![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 23 months ago
Closed 23 months ago
#10309 closed defect (can't reproduce)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| 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-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6rc202304150037 (2023-04-15 00:37:23 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 0x00007ff84f853b40 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/_internal.py", line 251 in __init__
File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molc.py", line 322 in pointer
File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molc.py", line 240 in set_cvec_pointer
File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 122 in __init__
File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 382 in __init__
File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molobject.py", line 2186 in process_changes
File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molobject.py", line 2191 in changes
File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/changes.py", line 25 in check_for_changes
File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 58 in draw_new_frame
File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 280000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,2",
"coalitionID" : 5276,
"osVersion" : {
"train" : "macOS 14.1.1",
"build" : "23B81",
"releaseType" : "User"
},
"captureTime" : "2023-12-08 13:15:36.9641 +0100",
"codeSigningMonitor" : 0,
"incident" : "8CE7EFF0-F16F-49C3-BCA0-2345DF76FE26",
"pid" : 90015,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-12-08 12:22:44.3893 +0100",
"procStartAbsTime" : 285277527570301,
"procExitAbsTime" : 288450010184216,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6-rc2023.04.15.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.0","CFBundleVersion":"1.6.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"D4B84B47-846E-5515-A255-E5818514FA5B","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "9B98626C-34AA-4037-BF37-43F9688AEC0C",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 13004,
"bridgeVersion" : {"build":"21P1069","train":"8.1"},
"sleepWakeUUID" : "3E428BA1-6870-4426-B693-34DB2CB0F205",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140737487716183\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff64000-7ffffff65000 [ 4K] r-x\/r-x SM=SHM ",
"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":90015},
"ktriageinfo" : "VM - (arg = 0x0) Waiting on busy page was interrupted\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140737487716183\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff64000-7ffffff65000 [ 4K] r-x\/r-x SM=SHM ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.6rc202304150037 (2023-04-15)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show AlphaFold
> alphafold predict
> VKLENILIKNGGGHGRDTYGASGKIAKGDAKKSDSDVYSIDEIL,MSFFQFIKGDERKMNQHVKVTFDFTNYNYGTYDLAVPAYLPIKNLIALVLDSLDISIFDVNTQIKVMTKGQLLVENDRLIDYQIADGDILKLL
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/gabrielumajioka/Downloads/ChimeraX/AlphaFold/prediction_78
> open
> /Users/gabrielumajioka/Downloads/ChimeraX/AlphaFold/prediction_78/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> alphafold predict
> VKLENILIKNGGGHGRDTYGASGKIAKGDAKKSDSDVYSIDEIL,DKTIYMINDYGQLQAINKDLS
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/gabrielumajioka/Downloads/ChimeraX/AlphaFold/prediction_79
> open
> /Users/gabrielumajioka/Downloads/ChimeraX/AlphaFold/prediction_79/best_model.pdb
Chain information for best_model.pdb #2
---
Chain | Description
A | No description available
B | No description available
> hide #2 models
> show #2 models
> hide #1 models
> alphafold pae #2 file
> /Users/gabrielumajioka/Downloads/ChimeraX/AlphaFold/prediction_79/best_model_pae.json
> color #2/A:5-37 lime
> color #2/B:8-17 lime
> color #2/A:4-37 magenta
> alphafold pae #2 colorDomains true
> ui tool show "Show Sequence Viewer"
> sequence chain #2/B
Alignment identifier is 2/B
> select #2/B:21
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/B
170 atoms, 171 bonds, 21 residues, 1 model selected
> color sel magenta
> select #2/A
325 atoms, 327 bonds, 44 residues, 1 model selected
> color sel light gray
> select clear
> save "/Users/gabrielumajioka/Desktop/project T7SS /T7SS structure
> related/bioinformatic/SAO_YukB_Btb_vs_Toxin_prepretoxinmotiv.cxs"
> open "/Users/gabrielumajioka/Desktop/project T7SS /T7SS structure
> related/SAO_YukB_BtB_YukD_PPTXmotv.cxs"
opened ChimeraX session
> close
> open "/Users/gabrielumajioka/Desktop/project T7SS /T7SS structure
> related/SAO_YukB_BtB_YukD_PPTXmotv.cxs"
opened ChimeraX session
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> sequence chain /B
Alignment identifier is 1/B
> sequence chain /C
Alignment identifier is 1/C
> open
> /Users/gabrielumajioka/Downloads/ChimeraX/AlphaFold/prediction_79/best_model.pdb
Chain information for best_model.pdb #2
---
Chain | Description
A | No description available
B | No description available
> hide #2 models
> show #2 models
> select add #2
665 atoms, 669 bonds, 86 residues, 2 models selected
> hide #1 models
> select add #1
1782 atoms, 1802 bonds, 227 residues, 2 models selected
> select subtract #1
495 atoms, 498 bonds, 65 residues, 1 model selected
> show #1 models
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-17.774,0,1,0,34.757,0,0,1,-12.016
> select #2/A
325 atoms, 327 bonds, 44 residues, 1 model selected
> color sel white
> select #2/B
170 atoms, 171 bonds, 21 residues, 1 model selected
> color sel magenta
> select clear
> select add #2
495 atoms, 498 bonds, 65 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.26188,0.91932,-0.29373,-18.175,-0.87555,-0.35434,-0.32842,40.457,-0.406,0.17117,0.8977,-11.771
> view matrix models
> #2,-0.37625,0.88556,0.27243,-16.049,-0.92643,-0.36366,-0.097363,41.322,0.012853,-0.28902,0.95724,-11.258
> view matrix models
> #2,0.066154,0.89172,0.44773,-16.737,-0.98009,-0.026126,0.19685,41.279,0.18723,-0.45184,0.87223,-11.468
> view matrix models
> #2,-0.076723,0.82126,-0.56537,-19.184,-0.97598,-0.17782,-0.12586,40.778,-0.2039,0.54213,0.81518,-13.751
> view matrix models
> #2,-0.39737,0.6668,-0.63045,-18.019,-0.87009,-0.4921,0.02794,41.958,-0.29162,0.55965,0.77573,-13.688
> view matrix models
> #2,-0.64379,0.56386,-0.5173,-16.682,-0.73416,-0.64576,0.20979,42.629,-0.21576,0.51484,0.82969,-13.588
> view matrix models
> #2,-0.60641,0.70218,-0.37312,-16.789,-0.79507,-0.54237,0.27149,42.65,-0.011732,0.46128,0.88717,-13.796
> view matrix models
> #2,-0.42776,0.79932,-0.42204,-17.73,-0.90382,-0.37208,0.21136,42.22,0.011915,0.47186,0.88159,-13.911
> view matrix models
> #2,-0.66462,0.63827,-0.38846,-16.474,-0.74717,-0.56476,0.3504,42.83,0.0042678,0.52313,0.85224,-14.142
> select add #1
1782 atoms, 1802 bonds, 227 residues, 2 models selected
> select subtract #2
1287 atoms, 1304 bonds, 162 residues, 1 model selected
> view matrix models
> #1,0.91137,-0.24024,-0.33419,0.098075,0.1648,0.95704,-0.23855,-0.3079,0.37715,0.16233,0.91182,-0.6378
> view matrix models
> #1,0.94814,0.047907,-0.31421,0.26087,-0.081321,0.99224,-0.094109,0.20005,0.30726,0.11478,0.94468,-0.54038
> view matrix models
> #1,0.94912,0.048674,-0.31112,0.25837,-0.081314,0.99236,-0.092808,0.19969,0.30423,0.11338,0.94583,-0.53549
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.94912,0.048674,-0.31112,7.0268,-0.081314,0.99236,-0.092808,-20.437,0.30423,0.11338,0.94583,-6.9056
> ui tool show AlphaFold
> help help:user/tools/alphafold.html
> alphafold predict
> MSFFQFIKGDERKMNQHVKVTFDFTNYNYGTYDLAVPAYLPIKNLIALVLDSLDISIFDVNTQIKVMTKGQLLVENDRLIDYQIADGDILKLL,VKLENILIKNGGGHGRDTYGASGKIAKGDAKKSDSDVYSIDEIL
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/gabrielumajioka/Downloads/ChimeraX/AlphaFold/prediction_80
> open
> /Users/gabrielumajioka/Downloads/ChimeraX/AlphaFold/prediction_80/best_model.pdb
Chain information for best_model.pdb #3
---
Chain | Description
A | No description available
B | No description available
> select add #2
1782 atoms, 1802 bonds, 227 residues, 2 models selected
> select subtract #2
1287 atoms, 1304 bonds, 162 residues, 1 model selected
> select add #3
2368 atoms, 2400 bonds, 299 residues, 2 models selected
> select subtract #1
1081 atoms, 1096 bonds, 137 residues, 1 model selected
> view matrix models #3,1,0,0,14.872,0,1,0,-47.034,0,0,1,15.977
> view matrix models #3,1,0,0,28.952,0,1,0,-73.398,0,0,1,0.38853
> select #3/A
756 atoms, 769 bonds, 93 residues, 1 model selected
> color sel orange
> select clear
> select #3/B
325 atoms, 327 bonds, 44 residues, 1 model selected
> color sel white
> select clear
> select add #3
1081 atoms, 1096 bonds, 137 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.99773,-0.065708,0.014415,29.151,0.066419,0.99621,-0.056137,-73.156,-0.010672,0.056968,0.99832,0.17168
> view matrix models
> #3,0.75751,-0.4448,0.47784,28.896,0.26977,0.87982,0.39132,-74.095,-0.59447,-0.16753,0.78647,1.3904
> view matrix models
> #3,0.58285,-0.69781,0.41635,29.959,0.6299,0.71169,0.31101,-72.976,-0.51334,0.080986,0.85436,0.26742
> view matrix models
> #3,0.3252,-0.90016,0.28975,31,0.5199,0.42613,0.74035,-73.395,-0.7899,-0.09012,0.60657,1.5847
> view matrix models
> #3,0.48592,-0.82392,0.2916,30.799,0.17803,0.41995,0.88991,-74.074,-0.85568,-0.38052,0.35075,3.5056
> view matrix models
> #3,0.35778,-0.88895,0.28595,30.989,0.45721,0.43377,0.7764,-73.582,-0.81422,-0.14704,0.56163,1.937
> view matrix models
> #3,0.63381,-0.35183,0.68885,27.763,-0.76328,-0.42871,0.48333,-70.044,0.12527,-0.83212,-0.54026,8.7828
> view matrix models
> #3,0.77879,0.43754,0.44949,25.654,-0.62594,0.49526,0.60242,-73.869,0.04097,-0.75052,0.65958,4.4021
> view matrix models
> #3,0.31191,-0.1341,0.9406,25.903,-0.79677,0.50236,0.33583,-73.103,-0.51756,-0.85419,0.049845,6.5107
> view matrix models
> #3,0.17202,-0.43846,0.88214,27.172,-0.19515,0.86257,0.46679,-74.556,-0.96557,-0.25244,0.062812,3.9199
> view matrix models
> #3,-0.53719,-0.65566,0.53059,28.758,-0.50289,0.754,0.42259,-74.176,-0.67715,-0.039816,-0.73477,5.9557
> view matrix models
> #3,-0.74138,-0.62118,-0.25396,31.136,-0.66958,0.71006,0.21789,-73.422,0.044978,0.33159,-0.94235,5.6664
> view matrix models
> #3,-0.78122,-0.60213,-0.16473,30.742,-0.61441,0.78833,0.03226,-73.064,0.11043,0.12641,-0.98581,6.6293
> view matrix models
> #3,-0.85682,-0.51497,-0.025656,29.9,-0.48072,0.81585,-0.3214,-71.904,0.18644,-0.26305,-0.9466,8.0207
> view matrix models
> #3,-0.89319,-0.44888,0.026897,29.452,-0.40268,0.77176,-0.49217,-71.119,0.20017,-0.45043,-0.87008,8.4836
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6rc202304150037 (2023-04-15)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-22.1.28
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2,3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2020.41.1.0.0 (iBridge: 21.16.1069.0.0,0)
OS Loader Version: 580~743
Software:
System Software Overview:
System Version: macOS 14.1.1 (23B81)
Kernel Version: Darwin 23.1.0
Time since boot: 9 days, 3 hours, 3 minutes
Graphics/Displays:
Intel Iris Plus Graphics 655:
Chipset Model: Intel Iris Plus Graphics 655
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea5
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG UltraFine:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 806NTKF1F589
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9
ChimeraX-AddH: 2.2.4
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
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: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
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: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6rc202304150037
ChimeraX-CoreFormats: 1.1
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: 1.1.1
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: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
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: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.2
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: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.4.1
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.2.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
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: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 23 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 , 23 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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