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Opened 19 months ago
Closed 19 months ago
#14823 closed defect (duplicate)
Crash in python_instances_of_class while saving session
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | 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-14.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202403220040 (2024-03-22 00:40:30 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 0x00000001e6091ec0 (most recent call first):
File "/private/var/folders/47/v2c4v0411rv3hpvg8xpz8qq00000gn/T/AppTranslocation/2FF645F4-6C5B-4F0D-8CE3-3D7E13D56C45/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 44 in python_instances_of_class
File "/private/var/folders/47/v2c4v0411rv3hpvg8xpz8qq00000gn/T/AppTranslocation/2FF645F4-6C5B-4F0D-8CE3-3D7E13D56C45/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 2636 in
File "/private/var/folders/47/v2c4v0411rv3hpvg8xpz8qq00000gn/T/AppTranslocation/2FF645F4-6C5B-4F0D-8CE3-3D7E13D56C45/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 256 in
File "/private/var/folders/47/v2c4v0411rv3hpvg8xpz8qq00000gn/T/AppTranslocation/2FF645F4-6C5B-4F0D-8CE3-3D7E13D56C45/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 256 in include_state
File "/private/var/folders/47/v2c4v0411rv3hpvg8xpz8qq00000gn/T/AppTranslocation/2FF645F4-6C5B-4F0D-8CE3-3D7E13D56C45/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 260 in discovery
File "/private/var/folders/47/v2c4v0411rv3hpvg8xpz8qq00000gn/T/AppTranslocation/2FF645F4-6C5B-4F0D-8CE3-3D7E13D56C45/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 641 in save
File "/private/var/folders/47/v2c4v0411rv3hpvg8xpz8qq00000gn/T/AppTranslocation/2FF645F4-6C5B-4F0D-8CE3-3D7E13D56C45/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 917 in save
File "/private/var/folders/47/v2c4v0411rv3hpvg8xpz8qq00000gn/T/AppTranslocation/2FF645F4-6C5B-4F0D-8CE3-3D7E13D56C45/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95 in save
File "/private/var/folders/47/v2c4v0411rv3hpvg8xpz8qq00000gn/T/AppTranslocation/2FF645F4-6C5B-4F0D-8CE3-3D7E13D56C45/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101 in provider_save
File "/private/var/folders/47/v2c4v0411rv3hpvg8xpz8qq00000gn/T/AppTranslocation/2FF645F4-6C5B-4F0D-8CE3-3D7E13D56C45/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/private/var/folders/47/v2c4v0411rv3hpvg8xpz8qq00000gn/T/AppTranslocation/2FF645F4-6C5B-4F0D-8CE3-3D7E13D56C45/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86 in cmd_save
File "/private/var/folders/47/v2c4v0411rv3hpvg8xpz8qq00000gn/T/AppTranslocation/2FF645F4-6C5B-4F0D-8CE3-3D7E13D56C45/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/private/var/folders/47/v2c4v0411rv3hpvg8xpz8qq00000gn/T/AppTranslocation/2FF645F4-6C5B-4F0D-8CE3-3D7E13D56C45/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/private/var/folders/47/v2c4v0411rv3hpvg8xpz8qq00000gn/T/AppTranslocation/2FF645F4-6C5B-4F0D-8CE3-3D7E13D56C45/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 62 in display
File "/private/var/folders/47/v2c4v0411rv3hpvg8xpz8qq00000gn/T/AppTranslocation/2FF645F4-6C5B-4F0D-8CE3-3D7E13D56C45/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138 in show_save_file_dialog
File "/private/var/folders/47/v2c4v0411rv3hpvg8xpz8qq00000gn/T/AppTranslocation/2FF645F4-6C5B-4F0D-8CE3-3D7E13D56C45/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 127 in
File "/private/var/folders/47/v2c4v0411rv3hpvg8xpz8qq00000gn/T/AppTranslocation/2FF645F4-6C5B-4F0D-8CE3-3D7E13D56C45/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
File "/private/var/folders/47/v2c4v0411rv3hpvg8xpz8qq00000gn/T/AppTranslocation/2FF645F4-6C5B-4F0D-8CE3-3D7E13D56C45/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/private/var/folders/47/v2c4v0411rv3hpvg8xpz8qq00000gn/T/AppTranslocation/2FF645F4-6C5B-4F0D-8CE3-3D7E13D56C45/d/ChimeraX_Daily.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.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, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 57)
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"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
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"coalitionID" : 74898,
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"captureTime" : "2024-03-26 08:24:20.0503 +0100",
"codeSigningMonitor" : 1,
"incident" : "80FF622C-FCBD-4CF7-9AA9-D4B8F9C8D526",
"pid" : 50152,
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"cpuType" : "ARM-64",
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"bug_type" : "309",
"procLaunch" : "2024-03-25 18:14:03.5332 +0100",
"procStartAbsTime" : 15965504665391,
"procExitAbsTime" : 16206492657249,
"procName" : "ChimeraX",
"procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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"crashReporterKey" : "1F60A6CC-BCB2-738C-804C-DC44412EC204",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
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"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"vmRegionInfo" : "0x5c1fb1 is not in any region. Bytes before following region: 4302348367\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100ccc000-100cd0000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
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"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":50152},
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"uuid" : "ec7a3ba0-f9bf-3ab8-a0f4-8622e5606b20",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
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"source" : "A",
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"uuid" : "00000000-0000-0000-0000-000000000000"
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"uuid" : "3702eede-997d-38e6-a6a1-c08eb22c375b",
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}
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"uuid" : "43b9f010-3c81-318c-ba80-29c673a7757a"
},
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "f1071b2b15ffb16dd1dd6f0a27750697978641a4",
"trialInfo" : {
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{
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],
"experiments" : [
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"experimentId" : "65f21aa774b6f500a45abd7d",
"deploymentId" : 400000002
}
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show AlphaFold
> alphafold predict
> VLLSRKRRRQHGQLWFPEGFKVSEASKKKRREPLGEDSVGLKPLKNASDGALMDDNQNEWGDEDLETKKFRFEEPVVLPDLDDQTDHRQWTQQHLDAADLRMSAMAPTPPQGEVDADCMDVNVRGPDGFTPLMIASCSGGGLETGNSEEEEDAPAVISDFIYQGASLHNQTDRTGETALHLAARYSRSDAAKRLLEASADANIQDNMGRTPLHAAVSADAQGVFQILIRNRATDLDARMHDGTTPLILAARLAVEGMLEDLINSHADVNAVDDLGKSALHWAAAVNNVDAAVVLLKNGANKDMQNNREETPLFLAAREGSYETAKVLLDHFANRDITDHMDRLPRDIAQERMHHDIVRLLDEYNLVRSPQLHGAPLGGTPTLSPPLCSPNGYLGSLKPGVQGKKVRKPSSKGLACGSKEAKDLKARRKKSQDGKGCLLDSSGMLSPVDSLESPHGYLSDVASPPLLPSPFQQSPSVPLNHLPGMPDTHLGIGHLNVAAKPEMAALGGGGRLAFETGPPRLSHLPVASGTSTVLGSSSGGALNFTVGGSTSLNGQCEWLSRLQSGMVPNQYNPLRGSVAPGPLSTQAPSLQHGMVGPLHSSLAASALSQMMSYQGLPSTRLATQPHLVQTQQVQPQNLQMQQQNLQPANIQQQQSLQPPPPPPQPHLGVSSAASGHLGRSFLSGEPSQADVQPLGPSSLAVHTILPQESPALPTSLPSSLVPPVTAAQFLTPPSQHSYSSPVDNTPSHQLQVPEHPFLTPSPESPDQWSSSSPHSNVSDWSEGVSSPPTSMQSQIARIPEAFK,MGLKLNGRYISLILAVQIAYLVQAVRAAGKCDAVFKGFSDCLLKLGDSMANYPQGLDDKTNIKTVCTYWEDFHSCTVTALTDCQEGAKDMWDKLRKESKNLNIQGSLFELCGSGNGAAGSLLPAFPVLLVSLSAALATWLSF
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
Alphafold prediction send sequence to Google Colab returned: None
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/luciahaller/Downloads/ChimeraX/AlphaFold/prediction_1
> open
> /Users/luciahaller/Downloads/ChimeraX/AlphaFold/prediction_1/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #1/B
Alignment identifier is 1/B
> select add #1
7101 atoms, 7263 bonds, 944 residues, 1 model selected
> select subtract #1
Nothing selected
> view
> select /A:1-802
6028 atoms, 6171 bonds, 802 residues, 1 model selected
> select /B:1-142
1073 atoms, 1092 bonds, 142 residues, 1 model selected
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> /Users/luciahaller/Downloads/ChimeraX/AlphaFold/prediction_1/best_model_pae.json
> color #1/A:218-218 lime
> color #1/A:245-245 magenta
> color #1/A:192-192 lime
> color #1/A:188-188 magenta
> color #1/A:134-134 lime
> color #1/A:192-192 magenta
> color #1/A:108-109 lime
> color #1/A:228-228 magenta
> color #1/A:115-115 lime
> color #1/A:327-327 magenta
> color #1/A:295-295 lime
> color #1/A:331-331 magenta
> color #1/A:318-318 lime
> color #1/A:197-197 magenta
> select /B:1-142
1073 atoms, 1092 bonds, 142 residues, 1 model selected
> select /A:1-802
6028 atoms, 6171 bonds, 802 residues, 1 model selected
> select /B:1-142
1073 atoms, 1092 bonds, 142 residues, 1 model selected
> color #1 #923a8cff
> color #1 #92658dff
> color #1 #929292ff
> alphafold pae #1 file
> /Users/luciahaller/Downloads/ChimeraX/AlphaFold/prediction_1/best_model_pae.json
> help help:user/tools/alphafold.html#pae
> color #1/A:215-215 lime
> color #1/A:243-243 magenta
> color #1/A:209-209 lime
> color #1/A:270-270 magenta
> color #1/A:209-209 lime
> color #1/A:283-283 magenta
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> /Users/luciahaller/Downloads/ChimeraX/AlphaFold/prediction_1/best_model_pae.json
> color sel bychain
Compositor returned null texture
Already setting window visible!
> select /A:1-802
6028 atoms, 6171 bonds, 802 residues, 1 model selected
> color sel bychain
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> toolshed show
> select add #1
7101 atoms, 7263 bonds, 944 residues, 1 model selected
> select subtract #1
Nothing selected
> color bfactor
7101 atoms, 944 residues, atom bfactor range 13.4 to 98.4
> select /A:1-802
6028 atoms, 6171 bonds, 802 residues, 1 model selected
> select /B:1-142
1073 atoms, 1092 bonds, 142 residues, 1 model selected
> color bfactor sel
1073 atoms, 142 residues, atom bfactor range 15.5 to 52.9
> select add #1
7101 atoms, 7263 bonds, 944 residues, 1 model selected
> select subtract #1
Nothing selected
> ui tool show "Color Actions"
> toolshed show
> close
> open
> /Users/luciahaller/Downloads/ChimeraX/AlphaFold/prediction_1/best_model.pdb
> format pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> save /Users/luciahaller/Desktop/N1ICD-NRN1.cxs
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: MLXY3D/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1 (23B74)
Kernel Version: Darwin 23.1.0
Time since boot: 78 days, 18 hours, 41 minutes
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: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
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: 2.12.1
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: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
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-Core: 1.8.dev202403220040
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4.2
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: 1.1.1
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: 1.1.9
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
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-Segmentations: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.37.1
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
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
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
superqt: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 19 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in python_instances_of_class while saving session |
comment:2 by , 19 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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