![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 21 months ago
Closed 17 months ago
#14449 closed defect (fixed)
Crash in garbage collection
| 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-14.0-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 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 0x000000020260f240 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mmcif/__init__.py", line 123 in save
File "/Applications/ChimeraX-1.7.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 "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.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 "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 62 in display
File "/Applications/ChimeraX-1.7.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 "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 127 in
File "/Applications/ChimeraX-1.7.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, 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.pdb_lib._load_libs, 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, chimerax.mmcif.mmcif_write, lxml._elementpath, lxml.etree, lxml.builder (total: 56)
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"procRole" : "Foreground",
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"coalitionID" : 3361,
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"releaseType" : "User"
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"captureTime" : "2024-01-22 15:42:54.7018 -0800",
"codeSigningMonitor" : 1,
"incident" : "FE8CC674-BF6F-44AB-8BE1-5A25F8AC5AFB",
"pid" : 9038,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-01-22 14:32:12.3606 -0800",
"procStartAbsTime" : 1198668859285,
"procExitAbsTime" : 1300483024057,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"DC33E73C-FA52-5625-BB1C-E16B2534C308","thirdParty":true},
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"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "D90B7D68-427E-98ED-CD16-515C91CC8B65",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 4497,
"sleepWakeUUID" : "EDE8CA60-DD36-425C-80A2-C1E200AB93A8",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140723131826007\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffca848c000-7ffccdbac000 [599.1M] r-x\/r-x SM=COW ...t_id=a97e7b63",
"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":9038},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140723131826007\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffca848c000-7ffccdbac000 [599.1M] r-x\/r-x SM=COW ...t_id=a97e7b63",
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},
"reportNotes" : [
"PC register does not match crashing frame (0x0 vs 0x7FF8A3E2EA78)"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM
> final/Aged_C2_class/helix_aged_class2_refined.pdb" format pdb
Summary of feedback from opening
/Users/yiyingli/Library/CloudStorage/OneDrive-
UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM
final/Aged_C2_class/helix_aged_class2_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.005 0.040 64360
Ignored bad PDB record found on line 24
ANGLE : 0.775 8.973 87080
18 messages similar to the above omitted
Chain information for helix_aged_class2_refined.pdb #1
---
Chain | Description
A C E G I K M O Q S U W Y a c e g i k m | No description available
> close
> open "/Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM
> final/ATP_C2_class2/FtsH_ATP_class2_refined.pdb" format pdb
Summary of feedback from opening
/Users/yiyingli/Library/CloudStorage/OneDrive-
UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM
final/ATP_C2_class2/FtsH_ATP_class2_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.005 0.031 3218
Ignored bad PDB record found on line 24
ANGLE : 0.753 8.833 4354
18 messages similar to the above omitted
Chain information for FtsH_ATP_class2_refined.pdb #1
---
Chain | Description
A | No description available
> windowsize 900 900
> sym H,9.1,157.5,5,-2
Missing or invalid "structures" argument: only initial part "H" of atom
specifier valid
> sym c1*h,9.1,157.5,5,-2
Missing or invalid "structures" argument: invalid atomic structures specifier
> sym #1 c1*h,9.1,157.5,5,-2
Made 5 copies for FtsH_ATP_class2_refined.pdb symmetry c1*h,9.1,157.5,5,-2
> sym #1 shift,5,10
Made 5 copies for FtsH_ATP_class2_refined.pdb symmetry shift,5,10
> sym #1 c1*h,9.1,157.5,5,-2 axis 10,10,10
Made 5 copies for FtsH_ATP_class2_refined.pdb symmetry c1*h,9.1,157.5,5,-2
> open "/Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/TO SAVE DATA
> W3/cryosparc_P3_J171_006_volume_map_sym_sharp.mrc" format mrc
Opened cryosparc_P3_J171_006_volume_map_sym_sharp.mrc as #5, grid size
448,448,448, pixel 0.86, shown at level 0.894, step 2, values float32
> ui tool show Log
> volume #5 step 1
> ui tool show "Map Coordinates"
> view orient
> close #2
> close #3
> close #4
> view orient
> log metadata #1
No models had metadata
> log chains #1
Chain information for FtsH_ATP_class2_refined.pdb #1
---
Chain | Description
A | No description available
> ui tool show "Map Statistics"
> measure mapstats
Map cryosparc_P3_J171_006_volume_map_sym_sharp.mrc #5, minimum -2.2, maximum
6.847, mean 0.01989, SD 0.2062, RMS 0.2072
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> view
> view orient
> ui tool show "Side View"
> toolshed show
> coordinates
Unknown command: coordinates
> mapcoor
Unknown command: mapcoor
> info
4 models
#1, FtsH_ATP_class2_refined.pdb, hidden
3176 atoms, 3218 bonds, 406 residues, 1 chains (A)
0 missing structure
#1.1, missing structure, shown, 0 pseudobonds
#5, cryosparc_P3_J171_006_volume_map_sym_sharp.mrc, shown size 448,448,448,
step 1, voxel size 0.86, level 0.894, value range -2.2001 - 6.8468, value type
float32, 0 symmetry operators
#5.1, surface, shown, 3666688 triangles
> ui tool show "Map Statistics"
> measure mapstats
Map cryosparc_P3_J171_006_volume_map_sym_sharp.mrc #5, minimum -2.2, maximum
6.847, mean 0.01989, SD 0.2062, RMS 0.2072
> ui tool show "Map Coordinates"
> volume #5 origin
Missing "origin" keyword's argument
> volume #5 origin 0,0,0
> volume #5 originIndex0,0,0
Expected a keyword
> volume #5 originIndex 0,0,0
> view orient
> show #!1 models
> hide #!5 models
> sym #1 c1*h,9.1,157.5,5
Made 5 copies for FtsH_ATP_class2_refined.pdb symmetry c1*h,9.1,157.5,5
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> sym #1 c1*h,9.1,157.5,5,-223.5
Made 5 copies for FtsH_ATP_class2_refined.pdb symmetry c1*h,9.1,157.5,5,-223.5
> view
> ui tool show "Side View"
> sym #1 c1*h,9.1,157.5,5,-2
Made 5 copies for FtsH_ATP_class2_refined.pdb symmetry c1*h,9.1,157.5,5,-2
> hide #!2 models
> close #2
> close #3
> close #4
> show #!1 models
> view
> sym #1 c1*h,9.1,157.5,5,-2 axis 0,0,1
Made 5 copies for FtsH_ATP_class2_refined.pdb symmetry c1*h,9.1,157.5,5,-2
> view
> close #2
> show #!1 models
> show #!5 models
> hide #!5 models
> view
> sym #1 c1*h,9.1,157.5,5,-2 coordinateSystem #5
Made 5 copies for FtsH_ATP_class2_refined.pdb symmetry c1*h,9.1,157.5,5,-2
> view
> select add #2
15880 atoms, 16090 bonds, 2030 residues, 6 models selected
> close #2
> show #!1 models
> sym #1 c1*h,9.1,157.5,5,-2 coordinateSystem #5 biomtSet true
Expected a keyword
> sym #1 c1*h,9.1,157.5,5,-2 coordinateSystem #5 biomtSet True
Expected a keyword
> sym #1 c1*h,9.1,157.5,5,-2 coordinateSystem #5 biomtSet true
Expected a keyword
> sym #1 c1*h,9.1,157.5,5,-2 biomtSet true coordinateSystem #5
Expected a keyword
> sym #1 c1*h,9.1,157.5,5,-2 axis 0,0,1 biomtSet
Expected a keyword
> sym #1 c1*h,9.1,157.5,5,-2 axis 0,0,1 biomt true
Expected a keyword
> sym #1 c1*h,9.1,157.5,5,-2 axis 0,0,1 BIOMT
Expected a keyword
> sym #1 c1*h,9.1,157.5,5,-2 axis 0,0,1 bioMT
Expected a keyword
> sym #1 c1*h,9.1,157.5,5,-2 axis 0,0,1 bio
Expected a keyword
> sym #1 c1*h,9.1,157.5,5,-2 axis 0,0,1 biomt
Expected a keyword
> sym #1 c1*h,9.1,157.5,5,-2 axis 0,0,1
Made 5 copies for FtsH_ATP_class2_refined.pdb symmetry c1*h,9.1,157.5,5,-2
No model chosen to save relative to
> save /Users/yiyingli/Desktop/5subunit.cif relModel #5
Not saving entity_poly_seq for non-authoritative sequences
> biomt
Unknown command: biomt
> help help:user
> sym #1 biomt c1*h,9.1,157.5,5,-2 axis 0,0,1
Expected a keyword
> sym #1 biomt true c1*h,9.1,157.5,5,-2 axis 0,0,1
Expected a keyword
> sym #1 biomt
Molecule FtsH_ATP_class2_refined.pdb has no biological unit info
> sym #1 biomt matri
Expected a keyword
> sym #1 biomt1
Unknown symmetry group "biomt1"
> sym #1 biomtSet
Unknown symmetry group "biomtSet"
> sym #1 biomtSet true
Expected a keyword
> sym #1 c1*h,9.1,157.5,5 biomtSet true
Expected a keyword
> toolshed show
> sym #1 c1*h,9.1,157.5,5 addMmcifAssembly true
Made 5 copies for FtsH_ATP_class2_refined.pdb symmetry c1*h,9.1,157.5,5
No model chosen to save relative to
> save /Users/yiyingli/Desktop/5subunit2.cif relModel #5
Not saving entity_poly_seq for non-authoritative sequences
> open /Users/yiyingli/Desktop/ATP_group1.pdb
Summary of feedback from opening /Users/yiyingli/Desktop/ATP_group1.pdb
---
warning | Ignored bad PDB record found on line 3180
Chain information for ATP_group1.pdb #4
---
Chain | Description
A | No description available
> open /Users/yiyingli/Desktop/ATP_group1.pdb
Summary of feedback from opening /Users/yiyingli/Desktop/ATP_group1.pdb
---
warning | Ignored bad PDB record found on line 3180
Chain information for ATP_group1.pdb #6
---
Chain | Description
A | No description available
> hide #!2 models
> show #!1 models
> hide #!2.1 models
> close #2
> close #3
> close #6
> show #!5 models
> hide #!4 models
> hide #!1 models
> show #!4 models
> hide #!5 models
> show #!5 models
> view orient
> show #!1 models
> close #1
> hide #!5 models
> show #!5 models
> volume #5 level 1
> volume #5 level 1.5
> view
> view orient
> hide #!5 models
> sym #4 c1*h,9.1,157.5,5 addMmcifAssembly true
Made 5 copies for ATP_group1.pdb symmetry c1*h,9.1,157.5,5
> view
> save /Users/yiyingli/Desktop/5subunit.cif relModel #5
Not saving entity_poly_seq for non-authoritative sequences
> sym #4 c1*h,9.1,157.5,5 biomt
Expected a keyword
> sym #4 biomt
Molecule ATP_group1.pdb has no biological unit info
> sym #4 c1*h,9.1,157.5,5 addMmcifAssembly true copies true
Made 5 copies for ATP_group1.pdb symmetry c1*h,9.1,157.5,5
> hide #!1 models
> show #!1 models
> close #1
> combine #2
Remapping chain ID 'A' in ATP_group1.pdb #2.2 to 'B'
Remapping chain ID 'A' in ATP_group1.pdb #2.3 to 'C'
Remapping chain ID 'A' in ATP_group1.pdb #2.4 to 'D'
Remapping chain ID 'A' in ATP_group1.pdb #2.5 to 'E'
> save /Users/yiyingli/Desktop/5subunit.cif relModel #5
Not saving entity_poly_seq for non-authoritative sequences
> sym #4 c1*h,9.1,157.5,5 addMmcifAssembly true copies true
Made 5 copies for ATP_group1.pdb symmetry c1*h,9.1,157.5,5
> sym #4 c1*h,9.1,157.5,5 addMmcifAssembly false copies true
Made 5 copies for ATP_group1.pdb symmetry c1*h,9.1,157.5,5
> close #4
> close #3
> close #2
> close #6
> hide #!1 models
> show #!1 models
> sym #1 c1*h,9.1,157.5,5 addMmcifAssembly false copies true
Made 5 copies for combination symmetry c1*h,9.1,157.5,5
> hide #!2 models
> show #!2 models
> save /Users/yiyingli/Desktop/5subunit_noaddMmcif.cif models #2 relModel #5
Not saving entity_poly_seq for non-authoritative sequences
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M2
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: Mac14,2
Model Number: FLY13LL/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.1.1
OS Loader Version: 10151.1.1
Software:
System Software Overview:
System Version: macOS 14.0 (23A344)
Kernel Version: Darwin 23.0.0
Time since boot: 3 days, 7 hours, 40 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
DELL U2414H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 50.00Hz
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.13
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: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
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-Core: 1.7
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
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: 1.5.13
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: 1.0.3
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: 1.12.3
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: 1.33.2
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: 0.2.0
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: 4.47.0
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: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
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: 10.0.1
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: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
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: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 21 months ago
| Cc: | added |
|---|---|
| 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 , 17 months ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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Fixed in 1.8 release candidate