id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15093 Copick: crash in QCoPickTableModel chimerax-bug-report@… Utz Ermel "{{{ 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, 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Address size fault""},""pc"":{""value"":6756620780},""far"":{""value"":0}}}], ""usedImages"" : [ [deleted to fit within ticket limits] { ""size"" : 0, ""source"" : ""A"", ""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" } ], ""sharedCache"" : { ""base"" : 6752387072, ""size"" : 4189880320, ""uuid"" : ""a53b7d2f-a773-3524-8828-248b33ef0b4e"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.7G resident=0K(0%) swapped_out_or_unallocated=1.7G(100%)\nWritable regions: Total=6.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=6.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 400K 19 \nColorSync 640K 30 \nCoreAnimation 1456K 91 \nCoreGraphics 144K 9 \nCoreUI image data 5744K 56 \nFoundation 32K 2 \nKernel Alloc Once 48K 2 \nMALLOC 5.0G 197 \nMALLOC guard page 384K 24 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 1120K 70 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""SIRI_TTS_DEVICE_TRAINING"" : ""6539d7f333b9b7499c6f1b63"" }, ""deploymentId"" : 240000073 } ], ""experiments"" : [ { ""treatmentId"" : ""2dffbe18-a39a-4f33-ada9-2cce30af39ca"", ""experimentId"" : ""6384d56b96e8d228551ec182"", ""deploymentId"" : 400000032 } ] } } ===== 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 }}} " defect assigned normal Third Party Tom Goddard all ChimeraX