![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 12 months ago
Closed 12 months ago
#16180 closed defect (can't reproduce)
Crash in Residue::connects_to() in alignment association
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.4-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000002b8007000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000002003a5e00 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1292 in estimate_assoc_params
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 281 in associate
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 265 in seqalign_chain
File "/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/show_sequences/tool.py", line 77 in show_seqs
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, 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, lxml._elementpath, lxml.etree, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, PIL._imagingmath, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio (total: 60)
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{
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"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
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"modelCode" : "Mac14,2",
"coalitionID" : 30823,
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"build" : "22F66",
"releaseType" : "User"
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"captureTime" : "2024-10-24 14:07:20.2189 +0200",
"incident" : "03BEDBC0-DB1E-4342-A99F-1EF3F48999DB",
"pid" : 1580,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-10-24 13:58:57.6736 +0200",
"procStartAbsTime" : 3690289280857,
"procExitAbsTime" : 3702350212127,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"8B16F2CA-1535-5FB5-98AB-D37A08467174","thirdParty":true},
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"crashReporterKey" : "A0A9E16B-7E59-F68B-AD30-EF50843866FB",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
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"wakeTime" : 6420,
"sleepWakeUUID" : "F0231BA2-7523-4DAD-A277-6FAFC1223F7B",
"sip" : "enabled",
"vmRegionInfo" : "0x1 is not in any region. Bytes before following region: 105553518919679\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600018000000-600020000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000001","rawCodes":[1,1],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000001"},
"ktriageinfo" : "VM - (arg = 0x0) pmap_enter retried due to resource shortage\nVM - (arg = 0x0) pmap_enter retried due to resource shortage\nVM - (arg = 0x0) pmap_enter retried due to resource shortage\nVM - (arg = 0x0) pmap_enter retried due to resource shortage\nVM - (arg = 0x0) pmap_enter retried due to resource shortage\n",
"vmregioninfo" : "0x1 is not in any region. Bytes before following region: 105553518919679\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600018000000-600020000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
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"faultingThread" : 0,
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=2.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 3328K 4 \nCG image 6768K 56 \nCG raster data 368K 1 \nColorSync 592K 30 \nCoreAnimation 21.0M 62 \nCoreGraphics 96K 6 \nCoreServices 624K 2 \nCoreUI image data 5120K 36 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 742.3M 187 \nMALLOC guard page 192K 10 \nMALLOC_MEDIUM (reserved) 792.0M 8 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 64K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.6M 36 \nStack 169.3M 36 \nVM_ALLOCATE 252.1M 146 \nVM_ALLOCATE (reserved) 128.0M 3 reserved VM address space (unallocated)\n__AUTH 1843K 369 \n__AUTH_CONST 28.8M 602 \n__CTF 824 1 \n__DATA 21.4M 749 \n__DATA_CONST 38.7M 757 \n__DATA_DIRTY 1973K 229 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 832.5M 154 \n__OBJC_RO 66.3M 1 \n__OBJC_RW 2011K 1 \n__TEXT 837.2M 777 \ndyld private memory 464K 4 \nmapped file 225.7M 58 \nshared memory 3360K 37 \n=========== ======= ======= \nTOTAL 4.4G 4380 \nTOTAL, minus reserved VM space 3.2G 4380 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "f4cc70ee1ad8a7c04bfd1ebe526f996d55531c73",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "62c751b6bcb0435c2153fe92",
"factorPackIds" : {
"SIRI_UNDERSTANDING_ASR_ASSISTANT" : "6552c036dc598031005cc0f4",
"SIRI_UNDERSTANDING_MORPHUN" : "64e514ddc83b9a3d50649ddc"
},
"deploymentId" : 240000366
},
{
"rolloutId" : "63582c5f8a53461413999550",
"factorPackIds" : {
},
"deploymentId" : 240000002
}
],
"experiments" : [
{
"treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000007
}
]
}
}
===== 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: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> save "/Users/zalaperko/OneDrive - Univerza v Ljubljani/MAGISTRSKO
> DELO/chimera/b1s2t-join-models.cxs"
> open "/Users/zalaperko/Library/CloudStorage/OneDrive-
> UniverzavLjubljani/MAGISTRSKO DELO/chimera/b1s2t-join-models.cxs"
opened ChimeraX session
> open "/Users/zalaperko/Library/CloudStorage/OneDrive-
> UniverzavLjubljani/MAGISTRSKO DELO/chimera/b1s2t-join-models.cxs" format
> session
opened ChimeraX session
> open "/Users/zalaperko/Library/CloudStorage/OneDrive-
> UniverzavLjubljani/MAGISTRSKO DELO/chimera/b1s2t-join-models.cxs" format
> session
opened ChimeraX session
> open "/Users/zalaperko/Library/CloudStorage/OneDrive-
> UniverzavLjubljani/MAGISTRSKO DELO/chimera/b1s2t-join-models.cxs" format
> session
opened ChimeraX session
> open "/Users/zalaperko/Library/CloudStorage/OneDrive-
> UniverzavLjubljani/MAGISTRSKO DELO/chimera/b1s2t-join-models.cxs" format
> session
opened ChimeraX session
> open "/Users/zalaperko/Library/CloudStorage/OneDrive-
> UniverzavLjubljani/MAGISTRSKO DELO/chimera/b1s2t-join-models.cxs" format
> session
opened ChimeraX session
> open
> /Users/zalaperko/Downloads/fold_l1_sso10a_l2_dimer/fold_l1_sso10a_l2_dimer_model_3.cif
Chain information for fold_l1_sso10a_l2_dimer_model_3.cif #1
---
Chain | Description
A B | .
> save "/Users/zalaperko/OneDrive - Univerza v Ljubljani/MAGISTRSKO
> DELO/chimera/b1s2t-join-models.cxs"
> open /Users/zalaperko/Downloads/fold_bsest/fold_bsest_model_0.cif
Chain information for fold_bsest_model_0.cif #2
---
Chain | Description
A | .
> open /Users/zalaperko/Downloads/fold_bsest/fold_bsest_model_0.cif
Chain information for fold_bsest_model_0.cif #3
---
Chain | Description
A | .
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> select #2/A:7
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
31 atoms, 30 bonds, 4 residues, 1 model selected
> select up
3749 atoms, 3853 bonds, 483 residues, 1 model selected
> view matrix models #2,1,0,0,48.54,0,1,0,-4.1943,0,0,1,-3.9758
> select add #3
7498 atoms, 7706 bonds, 966 residues, 2 models selected
> color sel blue
> select subtract #3
3749 atoms, 3853 bonds, 483 residues, 1 model selected
> select subtract #2
Nothing selected
> select clear
> select #3/A:483
10 atoms, 9 bonds, 1 residue, 1 model selected
> view matrix models #3,1,0,0,1.3563,0,1,0,-0.2978,0,0,1,-1.1899
> view matrix models #3,1,0,0,-3.7162,0,1,0,-8.3478,0,0,1,-7.1369
> select add #1/B:1
14 atoms, 12 bonds, 2 residues, 2 models selected
> ui tool show "Build Structure"
> build join peptide sel length 1.33 omega 180 phi -120 move small
Remapping chain ID 'A' in fold_l1_sso10a_l2_dimer_model_3.cif #1 to 'C'
> view matrix models #3,1,0,0,-41.331,0,1,0,-32.975,0,0,1,-33.695
> view matrix models #3,1,0,0,-47.864,0,1,0,-48.708,0,0,1,-46.303
> select #3/C:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #2/A:483
14 atoms, 12 bonds, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move small
> save "/Users/zalaperko/OneDrive - Univerza v Ljubljani/MAGISTRSKO
> DELO/chimera/b1s2t-join-models.cxs"
> open /Users/zalaperko/Downloads/fold_tpe_chis6/fold_tpe_chis6_model_1.cif
Chain information for fold_tpe_chis6_model_1.cif #1
---
Chain | Description
A | .
> open /Users/zalaperko/Downloads/fold_tpe_chis6/fold_tpe_chis6_model_1.cif
Chain information for fold_tpe_chis6_model_1.cif #2
---
Chain | Description
A | .
> select #1/A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
97 atoms, 100 bonds, 12 residues, 1 model selected
> select up
2033 atoms, 2087 bonds, 266 residues, 1 model selected
> select add #2
4066 atoms, 4174 bonds, 532 residues, 2 models selected
> color sel magenta
> color sel lime
> select subtract #2
2033 atoms, 2087 bonds, 266 residues, 1 model selected
> view matrix models #1,1,0,0,22.475,0,1,0,16.77,0,0,1,-53.856
> select #3/A:540
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #1/A:1
18 atoms, 17 bonds, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move small
> select #2/A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> view matrix models #2,1,0,0,-5.31,0,1,0,-16.303,0,0,1,-18.797
> select #2/A:266
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #3/C:540
23 atoms, 23 bonds, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move small
No chain-initial nitrogens in atoms
> select add #2
2045 atoms, 2099 bonds, 267 residues, 2 models selected
> select add #3
12359 atoms, 12680 bonds, 1612 residues, 2 models selected
> select subtract #3
2033 atoms, 2087 bonds, 266 residues, 1 model selected
> view matrix models #2,1,0,0,-42.399,0,1,0,-4.6509,0,0,1,-3.2973
> select subtract #2
Nothing selected
> select #2/A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> view matrix models #2,1,0,0,-33.432,0,1,0,-32.227,0,0,1,-14.395
> select add #3/C:540
18 atoms, 17 bonds, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move small
> save "/Users/zalaperko/OneDrive - Univerza v Ljubljani/MAGISTRSKO
> DELO/chimera/b1s2t-join-models.cxs"
> ui tool show "Show Sequence Viewer"
> sequence chain /A /C
Alignment identifier is 1
===== 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: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83.1
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: MacBook Air
Model Identifier: Mac14,2
Model Number: MLY13CR/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 8422.121.1
OS Loader Version: 8422.121.1
Software:
System Software Overview:
System Version: macOS 13.4 (22F66)
Kernel Version: Darwin 22.5.0
Time since boot: 9 days, 16 hours, 48 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: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-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: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 12 months ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in Residue::connects_to() in alignment association |
comment:2 by , 12 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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