![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17795 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-15.5-arm64-arm-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
Current thread 0x00000001fd705f00 (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.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.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, _pyKVFinder (total: 53)
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"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac16,8",
"coalitionID" : 13113,
"osVersion" : {
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"build" : "24F74",
"releaseType" : "User"
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"captureTime" : "2025-05-24 22:10:51.0337 -0700",
"codeSigningMonitor" : 2,
"incident" : "907C1C65-818D-4496-BBD5-72F90EE139DC",
"pid" : 12050,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-22 15:04:29.8591 -0700",
"procStartAbsTime" : 557700791072,
"procExitAbsTime" : 4027186253718,
"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":"85B4EC26-EB43-5C27-9F20-8C5094A931F4","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "50DE277B-8FAD-2DE9-B497-FCDF5EAFBDBC",
"appleIntelligenceStatus" : {"reasons":["siriAssetIsNotReady","assetIsNotReady","notOptedIn"],"state":"unavailable"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "3981FE06-C9C8-4168-BE30-66F30307432A",
"wakeTime" : 25890,
"sleepWakeUUID" : "D91A84F2-4708-4101-A92F-3F0E9C3F38E7",
"sip" : "enabled",
"vmRegionInfo" : "0x232135444b08 is not in any region. Bytes after previous region: 38144498223881 Bytes before following region: 66927581705464\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, 0x0000a32135444b08","rawCodes":[1,179363022916360],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000a32135444b08 -> 0x0000232135444b08 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":12050},
"vmregioninfo" : "0x232135444b08 is not in any region. Bytes after previous region: 38144498223881 Bytes before following region: 66927581705464\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: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV-
> CoV/20250521-pdb6U7K-PEDV-CoV-S2-res736-1242.pdb"
Chain information for 20250521-pdb6U7K-PEDV-CoV-S2-res736-1242.pdb #1
---
Chain | Description
A B C | No description available
> select ::name="BMA"::name="MAN"::name="NAG"
1098 atoms, 1125 bonds, 81 residues, 1 model selected
> delete sel
> show cartoons
> hide atoms
> save "/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV-
> CoV/20250522-pdb6U7K-PEDV-CoV-S2-res736-1242.pdb"
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B /C
Alignment identifier is 1
Could not find virtual screen for QCocoaScreen(0x6000026e46e0, "HDMI (2)",
QRect(0,0 1920x1080), dpr=1, displayId=6, ) with
displayId 6
> select #1/A-C:736-775
867 atoms, 885 bonds, 120 residues, 1 model selected
> select #1/A-C:736-770
765 atoms, 780 bonds, 105 residues, 1 model selected
> hide sel
> hide sel cartoons
> select #1/A-C:771-1242
10518 atoms, 10686 bonds, 3 pseudobonds, 1380 residues, 2 models selected
> show sel surfaces
> lighting soft
> set bgColor white
> select #1/A:791-793
28 atoms, 28 bonds, 3 residues, 1 model selected
> transparency #1 50 surfaces
> transparency #1 80 surfaces
> show sel atoms
> select #1/A:747,749,762,763,764,765
42 atoms, 40 bonds, 6 residues, 1 model selected
> show sel
> hide sel atoms
> select #1/A:773,775,776,1165,1166,1167
39 atoms, 37 bonds, 6 residues, 1 model selected
> show sel atoms
> select #1/A-C:736-770
765 atoms, 780 bonds, 105 residues, 1 model selected
> delete sel
> show cartoons
> save "/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV-
> CoV/20250522-pdb6U7K-PEDV-CoV-S2-res771-1242.pdb"
> open 6VC0
Summary of feedback from opening 6VC0 fetched from pdb
---
note | Fetching compressed mmCIF 6vc0 from http://files.rcsb.org/download/6vc0.cif
6vc0 title:
Crystal structure of the horse MLKL pseudokinase domain [more info...]
Chain information for 6vc0 #2
---
Chain | Description | UniProt
A B C | Mixed lineage kinase domain like pseudokinase | F6S337_HORSE 189-475
Non-standard residues in 6vc0 #2
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
6vc0 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
> hide #!1 models
> close #2
> open 6CV0
Summary of feedback from opening 6CV0 fetched from pdb
---
note | Fetching compressed mmCIF 6cv0 from http://files.rcsb.org/download/6cv0.cif
6cv0 title:
Cryo-electron microscopy structure of infectious bronchitis coronavirus spike
protein [more info...]
Chain information for 6cv0 #2
---
Chain | Description | UniProt
A B C | Spike glycoprotein | F4MIW6_9GAMC 19-1090
Non-standard residues in 6cv0 #2
---
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)
> select
> #1/A-C:804-811,813-821,825-849,852-860,871-876,892-904,913-919,925-933,943-960,970-981,991-1011,1014-1024,1027-1055,1063-1070,1072-1120,1234-1239
5526 atoms, 5547 bonds, 720 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A #2/B #2/C
Alignment identifier is 1
Could not find virtual screen for QCocoaScreen(0x6000026e46e0, "HDMI (2)",
QRect(0,0 1920x1080), dpr=1, displayId=6, ) with
displayId 6
> select #2/A:856-875
152 atoms, 151 bonds, 20 residues, 1 model selected
> select #2/A-C:1-701
15858 atoms, 16272 bonds, 2043 residues, 1 model selected
> select #2/A-C:1-600
13488 atoms, 13851 bonds, 1740 residues, 1 model selected
> select #2/A-C:1-500
11133 atoms, 11451 bonds, 1440 residues, 1 model selected
> select #2/A-C:1-414
9120 atoms, 9390 bonds, 1182 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select ::name="NAG"
1218 atoms, 1245 bonds, 87 residues, 1 model selected
> delete sel
> hide #!2 atoms
> select #2/A-C:415-500
2013 atoms, 2058 bonds, 258 residues, 1 model selected
> select #2/A-C:415-538
2919 atoms, 2973 bonds, 372 residues, 1 model selected
> hide sel cartoons
> select #2/A-C:1-537
12021 atoms, 12348 bonds, 1551 residues, 1 model selected
> delete sel
> save "/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/IBV-
> CoV/20250522-PDB-6CV0-res578-1022.pdb" models #2
> hide #!2 models
> show #!1 models
> hide #!1 models
> open 6U7K
6u7k title:
Prefusion structure of PEDV spike [more info...]
Chain information for 6u7k #3
---
Chain | Description | UniProt
A B C | Spike glycoprotein | SPIKE_PEDV7 1-1319
Non-standard residues in 6u7k #3
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
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)
> select ::name="BMA"::name="MAN"::name="NAG"
1098 atoms, 1125 bonds, 81 residues, 1 model selected
> delete sel
> hide #!3 atoms
> hide pseudobonds
> graphics silhouettes true
> select #3/A-C:1-755
13569 atoms, 13926 bonds, 15 pseudobonds, 1767 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> ~select
Nothing selected
> ui tool show "Show Sequence Viewer"
> select #3/A-C:1-755
13569 atoms, 13926 bonds, 15 pseudobonds, 1767 residues, 2 models selected
> select #3/A-C:892-910
423 atoms, 423 bonds, 57 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/B #1/C #3/A #3/B #3/C
Alignment identifier is 1
Could not find virtual screen for QCocoaScreen(0x6000026b2f70, "HDMI (2)",
QRect(0,0 1920x1080), dpr=1, displayId=9, ) with
displayId 9
> close #1
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A #3/B #3/C
Alignment identifier is 1
Could not find virtual screen for QCocoaScreen(0x6000026b2f70, "HDMI (2)",
QRect(0,0 1920x1080), dpr=1, displayId=9, ) with
displayId 9
> select
> #3/A-C:230-235,242-246,322-326,463-473,572-577,804-811,813-821,825-849,852-860,871-876,892-904,913-919,925-933,943-960,970-981,991-1011,1014-1024,1027-1055,1063-1070,1072-1120,1234-1239
6249 atoms, 6264 bonds, 819 residues, 1 model selected
> select #3/A-C:892
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #3/A-C:892-907
369 atoms, 369 bonds, 48 residues, 1 model selected
> select
> #3/A-C:230-235,242-246,322-326,463-473,572-577,804-811,813-821,825-849,852-860,871-876,892-904,913-919,925-933,943-960,970-981,991-1011,1014-1024,1027-1055,1063-1070,1072-1120,1234-1239
6249 atoms, 6264 bonds, 819 residues, 1 model selected
> ~select
Nothing selected
> select #3/A-C:1-755
13569 atoms, 13926 bonds, 15 pseudobonds, 1767 residues, 2 models selected
> hide sel cartoons
> select #3/A-C:756-770
330 atoms, 336 bonds, 45 residues, 1 model selected
> select #3/A-C:756-765
207 atoms, 210 bonds, 30 residues, 1 model selected
> ~select
Nothing selected
> color dim gray
> select #1/A
Nothing selected
> select #3/A
8139 atoms, 8318 bonds, 6 pseudobonds, 1064 residues, 2 models selected
> color sel gray
> select #3/B
8139 atoms, 8318 bonds, 6 pseudobonds, 1064 residues, 2 models selected
> color sel light gray
> ~select
Nothing selected
> select #3/A
8139 atoms, 8318 bonds, 6 pseudobonds, 1064 residues, 2 models selected
> color sel gray
> ui tool show "Color Actions"
> color sel gainsboro
> color sel silver
> ~select
Nothing selected
> select #3/A
8139 atoms, 8318 bonds, 6 pseudobonds, 1064 residues, 2 models selected
> color sel dim gray
> color sel dark gray
> ~select
Nothing selected
> color dim gray
> ui tool show "Side View"
> save /Users/adonisrubio/Desktop/image34.png supersample 3
> save /Users/adonisrubio/Desktop/image35.png supersample 3
> select #3/A:1069-1089
162 atoms, 161 bonds, 21 residues, 1 model selected
> show sel atoms
> hide sel atoms
> ~select
Nothing selected
> select #3/A-C:756-770
330 atoms, 336 bonds, 45 residues, 1 model selected
> select #3/A-C:756-760
84 atoms, 81 bonds, 15 residues, 1 model selected
> select #3/A-C:756-765
207 atoms, 210 bonds, 30 residues, 1 model selected
> delete sel
> ui tool show Contacts
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
Errors may have occurred when running pip:
pip standard error:
\---
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.
chimerax-bundlebuilder 1.4.0 requires numpy==1.26.4, but you have numpy 2.2.6
which is incompatible.
nptyping 2.5.0 requires numpy=1.20.0; python_version >= "3.8", but you
have numpy 2.2.6 which is incompatible.
\---
pip standard output:
\---
\---
> kvfinder #3
153 cavities found for 6u7k #3
6u7k Cavities
---
ID | | Volume | Area | Points
3.2.13 | | 18339.3 | 13561.8 | 84904
3.2.48 | | 2401.06 | 2036.74 | 11116
3.2.4 | | 1766.45 | 1396.08 | 8178
3.2.100 | | 1766.02 | 1418.94 | 8176
3.2.77 | | 1594.3 | 1364.02 | 7381
3.2.52 | | 841.75 | 669.43 | 3897
3.2.31 | | 840.67 | 682.51 | 3892
3.2.122 | | 839.38 | 650.22 | 3886
3.2.72 | | 581.26 | 579.22 | 2691
3.2.40 | | 527.69 | 496.57 | 2443
3.2.9 | | 475.2 | 509.15 | 2200
3.2.105 | | 440.42 | 403.09 | 2039
3.2.50 | | 416.88 | 384.47 | 1930
3.2.8 | | 382.54 | 357.89 | 1771
3.2.82 | | 367.63 | 337.31 | 1702
3.2.132 | | 325.08 | 317.33 | 1505
3.2.61 | | 287.28 | 278.92 | 1330
3.2.127 | | 267.41 | 196.08 | 1238
3.2.19 | | 265.25 | 246.76 | 1228
3.2.149 | | 254.66 | 197.86 | 1179
3.2.119 | | 239.98 | 215.93 | 1111
3.2.2 | | 237.17 | 169.72 | 1098
3.2.56 | | 222.48 | 197.57 | 1030
3.2.65 | | 217.3 | 223.92 | 1006
3.2.80 | | 217.3 | 252.08 | 1006
3.2.96 | | 216.86 | 160.57 | 1004
3.2.81 | | 203.04 | 235 | 940
3.2.29 | | 163.3 | 239.44 | 756
3.2.133 | | 158.11 | 154.66 | 732
3.2.59 | | 140.4 | 126.57 | 650
3.2.76 | | 129.38 | 117.17 | 599
3.2.108 | | 128.95 | 116.28 | 597
3.2.101 | | 114.48 | 120.7 | 530
3.2.102 | | 99.79 | 103.8 | 462
3.2.116 | | 97.63 | 100.11 | 452
3.2.85 | | 94.18 | 105.1 | 436
3.2.28 | | 81.22 | 91.64 | 376
3.2.120 | | 81.22 | 115.67 | 376
3.2.125 | | 79.49 | 95.85 | 368
3.2.70 | | 78.62 | 89.41 | 364
3.2.107 | | 77.98 | 87.95 | 361
3.2.91 | | 75.82 | 105.55 | 351
3.2.104 | | 74.09 | 95.42 | 343
3.2.20 | | 71.5 | 78.19 | 331
3.2.97 | | 71.06 | 90.89 | 329
3.2.11 | | 68.69 | 92.51 | 318
3.2.110 | | 63.07 | 89.74 | 292
3.2.124 | | 60.91 | 110.18 | 282
3.2.114 | | 60.7 | 87.89 | 281
3.2.7 | | 48.38 | 64.66 | 224
3.2.130 | | 48.38 | 68.94 | 224
3.2.60 | | 47.74 | 57.39 | 221
3.2.146 | | 47.74 | 62.71 | 221
3.2.6 | | 46.01 | 57.15 | 213
3.2.150 | | 43.63 | 61.99 | 202
3.2.42 | | 42.34 | 55.79 | 196
3.2.109 | | 42.34 | 68.31 | 196
3.2.62 | | 41.9 | 62.43 | 194
3.2.145 | | 41.69 | 54.72 | 193
3.2.14 | | 41.47 | 61.78 | 192
3.2.35 | | 40.39 | 53.98 | 187
3.2.16 | | 38.66 | 49.47 | 179
3.2.32 | | 38.02 | 55.01 | 176
3.2.23 | | 37.8 | 53.51 | 175
3.2.152 | | 37.8 | 58.72 | 175
3.2.38 | | 34.78 | 57.43 | 161
3.2.144 | | 34.78 | 50.38 | 161
3.2.1 | | 34.56 | 53.71 | 160
3.2.141 | | 34.13 | 43.42 | 158
3.2.88 | | 33.48 | 50.84 | 155
3.2.95 | | 33.48 | 47.02 | 155
3.2.139 | | 31.97 | 63.31 | 148
3.2.51 | | 31.32 | 44.68 | 145
3.2.37 | | 30.46 | 49.12 | 141
3.2.33 | | 28.94 | 46.13 | 134
3.2.143 | | 28.94 | 46.13 | 134
3.2.18 | | 28.73 | 37.55 | 133
3.2.41 | | 28.73 | 48.41 | 133
3.2.47 | | 28.51 | 38.59 | 132
3.2.27 | | 28.3 | 50.22 | 131
3.2.151 | | 27 | 38.44 | 125
3.2.103 | | 26.78 | 43.97 | 124
3.2.137 | | 24.62 | 45.13 | 114
3.2.135 | | 23.76 | 52.37 | 110
3.2.73 | | 23.33 | 41.55 | 108
3.2.94 | | 23.33 | 39.8 | 108
3.2.34 | | 23.11 | 40.33 | 107
3.2.68 | | 23.11 | 33.54 | 107
3.2.142 | | 20.95 | 29.21 | 97
3.2.36 | | 20.3 | 35.08 | 94
3.2.90 | | 19.22 | 34.5 | 89
3.2.113 | | 19.01 | 38.34 | 88
3.2.117 | | 19.01 | 38.34 | 88
3.2.58 | | 18.36 | 31.48 | 85
3.2.140 | | 18.36 | 26.35 | 85
3.2.79 | | 18.14 | 33.85 | 84
3.2.21 | | 17.06 | 35.72 | 79
3.2.64 | | 16.85 | 32.3 | 78
3.2.134 | | 16.85 | 32.3 | 78
3.2.98 | | 15.55 | 25.45 | 72
3.2.26 | | 15.34 | 26.6 | 71
3.2.3 | | 13.82 | 27.81 | 64
3.2.78 | | 12.74 | 22.92 | 59
3.2.15 | | 12.31 | 29.54 | 57
3.2.30 | | 12.31 | 29.54 | 57
3.2.43 | | 12.31 | 29.54 | 57
3.2.45 | | 12.31 | 29.54 | 57
3.2.46 | | 12.31 | 29.54 | 57
3.2.54 | | 12.31 | 29.54 | 57
3.2.71 | | 12.31 | 29.54 | 57
3.2.75 | | 12.31 | 29.54 | 57
3.2.84 | | 12.31 | 29.54 | 57
3.2.87 | | 12.31 | 29.54 | 57
3.2.89 | | 12.31 | 29.54 | 57
3.2.92 | | 12.31 | 29.54 | 57
3.2.99 | | 12.31 | 29.54 | 57
3.2.111 | | 12.31 | 29.54 | 57
3.2.126 | | 12.31 | 29.54 | 57
3.2.131 | | 12.31 | 21.78 | 57
3.2.136 | | 12.31 | 29.54 | 57
3.2.153 | | 12.31 | 29.54 | 57
3.2.49 | | 12.1 | 17.38 | 56
3.2.57 | | 11.66 | 19.36 | 54
3.2.25 | | 11.45 | 17.42 | 53
3.2.123 | | 11.45 | 26.1 | 53
3.2.138 | | 11.45 | 18.21 | 53
3.2.5 | | 11.23 | 24.74 | 52
3.2.115 | | 11.23 | 20 | 52
3.2.121 | | 10.58 | 19.65 | 49
3.2.39 | | 9.5 | 20.92 | 44
3.2.53 | | 9.5 | 17.04 | 44
3.2.74 | | 9.07 | 14.34 | 42
3.2.44 | | 8.64 | 19.12 | 40
3.2.93 | | 8.64 | 20.22 | 40
3.2.106 | | 7.78 | 18.22 | 36
3.2.129 | | 7.78 | 13.69 | 36
3.2.112 | | 7.56 | 13.14 | 35
3.2.10 | | 7.34 | 15.99 | 34
3.2.12 | | 7.13 | 13.14 | 33
3.2.17 | | 6.7 | 11.68 | 31
3.2.118 | | 6.26 | 15.22 | 29
3.2.63 | | 6.05 | 14.9 | 28
3.2.83 | | 6.05 | 11.67 | 28
3.2.86 | | 6.05 | 12.92 | 28
3.2.22 | | 5.83 | 13.64 | 27
3.2.128 | | 5.83 | 14.77 | 27
3.2.66 | | 5.62 | 13.93 | 26
3.2.67 | | 5.62 | 11.34 | 26
3.2.69 | | 5.62 | 12.9 | 26
3.2.55 | | 5.4 | 12.81 | 25
3.2.24 | | 5.18 | 10.2 | 24
3.2.147 | | 5.18 | 13.81 | 24
3.2.148 | | 5.18 | 12.05 | 24
Populating font family aliases took 116 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> view #3.2.13 @ zoom 0.75
moved plane near -92.38150187515349 [ 0.63441866 -0.77278985 -0.017591 ]
moved plane far -92.38150187515349 [ 0.63441866 -0.77278985 -0.017591 ]
> surface #3.2
> transparency #3.2 50
> ~surface #3.2
> surface #3.2.13
> show #!3 & (#3.2.13 : show #!3#!3.2.1-153 surfaces
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting simple
> lighting soft
> hide #!3#!3.2.1-153 surfaces
> close session
> open "/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV-
> CoV/20250522-pdb6U7K-PEDV-CoV-S2-res771-1242.pdb"
Chain information for 20250522-pdb6U7K-PEDV-CoV-S2-res771-1242.pdb #1
---
Chain | Description
A B C | No description available
> open "/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV-
> CoV/20250522-pdb6U7K-PEDV-CoV-S2-res736-1242.pdb"
Chain information for 20250522-pdb6U7K-PEDV-CoV-S2-res736-1242.pdb #2
---
Chain | Description
A B C | No description available
> hide #!1 models
> select #2/A-C:736-760
519 atoms, 525 bonds, 75 residues, 1 model selected
> select #2/A-C:736-765
642 atoms, 654 bonds, 90 residues, 1 model selected
> select #2/A-C:736-764
615 atoms, 627 bonds, 87 residues, 1 model selected
> delete sel
> save "/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV-
> CoV/20250523-pdb6U7K-PEDV-CoV-S2-res765-1242.pdb" models #2
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #2/A-C:736-770
150 atoms, 150 bonds, 18 residues, 1 model selected
> select #2/A-C:736-760
Nothing selected
> close #1
> close #2
> open "/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV-
> CoV/20250522-pdb6U7K-PEDV-CoV-S2-res736-1242.pdb" format pdb
Chain information for 20250522-pdb6U7K-PEDV-CoV-S2-res736-1242.pdb #1
---
Chain | Description
A B C | No description available
> color light gray
> select #1/A-C:736-765
642 atoms, 654 bonds, 90 residues, 1 model selected
> color sel blue
> ~select
Nothing selected
> hide psuedobonds
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide pseudobonds
> select #1/A-C:766-1242
10641 atoms, 10812 bonds, 3 pseudobonds, 1395 residues, 2 models selected
> color sel dim gray
> ~select
Nothing selected
> turn x 90
> turn x 270
> save /Users/adonisrubio/Desktop/image36.png supersample 3
> turn x 90
> save /Users/adonisrubio/Desktop/image37.png supersample 3
> turn x 270
> select #1/A-C:736-755
435 atoms, 441 bonds, 60 residues, 1 model selected
> delete sel
> save /Users/adonisrubio/Desktop/image38.png supersample 3
> save /Users/adonisrubio/Desktop/image39.png supersample 3
> turn x 90
> turn x 270
> turn x 90
> turn x 270
> save /Users/adonisrubio/Desktop/image40.png supersample 3
> turn x 90
> save /Users/adonisrubio/Desktop/image41.png supersample 3
> select #1/A-C:736-755
Nothing selected
> select #1/A-C:736-765
207 atoms, 210 bonds, 30 residues, 1 model selected
> delete sel
> save "/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV-
> CoV/20250523-pdb6U7K-PEDV-CoV-S2-res766-1242.pdb"
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B /C
Alignment identifier is 1
Could not find virtual screen for QCocoaScreen(0x6000026ec0b0, "HDMI (1)",
QRect(-1920,0 1920x1080), dpr=1, displayId=8, ) with
displayId 8
> select #1/A-C:766-780
324 atoms, 327 bonds, 45 residues, 1 model selected
> select #1/A-C:1073-1074
48 atoms, 45 bonds, 6 residues, 1 model selected
> select #1/A-C:1072-1073
48 atoms, 45 bonds, 6 residues, 1 model selected
> select ~sel & ##selected
10593 atoms, 10767 bonds, 3 pseudobonds, 1389 residues, 2 models selected
> select #1/A-C:1214
21 atoms, 18 bonds, 3 residues, 1 model selected
> show
> hide atoms
> select #1/A-C:1242
36 atoms, 36 bonds, 3 residues, 1 model selected
> close session
> open "/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV-
> CoV/AlphaFold-models/20250524-Tamarind-AlphaFoldresult-PEDV-
> CoV-S2-766-1242-postfusiontemplates/20250524-PEDV-CoV-S2-766-1319-unrelaxed-
> Alphafold2-multimer-rank-1-model-4-renumbered.pdb"
Chain information for 20250524-PEDV-CoV-S2-766-1319-unrelaxed-
Alphafold2-multimer-rank-1-model-4-renumbered.pdb #1
---
Chain | Description
A B C | No description available
Computing secondary structure
> open "/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV-
> CoV/20250523pdb6U7KPEDVS2res766to1319.pdb"
Chain information for 20250523pdb6U7KPEDVS2res766to1319.pdb #2
---
Chain | Description
A B C | No description available
> select #2
10641 atoms, 10812 bonds, 3 pseudobonds, 1395 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-199.61,0,1,0,-294.61,0,0,1,-219.36
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.85316,-0.51564,-0.078914,366.51,-0.21402,0.48397,-0.84851,95.212,0.47572,-0.70703,-0.52327,231.91
> view matrix models
> #2,-0.99223,-0.12163,0.026228,280.4,-0.081474,0.47579,-0.87578,73.692,0.094044,-0.87111,-0.482,346.79
> ~select
Nothing selected
> select #2/A-C:1069-1089
486 atoms, 483 bonds, 63 residues, 1 model selected
> color sel goldenrod
> select #2
10641 atoms, 10812 bonds, 3 pseudobonds, 1395 residues, 3 models selected
> color sel dim gray
> select #2/A-C:1069-1089
486 atoms, 483 bonds, 63 residues, 1 model selected
> color sel goldenrod
> select #2/A-C:892-910
423 atoms, 423 bonds, 57 residues, 1 model selected
> color sel red
> ~select
Nothing selected
> hide pseudobonds
> color #1 dimgray
> color #1/A-C:1069-1089 goldenrod
> color #1/A-C:892-910 red
> select #2
10641 atoms, 10812 bonds, 3 pseudobonds, 1395 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.99223,-0.12163,0.026228,303.82,-0.081474,0.47579,-0.87578,47.346,0.094044,-0.87111,-0.482,377.62
> ~select
Nothing selected
> save /Users/adonisrubio/Desktop/image42.png supersample 3
> open
> /Users/adonisrubio/Downloads/KVFinder_structures_4920176801590624244/input_4920176801590624244.pdb
Summary of feedback from opening
/Users/adonisrubio/Downloads/KVFinder_structures_4920176801590624244/input_4920176801590624244.pdb
---
warning | Ignored bad PDB record found on line 10643
Chain information for input_4920176801590624244.pdb #3
---
Chain | Description
A B C | No description available
Computing secondary structure
> open
> /Users/adonisrubio/Downloads/KVFinder_structures_4920176801590624244/cavity_4920176801590624244.pdb
Summary of feedback from opening
/Users/adonisrubio/Downloads/KVFinder_structures_4920176801590624244/cavity_4920176801590624244.pdb
---
warning | Ignored bad PDB record found on line 46927
> hide #!3 models
> hide #4 models
> select #1/A-C:1241 #2/A-C:1241
48 atoms, 42 bonds, 6 residues, 2 models selected
> view matrix models
> #1,1,0,0,-8.7051,0,1,0,-14.602,0,0,1,-24.547,#2,-0.99223,-0.12163,0.026228,295.12,-0.081474,0.47579,-0.87578,32.744,0.094044,-0.87111,-0.482,353.07
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.9694,0.010769,0.24524,-10.842,0.0035832,0.99831,-0.058,-14.209,-0.24545,0.057104,0.96773,-21.191,#2,-0.93968,-0.32642,-0.10221,376.8,-0.090346,0.52507,-0.84625,12.244,0.3299,-0.78597,-0.52289,272.37
> view matrix models
> #1,0.87307,-0.1924,0.44802,-10.4,0.25535,0.96319,-0.083978,-22.908,-0.41538,0.18772,0.89007,-11.638,#2,-0.80848,-0.58801,-0.024548,414.93,-0.33974,0.50037,-0.79637,68.566,0.48056,-0.63551,-0.60431,207.16
> color dim gray
> color sel red
> show sel atoms
> style sel sphere
Changed 48 atom styles
> view matrix models
> #1,0.74147,-0.27295,0.61295,-19.609,0.17971,0.96093,0.21052,-26.41,-0.64647,-0.045945,0.76155,-11.548,#2,-0.65583,-0.75401,-0.036949,424.21,-0.2368,0.25195,-0.93832,153.18,0.71681,-0.60663,-0.34379,77.442
> close #3
> close #4
> view matrix models
> #1,0.86755,-0.46791,0.16858,-26.363,0.48848,0.86536,-0.11197,-29.131,-0.093489,0.17949,0.97931,-6.7903,#2,-0.80683,-0.475,0.35128,278.72,-0.56572,0.44985,-0.69108,117.97,0.17024,-0.75631,-0.63167,343.11
> hide #!2 models
> show #!2 models
> hide #1 models
> view matrix models
> #1,0.20104,-0.6117,0.76512,-46.806,0.61843,0.68499,0.38514,-88.78,-0.75969,0.39574,0.51601,82.694,#2,-0.07769,-0.98199,0.17219,274.24,-0.63321,-0.084804,-0.76932,276.98,0.77007,-0.1688,-0.61522,65.474
> close session
> open "/Users/adonisrubio/Desktop/PhD_Research_Barnes_Lab/S2 Immunogens/PEDV-
> CoV/20250523-pdb6U7K-PEDV-CoV-S2-res766-1319.pdb"
Chain information for 20250523-pdb6U7K-PEDV-CoV-S2-res766-1319.pdb #1
---
Chain | Description
A B C | No description available
> hide pseudobonds
> select #1/A-C:1241
24 atoms, 21 bonds, 3 residues, 1 model selected
> color dim gray
> color sel red
> show sel atoms sphere
Expected ',' or a keyword
> show sel atoms
> style sel sphere
Changed 24 atom styles
> ~select
Nothing selected
> save /Users/adonisrubio/Desktop/image43.png supersample 3
===== 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 Metal - 89.4
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.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: Mac16,8
Model Number: MX2J3LL/A
Chip: Apple M4 Pro
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 3 days, 20 hours, 8 minutes
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 20
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
C305W-2560UN:
Resolution: 2560 x 1080 (UW-UXGA - Ultra Wide - Ultra Extended Graphics Array)
UI Looks like: 2560 x 1080 @ 85.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
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: 3.10.3
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
narwhals: 1.40.0
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: 2.2.6
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: 6.0.1
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: 0.8.0
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
tifffile: 2024.7.24
tinyarray: 1.2.4
tomlkit: 0.13.2
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 , 6 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 , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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