![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 18 months ago
Last modified 18 months ago
#15093 assigned defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-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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===== 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
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