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Opened 18 months ago
Last modified 18 months ago
#15093 assigned defect
Copick: crash in QCoPickTableModel
| Reported by: | Owned by: | Utz Ermel | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.4.1-arm64-arm-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: Bus error
Thread 0x00000003dc7e7000 (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 0x000000037718f000 (most recent call first):
File "/Users/yue.yu/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/smbprotocol/transport.py", line 137 in _recv
File "/Users/yue.yu/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/smbprotocol/transport.py", line 115 in recv
File "/Users/yue.yu/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/smbprotocol/connection.py", line 1309 in _process_message_thread
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 0x000000034408b000 (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 0x000000034307f000 (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 0x0000000342073000 (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 0x0000000341067000 (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 0x000000034005b000 (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 0x000000033f04f000 (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 0x000000033e043000 (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 0x000000033d037000 (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 0x000000033c02b000 (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 0x000000033b01f000 (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 0x000000033a013000 (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 0x0000000339007000 (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 0x000000032f18b000 (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 0x000000032e17f000 (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 0x000000032d173000 (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 0x00000001fa8e7ac0 (most recent call first):
File "/Users/yue.yu/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/copick/ui/QCoPickTableModel.py", line 58 in parent
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.surface._surface, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, pyarrow.lib, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pyarrow._compute, pandas._libs.ops, numexpr.interpreter, pandas._libs.hashing, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.internals, pandas._libs.indexing, pandas._libs.index, pandas._libs.writers, pandas._libs.join, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, lz4._version, lz4.frame._frame, numcodecs.compat_ext, numcodecs.blosc, numcodecs.zstd, numcodecs.lz4, numcodecs._shuffle, msgpack._cmsgpack, numcodecs.jenkins, numcodecs.vlen, numcodecs.fletcher32, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.linalg._flinalg, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy.optimize._trlib._trlib, numpy.linalg.lapack_lite, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize.__nnls, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.optimize._direct, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, scipy.ndimage._nd_image, _ni_label, scipy.ndimage._ni_label, _cffi_backend, chimerax.atomic._ribbons, chimerax.graphics._graphics (total: 169)
{"app_name":"ChimeraX","timestamp":"2024-05-02 11:11:34.00 -0700","app_version":"1.7.1","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","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 14.4.1 (23E224)","roots_installed":0,"name":"ChimeraX","incident_id":"EF33B987-BC07-4E65-84AD-2B74EF2F367D"}
{
"uptime" : 420000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,5",
"coalitionID" : 11524,
"osVersion" : {
"train" : "macOS 14.4.1",
"build" : "23E224",
"releaseType" : "User"
},
"captureTime" : "2024-05-02 11:11:33.5994 -0700",
"codeSigningMonitor" : 1,
"incident" : "EF33B987-BC07-4E65-84AD-2B74EF2F367D",
"pid" : 81528,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-05-02 10:13:11.4835 -0700",
"procStartAbsTime" : 10100106063417,
"procExitAbsTime" : 10184156183249,
"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":"06057A0A-C3A2-59B4-87A8-2FB033BF809D","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "E53845EB-2A8A-EF96-C294-D5FCD194E7D4",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 5023,
"sleepWakeUUID" : "75DBCE58-E400-416F-AA2E-F2445A420487",
"sip" : "enabled",
"vmRegionInfo" : "0x374cf1210 is in 0x374c00000-0x374d00000; bytes after start: 987664 bytes before end: 60911\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n VM_ALLOCATE 374b00000-374c00000 [ 1024K] rw-\/rwx SM=PRV \n---> VM_ALLOCATE 374c00000-374d00000 [ 1024K] rw-\/rwx SM=PRV \n GAP OF 0x64000 BYTES\n __TEXT 374d64000-374ed4000 [ 1472K] r-x\/rwx SM=COW \/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
"exception" : {"codes":"0x0000000000000002, 0x0000000374cf1210","rawCodes":[2,14844629520],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000000374cf1210"},
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Address size fault"},"pc":{"value":6756620780},"far":{"value":0}}}],
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[deleted to fit within ticket limits]
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===== Log before crash start =====
Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle
Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with
that from OME-Zarr bundle
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
> copick start /Users/yue.yu/Downloads/copick_config_yue_yu.json
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
> ui mousemode shift wheel 'move copick planes'
> ks
Opened TS_2_1 - 10.0 as #3, grid size 630,630,184, pixel 10,10,10, shown at
step 4, values float32
Opened TS_2_1 - 10.0 as #1.1.1, grid size 630,630,184, pixel 10,10,10, shown
at level 7.17e-06, step 4, values float32
> artiax clip off
> artiax tomo #1.1.1 sliceDirection 0,0,1
> artiax view xy
Opened TS_2_1 - 10.0 as #3, grid size 630,630,184, pixel 10,10,10, shown at
step 4, values float32
Opened TS_2_1 - 10.0 as #1.1.1, grid size 630,630,184, pixel 10,10,10, shown
at level 7.17e-06, step 4, values float32
> artiax clip off
> artiax tomo #1.1.1 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.1 step 1
> artiax clip off
Opened membrane-bound-protein as #1.2.1.1.1, grid size 32,32,32, pixel 1,
shown at level 0.0002, step 1, values float32
> volume #1.2.1.1.1 capFaces false
> artiax tomo #1.1.1 slice 135
> artiax clip off
Opened ribosome as #1.2.2.1.1, grid size 61,63,61, pixel 6.67,6.67,6.67, shown
at level 0.332, step 1, values float32
> volume #1.2.2.1.1 capFaces false
Locked all of models: ribosome #1.2.2
[, ]
> artiax clip off
Opened ribosome as #1.2.3.1.1, grid size 61,63,61, pixel 6.67,6.67,6.67, shown
at level 0.332, step 1, values float32
> volume #1.2.3.1.1 capFaces false
Traceback (most recent call last):
File "/Users/yue.yu/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent
parentItem = childItem.parent
^^^^^^^^^^^^^^^^
AttributeError: 'CopickParticleData' object has no attribute 'parent'
AttributeError: 'CopickParticleData' object has no attribute 'parent'
File "/Users/yue.yu/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent
parentItem = childItem.parent
^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "/Users/yue.yu/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent
parentItem = childItem.parent
^^^^^^^^^^^^^^^^
AttributeError: 'CopickParticleData' object has no attribute 'parent'
AttributeError: 'CopickParticleData' object has no attribute 'parent'
File "/Users/yue.yu/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent
parentItem = childItem.parent
^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "/Users/yue.yu/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent
parentItem = childItem.parent
^^^^^^^^^^^^^^^^
AttributeError: 'CopickParticleData' object has no attribute 'parent'
AttributeError: 'CopickParticleData' object has no attribute 'parent'
File "/Users/yue.yu/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent
parentItem = childItem.parent
^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> artiax clip toggle
Clipping thickness set to 300 A around slabs of #1.1.1.
> artiax view xy
# Keyboard Shortcuts
---
| Particles
---
\--| Remove Particle
aa| Previous Particle
dd| Next Particle
ss| Select particles mode
ww| Hide/Show ArtiaX particle lists
Picking
---
ap| Add on plane mode
dp| Delete picked mode
ds| Delete selected particles
Visualization
---
cc| Turn Clipping On/Off
ee| Switch to orthoplanes.
ff| Move planes mouse mode.
qq| Switch to single plane.
xx| View XY orientation.
yy| View YZ orientation.
zz| View XZ orientation.
Info
---
?| Show Shortcuts in Log
il| Toggle Info Label
> view matrix camera 1,0,0,5166.064,0,1,0,2999.752,0,0,1,15681.992
> view matrix camera 1,0,0,5239.668,0,1,0,3052.072,0,0,1,15426.715
> view matrix camera 1,0,0,5166.064,0,1,0,2999.752,0,0,1,15681.992
> view matrix camera 1,0,0,3389.669,0,1,0,3879.751,0,0,1,15558.389
> ui mousemode right select
> view matrix camera 1,0,0,5166.064,0,1,0,2999.752,0,0,1,15681.992
> view matrix camera 1,0,0,5239.668,0,1,0,3052.072,0,0,1,15426.715
> view matrix camera 1,0,0,5166.064,0,1,0,2999.752,0,0,1,15681.992
> view matrix camera 1,0,0,3389.669,0,1,0,3879.751,0,0,1,15558.389
> view matrix camera 1,0,0,5166.064,0,1,0,2999.752,0,0,1,15681.992
> view matrix camera 1,0,0,3389.669,0,1,0,3879.751,0,0,1,15558.389
clip back plane is in front of front plane
> view matrix camera 1,0,0,2897.268,0,1,0,6040.703,0,0,1,15948.471
> view matrix camera 1,0,0,3389.669,0,1,0,3879.751,0,0,1,15558.389
> view matrix camera 1,0,0,2897.268,0,1,0,6040.703,0,0,1,15948.471
> view matrix camera 1,0,0,3558.55,0,1,0,2776.066,0,0,1,15842.712
> ui mousemode right select
> view matrix camera 1,0,0,2897.268,0,1,0,6040.703,0,0,1,15948.471
> view matrix camera 1,0,0,3558.55,0,1,0,2776.066,0,0,1,15842.712
clip back plane is in front of front plane
> view matrix camera 1,0,0,3758.385,0,1,0,2706.067,0,0,1,16561.991
> view matrix camera 1,0,0,4936.064,0,1,0,2289.671,0,0,1,15566.069
clip back plane is in front of front plane
> view matrix camera 1,0,0,3761.989,0,1,0,3026.066,0,0,1,16584.394
> view matrix camera 1,0,0,3069.752,0,1,0,2850.706,0,0,1,15711.511
clip back plane is in front of front plane
> view matrix camera 1,0,0,1933.83,0,1,0,5898.383,0,0,1,16094.394
> view matrix camera 1,0,0,2579.753,0,1,0,2210.789,0,0,1,15776.714
> view matrix camera 1,0,0,3069.752,0,1,0,2850.706,0,0,1,15711.511
> view matrix camera 1,0,0,2579.753,0,1,0,2210.789,0,0,1,15776.714
> view matrix camera 1,0,0,3069.752,0,1,0,2850.706,0,0,1,15711.511
clip back plane is in front of front plane
> view matrix camera 1,0,0,3761.989,0,1,0,3026.066,0,0,1,16584.394
> view matrix camera 1,0,0,4936.064,0,1,0,2289.671,0,0,1,15566.069
> view matrix camera 1,0,0,3558.55,0,1,0,2776.066,0,0,1,15842.712
> view matrix camera 1,0,0,3389.669,0,1,0,3879.751,0,0,1,15558.389
clip back plane is in front of front plane
> view matrix camera 1,0,0,3558.55,0,1,0,2776.066,0,0,1,15842.712
> view matrix camera 1,0,0,4936.064,0,1,0,2289.671,0,0,1,15566.069
clip back plane is in front of front plane
> view matrix camera 1,0,0,3761.989,0,1,0,3026.066,0,0,1,16584.394
> view matrix camera 1,0,0,3069.752,0,1,0,2850.706,0,0,1,15711.511
> view matrix camera 1,0,0,2579.753,0,1,0,2210.789,0,0,1,15776.714
> view matrix camera 1,0,0,3919.751,0,1,0,5888.383,0,0,1,16028.471
> view matrix camera 1,0,0,5293.744,0,1,0,4626.546,0,0,1,15470.791
clip back plane is in front of front plane
> view matrix camera 1,0,0,3167.267,0,1,0,1246.068,0,0,1,16569.671
> view matrix camera 1,0,0,5293.744,0,1,0,4626.546,0,0,1,15470.791
clip back plane is in front of front plane
> view matrix camera 1,0,0,3167.267,0,1,0,1246.068,0,0,1,16569.671
> view matrix camera 1,0,0,4002.071,0,1,0,2597.268,0,0,1,16573.11
> view matrix camera 1,0,0,5262.07,0,1,0,2749.752,0,0,1,15694.312
> view matrix camera 1,0,0,5166.064,0,1,0,2999.752,0,0,1,15681.992
> view matrix camera 1,0,0,3389.669,0,1,0,3879.751,0,0,1,15558.389
> view matrix camera 1,0,0,3558.55,0,1,0,2776.066,0,0,1,15842.712
> view matrix camera 1,0,0,4936.064,0,1,0,2289.671,0,0,1,15566.069
> view matrix camera 1,0,0,3558.55,0,1,0,2776.066,0,0,1,15842.712
> view matrix camera 1,0,0,4936.064,0,1,0,2289.671,0,0,1,15566.069
clip back plane is in front of front plane
> view matrix camera 1,0,0,3761.989,0,1,0,3026.066,0,0,1,16584.394
> view matrix camera 1,0,0,3069.752,0,1,0,2850.706,0,0,1,15711.511
> view matrix camera 1,0,0,2579.753,0,1,0,2210.789,0,0,1,15776.714
clip back plane is in front of front plane
> view matrix camera 1,0,0,4002.071,0,1,0,2597.268,0,0,1,16573.11
> view matrix camera 1,0,0,5262.07,0,1,0,2749.752,0,0,1,15694.312
clip back plane is in front of front plane
> view matrix camera 1,0,0,3341.907,0,1,0,1236.068,0,0,1,16289.672
> view matrix camera 1,0,0,4006.065,0,1,0,3108.469,0,0,1,16464.311
> view matrix camera 1,0,0,5166.064,0,1,0,2999.752,0,0,1,15681.992
> view matrix camera 1,0,0,3389.669,0,1,0,3879.751,0,0,1,15558.389
> view matrix camera 1,0,0,3558.55,0,1,0,2776.066,0,0,1,15842.712
> view matrix camera 1,0,0,4936.064,0,1,0,2289.671,0,0,1,15566.069
clip back plane is in front of front plane
> view matrix camera 1,0,0,3761.989,0,1,0,3026.066,0,0,1,16584.394
> view matrix camera 1,0,0,3069.752,0,1,0,2850.706,0,0,1,15711.511
> view matrix camera 1,0,0,2579.753,0,1,0,2210.789,0,0,1,15776.714
clip back plane is in front of front plane
> view matrix camera 1,0,0,4002.071,0,1,0,2597.268,0,0,1,16573.11
> view matrix camera 1,0,0,4006.065,0,1,0,3108.469,0,0,1,16464.311
> view matrix camera 1,0,0,4002.071,0,1,0,2597.268,0,0,1,16573.11
> view matrix camera 1,0,0,4006.065,0,1,0,3108.469,0,0,1,16464.311
> view matrix camera 1,0,0,3618.386,0,1,0,5288.466,0,0,1,16678.388
> view matrix camera 1,0,0,4899.03,0,1,0,4963.744,0,0,1,15763.831
> ui mousemode right select
> select #1.1.1
3 models selected
> select #1.1.1
3 models selected
> ui mousemode right select
> ui mousemode right "mark plane"
> marker #1.2.3.3 position 943.3,4515,763.8 color #005c3180 radius 10.01
> marker #1.2.3.3 position 2828,2640,763.8 color #005c3180 radius 10.01
> marker #1.2.3.3 position 3474,2458,763.8 color #005c3180 radius 10.01
> marker #1.2.3.3 position 3903,1926,763.8 color #005c3180 radius 10.01
> artiax view xy
> marker #1.2.3.3 position 3833,4973,663.7 color #005c3180 radius 10.01
> marker #1.2.3.3 position 3833,4974,663.7 color #005c3180 radius 10.01
> marker #1.2.3.3 position 5108,2609,433.4 color #005c3180 radius 10.01
> marker #1.2.3.3 position 1012,4273,1677 color #005c3180 radius 10.01
> marker #1.2.3.3 position 4259,2892,1427 color #005c3180 radius 10.01
> marker #1.2.3.3 position 3544,3348,1467 color #005c3180 radius 10.01
> marker #1.2.3.3 position 4309,2607,1166 color #005c3180 radius 10.01
> marker #1.2.3.3 position 3513,3060,1397 color #005c3180 radius 150
> marker #1.2.3.3 position 2947,2214,816 color #005c3180 radius 150
> marker #1.2.1.3 position 1493,4586,265.3 color #80808080 radius 130
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1302, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/yue.yu/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/__init__.py", line 31, in run_provider
run_provider(session, name)
File "/Users/yue.yu/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/toolbar/toolbar.py", line 42, in run_provider
what(session)
File "/Users/yue.yu/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/ParticleList.py", line 1335, in
delete_selected_particles
ids = col.child_ids[ma]
~~~~~~~~~~~~~^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File "/Users/yue.yu/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/ParticleList.py", line 1335, in
delete_selected_particles
ids = col.child_ids[ma]
~~~~~~~~~~~~~^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1302, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/yue.yu/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/__init__.py", line 31, in run_provider
run_provider(session, name)
File "/Users/yue.yu/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/toolbar/toolbar.py", line 42, in run_provider
what(session)
File "/Users/yue.yu/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/ParticleList.py", line 1335, in
delete_selected_particles
ids = col.child_ids[ma]
~~~~~~~~~~~~~^^^^
IndexError: arrays used as indices must be of integer (or boolean) type
IndexError: arrays used as indices must be of integer (or boolean) type
File "/Users/yue.yu/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/ParticleList.py", line 1335, in
delete_selected_particles
ids = col.child_ids[ma]
~~~~~~~~~~~~~^^^^
See log for complete Python traceback.
> ui mousemode right "delete picked particle"
> ui mousemode right "mark plane"
> marker #1.2.2.3 position 3418,3890,535.7 color #80808080 radius 130
> marker #1.2.1.3 position 3439,3816,535.7 color #80808080 radius 130
> ui mousemode right "mark plane"
> marker #1.2.1.3 position 1181,4819,535.7 color #80808080 radius 130
> marker #1.2.1.3 position 1383,4712,535.7 color #80808080 radius 130
> marker #1.2.1.3 position 1429,4399,535.7 color #80808080 radius 130
> marker #1.2.1.3 position 1811,3883,535.7 color #80808080 radius 130
> marker #1.2.1.3 position 1900,3346,535.7 color #80808080 radius 130
> marker #1.2.1.3 position 1298,3541,535.7 color #80808080 radius 130
> marker #1.2.1.3 position 1437,4209,535.7 color #80808080 radius 130
> ui mousemode right "delete picked particle"
> ui mousemode right "mark plane"
> marker #1.2.1.3 position 3510,2965,535.7 color #80808080 radius 130
> marker #1.2.1.3 position 4884,2885,535.7 color #80808080 radius 130
> marker #1.2.1.3 position 3894,1897,725.9 color #80808080 radius 130
> marker #1.2.1.3 position 5670,2780,295.4 color #80808080 radius 130
> ui mousemode right "delete picked particle"
> ui mousemode right "mark plane"
> marker #1.2.1.3 position 3412,3537,495.6 color #80808080 radius 130
> marker #1.2.1.3 position 1139,1631,1337 color #80808080 radius 130
> marker #1.2.1.3 position 1624,2114,1367 color #80808080 radius 130
> marker #1.2.1.3 position 1449,1928,1367 color #80808080 radius 130
> marker #1.2.1.3 position 745.5,1323,1297 color #80808080 radius 130
[, ]
> artiax clip off
Opened virus-like-particle as #1.2.4.1.1, grid size 78,78,78, pixel 6.67,
shown at level 0.566, step 1, values float32
> volume #1.2.4.1.1 capFaces false
===== Log before crash end =====
Log:
Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle
Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with
that from OME-Zarr bundle
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 Metal - 88
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
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: Mac14,5
Model Number: MPHK3LL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: 10151.101.3
OS Loader Version: 10151.101.3
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 20 days, 1 hour, 47 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U3423WE:
Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
UI Looks like: 3440 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
aiobotocore: 2.12.3
aiohttp: 3.9.5
aioitertools: 0.11.0
aiosignal: 1.3.1
alabaster: 0.7.16
annotated-types: 0.6.0
appdirs: 1.4.4
appnope: 0.1.3
asciitree: 0.3.3
asttokens: 2.4.1
attrs: 23.2.0
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
botocore: 1.34.69
build: 0.10.0
certifi: 2022.12.7
cffi: 1.16.0
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-ArtiaX: 0.4.7
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-copick: 0.2.3
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-OME-Zarr: 0.5.3
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
click: 8.1.7
cloudpickle: 3.0.0
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
copick: 0.4.0
cryptography: 42.0.5
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
dask: 2024.4.2
debugpy: 1.8.0
decorator: 5.1.1
distributed: 2024.4.2
docutils: 0.19
executing: 2.0.1
fasteners: 0.19
filelock: 3.9.0
fonttools: 4.47.2
frozenlist: 1.4.1
fsspec: 2024.3.1
funcparserlib: 2.0.0a0
geomdl: 5.3.1
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
hatchling: 1.24.2
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imageio: 2.34.1
imagesize: 1.4.1
importlib-metadata: 7.1.0
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
jmespath: 1.0.1
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
lazy-loader: 0.4
line-profiler: 4.0.2
locket: 1.0.0
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
multidict: 6.0.5
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numcodecs: 0.12.1
numexpr: 2.8.8
numpy: 1.25.1
ome-zarr: 0.8.3
openvr: 1.23.701
packaging: 24.0
pandas: 2.2.2
ParmEd: 3.4.3
parso: 0.8.3
partd: 1.4.1
pathspec: 0.12.1
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
pluggy: 1.5.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pyarrow: 16.0.0
pycollada: 0.7.2
pycparser: 2.22
pydantic: 2.7.1
pydantic-core: 2.18.2
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
pyspnego: 0.10.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
PyYAML: 6.0.1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
s3fs: 2024.3.1
scikit-image: 0.23.2
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
smbprotocol: 1.13.0
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
starfile: 0.5.6
superqt: 0.5.0
tables: 3.8.0
tblib: 3.0.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
toolz: 0.12.1
tornado: 6.4
traitlets: 5.9.0
trimesh: 4.3.1
trove-classifiers: 2024.4.10
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
wrapt: 1.16.0
yarl: 1.9.4
zarr: 2.17.2
zict: 3.0.0
zipp: 3.18.1
Change History (2)
comment:1 by , 18 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Third Party |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Copick: crash in QCoPickTableModel |
comment:2 by , 18 months ago
Note:
See TracTickets
for help on using tickets.
Seems it crashed in Qt call QItemSelectionRange(). We don't have any other crash reports in that call. This was in ChimeraX 1.7.1 which uses Qt 6.3 while our current ChimeraX daily builds (and 1.8 to be released around June) uses Qt 6.6.