![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#16896 closed defect (can't reproduce)
Crash in event loop releasing memory
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | 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-15.3.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001f6618840 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, lxml._elementpath, lxml.etree, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 58)
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{
"uptime" : 3100,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"coalitionID" : 1329,
"osVersion" : {
"train" : "macOS 15.3.1",
"build" : "24D70",
"releaseType" : "User"
},
"captureTime" : "2025-02-18 18:58:21.5881 +0100",
"codeSigningMonitor" : 1,
"incident" : "77AFF539-98C9-4D63-A857-33E75FE3AF96",
"pid" : 1066,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-18 17:37:16.8291 +0100",
"procStartAbsTime" : 3789814137,
"procExitAbsTime" : 74765222065,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"A8C654F3-8E06-5A7D-8F04-9285A7AD7633","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "F7545098-703F-1A56-913E-C029D7FC81E3",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "72C6953D-A908-4CA9-82AB-8D9092BF4465",
"wakeTime" : 2320,
"sleepWakeUUID" : "921F52B8-91EE-4EFA-A4FB-49DE3B784A7F",
"sip" : "enabled",
"vmRegionInfo" : "0x6193d0e056d0 is not in any region. Bytes after previous region: 1729541756625 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [ 2528K] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x00006193d0e056d0","rawCodes":[1,107287492450000],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00006193d0e056d0"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":1066},
"vmregioninfo" : "0x6193d0e056d0 is not in any region. Bytes after previous region: 1729541756625 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [ 2528K] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 3iyu fromDatabase pdb format mmcif
Summary of feedback from opening 3iyu fetched from pdb
---
warning | PDB entry 3IYU has been replaced by 4V7Q
notes | Fetching compressed mmCIF 3iyu from http://files.rcsb.org/download/3iyu.cif
Fetching CCD NAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif
3iyu title:
Atomic model of an infectious rotavirus particle [more info...]
Chain information for 3iyu #1
---
Chain | Description | UniProt
A F G H I J K L M N O P Q | Outer layer protein VP7 | C3RX25_9REOV 51-326
X Y Z | Outer capsid protein VP4 | C3RX20_9REOV 1-776
Non-standard residues in 3iyu #1
---
NAG — N-acetyl-D-glucosamine
3iyu mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
> ui mousemode right "next docked"
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
> open C3RX25 fromDatabase uniprot associate #1/A,F,G,H,I,J,K,L,M,N,O,P,Q
Summary of feedback from opening C3RX25 fetched from uniprot
---
notes | UniProt identifier C3RX25 maps to entry P12476
Fetching compressed P12476 UniProt info from
https://www.uniprot.org/uniprot/P12476.xml
Alignment identifier is C3RX25
Associated 3iyu chain A to C3RX25 with 0 mismatches
Associated 3iyu chain F to C3RX25 with 0 mismatches
Associated 3iyu chain G to C3RX25 with 0 mismatches
Associated 3iyu chain H to C3RX25 with 0 mismatches
Associated 3iyu chain I to C3RX25 with 0 mismatches
8 messages similar to the above omitted
Opened UniProt C3RX25
QAccessibleList::child: Invalid index at: 0 0
> select /A,H,M,Q:58-312/F:58-320/G,J-L,P/I:52-324/N:52-326/O:52-325
27379 atoms, 28004 bonds, 3466 residues, 1 model selected
> select /A,H,M,Q:58-312/F:58-320/G,J-L,P/I:52-324/N:52-326/O:52-325
27379 atoms, 28004 bonds, 3466 residues, 1 model selected
> select /P:51
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A-F,H,M,Q:58-240/G,I-J,L,N-O:52-240/K:53-240/P:51-240
19053 atoms, 19477 bonds, 2427 residues, 1 model selected
> select /P:51
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A-F,H,M,Q:58-78/G,I-J,L,N-O:52-78/K:53-78/P:51-78
2439 atoms, 2473 bonds, 321 residues, 1 model selected
> ui tool show "Side View"
> select /A,H,M,Q:58-312/F:58-320/G,J-L,P/I:52-324/N:52-326/O:52-325
27379 atoms, 28004 bonds, 3466 residues, 1 model selected
> select clear
> style stick
Changed 43239 atom styles
> style sphere
Changed 43239 atom styles
> style ball
Changed 43239 atom styles
> color byhetero
> color bychain
> rainbow
> coulombic
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
/Y LEU 776 OXT
/Z LEU 776 OXT
/N ILE 326 OXT
/X LEU 776 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 3iyu_A SES surface #1.2: minimum, -21.87, mean -4.32,
maximum 7.32
Coulombic values for 3iyu_F SES surface #1.3: minimum, -24.05, mean -3.70,
maximum 10.21
Coulombic values for 3iyu_G SES surface #1.4: minimum, -24.38, mean -3.77,
maximum 7.52
Coulombic values for 3iyu_H SES surface #1.5: minimum, -28.51, mean -4.38,
maximum 6.99
Coulombic values for 3iyu_I SES surface #1.6: minimum, -22.38, mean -3.74,
maximum 11.07
Coulombic values for 3iyu_J SES surface #1.7: minimum, -22.17, mean -3.37,
maximum 8.36
Coulombic values for 3iyu_K SES surface #1.8: minimum, -22.12, mean -3.67,
maximum 10.67
Coulombic values for 3iyu_L SES surface #1.9: minimum, -28.42, mean -3.70,
maximum 8.68
Coulombic values for 3iyu_M SES surface #1.10: minimum, -27.92, mean -4.45,
maximum 6.35
Coulombic values for 3iyu_N SES surface #1.11: minimum, -23.43, mean -3.77,
maximum 7.68
Coulombic values for 3iyu_O SES surface #1.12: minimum, -25.92, mean -3.40,
maximum 7.46
Coulombic values for 3iyu_P SES surface #1.13: minimum, -22.42, mean -3.41,
maximum 8.85
Coulombic values for 3iyu_Q SES surface #1.14: minimum, -23.89, mean -4.58,
maximum 7.31
Coulombic values for 3iyu_X SES surface #1.15: minimum, -19.60, mean -1.92,
maximum 12.57
Coulombic values for 3iyu_Y SES surface #1.16: minimum, -18.05, mean -1.92,
maximum 12.75
Coulombic values for 3iyu_Z SES surface #1.17: minimum, -18.42, mean -1.44,
maximum 13.24
To also show corresponding color key, enter the above coulombic command and
add key true
Alignment identifier is 1
Alignment identifier is 2
> interfaces ~solvent
25 buried areas: Y X 4731, Y Z 3104, X Z 1734, J K 1367, N L 1356, G F 1329, L
M 1317, F H 1312, P Q 1309, O Q 1305, N M 1305, I K 1295, J L 1294, G H 1273,
O P 1273, N P 1253, O G 1219, I J 1077, A Q 843, Y G 592, X N 558, Z F 434, Y
F 344, X L 332, X P 331
Alignment identifier is 3
Alignment identifier is 4
> ~hbonds
> hbonds reveal true
3733 hydrogen bonds found
> mlp
Map values for surface "3iyu_A SES surface": minimum -28.06, mean -5.043,
maximum 25.73
Map values for surface "3iyu_F SES surface": minimum -28.12, mean -5.356,
maximum 25.65
Map values for surface "3iyu_G SES surface": minimum -28.5, mean -4.82,
maximum 25.25
Map values for surface "3iyu_H SES surface": minimum -30.53, mean -5.043,
maximum 24.61
Map values for surface "3iyu_I SES surface": minimum -28.87, mean -4.658,
maximum 25.39
Map values for surface "3iyu_J SES surface": minimum -28.9, mean -4.896,
maximum 25.63
Map values for surface "3iyu_K SES surface": minimum -28.4, mean -5.031,
maximum 24.76
Map values for surface "3iyu_L SES surface": minimum -27.69, mean -4.935,
maximum 27.29
Map values for surface "3iyu_M SES surface": minimum -28.06, mean -5.318,
maximum 25.36
Map values for surface "3iyu_N SES surface": minimum -29.15, mean -5.026,
maximum 25.35
Map values for surface "3iyu_O SES surface": minimum -29.31, mean -4.699,
maximum 25.72
Map values for surface "3iyu_P SES surface": minimum -27.78, mean -4.937,
maximum 26.36
Map values for surface "3iyu_Q SES surface": minimum -28.82, mean -4.99,
maximum 25.95
Map values for surface "3iyu_X SES surface": minimum -28.38, mean -5.377,
maximum 24.71
Map values for surface "3iyu_Y SES surface": minimum -28.65, mean -5.228,
maximum 25.36
Map values for surface "3iyu_Z SES surface": minimum -28, mean -4.98, maximum
26.18
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic
Coulombic values for 3iyu_A SES surface #1.2: minimum, -21.87, mean -4.32,
maximum 7.32
Coulombic values for 3iyu_F SES surface #1.3: minimum, -24.05, mean -3.70,
maximum 10.21
Coulombic values for 3iyu_G SES surface #1.4: minimum, -24.38, mean -3.77,
maximum 7.52
Coulombic values for 3iyu_H SES surface #1.5: minimum, -28.51, mean -4.38,
maximum 6.99
Coulombic values for 3iyu_I SES surface #1.6: minimum, -22.38, mean -3.74,
maximum 11.07
Coulombic values for 3iyu_J SES surface #1.7: minimum, -22.17, mean -3.37,
maximum 8.36
Coulombic values for 3iyu_K SES surface #1.8: minimum, -22.12, mean -3.67,
maximum 10.67
Coulombic values for 3iyu_L SES surface #1.9: minimum, -28.42, mean -3.70,
maximum 8.68
Coulombic values for 3iyu_M SES surface #1.10: minimum, -27.92, mean -4.45,
maximum 6.35
Coulombic values for 3iyu_N SES surface #1.11: minimum, -23.43, mean -3.77,
maximum 7.68
Coulombic values for 3iyu_O SES surface #1.12: minimum, -25.92, mean -3.40,
maximum 7.46
Coulombic values for 3iyu_P SES surface #1.13: minimum, -22.42, mean -3.41,
maximum 8.85
Coulombic values for 3iyu_Q SES surface #1.14: minimum, -23.89, mean -4.58,
maximum 7.31
Coulombic values for 3iyu_X SES surface #1.15: minimum, -19.60, mean -1.92,
maximum 12.57
Coulombic values for 3iyu_Y SES surface #1.16: minimum, -18.05, mean -1.92,
maximum 12.75
Coulombic values for 3iyu_Z SES surface #1.17: minimum, -18.42, mean -1.44,
maximum 13.24
To also show corresponding color key, enter the above coulombic command and
add key true
> color bypolymer
> color bychain
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
> close session
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: Z160000VFY/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 1 hora y 24 minutos
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
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-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (3)
comment:1 by , 8 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop releasing memory |
comment:2 by , 8 months ago
comment:3 by , 8 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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"Cell requested for row 0 is out of bounds for table with 0 rows! Resizing table model." was also in the log.