![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Closed 15 months ago
#15643 closed defect (duplicate)
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-14.4.1-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 0x00007ff8527ac100 (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 1613 in remove_deleted_pointers
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 134 in __init__
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 391 in __init__
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2226 in process_changes
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2231 in changes
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 36 in check_for_changes
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 69 in draw_new_frame
File "/Applications/ChimeraX-1.7.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.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.surface._surface, 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.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.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 55)
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{
"uptime" : 110000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "iMac20,1",
"coalitionID" : 4188,
"osVersion" : {
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"build" : "23E224",
"releaseType" : "User"
},
"captureTime" : "2024-07-20 18:34:55.1338 +0100",
"codeSigningMonitor" : 0,
"incident" : "BD2F5230-694C-45E9-8CA6-AC5A11110345",
"pid" : 78508,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-07-20 18:15:40.2151 +0100",
"procStartAbsTime" : 112361448316989,
"procExitAbsTime" : 113516353966582,
"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":"F8CBA00B-4C73-5861-A9DF-4647AA77FA4B","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "BD311670-CA44-CC15-4795-472285C0C952",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 109732,
"bridgeVersion" : {"build":"21P4222","train":"8.4"},
"sleepWakeUUID" : "2228FC4F-DF63-4E18-9F26-15C74E9CE96D",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 4404170583\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 106825000-106829000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.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":78508},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 4404170583\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 106825000-106829000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
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/will/Downloads/tetramermodelsaturday.pdb format pdb
Summary of feedback from opening
/Users/will/Downloads/tetramermodelsaturday.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 241
VAL A 255 1 15
Start residue of secondary structure not found: HELIX 2 2 SER A 290 THR A 298
1 9
Start residue of secondary structure not found: HELIX 3 3 ASP A 301 ILE A 321
1 21
Start residue of secondary structure not found: HELIX 4 4 LYS A 338 LYS A 340
1 3
Start residue of secondary structure not found: HELIX 5 5 THR A 378 MET A 382
1 5
37 messages similar to the above omitted
Chain information for tetramermodelsaturday.pdb
---
Chain | Description
1.1/A | No description available
1.2/A | No description available
1.3/A | No description available
1.4/B | No description available
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.2 models
> show #1.2 models
> hide #1.1 models
> show #1.1 models
> hide #1.2 models
> show #1.2 models
> hide #1.3 models
> show #1.3 models
> hide #!1.4 models
> hide #1.3 models
> close #1.3
> close #1.4
> save /Users/will/Downloads/selenA.pdb
> close #1
> open /Users/will/Downloads/x1226/sculpt_tetramermodelsaturday.pdb format pdb
No such file/path:
/Users/will/Downloads/x1226/sculpt_tetramermodelsaturday.pdb
> open /Users/will/Downloads/tetramermodelsaturday.pdb format pdb
Summary of feedback from opening
/Users/will/Downloads/tetramermodelsaturday.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 241
VAL A 255 1 15
Start residue of secondary structure not found: HELIX 2 2 SER A 290 THR A 298
1 9
Start residue of secondary structure not found: HELIX 3 3 ASP A 301 ILE A 321
1 21
Start residue of secondary structure not found: HELIX 4 4 LYS A 338 LYS A 340
1 3
Start residue of secondary structure not found: HELIX 5 5 THR A 378 MET A 382
1 5
37 messages similar to the above omitted
Chain information for tetramermodelsaturday.pdb
---
Chain | Description
1.1/A | No description available
1.2/A | No description available
1.3/A | No description available
1.4/B | No description available
> hide #1.3 models
> hide #!1.4 models
> open /Users/will/Downloads/selenA.pdb
Chain information for selenA.pdb
---
Chain | Description
2.1/A | No description available
2.2/A | No description available
> hide #!2 models
> show #!2 models
> close #2
> show #1.3 models
> show #!1.4 models
> save /Users/will/Downloads/selenA.pdb models #1.1-2
> save /Users/will/Downloads/SelenB.pdb models #1.3-4
> save /Users/will/Downloads/selenA.pdb models #1.1
> save /Users/will/Downloads/SelenB.pdb models #1.2
> save /Users/will/Downloads/selenC.pdb models #1.3
> save /Users/will/Downloads/SelenD.pdb models #1.4
> hide #1.2 models
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> show #1.2 models
> show #1.3 models
> open /Users/will/Downloads/x1226/AutoBuild_run_159_/working_best_placed.pdb
Summary of feedback from opening
/Users/will/Downloads/x1226/AutoBuild_run_159_/working_best_placed.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK THIS IS AutoBuild_run_159_/working_best.pdb
Ignored bad PDB record found on line 2
REMARK WITH UNPLACED RESIDUES REMOVED
Ignored bad PDB record found on line 3
Sat Jul 20 16:19:27 2024
Chain information for working_best_placed.pdb #2
---
Chain | Description
U | No description available
> ui mousemode right "translate selected models"
> select clear
> select #2/U:715
4 atoms, 3 bonds, 1 residue, 1 model selected
> view matrix models #2,1,0,0,-2.991,0,1,0,-11.588,0,0,1,-23.305
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.74386,-0.58338,0.3261,-12.329,0.071743,-0.41541,-0.9068,71.561,0.66447,0.69793,-0.26715,42.516
> view matrix models
> #2,0.78767,-0.5741,0.22358,-6.1158,0.14997,-0.17332,-0.97338,71.152,0.59757,0.80023,-0.050424,27.085
> view matrix models
> #2,0.82085,-0.54974,0.15488,-2.2933,0.19189,0.010049,-0.98136,68.198,0.53794,0.83528,0.11374,16.196
> view matrix models
> #2,0.81932,-0.55116,0.15789,-2.4542,0.19026,0.0015985,-0.98173,68.38,0.54084,0.8344,0.10618,16.684
> view matrix models
> #2,0.76902,-0.58151,0.26544,-8.5843,0.12013,-0.27638,-0.95351,71.854,0.62783,0.76516,-0.14268,33.495
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.76902,-0.58151,0.26544,-3.3891,0.12013,-0.27638,-0.95351,40.697,0.62783,0.76516,-0.14268,4.676
> view matrix models
> #2,0.76902,-0.58151,0.26544,-15.088,0.12013,-0.27638,-0.95351,39.611,0.62783,0.76516,-0.14268,19.178
> close #2
> open /Users/will/Downloads/x1226/AutoBuild_run_158_/overall_best.pdb
Chain information for overall_best.pdb #2
---
Chain | Description
A | No description available
U | No description available
> ui tool show Matchmaker
> matchmaker #!2 to #1.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker tetramermodelsaturday.pdb, chain A (#1.1) with overall_best.pdb,
chain A (#2), sequence alignment score = 1018
RMSD between 110 pruned atom pairs is 1.386 angstroms; (across all 286 pairs:
3.127)
> hide #!1.4 models
> show #!1.4 models
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> open /Users/will/Downloads/x1226/AutoBuild_run_159_/working_best.pdb
Chain information for working_best.pdb #3
---
Chain | Description
U | No description available
Drag select of 2 residues
Drag select of 3 residues
> view matrix models #3,1,0,0,-40.017,0,1,0,-28.346,0,0,1,-56.695
> view matrix models #3,1,0,0,-31.43,0,1,0,-38.699,0,0,1,-63.463
> view matrix models #3,1,0,0,-27.277,0,1,0,-113.88,0,0,1,-80.336
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.60863,-0.75532,-0.24301,15.761,0.019834,0.32066,-0.94699,-32.854,0.7932,0.57155,0.21014,-56.335
> view matrix models
> #3,-0.86697,0.13725,-0.47909,86.333,-0.30623,-0.90514,0.29485,-105.3,-0.39318,0.40234,0.82676,-54.462
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.86697,0.13725,-0.47909,84.021,-0.30623,-0.90514,0.29485,-40.727,-0.39318,0.40234,0.82676,-39.514
> ui tool show "Show Sequence Viewer"
> sequence chain #1.1/A
Alignment identifier is 1.1/A
> sequence chain #1.2/A
Alignment identifier is 1.2/A
> sequence chain #1.3/A
Alignment identifier is 1.3/A
> sequence chain #1.4/B
Alignment identifier is 1.4/B
> close #1.2-3
> close #2
> select #1.4/B:191-192
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #1.4/B
2295 atoms, 2346 bonds, 289 residues, 1 model selected
> colour sel lime
> view matrix models #1.4,1,0,0,31.652,0,1,0,-6.2748,0,0,1,-3.733
> undo
> view matrix models #1.4,1,0,0,0.36801,0,1,0,0.72714,0,0,1,-0.28754
> undo
> select clear
Drag select of 7 residues
> view matrix models
> #1.1,1,0,0,-10.196,0,1,0,-1.8448,0,0,1,12.212,#3,-0.86697,0.13725,-0.47909,73.825,-0.30623,-0.90514,0.29485,-42.572,-0.39318,0.40234,0.82676,-27.302
> undo
> select add #1
4612 atoms, 4683 bonds, 580 residues, 4 models selected
> select subtract #1.1
2327 atoms, 2346 bonds, 294 residues, 3 models selected
> select add #1
4612 atoms, 4683 bonds, 580 residues, 4 models selected
> select subtract #1.4
2317 atoms, 2337 bonds, 291 residues, 3 models selected
> select add #3
3750 atoms, 3780 bonds, 504 residues, 3 models selected
> select add #1
6045 atoms, 6126 bonds, 793 residues, 4 models selected
> select subtract #1
1465 atoms, 1443 bonds, 218 residues, 1 model selected
> view matrix models
> #3,-0.86697,0.13725,-0.47909,74.037,-0.30623,-0.90514,0.29485,-44.226,-0.39318,0.40234,0.82676,-27.8
> view matrix models
> #3,-0.86697,0.13725,-0.47909,78.994,-0.30623,-0.90514,0.29485,-44.207,-0.39318,0.40234,0.82676,-34.393
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
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/will/Downloads/tetramermodelsaturday.pdb
Summary of feedback from opening
/Users/will/Downloads/tetramermodelsaturday.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 241
VAL A 255 1 15
Start residue of secondary structure not found: HELIX 2 2 SER A 290 THR A 298
1 9
Start residue of secondary structure not found: HELIX 3 3 ASP A 301 ILE A 321
1 21
Start residue of secondary structure not found: HELIX 4 4 LYS A 338 LYS A 340
1 3
Start residue of secondary structure not found: HELIX 5 5 THR A 378 MET A 382
1 5
37 messages similar to the above omitted
Chain information for tetramermodelsaturday.pdb
---
Chain | Description
1.1/A | No description available
1.2/A | No description available
1.3/A | No description available
1.4/B | No description available
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5500 XT OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
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: iMac20,1
Processor Name: 8-Core Intel Core i7
Processor Speed: 3.8 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.4222.0.0,0)
OS Loader Version: 580~1678
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 1 day, 7 hours, 50 minutes
Graphics/Displays:
AMD Radeon Pro 5500 XT:
Chipset Model: AMD Radeon Pro 5500 XT
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0041
ROM Revision: 113-D3220I-231
VBIOS Version: 113-D322A1XT-011
Option ROM Version: 113-D322A1XT-011
EFI Driver Version: 01.01.231
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
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 , 15 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 , 15 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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