribosomal protein L27, mitochondrial | RM27_HUMAN 1-148
W6 | 28S ribosomal protein S28, mitochondrial | RT28_HUMAN 1-187
X3 | 39S ribosomal protein L28, mitochondrial | RM28_HUMAN 1-256
X6 | 28S ribosomal protein S29, mitochondrial | RT29_HUMAN 1-398
Y2 | nascent chain |
Y3 | 39S ribosomal protein L47, mitochondrial | RM47_HUMAN 1-250
Y6 | 28S ribosomal protein S31, mitochondrial | RT31_HUMAN 1-395
Z3 | 39S ribosomal protein L30, mitochondrial | RM30_HUMAN 1-161
Z6 | 28S ribosomal protein S33, mitochondrial | RT33_HUMAN 1-106
a3 | 39S ribosomal protein L42, mitochondrial | RM42_HUMAN 1-142
a6 | 28S ribosomal protein S34, mitochondrial | RT34_HUMAN 1-218
b3 | 39S ribosomal protein L43, mitochondrial | RM43_HUMAN 1-155
b6 | 28S ribosomal protein S35, mitochondrial | RT35_HUMAN 1-323
c3 | 39S ribosomal protein L44, mitochondrial | RM44_HUMAN 1-332
c6 | Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 |
CHCH1_HUMAN 1-118
d3 | 39S ribosomal protein L45, mitochondrial | RM45_HUMAN 1-306
d6 | Aurora kinase A-interacting protein | AKIP_HUMAN 1-199
e3 | 39S ribosomal protein L46, mitochondrial | RM46_HUMAN 1-279
e6 | Pentatricopeptide repeat domain-containing protein 3, mitochondrial |
PTCD3_HUMAN 1-689
f3 | 39S ribosomal protein L48, mitochondrial | RM48_HUMAN 1-194
g3 | 39S ribosomal protein L49, mitochondrial | RM49_HUMAN 1-166
h3 | 39S ribosomal protein L50, mitochondrial | RM50_HUMAN 1-158
i3 | 39S ribosomal protein L51, mitochondrial | RM51_HUMAN 1-128
j3 | cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal
protein L52 (MRPL52), transcript variant 1, mRNA | A8K7J6_HUMAN 1-123
k3 | 39S ribosomal protein L53, mitochondrial | RM53_HUMAN 1-112
l3 | 39S ribosomal protein L54, mitochondrial | RM54_HUMAN 1-138
m3 | 39S ribosomal protein L55, mitochondrial | RM55_HUMAN 1-128
n | 39S ribosomal protein L1, mitochondrial | RM01_HUMAN 23-308
o3 | Ribosomal protein 63, mitochondrial | RT63_HUMAN 1-102
p3 | Peptidyl-tRNA hydrolase ICT1, mitochondrial | ICT1_HUMAN 1-206
q3 | Growth arrest and DNA damage-inducible proteins-interacting protein 1 |
G45IP_HUMAN 1-222
r1 | Elongation factor G, mitochondrial | EFGM_HUMAN 1-751
r3 | 39S ribosomal protein S18a, mitochondrial | RT18A_HUMAN 1-196
s3 | 39S ribosomal protein S30, mitochondrial | RT30_HUMAN 1-439
u3 | RNA |
Non-standard residues in 7a5k #1
---
GCP — phosphomethylphosphonic acid guanylate ester
GDP — guanosine-5'-diphosphate
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
ZN — zinc ion
> open EMBD:11646
No such database 'embd'
> open EMDB:11646
Summary of feedback from opening 11646 fetched from emdb
---
notes | Fetching compressed map 11646 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-11646/map/emd_11646.map.gz
Fetching map header 11646 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-11646/header/emd-11646.xml
Opened emdb 11646 as #2, grid size 512,512,512, pixel 1.04, shown at level
0.05, step 2, values float32, fit PDB 7a5k
> volume hide
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-4.8.54
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 64 GB
System Firmware Version: 1731.120.10.0.0 (iBridge: 19.16.15071.0.0,0)
OS Loader Version: 540.120.3~6
Software:
System Software Overview:
System Version: macOS 12.4 (21F79)
Kernel Version: Darwin 21.5.0
Time since boot: 6:40
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
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
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 20 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 20 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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