![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 10 months ago
Closed 10 months ago
#16468 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.4.1-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001fdeffac0 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/_weakrefset.py", line 58 in _commit_removals
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/_weakrefset.py", line 33 in __exit__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/_weakrefset.py", line 64 in __iter__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/nucleotides/_data.py", line 519 in
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/nucleotides/_data.py", line 519 in rebuild
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 65 in draw_new_frame
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
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, openmm._openmm, openmm.app.internal.compiled, 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, PIL._webp (total: 56)
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{
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"procRole" : "Foreground",
"version" : 2,
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"modelCode" : "iMac21,1",
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"build" : "23E224",
"releaseType" : "User"
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"captureTime" : "2024-12-13 18:13:54.2646 -0600",
"codeSigningMonitor" : 1,
"incident" : "7022FF9F-5816-430F-90B7-2C4E146DF6B6",
"pid" : 69720,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-12-13 13:18:45.0973 -0600",
"procStartAbsTime" : 2582679268221,
"procExitAbsTime" : 3007702828413,
"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":"6AB11F68-765C-5A0C-8DF7-81415150FE35","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "4BEC5592-54B3-48B5-D63A-225C2533156F",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 18175,
"sleepWakeUUID" : "FBA132EC-A42A-47C4-A2E2-9194B8E03D99",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 4365582167\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104358000-10435c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":69720},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 4365582167\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104358000-10435c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
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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 '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
> open "/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final
> Structures/State4b_J92.pdb"
Chain information for State4b_J92.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> open "/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final
> Structures/State4a_98.pdb"
Chain information for State4a_98.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> hide #!1 models
> close session
> open "/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final
> Structures/Maps/J98 z flip.mrc"
Opened J98 z flip.mrc as #1, grid size 280,280,280, pixel 0.86, shown at level
0.0408, step 2, values float32
> surface dust #1 size 8.6
> open "/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final
> Structures/State4a_98-121324_real_space_refined_027.pdb"
Chain information for State4a_98-121324_real_space_refined_027.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> volume #1 level 0.03299
> transparency 50
> set bgColor white
> set bgColor #ffffff00
> lighting soft
> open
> /Users/chhandoseeganguly/Desktop/Cas12a_models/Half_maps/J98_008_volume_map_half_A.mrc
Opened J98_008_volume_map_half_A.mrc as #3, grid size 280,280,280, pixel 0.86,
shown at level 0.322, step 2, values float32
> open
> /Users/chhandoseeganguly/Desktop/Cas12a_models/Half_maps/J98_008_volume_map_half_B.mrc
Opened J98_008_volume_map_half_B.mrc as #4, grid size 280,280,280, pixel 0.86,
shown at level 0.323, step 2, values float32
> volume flip #3
Opened J98_008_volume_map_half_A.mrc z flip as #5, grid size 280,280,280,
pixel 0.86, shown at step 1, values float32
> volume flip #4
Opened J98_008_volume_map_half_B.mrc z flip as #6, grid size 280,280,280,
pixel 0.86, shown at step 1, values float32
> volume #5 level 0.1226
> volume #5 level 0.3097
> save "/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final
> Structures/Maps/98_half_map_A_zflipped.mrc" models #5
> save "/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final
> Structures/Maps/98_half_map_B_zflipped.mrc" models #6
> volume #5 level 0.4848
> volume #5 level 0.3335
> hide #!1 models
> volume #5 level 0.242
> surface dust #5 size 8.6
> volume #5 level 0.1306
> volume #5 level 0.16
> volume #5 level 0.17
> volume #5 level 0.18
> volume #5 level 0.16
> surface dust #6 size 8.6
> volume #6 level 0.16
> hide #!6 models
> show #!1 models
> hide #!2 models
> volume #!1 style surface
> color #1 #797979ff models
> volume #!1 step 1
> volume #1 level 0.03581
> save "/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final
> Structures/Maps/S4a_J98.tif" width 893 height 939 supersample 3
> transparentBackground true
> save "/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final
> Structures/Maps/S4a_98.png" width 893 height 939 supersample 3
> transparentBackground true
> show #!2 models
> hide #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 2/B
> select /B:-19
22 atoms, 24 bonds, 1 residue, 1 model selected
> select /B
764 atoms, 854 bonds, 36 residues, 1 model selected
> open "/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final
> Structures/State4a_98-121324_real_space_refined_027.pdb"
Chain information for State4a_98-121324_real_space_refined_027.pdb #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> open
> /Users/chhandoseeganguly/Desktop/Cas12a_models/Half_maps/J94_008_volume_map_half_A.mrc
> /Users/chhandoseeganguly/Desktop/Cas12a_models/Half_maps/J94_008_volume_map_half_B.mrc
Opened J94_008_volume_map_half_A.mrc as #8.1, grid size 280,280,280, pixel
0.86, shown at level 0.311, step 2, values float32
Opened J94_008_volume_map_half_B.mrc as #8.2, grid size 280,280,280, pixel
0.86, shown at level 0.312, step 2, values float32
> hide #!7 models
> hide #!8 models
> close session
> open
> /Users/chhandoseeganguly/Desktop/Cas12a_models/Half_maps/J94_008_volume_map_half_A.mrc
Opened J94_008_volume_map_half_A.mrc as #1, grid size 280,280,280, pixel 0.86,
shown at level 0.311, step 2, values float32
> open
> /Users/chhandoseeganguly/Desktop/Cas12a_models/Half_maps/J94_008_volume_map_half_B.mrc
Opened J94_008_volume_map_half_B.mrc as #2, grid size 280,280,280, pixel 0.86,
shown at level 0.312, step 2, values float32
> open "/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final
> Structures/Maps/J94 z flip.mrc"
Opened J94 z flip.mrc as #3, grid size 280,280,280, pixel 0.86, shown at level
0.059, step 2, values float32
> volume flip #1
Opened J94_008_volume_map_half_A.mrc z flip as #4, grid size 280,280,280,
pixel 0.86, shown at step 1, values float32
> volume flip #2
Opened J94_008_volume_map_half_B.mrc z flip as #5, grid size 280,280,280,
pixel 0.86, shown at step 1, values float32
> open "/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final
> Structures/State3_94 121324_real_space_refined_030.pdb"
Chain information for State3_94 121324_real_space_refined_030.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> surface dust #3 size 8.6
> surface dust #4 size 8.6
> surface dust #5 size 8.6
> transparency #3.1#4.1#5.1 50
> volume #3 level 0.082
> volume #!3-5 style surface
> color #3 #797979ff models
> volume #3 level 0.07048
> volume #!3-5 step 1
> volume #3 level 0.06516
> hide #!3 models
> hide #!5 models
> volume #4 level 0.2766
> volume #4 level 0.2268
> volume #4 level 0.1847
> volume #4 level 0.1426
> surface dust #4 size 8.6
> volume #4 level 0.177
> save "/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final
> Structures/Maps/94_half_map_A_zflipped.mrc" models #4
> save "/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final
> Structures/Maps/94_half_map_B_zflipped.mrc" models #5
> volume #5 level 0.177
> hide #!3 models
> show #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> save "/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final
> Structures/Maps/S3_94.png" width 597 height 939 supersample 3
> transparentBackground true
> close session
> open "/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final
> Structures/J96_State2/J96 z flip.mrc"
Opened J96 z flip.mrc as #1, grid size 280,280,280, pixel 0.86, shown at level
0.0288, step 2, values float32
> open "/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final
> Structures/J96_State2/State2_96_121324_real_space_refined_029.pdb"
Chain information for State2_96_121324_real_space_refined_029.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open
> /Users/chhandoseeganguly/Desktop/Cas12a_models/Half_maps/J96_008_volume_map_half_A.mrc
Opened J96_008_volume_map_half_A.mrc as #3, grid size 280,280,280, pixel 0.86,
shown at level 0.311, step 2, values float32
> open
> /Users/chhandoseeganguly/Desktop/Cas12a_models/Half_maps/J96_008_volume_map_half_B.mrc
Opened J96_008_volume_map_half_B.mrc as #4, grid size 280,280,280, pixel 0.86,
shown at level 0.311, step 2, values float32
> surface dust #1 size 8.6
> surface dust #3 size 8.6
> surface dust #4 size 8.6
> volume flip #3
Opened J96_008_volume_map_half_A.mrc z flip as #5, grid size 280,280,280,
pixel 0.86, shown at step 1, values float32
> volume flip #4
Opened J96_008_volume_map_half_B.mrc z flip as #6, grid size 280,280,280,
pixel 0.86, shown at step 1, values float32
> volume #3 level 0.16
> close #3
> close #4
> volume #5 level 0.177
> volume #5 level 0.2
> volume #5 level 0.3
> hide #!1 models
> hide #!6 models
===== 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 '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 M1
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: iMac
Model Identifier: iMac21,1
Model Number: Z12Q000NULL/A
Chip: Apple M1
Total Number of Cores: 8 (4 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: 4 days, 7 hours, 21 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 4.5K (4480 x 2520)
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: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
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-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-Clipper: 0.22.4
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: 1.7.1
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-ISOLDE: 1.7.1
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-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.2.2
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-QScore: 1.1
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
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
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
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
MolecularDynamicsViewer: 1.4
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
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
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
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
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
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
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
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
Change History (2)
comment:1 by , 10 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 10 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Chhandosee,
--Eric