Opened 18 months ago

Last modified 18 months ago

#15075 assigned defect

Copick: QCoPickTableModel: child item has no parent

Reported by: chimerax-bug-report@… Owned by: Utz Ermel
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-14.4.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Using Copick
Fatal Python error: Segmentation fault

Thread 0x000000031099e000 (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 0x0000000311d45000 (most recent call first):
 File "/Users/bisco.hill/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/smbprotocol/transport.py", line 137 in _recv
 File "/Users/bisco.hill/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/smbprotocol/transport.py", line 115 in recv
 File "/Users/bisco.hill/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

Current thread 0x00000002006bd240 (most recent call first):
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 486 in _invoke_rule
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 561 in _zone_selector_
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 187 in _model_
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 157 in block0
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 787 in _positive_closure
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 159 in _model_list_
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 136 in _as_term_
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 89 in _atom_specifier_
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 206 in parse
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 192 in _parse_unquoted
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 121 in parse
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/markers/cmd.py", line 313 in parse
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 901 in parse
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2499 in _parse_arg
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2640 in _process_positional_arguments
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2864 in run
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/logging.py", line 40 in log_equivalent_command
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/markers/mouse.py", line 547 in _log_place_marker
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/markers/mouse.py", line 514 in _mouse_place_marker
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/markers/mouse.py", line 116 in place_on_plane
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/markers/mouse.py", line 68 in mouse_down
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 550 in _dispatch_mouse_event
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 650 in 
 File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 61 in event
 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, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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.graphics._graphics, chimerax.atomic._ribbons (total: 169)


{"app_name":"ChimeraX","timestamp":"2024-04-30 11:23:50.00 -0700","app_version":"1.7.1","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.7.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.4.1 (23E224)","roots_installed":0,"name":"ChimeraX","incident_id":"906BDFB5-7560-4B5F-84D5-BF282B7D57E6"}
{
 "uptime" : 440000,
 "procRole" : "Foreground",
 "version" : 2,
 "userID" : 502,
 "deployVersion" : 210,
 "modelCode" : "Mac14,9",
 "coalitionID" : 59492,
 "osVersion" : {
   "train" : "macOS 14.4.1",
   "build" : "23E224",
   "releaseType" : "User"
 },
 "captureTime" : "2024-04-30 11:23:46.8378 -0700",
 "codeSigningMonitor" : 1,
 "incident" : "906BDFB5-7560-4B5F-84D5-BF282B7D57E6",
 "pid" : 29923,
 "translated" : true,
 "cpuType" : "X86-64",
 "roots_installed" : 0,
 "bug_type" : "309",
 "procLaunch" : "2024-04-30 11:02:26.0644 -0700",
 "procStartAbsTime" : 10652980607292,
 "procExitAbsTime" : 10683717541998,
 "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":"F47B4D8E-461B-51E2-BC2F-AF40381AA792","thirdParty":true},
 "parentProc" : "launchd",
 "parentPid" : 1,
 "coalitionName" : "edu.ucsf.cgl.ChimeraX",
 "crashReporterKey" : "C35A3D9E-E230-9A00-EB4F-C65538F4BBB2",
 "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
 "codeSigningTeamID" : "LWV8X224YF",
 "codeSigningFlags" : 570491649,
 "codeSigningValidationCategory" : 6,
 "codeSigningTrustLevel" : 4294967295,
 "wakeTime" : 2026,
 "sleepWakeUUID" : "FC2105FE-1BF3-4328-A2E1-4506BA5F46D3",
 "sip" : "enabled",
 "vmRegionInfo" : "0x13 is not in any region.  Bytes before following region: 4298272749\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      100327000-10032b000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
 "exception" : {"codes":"0x0000000000000001, 0x0000000000000013","rawCodes":[1,19],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000013"},
 "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":29923},
 "ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
 "vmregioninfo" : "0x13 is not in any region.  Bytes before following region: 4298272749\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      100327000-10032b000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
 "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
 "faultingThread" : 0,
 "threads" : 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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/Bisco.Hill/Downloads/copick_config_bisco_hill.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_1_4 - 10.0 as #3, grid size 630,630,184, pixel 10,10,10, shown at
step 4, values float32  
Opened TS_1_4 - 10.0 as #1.1.1, grid size 630,630,184, pixel 10,10,10, shown
at level -0.0408, step 4, values float32  

> artiax clip off

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

> volume #1.1.1 step 1,1,1

> volume #1.1.1 colorMode l8 orthoplanes xyz positionPlanes 316,316,93
> imageMode orthoplanes step 1,1,1

> volume #1.1.1 style surface step 1,1,1

> artiax tomo #1.1.1 slice 95

> artiax tomo #1.1.1 slice 0

> artiax tomo #1.1.1 slice 39

> artiax clip off

Opened virus-like-particle as #1.2.1.1.1, grid size 78,78,78, pixel 6.67,
shown at level 0.566, step 1, values float32  

> volume #1.2.1.1.1 capFaces false

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'deb32cba-f0bc-4be5-9217-de1ca3e9f476',
'805a3fce-3521-4956-b624-43d765d3b547',
'2f09094a-3697-4846-a8b9-380b6f26c299',
'155cea1a-2a38-4f27-9c10-3b4687a30c9c',
'23ad2621-64a0-4006-8829-795ea3a5249c',
'ab65dbd5-4709-4511-8295-e9829c1929fb']  

> artiax particles #1.2.1 color 100,80,60,18

> artiax tomo #1.1.1 slice 71

> artiax tomo #1.1.1 slice 0

[, ]  

> artiax clip off

Opened apo-ferritin as #1.2.2.1.1, grid size 37,37,37, pixel 6.67, shown at
level 0.303, step 1, values float32  

> volume #1.2.2.1.1 capFaces false

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'7739aeba-b309-42e3-901c-42577ad8f5bf',
'36caeebb-9b5c-4793-b5b1-5312a2ce9320']  
Traceback (most recent call last):  
File "/Users/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  


[deleted to fit within ticket length limits]

See log for complete Python traceback.  

Traceback (most recent call last):  
File "/Users/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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/bisco.hill/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/copick/ui/QCoPickTableModel.py", line 58, in parent  
parentItem = childItem.parent  
^^^^^^^^^^^^^^^^  
AttributeError: '' object has no attribute 'parent'  

AttributeError: '' object has no attribute 'parent'  

File "/Users/bisco.hill/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.  

['409aeba7-f9ad-4b98-97d1-1e843149bf2d',
'4e554bb8-ab90-4366-9d2b-2c2de1e15e8a',
'afac1cfd-f06c-4192-8f81-0c78c9cf068e',
'd9cd5746-520c-4841-8956-01ca944fe0b7',
'f835c858-aff7-4f7a-b472-7d4d4d3c1823',
'898539e7-938f-4853-9d32-c1ff3018dd67',
'319cd430-c12d-4205-8e2c-9db75f3e88df',
'78bd5f46-2ecc-42d8-b3b6-ac7afd7f6ef1',
'1809deae-e2f9-41e7-bf6e-08ef4f31e55a',
'cc163cc4-0a0d-4220-a432-fbba19b32b7d',
'954d2797-4cb7-457d-9b4a-8b94bd17442b',
'7739aeba-b309-42e3-901c-42577ad8f5bf',
'36caeebb-9b5c-4793-b5b1-5312a2ce9320']  

> view matrix camera 1,0,0,5737.130696,0,1,0,2092.6009,0,0,1,6921.144894

> view matrix camera 1,0,0,760.945782,0,1,0,1481.841785,0,0,1,7141.418673

> view matrix camera 1,0,0,6057.52892,0,1,0,1662.065786,0,0,1,7131.406228

> view matrix camera 1,0,0,5647.018696,0,1,0,5456.78225,0,0,1,7371.704896

> view matrix camera
> 1,0,0,5176.433805,0,1,0,2753.422236,0,0,1,7391.7297849999995

> artiax particles #1.2.2 color 0,46,86,3

> view matrix camera 1,0,0,5186.446249,0,1,0,3784.70402,0,0,1,7421.767118

> view matrix camera 1,0,0,4325.376022,0,1,0,5076.30936,0,0,1,6170.211556

> view matrix camera 1,0,0,4545.649801,0,1,0,1972.451566,0,0,1,6220.273779

> view matrix camera 1,0,0,5626.993807,0,1,0,1692.10312,0,0,1,6040.049778

> view matrix camera
> 1,0,0,1201.49334,0,1,0,2743.409792,0,0,1,6320.3982240000005

> view matrix camera 1,0,0,3294.094239,0,1,0,2132.650678,0,0,1,6530.659558

> view matrix camera 1,0,0,1632.028453,0,1,0,3604.480019,0,0,1,6500.622225

> view matrix camera 1,0,0,1682.090675,0,1,0,5576.931584,0,0,1,6891.10756

> ui mousemode right "move picked models"

> view matrix models #1.1.1,1,0,0,0,0,1,0,0,0,0,1,0

> ui mousemode right "move picked models"

> view matrix models #1.1.1,1,0,0,0,0,1,0,0,0,0,1,0

> ui mousemode right "translate selected particles"

> ui mousemode right translate

['409aeba7-f9ad-4b98-97d1-1e843149bf2d',
'4e554bb8-ab90-4366-9d2b-2c2de1e15e8a',
'f835c858-aff7-4f7a-b472-7d4d4d3c1823',
'78bd5f46-2ecc-42d8-b3b6-ac7afd7f6ef1',
'7739aeba-b309-42e3-901c-42577ad8f5bf',
'36caeebb-9b5c-4793-b5b1-5312a2ce9320']  

> artiax particles #1.2.2 color 0,46,86,9

> artiax tomo #1.1.1 slice 19

> volume #1.1.1 step 1,1,1

> ui mousemode right "mark plane"

> marker #1.2.2.3 position 5968,3546,185.2 color #0075dc17 radius 10.01

> marker #1.2.2.3 position 5988,2231,185.2 color #0075dc17 radius 10.01

> artiax tomo #1.1.1 slice 49

> marker #1.2.2.3 position 3134,4080,485.6 color #0075dc17 radius 10.01

> artiax tomo #1.1.1 slice 97

> artiax tomo #1.1.1 slice 98

> marker #1.2.2.3 position 5614,4015,976.2 color #0075dc17 radius 10.01

> artiax tomo #1.1.1 slice 151

> marker #1.2.2.3 position 3907,5577,1507 color #0075dc17 radius 10.01

> artiax tomo #1.1.1 slice 169

> marker #1.2.2.3 position 3240,5079,1687 color #0075dc17 radius 10.01

> artiax tomo #1.1.1 slice 169

> marker #1.2.2.3 position 1177,5676,1687 color #0075dc17 radius 10.01

> artiax tomo #1.1.1 slice 168

> marker #1.2.2.3 position 3879,4760,1677 color #0075dc17 radius 10.01

> artiax tomo #1.1.1 slice 162

> marker #1.2.2.3 position 4847,4097,1617 color #0075dc17 radius 10.01

> artiax tomo #1.1.1 slice 173

> marker #1.2.2.3 position 1277,5379,1727 color #0075dc17 radius 10.01


===== 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 Pro
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: Mac
     Model Identifier: Mac14,9
     Model Number: MPHH3LL/A
     Chip: Unknown
     Total Number of Cores: 10 (6 performance and 4 efficiency)
     Memory: 16 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, 48 minutes

Graphics/Displays:

   Apple M2 Pro:

     Chipset Model: Apple M2 Pro
     Type: GPU
     Bus: Built-In
     Total Number of Cores: 16
     Vendor: Apple (0x106b)
     Metal Support: Metal 3
     Displays:
       DELL U3423WE:
         Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
         UI Looks like: 3440 x 1440 @ 60.00Hz
         Main Display: Yes
         Mirror: Off
         Online: Yes


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: 0.2.2
   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: 0.5.4
   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: 0.5.7
   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 (1)

comment:1 by Eric Pettersen, 18 months ago

Component: Unassigned → Third Party
Description: modified (diff)
Owner: set to Utz Ermel
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Copick: QCoPickTableModel: child item has no parent
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