![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#16854 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.9rc202411012347 (2024-11-01 23:47:45 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 0x00000001f41b4f40 (most recent call first):
File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp, _pyKVFinder, chimerax.mmcif.mmcif_write (total: 61)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 934835242,
"deployVersion" : 210,
"modelCode" : "Mac15,6",
"coalitionID" : 183787,
"osVersion" : {
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"build" : "23G93",
"releaseType" : "User"
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"captureTime" : "2025-02-12 17:50:36.1560 -0600",
"codeSigningMonitor" : 1,
"incident" : "BF29F666-3CE8-4877-9314-D0E0B12E960A",
"pid" : 17453,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-12 16:16:38.0602 -0600",
"procStartAbsTime" : 49289668822725,
"procExitAbsTime" : 49424982809075,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9-rc2024.11.01.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"AC3A9B65-9C73-5A3A-B113-4B8F604B002C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B9AE1EFD-02FB-CFC1-D9DC-825F4F8F9160",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 116888,
"sleepWakeUUID" : "5E9A5B76-09DD-42EC-ACF2-2FF99ED4EDDB",
"sip" : "enabled",
"vmRegionInfo" : "0x37ac85cd96b8 is not in any region. Bytes after previous region: 60733082408633 Bytes before following region: 44338997520712\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x000037ac85cd96b8","rawCodes":[1,61214118745784],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000037ac85cd96b8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":17453},
"vmregioninfo" : "0x37ac85cd96b8 is not in any region. Bytes after previous region: 60733082408633 Bytes before following region: 44338997520712\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9rc202411012347 (2024-11-01)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/sb2364/Downloads/fold_cseda01_deaminase_only/fold_cseda01_deaminase_only_model_4.cif
Chain information for fold_cseda01_deaminase_only_model_4.cif #1
---
Chain | Description
A | .
Computing secondary structure
> open
> /Users/sb2364/Downloads/fold_cseda01_mci8316215_imm1/fold_cseda01_mci8316215_imm1_model_4.cif
Chain information for fold_cseda01_mci8316215_imm1_model_4.cif #2
---
Chain | Description
A | .
B | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2 to #1
Computing secondary structure
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 fold_cseda01_deaminase_only_model_4.cif, chain A (#1) with
fold_cseda01_mci8316215_imm1_model_4.cif, chain A (#2), sequence alignment
score = 886.4
RMSD between 163 pruned atom pairs is 0.583 angstroms; (across all 178 pairs:
2.417)
> ui dockable false "Model Panel"
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> ui tool show Log
> select add #1
1395 atoms, 1416 bonds, 178 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #2
2676 atoms, 2728 bonds, 338 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #2
2676 atoms, 2728 bonds, 338 residues, 1 model selected
> hide #2 models
> show #2 models
> hide #1 models
> delete 2/A
Missing or invalid "atoms" argument: invalid atoms specifier
> delete 2/a
Missing or invalid "atoms" argument: invalid atoms specifier
> delete /a
> open
> /Users/sb2364/Downloads/fold_cseda01_deaminase_only/fold_cseda01_deaminase_only_model_4.cif
Chain information for fold_cseda01_deaminase_only_model_4.cif #1
---
Chain | Description
A | .
Computing secondary structure
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_cseda01_mci8316215_imm1_model_4.cif_B SES surface
#2.1: minimum, -23.11, mean -7.33, maximum 6.64
To also show corresponding color key, enter the above coulombic command and
add key true
> select subtract #2
1 model selected
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_cseda01_mci8316215_imm1_model_4.cif_B SES surface
#2.1: minimum, -23.11, mean -7.33, maximum 6.64
Coulombic values for fold_cseda01_deaminase_only_model_4.cif_A SES surface
#1.1: minimum, -16.11, mean 0.09, maximum 20.59
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic
Coulombic values for fold_cseda01_mci8316215_imm1_model_4.cif_B SES surface
#2.1: minimum, -23.11, mean -7.33, maximum 6.64
Coulombic values for fold_cseda01_deaminase_only_model_4.cif_A SES surface
#1.1: minimum, -16.11, mean 0.09, maximum 20.59
To also show corresponding color key, enter the above coulombic command and
add key true
> hide surfaces
> show surfaces
> hide surfaces
> transparency 40
> coulombic
Coulombic values for fold_cseda01_mci8316215_imm1_model_4.cif_B SES surface
#2.1: minimum, -23.11, mean -7.33, maximum 6.64
Coulombic values for fold_cseda01_deaminase_only_model_4.cif_A SES surface
#1.1: minimum, -16.11, mean 0.09, maximum 20.59
To also show corresponding color key, enter the above coulombic command and
add key true
> transparency 30
> transparency 80
> combine
> hide #!2 models
> hide #!1 models
> hide #3 models
> show #3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> mlp #3
Map values for surface "combination_A SES surface": minimum -29.3, mean
-5.584, maximum 22
Map values for surface "combination_B SES surface": minimum -27.58, mean
-5.263, maximum 22.24
To also show corresponding color key, enter the above mlp command and add key
true
> transparency #3 80
> hide #3.2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!3 models
> show #!2 models
> hide #2.1 models
> hide #!1-2 cartoons
> hide #!2 models
> show #!2 models
> show #2.1 models
> hide #1.1 models
> hide #2.1 models
> show #1.1 models
> show #2.1 models
> hide #1.1 models
> hide #2.1 models
> show #1.1 models
> show #2.1 models
> transparency #1-2 80
> transparency #1-2 70
> transparency #1-2 90
> hide #!1-2 cartoons
> show #!1-2 cartoons
> transparency #1-2 50
> hide #1.1 models
> show #1.1 models
> hide #2.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #2.1 models
> hide #1.1 models
> findclash
Unknown command: findclash
> ~findclash
Unknown command: ~findclash
> ~findclash
Unknown command: ~findclash
> interfaces ~solvent
6 buried areas: #1/A #3/A 7759, #3/B #2/B 4427, #1/A #3/B 1527, #1/A #2/B
1527, #3/A #2/B 1527, #3/A #3/B 1527
> ~hbonds
> hbonds reveal true
1247 hydrogen bonds found
> ~hbonds
> hbonds reveal true
1247 hydrogen bonds found
> ~hbonds
> hbonds reveal true
1247 hydrogen bonds found
> hbonds reveal true
1247 hydrogen bonds found
> style stick
Changed 5352 atom styles
> style sphere
Changed 5352 atom styles
> style ball
Changed 5352 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides fill
> style nucleic stick
Changed 0 atom styles
> hide atoms
> ~distance all
> ui windowfill toggle
> ~distance all
> ui tool show Log
> ~distance all
> ui tool show "Side View"
> ui tool show "Volume Viewer"
> ui tool show ViewDockX
No suitable models found for ViewDockX
> ui tool show Clashes
> clashes ignoreHiddenModels true color #0cdc07
15622 clashes
> ui tool show "Model Panel"
> hide #4 models
> hide #!3 models
> hide #2.1 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> show #4 models
> hide #4 models
> hide #5 models
> show #5 models
> show #!1 models
> close #5
> close #3.1
> close #3.2
> hide #3 models
> show #3 models
> hide #!1 models
> show #!1 models
> ui tool show Clashes
> clashes overlapCutoff 1.3 ignoreHiddenModels true color #0cdc07
4379 clashes
> hide #5 models
> show #5 models
> show #4 models
> hide #4 models
> hide #5 models
> show #5 models
> hide #5 models
> close #5
> ui tool show Clashes
> clashes ignoreHiddenModels true color #15dc18 radius 0.21
8058 clashes
> show #2.1 models
> ui tool show "Find Cavities"
> kvfinder #1,3
10 cavities found for fold_cseda01_deaminase_only_model_4.cif #1
fold_cseda01_deaminase_only_model_4.cif Cavities
---
ID | | Volume | Area | Points
1.2.4 | | 109.08 | 114.5 | 505
1.2.6 | | 45.36 | 64.37 | 210
1.2.8 | | 44.06 | 61.64 | 204
1.2.2 | | 34.34 | 50.72 | 159
1.2.3 | | 25.7 | 36.48 | 119
1.2.1 | | 22.46 | 32.23 | 104
1.2.9 | | 22.03 | 39.42 | 102
1.2.5 | | 12.31 | 29.54 | 57
1.2.7 | | 10.58 | 18.96 | 49
1.2.10 | | 6.26 | 15.59 | 29
14 cavities found for combination #3
combination Cavities
---
ID | | Volume | Area | Points
3.1.11 | | 500.9 | 382.98 | 2319
3.1.4 | | 290.52 | 262.41 | 1345
3.1.5 | | 264.6 | 222.43 | 1225
3.1.1 | | 228.53 | 232.81 | 1058
3.1.10 | | 73.66 | 88.2 | 341
3.1.12 | | 43.2 | 57.66 | 200
3.1.8 | | 26.14 | 46.24 | 121
3.1.3 | | 21.38 | 33.27 | 99
3.1.9 | | 19.87 | 36.19 | 92
3.1.14 | | 19.01 | 31.31 | 88
3.1.7 | | 17.28 | 36.68 | 80
3.1.6 | | 7.34 | 13.91 | 34
3.1.2 | | 6.91 | 14.38 | 32
3.1.13 | | 5.62 | 13.39 | 26
> show #1.1 models
> hide #1.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> ui tool show Foldseek
> foldseek #!3/B
Found 20 similar structures to combination #!3/B in pdb database using
foldseek, name fs1
> open 6anz
Summary of feedback from opening 6anz fetched from pdb
---
notes | Fetching compressed mmCIF 6anz from http://files.rcsb.org/download/6anz.cif
Fetching CCD SO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SO4/SO4.cif
6anz title:
Crystal structure of a hypothetical protein from Neisseria gonorrhoeae [more
info...]
Chain information for 6anz #6
---
Chain | Description | UniProt
A | Uncharacterized protein | B4RQJ2_NEIG2 1-138
Non-standard residues in 6anz #6
---
SO4 — sulfate ion
6anz mmCIF Assemblies
---
1| software_defined_assembly
61 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 5 C-terminal residues, 37 non-polymer residues more than 3.0 Angstroms
away.
Alignment of 6anz chain A to query has RMSD 1.18 using 47 of 124 paired
residues within cutoff distance 2.0
> open 6anz
6anz title:
Crystal structure of a hypothetical protein from Neisseria gonorrhoeae [more
info...]
Chain information for 6anz #7
---
Chain | Description | UniProt
A | Uncharacterized protein | B4RQJ2_NEIG2 1-138
Non-standard residues in 6anz #7
---
SO4 — sulfate ion
6anz mmCIF Assemblies
---
1| software_defined_assembly
61 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 5 C-terminal residues, 37 non-polymer residues more than 3.0 Angstroms
away.
Alignment of 6anz chain A to query has RMSD 1.18 using 47 of 124 paired
residues within cutoff distance 2.0
> hide #7 models
> hide #6 models
> show #7 models
> close #7
> close #6
> hide #!3.1 models
> hide #!1.2 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9rc202411012347 (2024-11-01)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: MRX33LL/A
Chip: Apple M3 Pro
Total Number of Cores: 11 (5 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 11881.1.1
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 29 days, 20 hours, 33 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP Z24n G2:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
HP Z24i G2:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.7.1
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.7
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.7
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9rc202411012347
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.5
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2
ChimeraX-Label: 1.1.11
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.17
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-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 3.2.4
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
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: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.7
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.54.1
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.12.1
html2text: 2024.2.26
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.1
numpy: 2.1.3
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
plotly: 5.24.1
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pyKVFinder: 0.7.1
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.1
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tenacity: 9.0.0
tifffile: 2024.7.24
tinyarray: 1.2.4
toml: 0.10.2
tornado: 6.4.1
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 8 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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