![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#16979 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-12.7.4-x86_64-i386-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Thread 0x000070001479a000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x0000000119a71600 (most recent call first):
File "/Applications/ChimeraX-1.9.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.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.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.map._map, chimerax.pdb_lib._load_libs, 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath (total: 55)
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{
"uptime" : 260000,
"procLaunch" : "2025-02-27 14:15:30.1633 -0500",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"procStartAbsTime" : 261749505099220,
"coalitionID" : 26311,
"osVersion" : {
"train" : "macOS 12.7.4",
"build" : "21H1123",
"releaseType" : "User"
},
"captureTime" : "2025-02-27 15:09:44.9367 -0500",
"incident" : "C8788889-66D7-419B-8A57-3050D22EFBDA",
"bug_type" : "309",
"pid" : 41818,
"procExitAbsTime" : 264662830329399,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"6DB02E18-D3E1-5983-A034-4BB50DEDC1ED","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "D95D607A-60CC-90A5-EED4-ED93596DA988",
"wakeTime" : 7,
"bridgeVersion" : {"build":"21P4222","train":"8.4"},
"sleepWakeUUID" : "0182A155-156E-4509-9019-B62DBFFF6366",
"sip" : "enabled",
"vmRegionInfo" : "0x346591e8ba78 is not in any region. Bytes after previous region: 57604869483129 Bytes before following region: 47942271976840\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n mapped file 163dc1000-164205000 [ 4368K] r--\/rwx SM=COW ...t_id=7223fb47\n---> GAP OF 0x5ffe9bdfb000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000346591e8ba78","rawCodes":[1,57610844289656],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000346591e8ba78"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Compressor failed a blocking pager_get\nVM - Fault hit memory shortage\n",
"vmregioninfo" : "0x346591e8ba78 is not in any region. Bytes after previous region: 57604869483129 Bytes before following region: 47942271976840\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n mapped file 163dc1000-164205000 [ 4368K] r--\/rwx SM=COW ...t_id=7223fb47\n---> GAP OF 0x5ffe9bdfb000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"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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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so",
"name" : "QtWidgets.abi3.so"
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}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 3m7p format mmcif fromDatabase pdb
3m7p title:
Fibronectin fragment [more info...]
Chain information for 3m7p #1
---
Chain | Description | UniProt
A | FN1 protein | B7ZLE5_HUMAN 297-604
Non-standard residues in 3m7p #1
---
12P — dodecaethylene glycol (polyethylene glycol PEG400)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
ZN — zinc ion
3m7p mmCIF Assemblies
---
1| author_and_software_defined_assembly
> color #1 #7bd5d7ff
> color #1 #8fd7c2ff
> color #1 #5fd7bcff
> color #1 #74bfd7ff
> color #1 #7bd781ff
> color #1 #83d7c2ff
> select /A:955@ZN
1 atom, 1 residue, 1 model selected
> select /A:955@ZN
1 atom, 1 residue, 1 model selected
> color sel hot pink
> select clear
> select /A:537@CD
1 atom, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> color #1.3 #6366ffff models
> color #1.3 #eaffe0ff models
> color #1.3 #6983ffff models
> color #1.3 #2a2bffff models
> color #1.3 #03030fff models
> color #1.3 #15157eff models
> color #1.3 #8b1910ff models
> color #1.3 #8b060eff models
> color #1.3 #8b3e3eff models
> color #1.3 #ff2600ff models
> select /A:956@ZN
1 atom, 1 residue, 1 model selected
> color sel hot pink
> label sel text "{0.name} {0.number}{0.insertion_code}"
> color #1.2.1 #ff2600ff models
> color #1.2.1 white models
> select clear
Drag select of 2 atoms, 4 residues, 1 bonds
Drag select of 2 atoms, 4 residues, 3 bonds
> select clear
Drag select of 4 atoms, 5 bonds
> label sel text "{0.name} {0.number}{0.insertion_code}"
> color sel red
> color #1.3 #ff2600ff models
> close #1
> open 3m7p format mmcif fromDatabase pdb
3m7p title:
Fibronectin fragment [more info...]
Chain information for 3m7p #1
---
Chain | Description | UniProt
A | FN1 protein | B7ZLE5_HUMAN 297-604
Non-standard residues in 3m7p #1
---
12P — dodecaethylene glycol (polyethylene glycol PEG400)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
ZN — zinc ion
3m7p mmCIF Assemblies
---
1| author_and_software_defined_assembly
> open "/Users/gracesappington/Downloads/3m7p alphafold 2
> prediction/test_69270_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
Chain information for
test_69270_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #2
---
Chain | Description
A | No description available
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 3m7p, chain A (#1) with
test_69270_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#2), sequence alignment score = 643
RMSD between 7 pruned atom pairs is 1.179 angstroms; (across all 226 pairs:
30.016)
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #2/A
Alignment identifier is 2/A
> select #1/A:314
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:314-427
883 atoms, 907 bonds, 114 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2 to #1 & sel
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 3m7p, chain A (#1) with
test_69270_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#2), sequence alignment score = 253.3
RMSD between 16 pruned atom pairs is 0.776 angstroms; (across all 89 pairs:
21.193)
> select clear
> color bychain
> color #1 #ff9300ff
> select #2/A:196
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #2/A:188
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #2/A:179
26 atoms, 24 bonds, 3 residues, 1 model selected
> select up
109 atoms, 109 bonds, 13 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #!1 to #2 & sel
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 test_69270_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#2) with 3m7p, chain A (#1), sequence alignment score = 53.6
RMSD between 9 pruned atom pairs is 0.775 angstroms; (across all 13 pairs:
13.280)
> select clear
> select #2/A:12
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
25 atoms, 25 bonds, 3 residues, 1 model selected
> select up
1774 atoms, 1821 bonds, 231 residues, 1 model selected
> select down
25 atoms, 25 bonds, 3 residues, 1 model selected
> select #2/A:5
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #2/A:13
18 atoms, 17 bonds, 2 residues, 1 model selected
> select add #2/A:33
24 atoms, 22 bonds, 3 residues, 1 model selected
> select up
79 atoms, 78 bonds, 11 residues, 1 model selected
> select add #2/A:17
87 atoms, 85 bonds, 12 residues, 1 model selected
> select add #2/A:25
93 atoms, 90 bonds, 13 residues, 1 model selected
> select up
157 atoms, 156 bonds, 21 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #!1 to #2 & sel
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 test_69270_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#2) with 3m7p, chain A (#1), sequence alignment score = 69.8
RMSD between 16 pruned atom pairs is 0.870 angstroms; (across all 21 pairs:
2.690)
> open 3EJH format mmcif fromDatabase pdb
3ejh title:
Crystal Structure of the Fibronectin 8-9FnI Domain Pair in Complex with a
Type-I Collagen Peptide [more info...]
Chain information for 3ejh #3
---
Chain | Description | UniProt
A B | Fibronectin | FINC_HUMAN 516-608
E F | Collagen type-I a1 chain |
Non-standard residues in 3ejh #3
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
3ejh mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
80 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!1 models
> hide #2 models
> select add #3
2033 atoms, 1985 bonds, 1 pseudobond, 344 residues, 4 models selected
> hide #!3 models
> show #!3 models
> select add #2
3650 atoms, 3650 bonds, 1 pseudobond, 554 residues, 4 models selected
> select subtract #2
1876 atoms, 1829 bonds, 1 pseudobond, 323 residues, 3 models selected
> select subtract #3
Nothing selected
> ui tool show "Side View"
> select #3/E:960-974
109 atoms, 111 bonds, 15 residues, 1 model selected
> select #3/F:956-978
165 atoms, 168 bonds, 1 pseudobond, 22 residues, 2 models selected
> color sel bychain
> select clear
> color #!3 bychain
> view
> rock
> encode
Unknown command: encode
> stop
> rock
>
Incomplete command: movie
> movie record
> stop
> encode
Unknown command: encode
> movie record
Already recording a movie
> rock
> encode
Unknown command: encode
> stop
> open "/Users/gracesappington/Downloads/alphafold2 prediction 3ejh
> /test_64482_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
Chain information for
test_64482_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #4
---
Chain | Description
A | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #4 to #3
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 3ejh, chain A (#3) with
test_64482_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb, chain A
(#4), sequence alignment score = 167.9
RMSD between 12 pruned atom pairs is 1.083 angstroms; (across all 66 pairs:
20.262)
> ui tool show "Render/Select by Attribute"
> color byattribute a:bfactor #!3 target abcs palette
> 20.46,blue:82.605,white:144.75,red
1876 atoms, 323 residues, atom bfactor range 20.5 to 145
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-18.8.16
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
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: MacBookPro16,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.4222.0.0,0)
OS Loader Version: 540.120.3~37
Software:
System Software Overview:
System Version: macOS 12.7.4 (21H1123)
Kernel Version: Darwin 21.6.0
Time since boot: 21 days 3:29
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal Family: Supported, Metal GPUFamily macOS 2
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
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
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: 1.58.8
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: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
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: 1.9
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: 1.2.6
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: 1.2.1
ChimeraX-Label: 1.1.14
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: 2.7.2
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: 1.5.18
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: 1.6.2
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: 3.5.6
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: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
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: 3.10.0
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: 2.10.2
numpy: 2.2.2
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: 0.7.2
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: 2.4.2
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
sniffio: 1.3.1
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: 6.4.2
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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