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Opened 19 months ago
Closed 19 months ago
#14937 closed defect (duplicate)
Crash in python_instances_of_class
| 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-13.6.3-x86_64-i386-64bit
ChimeraX Version: 1.8.dev202403210048 (2024-03-21 00:48:29 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007000116ec000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700007e06000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007ff85fb85780 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 44 in python_instances_of_class
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 176 in _copy_custom_attrs
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 149 in combine
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/mod.py", line 522 in bind
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/mod.py", line 376 in cn_peptide_bond
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/cmd.py", line 205 in cmd_join_peptide
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/tool.py", line 774 in _jm_apply_cb
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/tool.py", line 1193 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, 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, 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, chimerax.chem_group._chem_group, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atom_search.ast, chimerax.dssp._dssp (total: 60)
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{
"uptime" : 550000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 13774,
"osVersion" : {
"train" : "macOS 13.6.3",
"build" : "22G436",
"releaseType" : "User"
},
"captureTime" : "2024-04-08 14:41:33.5493 -0700",
"incident" : "E8858DD8-0EB4-4BF9-92D7-8E184E517E21",
"pid" : 99418,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-04-08 14:22:22.9902 -0700",
"procStartAbsTime" : 556385885610346,
"procExitAbsTime" : 557536420396158,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"7C6B2945-57E4-54F2-8371-8C23A25F1144","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "4B8C08D7-14BD-7948-C61A-CC411D179A37",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 20002,
"bridgeVersion" : {"build":"21P2057","train":"8.2"},
"sleepWakeUUID" : "4470E603-5409-4DED-9EC4-7C06B576561A",
"sip" : "enabled",
"vmRegionInfo" : "0x1 is not in any region. Bytes before following region: 140737487351807\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff0b000-7ffffff0c000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000001","rawCodes":[1,1],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000001"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":99418},
"vmregioninfo" : "0x1 is not in any region. Bytes before following region: 140737487351807\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff0b000-7ffffff0c000 [ 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: 1.8.dev202403210048 (2024-03-21)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/yingyingjin/Box Sync/Alpha-S/NAC PDB
> build/NAC_rebuild/102723_tutorial/NAC_cylindrin.pdb"
Chain information for NAC_cylindrin.pdb
---
Chain | Description
1.1/? 1.2/? 1.3/? 1.4/? 1.5/? 1.6/? | No description available
> open "/Users/yingyingjin/Box Sync/Alpha-S/NAC PDB
> build/NAC_rebuild/102723_tutorial/preNAC_cylindrin.pdb"
Chain information for preNAC_cylindrin.pdb
---
Chain | Description
2.1/? 2.2/? 2.3/? 2.4/? 2.5/? 2.6/? | No description available
> show cartoons
> hide atoms
> hide #2.1 models
> hide #2.3 models
> hide #2.5 models
> show #2.5 models
> hide #2.4 models
> show #2.4 models
> hide #2.6 models
> show #2.6 models
> hide #2.5 models
> show #2.5 models
> hide #2.6 models
> show #2.6 models
> hide #2.2 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> hide #1.5 models
> show #1.5 models
> hide #1.4 models
> show #1.4 models
> hide #1.6 models
> show #1.6 models
> show #1.1 models
> hide #1.1 models
> hide #1.2 models
> select clear
Drag select of 63 residues
> save "/Users/yingyingjin/Desktop/NAC_paper/structure PDB/NACpreNACmodel.pdb"
> displayedOnly true
Drag select of 63 residues
> select clear
> save "/Users/yingyingjin/Desktop/NAC_paper/structure PDB/NACpreNACmodel.pdb"
> selectedOnly true
> ui tool show "Change Chain IDs"
> select add #1.1
139 atoms, 138 bonds, 11 residues, 1 model selected
> select subtract #1.1
Nothing selected
> save "/Users/yingyingjin/Desktop/NAC_paper/structure
> PDB/NACpreNACmodel.mol2"
> select add #1.1
139 atoms, 138 bonds, 11 residues, 1 model selected
> select add #1.2
278 atoms, 276 bonds, 22 residues, 2 models selected
> select add #1.3
417 atoms, 414 bonds, 33 residues, 3 models selected
> select add #2.1
551 atoms, 548 bonds, 43 residues, 4 models selected
> select add #2.2
685 atoms, 682 bonds, 53 residues, 5 models selected
> select subtract #2.2
551 atoms, 548 bonds, 43 residues, 4 models selected
> select add #2.2
685 atoms, 682 bonds, 53 residues, 5 models selected
> select add #2.3
819 atoms, 816 bonds, 63 residues, 6 models selected
> hide #1.4 models
> hide #1.5 models
> hide #1.6 models
> hide #2.4 models
> hide #2.5 models
> hide #2.6 models
> delete atoms #!1-2
> delete bonds #!1-2
> show #2.1 models
> show #2.2 models
> show #2.3 models
> show #1.1 models
> show #1.2 models
> show #1.3 models
> delete atoms sel
> delete bonds sel
> show #1.4 models
> show #1.5 models
> show #1.6 models
> show #2.4 models
> show #2.5 models
> show #2.6 models
> save "/Users/yingyingjin/Desktop/NAC_paper/structure
> PDB/NACpreNACmodel.mol2"
> save "/Users/yingyingjin/Desktop/NAC_paper/structure PDB/nacprenac.cxs"
> ui tool show "Change Chain IDs"
> changechains A
Chain IDs of 63 residues changed
> changechains A
Chain IDs of 0 residues changed
> changechains #* B
Chain IDs of 63 residues changed
> select add #1.4
139 atoms, 138 bonds, 11 residues, 1 model selected
> changechains sel A
Chain IDs of 11 residues changed
> select subtract #1.4
Nothing selected
> select add #1.5
139 atoms, 138 bonds, 11 residues, 1 model selected
> changechains sel B
Chain IDs of 0 residues changed
> changechains sel B
Chain IDs of 0 residues changed
> select subtract #1.5
Nothing selected
> select add #1.4
139 atoms, 138 bonds, 11 residues, 1 model selected
> select add #1.5
278 atoms, 276 bonds, 22 residues, 2 models selected
> select subtract #1.5
139 atoms, 138 bonds, 11 residues, 1 model selected
> select add #2.4
273 atoms, 272 bonds, 21 residues, 2 models selected
> select subtract #2.4
139 atoms, 138 bonds, 11 residues, 1 model selected
> select add #2.5
273 atoms, 272 bonds, 21 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel A
Chain IDs of 10 residues changed
> select subtract #1.4
134 atoms, 134 bonds, 10 residues, 1 model selected
> select subtract #2.5
Nothing selected
> select add #1.5
139 atoms, 138 bonds, 11 residues, 1 model selected
> select add #2.4
273 atoms, 272 bonds, 21 residues, 2 models selected
> select subtract #2.4
139 atoms, 138 bonds, 11 residues, 1 model selected
> select add #2.6
273 atoms, 272 bonds, 21 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel B
Chain IDs of 0 residues changed
> select add #2.5
407 atoms, 406 bonds, 31 residues, 3 models selected
> select subtract #2.5
273 atoms, 272 bonds, 21 residues, 2 models selected
> select add #2.4
407 atoms, 406 bonds, 31 residues, 3 models selected
> select subtract #2.6
273 atoms, 272 bonds, 21 residues, 2 models selected
> select subtract #1.5
134 atoms, 134 bonds, 10 residues, 1 model selected
> select add #1.6
273 atoms, 272 bonds, 21 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel C
Chain IDs of 21 residues changed
> changechains sel C
Chain IDs of 0 residues changed
> ui tool show "Build Structure"
> build start peptide "custom built" EKTKEQVTNVG -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 rotLib Dunbrack
Chain information for custom built #3
---
Chain | Description
A | No description available
> select add #3
359 atoms, 357 bonds, 32 residues, 3 models selected
> select add #1
637 atoms, 633 bonds, 54 residues, 6 models selected
> select subtract #1
220 atoms, 219 bonds, 21 residues, 2 models selected
> select add #2
488 atoms, 487 bonds, 41 residues, 5 models selected
> select subtract #2.4
354 atoms, 353 bonds, 31 residues, 4 models selected
> select subtract #2.5
220 atoms, 219 bonds, 21 residues, 3 models selected
> select subtract #2.6
86 atoms, 85 bonds, 11 residues, 2 models selected
> select add #2
488 atoms, 487 bonds, 41 residues, 5 models selected
> select subtract #2
86 atoms, 85 bonds, 11 residues, 1 model selected
> ui mousemode right select
> ui mousemode right translate
> select clear
> select add #3
86 atoms, 85 bonds, 11 residues, 1 model selected
> ui mousemode right translate
> hide #!1 models
> hide #!2 models
> select clear
Drag select of 11 residues
> show #!2 models
> hide #!2 models
> show #!2 models
Drag select of 1 residues
Alignment identifier is 3/A
> show #!1 models
Drag select of 1 residues
Alignment identifier is 1.6/C
Drag select of 3 residues
> select #1.6/C:2-3
26 atoms, 25 bonds, 2 residues, 1 model selected
Drag select of 2 residues
> ui tool show "Build Structure"
> build join peptide sel length 1.33 omega 180 phi -120 move small
> build start peptide "custom built" EKTKEQVTNVG -57.0,-70.0 -57.0,-70.0
> -57.0,-70.0 -57.0,-70.0 -57.0,-70.0 -57.0,-70.0 -57.0,-70.0 -57.0,-70.0
> -57.0,-70.0 -57.0,-70.0 -57.0,-70.0 rotLib Dunbrack
Chain information for custom built #3
---
Chain | Description
A | No description available
Drag select of 2 residues
Alignment identifier is 1.4/A
Alignment identifier is 3/A
> ui tool show "Build Structure"
> build join peptide sel length 1.33 omega 180 phi -120 move small
> build start peptide "custom built" EKTKEQVTNVG -57.0,-70.0 -57.0,-70.0
> -57.0,-70.0 -57.0,-70.0 -57.0,-70.0 -57.0,-70.0 -57.0,-70.0 -57.0,-70.0
> -57.0,-70.0 -57.0,-70.0 -57.0,-70.0 rotLib Dunbrack
Chain information for custom built #3
---
Chain | Description
A | No description available
Drag select of 5 residues
Drag select of 3 residues
> select add #3
114 atoms, 85 bonds, 13 residues, 2 models selected
> select subtract #3
28 atoms, 2 residues, 1 model selected
> select add #3
114 atoms, 85 bonds, 13 residues, 2 models selected
> hide #3 models
> select subtract #3
28 atoms, 2 residues, 1 model selected
> hide #!1 models
> show #!1 models
> build start peptide "custom built" EKTKEQVTNVG -119.0,113.0 -119.0,113.0
> -119.0,113.0 -119.0,113.0 -119.0,113.0 -119.0,113.0 -119.0,113.0
> -119.0,113.0 -119.0,113.0 -119.0,113.0 -119.0,113.0 rotLib Dunbrack
Chain information for custom built #4
---
Chain | Description
A | No description available
Drag select of 2 residues
Alignment identifier is 1.5/B
Alignment identifier is 4/A
> build join peptide sel length 1.33 omega 180 phi -120 move small
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8.dev202403210048 (2024-03-21)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2020.61.1.0.0 (iBridge: 21.16.2057.0.0,0)
OS Loader Version: 577.140.2~22
Software:
System Software Overview:
System Version: macOS 13.6.3 (22G436)
Kernel Version: Darwin 22.6.0
Time since boot: 20 days, 5 hours, 54 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-019
Option ROM Version: 113-D32207P1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
27GL650F:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 72.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 909NTZN6Y069
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
LG FULL HD:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number:
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202403210048
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.37.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 19 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in python_instances_of_class |
comment:2 by , 19 months ago
| Cc: | added |
|---|---|
| Resolution: | → duplicate |
| Status: | accepted → closed |
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