![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Closed 5 months ago
#17883 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-13.7.5-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff85429ba00 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, 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, psutil._psutil_osx, psutil._psutil_posix (total: 54)
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{
"uptime" : 230000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro14,1",
"coalitionID" : 14578,
"osVersion" : {
"train" : "macOS 13.7.5",
"build" : "22H527",
"releaseType" : "User"
},
"captureTime" : "2025-06-03 13:08:43.4591 -0400",
"incident" : "3C0614CA-C9D7-49D3-8247-BF0617A31EA8",
"pid" : 32782,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-06-03 08:56:31.1561 -0400",
"procStartAbsTime" : 222412189000107,
"procExitAbsTime" : 234676368408468,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"9EE87E99-633C-58F2-BE90-E5AA3015234A","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "C07FE766-0CC2-1B3A-1E8B-8D588696AC95",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 972,
"sleepWakeUUID" : "59EE9EAC-F8DD-4023-B847-1B9A2380B683",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 140737487093399\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffecc000-7fffffecd000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":32782},
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 140737487093399\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffecc000-7fffffecd000 [ 4K] r-x\/r-x SM=SHM ",
"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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"size" : 9998322,
"uuid" : "79aaebf4-871c-37c3-9bdb-9d53c11ee075",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
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"arch" : "x86_64",
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"name" : "SkyLight"
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"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=5.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=5.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 2880K 8 \nCG image 632K 52 \nColorSync 268K 30 \nCoreAnimation 744K 102 \nCoreGraphics 16K 3 \nCoreImage 8K 2 \nCoreUI image data 5084K 60 \nFoundation 32K 2 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 4.4G 1034 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 120K 30 \nStack 173.2M 31 \nStack Guard 56.0M 1 \nVM_ALLOCATE 303.5M 901 \n__CTF 824 1 \n__DATA 40.8M 766 \n__DATA_CONST 49.5M 441 \n__DATA_DIRTY 1856K 236 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 201.6M 149 \n__OBJC_RO 66.3M 1 \n__OBJC_RW 2013K 2 \n__TEXT 969.5M 776 \ndyld private memory 292K 4 \nmapped file 241.5M 63 \nshared memory 3156K 35 \n=========== ======= ======= \nTOTAL 6.7G 4757 \nTOTAL, minus reserved VM space 6.5G 4757 \n",
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"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
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{
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"factorPackIds" : {
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}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/julienadeau/Downloads/MpIBP_R35figure.pdb
Summary of feedback from opening
/Users/julienadeau/Downloads/MpIBP_R35figure.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN A 30 LYS A 41 1 12
Start residue of secondary structure not found: HELIX 2 2 THR A 65 GLY A 72 1
8
Start residue of secondary structure not found: HELIX 3 3 SER A 73 LEU A 78 1
6
Start residue of secondary structure not found: SHEET 1 1 1 LEU A 17 THR A 24
0
Start residue of secondary structure not found: SHEET 2 2 1 ALA A 45 ALA A 49
0
End residue of secondary structure not found: SHEET 3 3 1 TYR A 54 GLY A 57 0
Start residue of secondary structure not found: SHEET 4 4 1 ASP A 87 LEU A 98
0
Start residue of secondary structure not found: SHEET 5 5 1 GLY A 101 ASP A
110 0
Start residue of secondary structure not found: SHEET 6 6 1 TYR A 113 ILE A
117 0
Start residue of secondary structure not found: SHEET 7 7 1 ASN A 120 VAL A
125 0
Start residue of secondary structure not found: SHEET 8 8 1 TYR A 132 THR A
135 0
71 messages similar to the above omitted
End residue of secondary structure not found: SHEET 5 5 1 GLY A 101 ASP A 110
0
Start residue of secondary structure not found: SHEET 6 6 1 TYR A 113 ILE A
117 0
Start residue of secondary structure not found: SHEET 7 7 1 ASN A 120 VAL A
125 0
Start residue of secondary structure not found: SHEET 8 8 1 TYR A 132 THR A
135 0
Start residue of secondary structure not found: SHEET 9 9 1 PHE A 139 ILE A
141 0
Start residue of secondary structure not found: SHEET 10 10 1 GLY A 145 ASP A
155 0
17 messages similar to the above omitted
80 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
5 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
5 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
25 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for MpIBP_R35figure.pdb
---
Chain | Description
1.1/A | No description available
1.2/A | No description available
1.3/A | No description available
1.4/A | No description available
1.5/A | No description available
1.6/A | No description available
1.7/A | No description available
1.8/A | No description available
> hide #1.8 models
> show #1.8 models
> hide #1.7 models
> show #1.7 models
> rename #1.7 MpIBP_AlphaFold
> hide #1.7 models
> select add #1
17350 atoms, 17050 bonds, 167 pseudobonds, 2831 residues, 16 models selected
> select subtract #1
Nothing selected
> select add #1.1
1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 2 models selected
> select subtract #1.1
Nothing selected
> select add #1.2
722 atoms, 720 bonds, 15 pseudobonds, 109 residues, 2 models selected
> select subtract #1.2
Nothing selected
> select add #1.2
722 atoms, 720 bonds, 15 pseudobonds, 109 residues, 2 models selected
> rename #1.2 RIII_1
> select subtract #1.2
Nothing selected
> select add #1.1
1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 2 models selected
> select subtract #1.1
Nothing selected
> select add #1.3
652 atoms, 661 bonds, 9 pseudobonds, 88 residues, 2 models selected
> rename #1.3 RIII_2
> select subtract #1.3
Nothing selected
> select add #1.4
1621 atoms, 1648 bonds, 28 pseudobonds, 216 residues, 2 models selected
> rename #1.4 RIII_#
> rename #1.4 RIII_3
> select subtract #1.4
Nothing selected
> select add #1.5
782 atoms, 788 bonds, 10 pseudobonds, 114 residues, 3 models selected
> rename #1.5 RIII_4
> select subtract #1.5
Nothing selected
> select add #1.6
1190 atoms, 1010 bonds, 52 pseudobonds, 326 residues, 2 models selected
> select subtract #1.6
Nothing selected
> select add #1.8
627 atoms, 631 bonds, 87 residues, 1 model selected
> select subtract #1.8
Nothing selected
> select add #1.1
1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 2 models selected
> rename #1.1 RIII_5
> select add #1.6
2943 atoms, 2483 bonds, 105 pseudobonds, 827 residues, 4 models selected
> select subtract #1.6
1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 2 models selected
> select add #1.8
2380 atoms, 2104 bonds, 53 pseudobonds, 588 residues, 3 models selected
> rename #1.8 missingdomain
> select subtract #1.8
1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 2 models selected
> select subtract #1.1
Nothing selected
> select add #1.6
1190 atoms, 1010 bonds, 52 pseudobonds, 326 residues, 2 models selected
> rename #1.6 RV
> select subtract #1.6
Nothing selected
> open /Users/julienadeau/Downloads/MpIBP_R35figure.pdb format pdb
Summary of feedback from opening
/Users/julienadeau/Downloads/MpIBP_R35figure.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN A 30 LYS A 41 1 12
Start residue of secondary structure not found: HELIX 2 2 THR A 65 GLY A 72 1
8
Start residue of secondary structure not found: HELIX 3 3 SER A 73 LEU A 78 1
6
Start residue of secondary structure not found: SHEET 1 1 1 LEU A 17 THR A 24
0
Start residue of secondary structure not found: SHEET 2 2 1 ALA A 45 ALA A 49
0
End residue of secondary structure not found: SHEET 3 3 1 TYR A 54 GLY A 57 0
Start residue of secondary structure not found: SHEET 4 4 1 ASP A 87 LEU A 98
0
Start residue of secondary structure not found: SHEET 5 5 1 GLY A 101 ASP A
110 0
Start residue of secondary structure not found: SHEET 6 6 1 TYR A 113 ILE A
117 0
Start residue of secondary structure not found: SHEET 7 7 1 ASN A 120 VAL A
125 0
Start residue of secondary structure not found: SHEET 8 8 1 TYR A 132 THR A
135 0
71 messages similar to the above omitted
End residue of secondary structure not found: SHEET 5 5 1 GLY A 101 ASP A 110
0
Start residue of secondary structure not found: SHEET 6 6 1 TYR A 113 ILE A
117 0
Start residue of secondary structure not found: SHEET 7 7 1 ASN A 120 VAL A
125 0
Start residue of secondary structure not found: SHEET 8 8 1 TYR A 132 THR A
135 0
Start residue of secondary structure not found: SHEET 9 9 1 PHE A 139 ILE A
141 0
Start residue of secondary structure not found: SHEET 10 10 1 GLY A 145 ASP A
155 0
17 messages similar to the above omitted
80 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
5 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
5 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
25 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for MpIBP_R35figure.pdb
---
Chain | Description
2.1/A | No description available
2.2/A | No description available
2.3/A | No description available
2.4/A | No description available
2.5/A | No description available
2.6/A | No description available
2.7/A | No description available
2.8/A | No description available
> hide #2.8 models
> show #2.8 models
> select add #2.7
10003 atoms, 10119 bonds, 1390 residues, 1 model selected
> select subtract #2.7
Nothing selected
> select add #2.7
10003 atoms, 10119 bonds, 1390 residues, 1 model selected
> delete sel
> select add #2.8
627 atoms, 631 bonds, 87 residues, 1 model selected
> select subtract #2.8
Nothing selected
> select add #2
7347 atoms, 6931 bonds, 167 pseudobonds, 1441 residues, 15 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-17.137,0,1,0,40.382,0,0,1,119.14
> select subtract #2
Nothing selected
> select add #2.2
722 atoms, 720 bonds, 15 pseudobonds, 109 residues, 2 models selected
> rename #2.2 RIII_1
> select subtract #2.2
Nothing selected
> hide #!2.2 models
> hide #!1.2 models
> select add #2.8
627 atoms, 631 bonds, 87 residues, 1 model selected
> select add #2
7347 atoms, 6931 bonds, 167 pseudobonds, 1441 residues, 15 models selected
> select subtract #2
Nothing selected
> select add #2.8
627 atoms, 631 bonds, 87 residues, 1 model selected
> delete sel
> select add #2.6
1190 atoms, 1010 bonds, 52 pseudobonds, 326 residues, 2 models selected
> select subtract #2.6
Nothing selected
> hide #!2.6 models
> select add #2.1
1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 2 models selected
> select subtract #2.1
Nothing selected
> select add #2.4
1621 atoms, 1648 bonds, 28 pseudobonds, 216 residues, 2 models selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui mousemode right "rotate selected models"
> view matrix models
> #2.4,0.69762,-0.1137,-0.70739,186.48,0.26489,0.9583,0.1072,-51.609,0.6657,-0.26216,0.69865,-5.2424
> view matrix models
> #2.4,0.33073,-0.6945,-0.63897,334.36,0.76243,0.59565,-0.25279,-3.1966,0.55616,-0.40357,0.72651,31.981
> view matrix models
> #2.4,-0.046131,0.036944,0.99825,-14.131,0.91589,0.40049,0.027503,-39.732,-0.39877,0.91556,-0.052312,77.428
> view matrix models
> #2.4,-0.85109,0.21114,-0.4807,329.44,0.016306,0.92576,0.37776,-53.294,0.52477,0.31367,-0.79134,166.65
> view matrix models
> #2.4,0.28901,-0.51163,-0.80914,337.2,-0.21999,0.7871,-0.57626,169.16,0.93171,0.34455,0.11493,-54.941
> view matrix models
> #2.4,0.63035,-0.22191,-0.74391,222.2,-0.40996,0.71859,-0.56174,208.13,0.65923,0.65908,0.36199,-110.43
> ui mousemode right "translate selected models"
> view matrix models
> #2.4,0.63035,-0.22191,-0.74391,221.08,-0.40996,0.71859,-0.56174,202.26,0.65923,0.65908,0.36199,-110.98
> view matrix models
> #2.4,0.63035,-0.22191,-0.74391,214.27,-0.40996,0.71859,-0.56174,194.89,0.65923,0.65908,0.36199,-100.92
> select subtract #2.4
Nothing selected
> select add #2.1
1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 2 models selected
> view matrix models #2.1,1,0,0,-3.3535,0,1,0,4.3358,0,0,1,13.735
> ui mousemode right "rotate selected models"
> view matrix models
> #2.1,-0.062952,0.77855,-0.62441,145.49,-0.79048,0.34304,0.50741,167.19,0.60925,0.52553,0.59383,-112.6
> view matrix models
> #2.1,-0.92154,0.3412,-0.18532,298.76,-0.29897,-0.31899,0.89937,126.58,0.24775,0.88421,0.39597,-76.108
> view matrix models
> #2.1,-0.91653,0.38936,-0.091554,280.82,-0.25431,-0.39059,0.88474,130.18,0.30872,0.83417,0.45701,-86.775
> view matrix models
> #2.1,-0.8666,0.49573,-0.057031,254.3,-0.30011,-0.42647,0.85326,146.3,0.39866,0.75656,0.51835,-98.732
> ui mousemode right "translate selected models"
> view matrix models
> #2.1,-0.8666,0.49573,-0.057031,260.98,-0.30011,-0.42647,0.85326,156.74,0.39866,0.75656,0.51835,-102.33
> view matrix models
> #2.1,-0.8666,0.49573,-0.057031,260.87,-0.30011,-0.42647,0.85326,155.91,0.39866,0.75656,0.51835,-105.31
> view matrix models
> #2.1,-0.8666,0.49573,-0.057031,260.24,-0.30011,-0.42647,0.85326,155.24,0.39866,0.75656,0.51835,-103.23
> ui mousemode right "rotate selected models"
> view matrix models
> #2.1,-0.86366,0.50391,0.013203,250.63,-0.26718,-0.47983,0.83569,158.75,0.42745,0.71822,0.54904,-106.53
> view matrix models
> #2.1,-0.81653,0.54138,0.20045,216.25,-0.21813,-0.61082,0.76113,176.34,0.5345,0.57776,0.61684,-113.8
> view matrix models
> #2.1,-0.90803,0.4056,-0.10473,284.65,-0.28788,-0.42258,0.85939,151.97,0.30431,0.8105,0.50048,-92.342
> ui mousemode right "translate selected models"
> view matrix models
> #2.1,-0.90803,0.4056,-0.10473,279.98,-0.28788,-0.42258,0.85939,154.01,0.30431,0.8105,0.50048,-79.428
> view matrix models
> #2.1,-0.90803,0.4056,-0.10473,278.15,-0.28788,-0.42258,0.85939,151.43,0.30431,0.8105,0.50048,-75.033
> view matrix models
> #2.1,-0.90803,0.4056,-0.10473,273.11,-0.28788,-0.42258,0.85939,157.98,0.30431,0.8105,0.50048,-70.726
> view matrix models
> #2.1,-0.90803,0.4056,-0.10473,265.36,-0.28788,-0.42258,0.85939,147.03,0.30431,0.8105,0.50048,-92.793
> view matrix models
> #2.1,-0.90803,0.4056,-0.10473,265.57,-0.28788,-0.42258,0.85939,147.52,0.30431,0.8105,0.50048,-92.974
> view matrix models
> #2.1,-0.90803,0.4056,-0.10473,264.97,-0.28788,-0.42258,0.85939,144.99,0.30431,0.8105,0.50048,-92.492
> ui mousemode right "translate selected models"
> view matrix models
> #2.1,-0.90803,0.4056,-0.10473,268.04,-0.28788,-0.42258,0.85939,152.57,0.30431,0.8105,0.50048,-90.246
> ui mousemode right select
> select clear
> ui mousemode right translate
> select add #2.1
1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2.1,-0.90803,0.4056,-0.10473,274.96,-0.28788,-0.42258,0.85939,165.61,0.30431,0.8105,0.50048,-99.845
> ui mousemode right "rotate selected models"
> view matrix models
> #2.1,-0.86521,0.45995,-0.19966,271.34,-0.39086,-0.36924,0.84315,177.85,0.31408,0.80753,0.49924,-100.97
> view matrix models
> #2.1,-0.90773,0.41518,-0.060466,268.57,-0.28065,-0.49372,0.82309,177.95,0.31188,0.76411,0.56469,-102.35
> view matrix models
> #2.1,-0.68924,0.29214,-0.66303,316.65,-0.72204,-0.35276,0.59515,260.18,-0.060025,0.88894,0.45408,-43.338
> view matrix models
> #2.1,-0.48798,0.85411,-0.17991,153.15,-0.86341,-0.4421,0.24305,336.24,0.12805,0.27394,0.95318,-51.17
> view matrix models
> #2.1,-0.87896,0.46871,-0.088008,259.87,-0.46946,-0.81792,0.3326,308.96,0.083908,0.33365,0.93895,-49.966
> view matrix models
> #2.1,-0.79545,0.47583,-0.37529,277.48,-0.40189,-0.8777,-0.261,373.63,-0.45358,-0.056792,0.8894,98.13
> view matrix models
> #2.1,-0.94762,0.0091359,-0.31926,358.63,0.058283,-0.97786,-0.20098,302.1,-0.31403,-0.20906,0.92611,90.469
> ui mousemode right "translate selected models"
> view matrix models
> #2.1,-0.94762,0.0091359,-0.31926,360.91,0.058283,-0.97786,-0.20098,300.44,-0.31403,-0.20906,0.92611,105.26
> view matrix models
> #2.1,-0.94762,0.0091359,-0.31926,360.95,0.058283,-0.97786,-0.20098,301.04,-0.31403,-0.20906,0.92611,103.59
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #2.1,-0.94762,0.0091359,-0.31926,360.84,0.058283,-0.97786,-0.20098,308.79,-0.31403,-0.20906,0.92611,111.95
> view matrix models
> #2.1,-0.94762,0.0091359,-0.31926,358.75,0.058283,-0.97786,-0.20098,301.55,-0.31403,-0.20906,0.92611,110.18
> ui mousemode right "rotate selected models"
> view matrix models
> #2.1,0.012894,0.77708,0.62927,-13.915,-0.99908,0.035703,-0.023619,326.32,-0.04082,-0.62839,0.77683,136.43
> view matrix models
> #2.1,0.6359,0.36127,0.68199,-70.278,-0.76521,0.41011,0.49625,177.62,-0.10041,-0.83743,0.53724,201.63
> view matrix models
> #2.1,0.65287,0.34072,0.67652,-69.804,-0.74944,0.42029,0.51157,171.84,-0.11003,-0.84099,0.52974,204.59
> ui mousemode right "translate selected models"
> view matrix models
> #2.1,0.65287,0.34072,0.67652,-77.3,-0.74944,0.42029,0.51157,153.76,-0.11003,-0.84099,0.52974,208.41
> view matrix models
> #2.1,0.65287,0.34072,0.67652,-74.511,-0.74944,0.42029,0.51157,159.49,-0.11003,-0.84099,0.52974,204.23
> ui mousemode right "rotate selected models"
> view matrix models
> #2.1,0.66206,0.33462,0.6706,-74.584,-0.74138,0.42338,0.52068,156.67,-0.10969,-0.84189,0.52839,204.45
> view matrix models
> #2.1,0.66739,0.31304,0.67572,-73.21,-0.73328,0.43464,0.52288,153.56,-0.13001,-0.84445,0.51961,209.24
> view matrix models
> #2.1,0.50732,0.61012,0.60858,-77.661,-0.766,-0.0042599,0.64282,203.48,0.39479,-0.7923,0.46519,119.63
> view matrix models
> #2.1,0.88892,-0.13047,0.43909,-24.974,-0.24857,0.66778,0.70163,20.053,-0.38476,-0.73283,0.56117,232.85
> ui mousemode right "translate selected models"
> view matrix models
> #2.1,0.88892,-0.13047,0.43909,-30.384,-0.24857,0.66778,0.70163,14.859,-0.38476,-0.73283,0.56117,238.4
> select subtract #2.1
Nothing selected
> lighting simple
> set bgColor white
> show #1.8#!1.1,3-6#!2.1,3-5 cartoons
> select add #2
6720 atoms, 6300 bonds, 167 pseudobonds, 1354 residues, 14 models selected
> show sel & #!2.1,3-5 cartoons
> select subtract #2
Nothing selected
> graphics silhouettes true
> select add #2
6720 atoms, 6300 bonds, 167 pseudobonds, 1354 residues, 14 models selected
> view matrix models #2,1,0,0,7.4703,0,1,0,99.175,0,0,1,162.02
> select subtract #2
Nothing selected
> select add #1
17350 atoms, 17050 bonds, 167 pseudobonds, 2831 residues, 16 models selected
> view matrix models #1,1,0,0,-10.641,0,1,0,-6.7046,0,0,1,60.639
> view matrix models #1,1,0,0,-14.341,0,1,0,-11.353,0,0,1,79.589
> view matrix models #1,1,0,0,-10.65,0,1,0,-2.656,0,0,1,84.174
> select subtract #1
Nothing selected
> hide #!1.6 models
> select add #1.7
10003 atoms, 10119 bonds, 1390 residues, 1 model selected
> select subtract #1.7
Nothing selected
> show #1.7 models
> hide #!2 models
> show #!2 models
> hide #1.8 models
> show #1.8 models
> hide #1.7 models
> open "/Users/julienadeau/Desktop/Master's
> degree/data/cryosparc/MpIBP/cryosparc_P43_J1976_006_volume_map_sharp.mrc"
> format mrc
Opened cryosparc_P43_J1976_006_volume_map_sharp.mrc as #3, grid size
440,440,440, pixel 0.675, shown at level 0.00933, step 2, values float32
> volume #3 level 0.03011
> vop gaussian #3 sdev 2.03
Opened cryosparc_P43_J1976_006_volume_map_sharp.mrc gaussian as #4, grid size
440,440,440, pixel 0.675, shown at step 1, values float32
> transparency #4.1 50
> volume #!4 style mesh
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!3 models
> volume #4 level 0.003749
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 9 atomic models, 1 maps.
> select add #1
17350 atoms, 17050 bonds, 167 pseudobonds, 2831 residues, 16 models selected
> view matrix models #1,1,0,0,-4.9848,0,1,0,2.0599,0,0,1,-1.1115
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 9 atomic models, 1 maps.
> select subtract #1
Nothing selected
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #4 level 0.003749
> volume #4 color #ffffb21b
> volume #4 color #ffffb245
> volume #4 color #ffffb200
> volume #4 color #ffffb245
> hide #1.8#!1.1,3-5#!2.1,3-5 cartoons
> show #1.8#!1.1,3-5#!2.1,3-5 surfaces
> hide #!1.1,3-5,8#!2.1,3-5 surfaces
> show #!1.1,3-5,8#!2.1,3-5 cartoons
> ui tool show "Side View"
> volume #4 color #fbfff845
> volume #4 color white
> volume #4 color #ffffff32
> open /Users/julienadeau/Downloads/MpIBP_R35figure.pdb format pdb
Summary of feedback from opening
/Users/julienadeau/Downloads/MpIBP_R35figure.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN A 30 LYS A 41 1 12
Start residue of secondary structure not found: HELIX 2 2 THR A 65 GLY A 72 1
8
Start residue of secondary structure not found: HELIX 3 3 SER A 73 LEU A 78 1
6
Start residue of secondary structure not found: SHEET 1 1 1 LEU A 17 THR A 24
0
Start residue of secondary structure not found: SHEET 2 2 1 ALA A 45 ALA A 49
0
End residue of secondary structure not found: SHEET 3 3 1 TYR A 54 GLY A 57 0
Start residue of secondary structure not found: SHEET 4 4 1 ASP A 87 LEU A 98
0
Start residue of secondary structure not found: SHEET 5 5 1 GLY A 101 ASP A
110 0
Start residue of secondary structure not found: SHEET 6 6 1 TYR A 113 ILE A
117 0
Start residue of secondary structure not found: SHEET 7 7 1 ASN A 120 VAL A
125 0
Start residue of secondary structure not found: SHEET 8 8 1 TYR A 132 THR A
135 0
71 messages similar to the above omitted
End residue of secondary structure not found: SHEET 5 5 1 GLY A 101 ASP A 110
0
Start residue of secondary structure not found: SHEET 6 6 1 TYR A 113 ILE A
117 0
Start residue of secondary structure not found: SHEET 7 7 1 ASN A 120 VAL A
125 0
Start residue of secondary structure not found: SHEET 8 8 1 TYR A 132 THR A
135 0
Start residue of secondary structure not found: SHEET 9 9 1 PHE A 139 ILE A
141 0
Start residue of secondary structure not found: SHEET 10 10 1 GLY A 145 ASP A
155 0
17 messages similar to the above omitted
80 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
5 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
5 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
25 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for MpIBP_R35figure.pdb
---
Chain | Description
5.1/A | No description available
5.2/A | No description available
5.3/A | No description available
5.4/A | No description available
5.5/A | No description available
5.6/A | No description available
5.7/A | No description available
5.8/A | No description available
> hide #5.7 models
> hide #!5.6 models
> show #!5.6 models
> hide #!5.5 models
> show #!5.5 models
> hide #5.8 models
> show #5.8 models
> hide #!5.2 models
> select add #5
17350 atoms, 17050 bonds, 167 pseudobonds, 2831 residues, 16 models selected
> view matrix models #5,1,0,0,-7.3432,0,1,0,12.188,0,0,1,124.46
> view matrix models #5,1,0,0,-23.356,0,1,0,-35.477,0,0,1,162.79
> select subtract #5
Nothing selected
> select add #2
6720 atoms, 6300 bonds, 167 pseudobonds, 1354 residues, 14 models selected
> view matrix models #2,1,0,0,11.652,0,1,0,129.46,0,0,1,201.55
> view matrix models #2,1,0,0,12.894,0,1,0,162.66,0,0,1,255.33
> select subtract #2
4 models selected
> select add #5
17350 atoms, 17050 bonds, 167 pseudobonds, 2831 residues, 16 models selected
> view matrix models #5,1,0,0,-4.3526,0,1,0,80.084,0,0,1,142.25
> show #!5.2 models
> hide #!5.2 models
> select subtract #5
Nothing selected
> ui mousemode right "rotate selected models"
> select add #2
6720 atoms, 6300 bonds, 167 pseudobonds, 1354 residues, 14 models selected
> show #1.7 models
> hide #1.7 models
> show #!1.6 models
> hide #!1.6 models
> select subtract #2
4 models selected
> ui mousemode right "translate selected models"
> show #!1.6 models
> hide #!5.6 models
> color #2.5 #c2c2c2ff
> select add #2.5
782 atoms, 788 bonds, 10 pseudobonds, 114 residues, 3 models selected
> color #2.5 skyblue
> select subtract #2.5
1 model selected
> select add #2.4
1621 atoms, 1648 bonds, 28 pseudobonds, 216 residues, 2 models selected
> select subtract #2.4
1 model selected
> select add #2.3
652 atoms, 661 bonds, 9 pseudobonds, 88 residues, 2 models selected
> select subtract #2.3
1 model selected
> select add #2.1
1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 2 models selected
> color #2.5 #ef574bff
> color #2.5 skyblue
> select add #2.3
2405 atoms, 2134 bonds, 62 pseudobonds, 589 residues, 5 models selected
> select subtract #2.3
1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 4 models selected
> select add #2.3
2405 atoms, 2134 bonds, 62 pseudobonds, 589 residues, 5 models selected
> select subtract #2.3
1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 4 models selected
> color #2.5 #ef574bff
> color #2.5 skyblue
> color #2.5 #ef574bff
> color #2.5 skyblue
> select subtract #2.1
1 model selected
> select add #2.1
1753 atoms, 1473 bonds, 53 pseudobonds, 501 residues, 2 models selected
> color #2.1 #ef574bff
> select subtract #2.1
1 model selected
> color #5.1 skyblue
> color #5.1 #ef574bff
> color #5.3 skyblue
> color #5.4 #ef574bff
> color #5.4 skyblue
> hide #!5.5 models
> show #!5.5 models
> color #5.5 skyblue
> select add #5.8
627 atoms, 631 bonds, 87 residues, 1 model selected
> color #5.8 lightgrey
> color #5.8 #11d1e1ff
> color #5.8 #627be4ff
> color #5.8 #4e41e4ff
> select subtract #5.8
Nothing selected
> hide #!1.6 models
> color #1.1 skyblue
> color #1.1 #ef574bff
> select add #1.3
652 atoms, 661 bonds, 9 pseudobonds, 88 residues, 2 models selected
> select subtract #1.3
1 model selected
> color #1.3 skyblue
> hide #!1.8 models
> show #!1.8 models
> color #1.8 #4e41e4ff
> color #1.5 skyblue
> color #1.4 skyblue
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right translate
> ui mousemode right rotate
> lighting simple
> show #!1.2 models
> hide #!1.2 models
> show #!1.6 models
> hide #!1.6 models
> show #!1.6 models
> hide #!1.6 models
> show #1.7 models
> ui mousemode right translate
> show #!1.6 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.7.3
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro14,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 529.140.2.0.0
OS Loader Version: 577.140.2~30
SMC Version (system): 2.43f11
Software:
System Software Overview:
System Version: macOS 13.7.5 (22H527)
Kernel Version: Darwin 22.6.0
Time since boot: 20 days, 4 hours, 12 minutes
Graphics/Displays:
Intel Iris Plus Graphics 640:
Chipset Model: Intel Iris Plus Graphics 640
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5926
Revision ID: 0x0006
Metal Support: Metal 3
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
VS278:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: H4LMQS080476
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
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: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 5 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 , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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