![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 7 months ago
#17047 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-14.1.2-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 0x00000001d6b89ec0 (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, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, PIL._imagingmath, 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 58)
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{
"uptime" : 760000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,3",
"coalitionID" : 3257,
"osVersion" : {
"train" : "macOS 14.1.2",
"build" : "23B2091",
"releaseType" : "User"
},
"captureTime" : "2025-03-08 16:55:03.7203 +0100",
"codeSigningMonitor" : 1,
"incident" : "07E3DBC5-D0BD-4A7E-8F4E-ADB93D072AEA",
"pid" : 80965,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-08 15:37:35.2272 +0100",
"procStartAbsTime" : 18276030183905,
"procExitAbsTime" : 18378973330152,
"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":"463518D6-ECCB-58B4-944B-1B5F4D9D1A65","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "D04DF421-CE34-E3CD-43E3-85AEAEB3A42B",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"sleepWakeUUID" : "B6E2FC45-56B4-4411-85F1-4F21960C5083",
"sip" : "enabled",
"vmRegionInfo" : "0x340b3d196aa8 is not in any region. Bytes after previous region: 56741838023337 Bytes before following region: 48330241906008\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000b40b3d196aa8","rawCodes":[1,197960362715816],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000b40b3d196aa8 -> 0x0000340b3d196aa8 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":80965},
"vmregioninfo" : "0x340b3d196aa8 is not in any region. Bytes after previous region: 56741838023337 Bytes before following region: 48330241906008\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(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/romainfrancois/Documents/CCP4/E1-ESO25/E1-ESO25_refine_010-coot-0_refmac2-coot-0.pdb
E1-ESO25_refine_010-coot-0_refmac2-coot-0.pdb title:
\--- [more info...]
Chain information for E1-ESO25_refine_010-coot-0_refmac2-coot-0.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Non-standard residues in E1-ESO25_refine_010-coot-0_refmac2-coot-0.pdb #1
---
ATP — (ATP)
MG — (MG)
ZN — (ZN)
14 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> set bgColor white
> lighting full
> lighting soft
> lighting simple
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting full
> lighting simple
> lighting soft
> lighting simple
> graphics silhouettes false
> lighting simple
> lighting full
> lighting flat
> lighting full
> ui tool show "Unit Cell"
> unitcell #1
> unitcell delete #1
> view #1 clip false
> ui tool show "Scale Bar"
> scalebar
> scalebar thickness 1
> scalebar off
> ui tool show "Selection Inspector"
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A
2411 atoms, 2452 bonds, 2 pseudobonds, 306 residues, 2 models selected
> ui tool show "Color Actions"
> color sel medium blue
> color sel royal blue
> color sel slate blue
> select /C
2431 atoms, 2474 bonds, 1 pseudobond, 309 residues, 2 models selected
> color sel royal blue
> color sel slate blue
Alignment identifier is 1/C
> hide sel cartoons
> show sel cartoons
> select
13145 atoms, 13209 bonds, 15 pseudobonds, 1824 residues, 3 models selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> undo
> select ::name="ATP"::name="HOH"::name="MG"::name="ZN"
242 atoms, 66 bonds, 182 residues, 1 model selected
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
12903 atoms, 13143 bonds, 7 pseudobonds, 1642 residues, 2 models selected
> hide sel atoms
> ui mousemode right select
> select /B:467
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select /B:468
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select /A:205
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select /B:115
5 atoms, 4 bonds, 1 residue, 1 model selected
Alignment identifier is 1/B
> select /B:6
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:6-42
254 atoms, 255 bonds, 37 residues, 1 model selected
> select /B:6-42
254 atoms, 255 bonds, 37 residues, 1 model selected
> select /B:6-42
254 atoms, 255 bonds, 37 residues, 1 model selected
> select /B:43-44
18 atoms, 18 bonds, 2 residues, 1 model selected
> select /B:43-147
842 atoms, 858 bonds, 105 residues, 1 model selected
> select /B:6-7
12 atoms, 11 bonds, 2 residues, 1 model selected
> select /B:6-192
1455 atoms, 1485 bonds, 187 residues, 1 model selected
> select /B:192-193
19 atoms, 19 bonds, 2 residues, 1 model selected
> select /B:190-193
40 atoms, 41 bonds, 4 residues, 1 model selected
> select clear
> select /B:167
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:6
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:6-167
1252 atoms, 1274 bonds, 162 residues, 1 model selected
> ui tool show "Color Actions"
> color sel hot pink
> color sel pale violet red
> select clear
> select /D:44
8 atoms, 7 bonds, 1 residue, 1 model selected
Alignment identifier is 1/D
> select /D:6
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /D:6-167
1252 atoms, 1274 bonds, 162 residues, 1 model selected
> color sel pale violet red
> select /B:168
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:384
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:384
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:168-384
1504 atoms, 1540 bonds, 2 pseudobonds, 186 residues, 2 models selected
> color sel salmon
> select clear
> select /B:439
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:439
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:384-439
419 atoms, 426 bonds, 56 residues, 1 model selected
> select /B:384
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:438
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:388-438
384 atoms, 389 bonds, 51 residues, 1 model selected
> select /B:439
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:385-439
411 atoms, 418 bonds, 55 residues, 1 model selected
> color sel hot pink
Drag select of 2 residues, 1 bonds
> select /B:439
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:385-439
411 atoms, 418 bonds, 55 residues, 1 model selected
> color sel pale violet red
> select /D:392
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /D:392
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /D:439
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:385-439
411 atoms, 418 bonds, 55 residues, 1 model selected
> color sel pale violet red
> select /D:440
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:440-548
852 atoms, 862 bonds, 109 residues, 1 model selected
> color sel red
> select clear
> select /B:440
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:440-549
860 atoms, 870 bonds, 110 residues, 1 model selected
> color sel red
> select clear
> select /B:354
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> select /B:168
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:384
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:168
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /D:168-384
1519 atoms, 1555 bonds, 2 pseudobonds, 188 residues, 2 models selected
> color sel dark salmon
> color sel light salmon
> color sel dark salmon
> color sel lime
> color sel dark salmon
> color sel salmon
> select clear
> select /D:549@C2'
1 atom, 1 residue, 1 model selected
> select ::name="ATP"
62 atoms, 66 bonds, 2 residues, 1 model selected
> color sel white
> color sel byelement
> color sel byhetero
> color sel byelement
Drag select of 12 residues
> select /D:549@C3'
1 atom, 1 residue, 1 model selected
> select /D:549@C4'
1 atom, 1 residue, 1 model selected
> view clip false
Drag select of 4 residues
Drag select of 1 residues
> select /D:549@C5'
1 atom, 1 residue, 1 model selected
> select /D:549@C4'
1 atom, 1 residue, 1 model selected
> select /D:549@C5'
1 atom, 1 residue, 1 model selected
> select /D:549@C4'
1 atom, 1 residue, 1 model selected
> select add /D:549@C2'
2 atoms, 2 bonds, 1 residue, 1 model selected
> select add /D:549@C8
3 atoms, 4 bonds, 1 residue, 1 model selected
> select add /D:549@C4
4 atoms, 4 bonds, 1 residue, 1 model selected
> select add /D:549@C2
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add /D:549@C5
6 atoms, 4 bonds, 1 residue, 1 model selected
> select add /D:549@C6
7 atoms, 4 bonds, 1 residue, 1 model selected
> color sel white
> select clear
> select /D:549@C5'
1 atom, 1 residue, 1 model selected
> select add /D:549@C3'
2 atoms, 1 residue, 1 model selected
> select add /D:549@C1'
3 atoms, 1 residue, 1 model selected
> color sel white
> select ::name="HOH"
176 atoms, 176 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /B:550@C4
1 atom, 1 residue, 1 model selected
> view sel
> select clear
> select add /B:550@C5'
1 atom, 1 residue, 1 model selected
> select add /B:550@C4'
2 atoms, 1 residue, 1 model selected
> view clip false
> select add /B:550@C3'
3 atoms, 1 residue, 1 model selected
> select add /B:550@C1'
4 atoms, 1 residue, 1 model selected
> select add /B:550@C8
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add /B:550@C5
6 atoms, 4 bonds, 1 residue, 1 model selected
> select add /B:550@C4
7 atoms, 4 bonds, 1 residue, 1 model selected
> select add /B:550@C6
8 atoms, 5 bonds, 1 residue, 1 model selected
> select add /B:550@C2
9 atoms, 5 bonds, 1 residue, 1 model selected
> color sel white
> select /B:550@C2'
1 atom, 1 residue, 1 model selected
> color sel white
Drag select of 4 residues
> save
> /Users/romainfrancois/Documents/Universite_de_Lorraine/CRM2/Projet_SUMOylation/Structures_E1/Structure_Analysis/ASU_contacts_ESO25.cxs
> select clear
> select /C
2431 atoms, 2474 bonds, 1 pseudobond, 309 residues, 2 models selected
> select /C
2431 atoms, 2474 bonds, 1 pseudobond, 309 residues, 2 models selected
> select /D
4067 atoms, 4145 bonds, 6 pseudobonds, 517 residues, 3 models selected
> select /C and /D
Expected a keyword
> select C/ D/
Expected an objects specifier or a keyword
> select /C /D
6498 atoms, 6619 bonds, 7 pseudobonds, 826 residues, 3 models selected
> create object
Unknown command: create object
> cofr sel
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> sequence chain /B
Alignment identifier is 1/B
> sequence chain /C
Alignment identifier is 1/C
> sequence chain /D
Alignment identifier is 1/D
Drag select of 56 residues
> select clear
> select /C:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C
2431 atoms, 2474 bonds, 1 pseudobond, 309 residues, 2 models selected
> select /D:6
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /D:6-548
4034 atoms, 4112 bonds, 2 pseudobonds, 514 residues, 2 models selected
> select /C /D
6498 atoms, 6619 bonds, 7 pseudobonds, 826 residues, 3 models selected
> select /B:519
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /B:517
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:355
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:355
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
Drag select of 1 residues
> select /B:183
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
25 atoms, 26 bonds, 3 residues, 1 model selected
> select up
1692 atoms, 1729 bonds, 217 residues, 1 model selected
> select up
1698 atoms, 1734 bonds, 218 residues, 1 model selected
> select up
2134 atoms, 2184 bonds, 269 residues, 1 model selected
> select up
2146 atoms, 2195 bonds, 271 residues, 1 model selected
> select up
4027 atoms, 4105 bonds, 513 residues, 1 model selected
> select down
2146 atoms, 2195 bonds, 271 residues, 1 model selected
> select down
2134 atoms, 2184 bonds, 269 residues, 1 model selected
> select down
1698 atoms, 1734 bonds, 218 residues, 1 model selected
> select up
2134 atoms, 2184 bonds, 269 residues, 1 model selected
> select up
2146 atoms, 2195 bonds, 271 residues, 1 model selected
> select up
4027 atoms, 4105 bonds, 513 residues, 1 model selected
> select up
4060 atoms, 4138 bonds, 516 residues, 1 model selected
> select up
12969 atoms, 13209 bonds, 1648 residues, 1 model selected
> select up
12969 atoms, 13209 bonds, 1648 residues, 1 model selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select down
4060 atoms, 4138 bonds, 516 residues, 1 model selected
> select ~sel & ##selected
8909 atoms, 9071 bonds, 9 pseudobonds, 1132 residues, 3 models selected
> select ~sel & ##selected
4060 atoms, 4138 bonds, 6 pseudobonds, 516 residues, 3 models selected
> select ~sel & ##selected
8909 atoms, 9071 bonds, 9 pseudobonds, 1132 residues, 3 models selected
> select ~sel & ##selected
4060 atoms, 4138 bonds, 6 pseudobonds, 516 residues, 3 models selected
> select ~sel & ##selected
8909 atoms, 9071 bonds, 9 pseudobonds, 1132 residues, 3 models selected
> select ~sel & ##selected
4060 atoms, 4138 bonds, 6 pseudobonds, 516 residues, 3 models selected
> select ~sel & ##selected
8909 atoms, 9071 bonds, 9 pseudobonds, 1132 residues, 3 models selected
Drag select of 6 atoms, 6 residues, 5 bonds
> select clear
> select add /A:20
8 atoms, 8 bonds, 1 residue, 1 model selected
> select add /B:48
16 atoms, 15 bonds, 2 residues, 1 model selected
> select add /B:92
28 atoms, 27 bonds, 3 residues, 1 model selected
> select /B:46
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:104
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /B:47
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add /B:92
29 atoms, 27 bonds, 3 residues, 1 model selected
Drag select of 32 atoms, 26 residues, 33 bonds
> view clip false
> select clear
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select C D
Expected a keyword
> select C,D
Expected an objects specifier or a keyword
> select /C /D
6498 atoms, 6619 bonds, 7 pseudobonds, 826 residues, 3 models selected
> view sel
> ui tool show "Side View"
> view orient
> view sel
> combine$ /C /D
Unknown command: combine$ /C /D
> combine /C /D
> hide #!3 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> close #3
> show #!1 models
> select clear
> ui tool show "Command Line Interface"
> ui tool show Contacts
> contacts intraMol false ignoreHiddenModels true
2135 contacts
> ui tool show Clashes
> undo
> show #!1 models
> ui tool show H-Bonds
> hbonds intraMol false reveal true
69 hydrogen bonds found
> hbonds intraMol false reveal true
69 hydrogen bonds found
Drag select of 1 atoms, 1 residues
> undo
> show #!1 models
> ui tool show Contacts
> select clear
> select add /D:435@CB
1 atom, 1 residue, 1 model selected
> select clear
> hide dahed lines
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide pbonds
> hide side chains
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ui tool show H-Bonds
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
12903 atoms, 13143 bonds, 2062 pseudobonds, 1642 residues, 4 models selected
> hide sel atoms
> select clear
> hbonds intraMol false intraRes false reveal true
69 hydrogen bonds found
Drag select of 19 residues
> select clear
> toolshed show
> ui tool show Contacts
> contacts intraMol false ignoreHiddenModels true
2135 contacts
Drag select of 1 atoms, 1 bonds
> select clear
> ui tool show Distances
> select /B:287
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:316@CB
1 atom, 1 residue, 1 model selected
> select add /B:287
8 atoms, 6 bonds, 2 residues, 1 model selected
Exactly two atoms must be selected!
> select clear
Exactly two atoms must be selected!
> select add /B:287
7 atoms, 6 bonds, 1 pseudobond, 1 residue, 2 models selected
> select clear
> select add /B:287
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add /B:316@CB
8 atoms, 6 bonds, 2 residues, 1 model selected
> select clear
> select add /B:316@CB
1 atom, 1 residue, 1 model selected
> select clear
> select /B:287
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> style sel stick
Changed 7 atom styles
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
> select clear
> select
12969 atoms, 13209 bonds, 2219 pseudobonds, 1648 residues, 5 models selected
> ui tool show "Color Actions"
> color sel byelement target a
> select clear
> select /B:287
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel ladder
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 7 atom styles
> show sel atoms
> style sel stick
Changed 7 atom styles
> style sel sphere
Changed 7 atom styles
> style sel ball
Changed 7 atom styles
> style sel stick
Changed 7 atom styles
> hide sel atoms
> select /B:287
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel main chain
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/romainfrancois/Documents/Universite_de_Lorraine/CRM2/Projet_SUMOylation/Structures_E1/Structure_Analysis/ASU_contacts_ESO25.cxs
Log from Sat Mar 8 16:02:15 2025 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/romainfrancois/Documents/CCP4/E1-ESO25/E1-ESO25_refine_010-coot-0_refmac2-coot-0.pdb
E1-ESO25_refine_010-coot-0_refmac2-coot-0.pdb title:
\--- [more info...]
Chain information for E1-ESO25_refine_010-coot-0_refmac2-coot-0.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Non-standard residues in E1-ESO25_refine_010-coot-0_refmac2-coot-0.pdb #1
---
ATP — (ATP)
MG — (MG)
ZN — (ZN)
14 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> set bgColor white
> lighting full
> lighting soft
> lighting simple
> lighting full
[Repeated 1 time(s)]
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting simple
[Repeated 1 time(s)]
> lighting shadows true
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting simple
> graphics silhouettes false
> lighting simple
> lighting full
> lighting flat
> lighting full
> ui tool show "Unit Cell"
> unitcell #1
> unitcell delete #1
[Repeated 1 time(s)]
> view #1 clip false
> ui tool show "Scale Bar"
> scalebar
> scalebar thickness 1
> scalebar off
> ui tool show "Selection Inspector"
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A
2411 atoms, 2452 bonds, 2 pseudobonds, 306 residues, 2 models selected
> ui tool show "Color Actions"
> color sel medium blue
> color sel royal blue
> color sel slate blue
> select /C
2431 atoms, 2474 bonds, 1 pseudobond, 309 residues, 2 models selected
> color sel royal blue
[Repeated 1 time(s)]
> color sel slate blue
Alignment identifier is 1/C
> hide sel cartoons
> show sel cartoons
> select
13145 atoms, 13209 bonds, 15 pseudobonds, 1824 residues, 3 models selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> undo
[Repeated 2 time(s)]
> select ::name="ATP"::name="HOH"::name="MG"::name="ZN"
242 atoms, 66 bonds, 182 residues, 1 model selected
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
12903 atoms, 13143 bonds, 7 pseudobonds, 1642 residues, 2 models selected
> hide sel atoms
> ui mousemode right select
> select /B:467
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select /B:468
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select /A:205
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select /B:115
5 atoms, 4 bonds, 1 residue, 1 model selected
Alignment identifier is 1/B
> select /B:6
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:6-42
254 atoms, 255 bonds, 37 residues, 1 model selected
> select /B:6-42
254 atoms, 255 bonds, 37 residues, 1 model selected
> select /B:6-42
254 atoms, 255 bonds, 37 residues, 1 model selected
> select /B:43-44
18 atoms, 18 bonds, 2 residues, 1 model selected
> select /B:43-147
842 atoms, 858 bonds, 105 residues, 1 model selected
> select /B:6-7
12 atoms, 11 bonds, 2 residues, 1 model selected
> select /B:6-192
1455 atoms, 1485 bonds, 187 residues, 1 model selected
> select /B:192-193
19 atoms, 19 bonds, 2 residues, 1 model selected
> select /B:190-193
40 atoms, 41 bonds, 4 residues, 1 model selected
> select clear
> select /B:167
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:6
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:6-167
1252 atoms, 1274 bonds, 162 residues, 1 model selected
> ui tool show "Color Actions"
> color sel hot pink
> color sel pale violet red
> select clear
> select /D:44
8 atoms, 7 bonds, 1 residue, 1 model selected
Alignment identifier is 1/D
> select /D:6
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /D:6-167
1252 atoms, 1274 bonds, 162 residues, 1 model selected
> color sel pale violet red
> select /B:168
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:384
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:384
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:168-384
1504 atoms, 1540 bonds, 2 pseudobonds, 186 residues, 2 models selected
> color sel salmon
> select clear
> select /B:439
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:439
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:384-439
419 atoms, 426 bonds, 56 residues, 1 model selected
> select /B:384
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:438
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:388-438
384 atoms, 389 bonds, 51 residues, 1 model selected
> select /B:439
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:385-439
411 atoms, 418 bonds, 55 residues, 1 model selected
> color sel hot pink
Drag select of 2 residues, 1 bonds
> select /B:439
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:385-439
411 atoms, 418 bonds, 55 residues, 1 model selected
> color sel pale violet red
> select /D:392
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /D:392
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /D:439
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:385-439
411 atoms, 418 bonds, 55 residues, 1 model selected
> color sel pale violet red
> select /D:440
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:440-548
852 atoms, 862 bonds, 109 residues, 1 model selected
> color sel red
> select clear
> select /B:440
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:440-549
860 atoms, 870 bonds, 110 residues, 1 model selected
> color sel red
> select clear
[Repeated 2 time(s)]
> select /B:354
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> select /B:168
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:384
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:168
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /D:168-384
1519 atoms, 1555 bonds, 2 pseudobonds, 188 residues, 2 models selected
> color sel dark salmon
[Repeated 1 time(s)]
> color sel light salmon
> color sel dark salmon
> color sel lime
> color sel dark salmon
> color sel salmon
> select clear
> select /D:549@C2'
1 atom, 1 residue, 1 model selected
> select ::name="ATP"
62 atoms, 66 bonds, 2 residues, 1 model selected
> color sel white
> color sel byelement
> color sel byhetero
> color sel byelement
Drag select of 12 residues
> select /D:549@C3'
1 atom, 1 residue, 1 model selected
> select /D:549@C4'
1 atom, 1 residue, 1 model selected
> view clip false
Drag select of 4 residues
Drag select of 1 residues
> select /D:549@C5'
1 atom, 1 residue, 1 model selected
> select /D:549@C4'
1 atom, 1 residue, 1 model selected
> select /D:549@C5'
1 atom, 1 residue, 1 model selected
> select /D:549@C4'
1 atom, 1 residue, 1 model selected
> select add /D:549@C2'
2 atoms, 2 bonds, 1 residue, 1 model selected
> select add /D:549@C8
3 atoms, 4 bonds, 1 residue, 1 model selected
> select add /D:549@C4
4 atoms, 4 bonds, 1 residue, 1 model selected
> select add /D:549@C2
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add /D:549@C5
6 atoms, 4 bonds, 1 residue, 1 model selected
> select add /D:549@C6
7 atoms, 4 bonds, 1 residue, 1 model selected
> color sel white
> select clear
> select /D:549@C5'
1 atom, 1 residue, 1 model selected
> select add /D:549@C3'
2 atoms, 1 residue, 1 model selected
> select add /D:549@C1'
3 atoms, 1 residue, 1 model selected
> color sel white
> select ::name="HOH"
176 atoms, 176 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /B:550@C4
1 atom, 1 residue, 1 model selected
> view sel
> select clear
> select add /B:550@C5'
1 atom, 1 residue, 1 model selected
> select add /B:550@C4'
2 atoms, 1 residue, 1 model selected
> view clip false
> select add /B:550@C3'
3 atoms, 1 residue, 1 model selected
> select add /B:550@C1'
4 atoms, 1 residue, 1 model selected
> select add /B:550@C8
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add /B:550@C5
6 atoms, 4 bonds, 1 residue, 1 model selected
> select add /B:550@C4
7 atoms, 4 bonds, 1 residue, 1 model selected
> select add /B:550@C6
8 atoms, 5 bonds, 1 residue, 1 model selected
> select add /B:550@C2
9 atoms, 5 bonds, 1 residue, 1 model selected
> color sel white
> select /B:550@C2'
1 atom, 1 residue, 1 model selected
> color sel white
Drag select of 4 residues
> save
> /Users/romainfrancois/Documents/Universite_de_Lorraine/CRM2/Projet_SUMOylation/Structures_E1/Structure_Analysis/ASU_contacts_ESO25.cxs
——— End of log from Sat Mar 8 16:02:15 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3
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: Mac15,3
Model Number: Z1C8000JJFN/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1.2 (23B2091)
Kernel Version: Darwin 23.1.0
Time since boot: 39 jours, 22 heures et 42 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
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
PHL 242B1:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
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: 3.9.2
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: 2.1.3
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: 2.4.2
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 , 7 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 , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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