![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17480 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 (last modified by )
The following bug report has been submitted:
Platform: macOS-15.4-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 0x00000001f3624c40 (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, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 60)
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"procRole" : "Background",
"version" : 2,
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"deployVersion" : 210,
"modelCode" : "Mac15,12",
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"build" : "24E248",
"releaseType" : "User"
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"captureTime" : "2025-04-24 13:00:40.6203 -0700",
"codeSigningMonitor" : 1,
"incident" : "CAD8A64C-F5B3-45AC-A783-18132580D9F1",
"pid" : 41041,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
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"procLaunch" : "2025-04-23 14:05:28.4251 -0700",
"procStartAbsTime" : 24810853477964,
"procExitAbsTime" : 26698181398076,
"procName" : "ChimeraX",
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"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"crashReporterKey" : "3587406A-7241-238D-D039-C9AD257A1AF4",
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"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
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"wakeTime" : 3,
"sleepWakeUUID" : "B6E70037-612D-4F8E-9D1A-0CC33A1316A8",
"sip" : "enabled",
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"exception" : {"codes":"0x0000000000000001, 0x0000a2024763d1e8","rawCodes":[1,178130671358440],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000a2024763d1e8 -> 0x000022024763d1e8 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":41041},
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===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/sphulera/Desktop/HVTN301/Map_session.cxs
Opened 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc as #1, grid size
400,400,400, pixel 1.03, shown at level 0.16, step 1, values float32
Opened 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc as #2, grid size
400,400,400, pixel 1.03, shown at level 0.23, step 1, values float32
Opened 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc as #3, grid size
400,400,400, pixel 1.03, shown at level 0.24, step 1, values float32
Opened 301_48FAB_GT1-1_RM20A3_J336_C3_map_sharp_2.98A.mrc as #4, grid size
400,400,400, pixel 1.03, shown at level 0.21, step 1, values float32
Opened 301_56Fab_426cSM_SOSIP_RM20A3_J1469_map_sharp_2.88A.mrc as #5, grid
size 400,400,400, pixel 1.03, shown at level 0.215, step 1, values float32
Opened 301_61FAB_426cSM_SOSIP_RM20A3_J1468_map_sharp_2.87A.mrc as #6, grid
size 400,400,400, pixel 1.03, shown at level 0.23, step 1, values float32
Log from Tue Apr 22 15:50:50 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/sphulera/Desktop/HVTN301/maps/301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc
Opened 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc as #1, grid size
400,400,400, pixel 1.03, shown at level 0.0574, step 2, values float32
> open
> /Users/sphulera/Desktop/HVTN301/maps/301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc
Opened 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc as #2, grid size
400,400,400, pixel 1.03, shown at level 0.0637, step 2, values float32
> open
> /Users/sphulera/Desktop/HVTN301/maps/301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc
Opened 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc as #3, grid size
400,400,400, pixel 1.03, shown at level 0.067, step 2, values float32
> open
> /Users/sphulera/Desktop/HVTN301/maps/301_48FAB_GT1-1_RM20A3_J336_C3_map_sharp_2.98A.mrc
Opened 301_48FAB_GT1-1_RM20A3_J336_C3_map_sharp_2.98A.mrc as #4, grid size
400,400,400, pixel 1.03, shown at level 0.0606, step 2, values float32
> open
> /Users/sphulera/Desktop/HVTN301/maps/301_56Fab_426cSM_SOSIP_RM20A3_J1469_map_sharp_2.88A.mrc
Opened 301_56Fab_426cSM_SOSIP_RM20A3_J1469_map_sharp_2.88A.mrc as #5, grid
size 400,400,400, pixel 1.03, shown at level 0.0655, step 2, values float32
> open
> /Users/sphulera/Desktop/HVTN301/maps/301_61FAB_426cSM_SOSIP_RM20A3_J1468_map_sharp_2.87A.mrc
Opened 301_61FAB_426cSM_SOSIP_RM20A3_J1468_map_sharp_2.87A.mrc as #6, grid
size 400,400,400, pixel 1.03, shown at level 0.0718, step 2, values float32
> surface dust #1 size 10.3
> surface dust #2 size 10.3
> surface dust #3 size 10.3
> surface dust #4 size 10.3
> surface dust #5 size 10.3
> surface dust #6 size 10.3
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select add #2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.68055,0.73228,-0.02489,-71.656,-0.73235,0.68088,0.0076984,213.17,0.022585,0.012989,0.99966,-7.1686
> fitmap #2 inMap #1
Fit map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc in map
301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc using 79679 points
correlation = 0.8247, correlation about mean = 0.7973, overlap = 1739
steps = 120, shift = 8.87, angle = 3.49 degrees
Position of 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) relative to
301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc (#1) coordinates:
Matrix rotation and translation
0.72068270 0.69325818 -0.00309118 -85.16213772
-0.69326501 0.72067722 -0.00282255 201.53581721
0.00027098 0.00417717 0.99999124 -0.24291772
Axis 0.00504832 -0.00242485 -0.99998432
Axis point 207.52227718 206.45020110 0.00000000
Rotation angle (degrees) 43.88971452
Shift along axis -0.67570642
> select clear
> volume #2 step 1
> volume #1 step 1
> hide #!2 models
> volume #1 level 0.08067
> volume #1 level 0.2202
> show #!2 models
> fitmap #1 inMap #2
Fit map 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc in map
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 81884 points
correlation = 0.9559, correlation about mean = 0.7508, overlap = 1.157e+04
steps = 40, shift = 0.00539, angle = 0.0285 degrees
Position of 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc (#1) relative to
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates:
Matrix rotation and translation
0.72098069 -0.69295515 0.00005930 201.01210114
0.69294854 0.72097417 0.00430886 -86.23281590
-0.00302860 -0.00306551 0.99999071 0.58334473
Axis -0.00532089 0.00222804 0.99998336
Axis point 207.58699714 206.48913474 0.00000000
Rotation angle (degrees) 43.86514598
Shift along axis -0.67835847
> fitmap #1 inMap #2
Fit map 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc in map
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 81884 points
correlation = 0.9558, correlation about mean = 0.7506, overlap = 1.158e+04
steps = 48, shift = 0.0118, angle = 0.00601 degrees
Position of 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc (#1) relative to
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates:
Matrix rotation and translation
0.72103666 -0.69289691 0.00005690 200.98869703
0.69289010 0.72102993 0.00437570 -86.24757234
-0.00307294 -0.00311561 0.99999042 0.59133203
Axis -0.00540573 0.00225849 0.99998284
Axis point 207.60609202 206.48162074 0.00000000
Rotation angle (degrees) 43.86053881
Shift along axis -0.68995794
> volume #2 level 0.1202
> lighting soft
> set bgColor white
> volume #2 level 0.2083
> fitmap #1 inMap #2
Fit map 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc in map
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 81884 points
correlation = 0.9558, correlation about mean = 0.7505, overlap = 1.159e+04
steps = 40, shift = 0.00345, angle = 0.00653 degrees
Position of 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc (#1) relative to
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates:
Matrix rotation and translation
0.72108006 -0.69285173 0.00014459 200.95025525
0.69284476 0.72107372 0.00433882 -86.23782963
-0.00311042 -0.00302846 0.99999058 0.57786141
Axis -0.00531658 0.00234896 0.99998311
Axis point 207.58433723 206.46143216 0.00000000
Rotation angle (degrees) 43.85692728
Shift along axis -0.69308527
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #2 level 0.22
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> surface dust #2 size 10.3
[Repeated 1 time(s)]
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> volume #3 level 0.22
> volume #3 step 1
> hide #!1 models
> show #!2 models
> hide #!3 models
> volume #2 level 0.1847
> surface dust #2 size 10.3
[Repeated 1 time(s)]
> ui tool show "Hide Dust"
> surface dust #2 size 1.03
> surface dust #2 size 1.09
> surface dust #2 size 1.6
[Repeated 1 time(s)]
> surface dust #2 size 1.5
> surface dust #2 size 5.28
[Repeated 1 time(s)]
> surface dust #2 size 5.46
> surface dust #2 size 13.76
> surface dust #2 size 10
[Repeated 1 time(s)]
> volume #2 level 0.2
> volume #2 level 0.201
> volume #2 level 0.2
> volume #2 level 0.205
> volume #2 level 0.209
> volume #2 level 0.22
> volume #2 level 0.2
> volume #2 level 0.18
> volume #2 level 0.19
> volume #2 level 0.1
> volume #2 level 0.15
> volume #2 level 0.16
> volume #2 level 0.17
> volume #2 level 0.19
> volume #2 level 0.2
> show #!3 models
> select add #3
2 models selected
> view matrix models
> #3,0.67263,0.70376,0.22866,-129.08,0.72859,-0.68387,-0.038439,212.71,0.12933,0.19246,-0.97275,349.38
> view matrix models
> #3,0.090582,0.90746,0.41025,-86.538,0.99416,-0.10667,0.016445,20.574,0.058685,0.40636,-0.91182,305.78
> view matrix models
> #3,0.0053953,0.99627,0.086076,-18.574,0.99998,-0.0056737,0.0029901,0.55108,0.0034673,0.086058,-0.99628,404.11
> view matrix models
> #3,0.12784,0.98971,0.064272,-38.772,0.99172,-0.12837,0.0041183,28.357,0.012326,0.063213,-0.99792,407.45
> fitmap #3 inMap #2
Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points
correlation = 0.4032, correlation about mean = 0.05819, overlap = 4262
steps = 164, shift = 2.58, angle = 10.1 degrees
Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative
to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates:
Matrix rotation and translation
-0.46454226 0.88503527 -0.03021685 124.58564296
0.88539497 0.46483037 0.00290874 -75.39081319
0.01662005 -0.02540261 -0.99953913 424.06340972
Axis -0.51729269 -0.85578331 0.00657234
Axis point 81.68795033 0.00000000 212.75016737
Rotation angle (degrees) 178.43190949
Shift along axis 2.85804462
> show #!1 models
> hide #!2 models
> select clear
> select subtract #3
Nothing selected
> select add #3
2 models selected
> view matrix models
> #3,0.10598,0.9943,-0.011975,-20.206,0.99432,-0.10608,-0.0081687,22.594,-0.0093924,-0.011041,-0.99989,427.34
> fitmap #3 inMap #1
Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map
301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc using 105956 points
correlation = 0.395, correlation about mean = 0.08193, overlap = 4058
steps = 180, shift = 2.14, angle = 10.6 degrees
Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative
to 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc (#1) coordinates:
Matrix rotation and translation
0.28424491 0.95867659 -0.01200103 -50.89752473
0.95853292 -0.28389039 0.02491736 61.68796215
0.02048071 -0.01858601 -0.99961747 422.50869425
Axis -0.80128428 -0.59827795 -0.00264617
Axis point 0.00000000 53.42444368 210.80184256
Rotation angle (degrees) 178.44445594
Shift along axis 2.75881144
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.28479,0.95851,-0.012008,-45.119,0.95837,-0.28444,0.02472,59.144,0.020279,-0.018548,-0.99962,423.37
> fitmap #3 inMap #1
Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map
301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc using 105956 points
correlation = 0.3936, correlation about mean = 0.09039, overlap = 4063
steps = 116, shift = 2.17, angle = 2.59 degrees
Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative
to 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc (#1) coordinates:
Matrix rotation and translation
0.29774158 0.95454612 0.01384345 -53.74675777
0.95463380 -0.29763152 -0.00947480 70.54085059
-0.00492389 0.01603647 -0.99985928 420.08974848
Axis 0.80551150 0.59257367 0.00276843
Axis point 0.00000000 52.97504125 210.48490537
Rotation angle (degrees) 179.09265783
Shift along axis -0.32999286
> view matrix models
> #3,0.29829,0.95438,0.013817,-54.211,0.95446,-0.29818,-0.0096868,73.551,-0.005125,0.016077,-0.99986,424.15
> view matrix models
> #3,0.29829,0.95438,0.013817,-55.606,0.95446,-0.29818,-0.0096868,74.218,-0.005125,0.016077,-0.99986,424.22
> fitmap #3 inMap #1
Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map
301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc using 105956 points
correlation = 0.7444, correlation about mean = 0.4384, overlap = 1.063e+04
steps = 56, shift = 1.35, angle = 1.67 degrees
Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative
to 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc (#1) coordinates:
Matrix rotation and translation
0.32035097 0.94729415 0.00300724 -56.17053089
0.94728987 -0.32036018 0.00335510 76.28573060
0.00414167 0.00177391 -0.99998985 425.49648100
Axis -0.81251176 -0.58294065 -0.00220026
Axis point 0.00000000 58.42016887 212.80141511
Rotation angle (degrees) 179.94424980
Shift along axis 0.23295894
> hide #!3 models
> show #!2 models
> show #!3 models
> select subtract #3
Nothing selected
> select add #2
2 models selected
> select subtract #2
Nothing selected
> hide #!1 models
> fitmap #2 inMap #3
Fit map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc in map
301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc using 102847 points
correlation = 0.7803, correlation about mean = 0.4458, overlap = 1.145e+04
steps = 48, shift = 0.173, angle = 0.039 degrees
Position of 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) relative to
301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) coordinates:
Matrix rotation and translation
-0.42483714 0.90526980 -0.00001636 107.44748660
0.90526980 0.42483714 0.00007650 -68.27029075
0.00007620 0.00001770 -1.00000000 426.17304121
Axis -0.53626559 -0.84404930 -0.00004244
Axis point 75.40454102 0.00000000 213.08998179
Rotation angle (degrees) 179.99685841
Shift along axis -0.01498541
> show #!1 models
> hide #!2 models
> fitmap #1 inMap #3
Fit map 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc in map
301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc using 81884 points
correlation = 0.7811, correlation about mean = 0.4261, overlap = 1.012e+04
steps = 40, shift = 0.0259, angle = 0.0171 degrees
Position of 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc (#1) relative to
301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) coordinates:
Matrix rotation and translation
0.32028343 0.94731170 0.00436808 -56.06305096
0.94731730 -0.32029267 0.00159397 76.90062542
0.00290905 0.00362744 -0.99998919 425.34770344
Axis 0.81249099 0.58296944 0.00223865
Axis point -0.00000000 58.39940114 212.78064492
Rotation angle (degrees) 179.92830103
Shift along axis 0.23219609
> hide #!3 models
> show #!3 models
> fitmap #1 inMap #3
Fit map 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc in map
301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc using 81884 points
correlation = 0.7811, correlation about mean = 0.4259, overlap = 1.012e+04
steps = 44, shift = 0.0153, angle = 0.00548 degrees
Position of 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc (#1) relative to
301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) coordinates:
Matrix rotation and translation
0.32026654 0.94731754 0.00433953 -56.05470088
0.94732278 -0.32027602 0.00168360 76.89189165
0.00298475 0.00357173 -0.99998917 425.34487757
Axis 0.81248581 0.58297661 0.00225313
Axis point 0.00000000 58.40411956 212.77760327
Rotation angle (degrees) 179.93342543
Shift along axis 0.24088441
> hide #!1 models
> show #!2 models
> surface dust #2 size 10.3
> surface dust #3 size 10.3
> ui tool show "Fit in Map"
> fitmap #3 inMap #2
Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points
correlation = 0.7771, correlation about mean = 0.4363, overlap = 1.159e+04
steps = 40, shift = 0.0225, angle = 0.0453 degrees
Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative
to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates:
Matrix rotation and translation
-0.42413851 0.90559733 -0.00007474 107.24333558
0.90559733 0.42413850 -0.00006687 -68.15706733
-0.00002885 -0.00009605 -0.99999999 426.22092767
Axis -0.53659058 -0.84384273 0.00001895
Axis point 75.28840961 0.00000000 213.11056241
Rotation angle (degrees) 179.99844201
Shift along axis -0.02384081
> fitmap #3 inMap #2
Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points
correlation = 0.7766, correlation about mean = 0.4362, overlap = 1.16e+04
steps = 28, shift = 0.016, angle = 0.0129 degrees
Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative
to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates:
Matrix rotation and translation
-0.42419054 0.90557295 -0.00002206 107.24376704
0.90557294 0.42419054 0.00014393 -68.21540991
0.00013969 0.00004108 -0.99999999 426.14533600
Axis -0.53656720 -0.84385759 -0.00006313
Axis point 75.29718197 0.00000000 213.07826444
Rotation angle (degrees) 179.99450876
Shift along axis -0.00629711
> fitmap #3 inMap #2
Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points
correlation = 0.7767, correlation about mean = 0.4363, overlap = 1.16e+04
steps = 44, shift = 0.00763, angle = 0.00962 degrees
Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative
to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates:
Matrix rotation and translation
-0.42415723 0.90558856 0.00005023 107.22521538
0.90558856 0.42415723 -0.00000315 -68.18250636
-0.00002416 0.00004415 -1.00000000 426.18239974
Axis 0.53658381 0.84384703 -0.00000594
Axis point 75.29605323 0.00000000 213.08955957
Rotation angle (degrees) 179.99747437
Shift along axis -0.00282250
> fitmap #3 inMap #2
Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points
correlation = 0.7774, correlation about mean = 0.4363, overlap = 1.157e+04
steps = 44, shift = 0.0177, angle = 0.00397 degrees
Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative
to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates:
Matrix rotation and translation
-0.42409701 0.90561676 0.00006090 107.20311177
0.90561676 0.42409701 0.00001301 -68.17909308
-0.00001404 0.00006067 -0.99999999 426.19455771
Axis 0.53661186 0.84382920 0.00000388
Axis point 75.28554877 0.00000000 213.09602508
Rotation angle (degrees) 179.99745575
Shift along axis -0.00339605
> fitmap #3 inMap #2
Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points
correlation = 0.7774, correlation about mean = 0.4363, overlap = 1.157e+04
steps = 44, shift = 0.00443, angle = 0.00847 degrees
Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative
to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates:
Matrix rotation and translation
-0.42411817 0.90560685 -0.00008466 107.23870306
0.90560685 0.42411817 0.00000227 -68.17491613
0.00003796 -0.00007571 -0.99999999 426.21268790
Axis -0.53660081 -0.84383622 0.00001079
Axis point 75.28660753 0.00000000 213.10821664
Rotation angle (degrees) 179.99583688
Shift along axis -0.01131451
> select add #3
2 models selected
> view matrix models
> #3,0.32165,0.94686,0.0028615,-56.803,0.94685,-0.32165,0.0032496,77.252,0.0039973,0.0016642,-0.99999,424.24
> view matrix models
> #3,0.32165,0.94686,0.0028615,-56.863,0.94685,-0.32165,0.0032496,76.477,0.0039973,0.0016642,-0.99999,425.05
> fitmap #3 inMap #2
Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points
correlation = 0.7772, correlation about mean = 0.4363, overlap = 1.158e+04
steps = 52, shift = 0.764, angle = 0.00805 degrees
Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative
to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates:
Matrix rotation and translation
-0.42412997 0.90560133 0.00003263 107.21681880
0.90560132 0.42412996 0.00007863 -68.19754869
0.00005737 0.00006290 -0.99999999 426.17522111
Axis -0.53659352 -0.84384085 -0.00009632
Axis point 75.28977250 0.00000000 213.09196817
Rotation angle (degrees) 179.99916032
Shift along axis -0.02502133
> fitmap #3 inMap #2
Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points
correlation = 0.7768, correlation about mean = 0.4363, overlap = 1.159e+04
steps = 40, shift = 0.0142, angle = 0.00614 degrees
Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative
to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates:
Matrix rotation and translation
-0.42414492 0.90559432 -0.00006281 107.24888311
0.90559432 0.42414493 0.00003275 -68.18644325
0.00005630 -0.00004299 -0.99999999 426.18590942
Axis -0.53658833 -0.84384416 -0.00000826
Axis point 75.29491885 0.00000000 213.09553069
Rotation angle (degrees) 179.99595654
Shift along axis -0.01328821
> fitmap #3 inMap #2
Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points
correlation = 0.7767, correlation about mean = 0.4362, overlap = 1.16e+04
steps = 40, shift = 0.00779, angle = 0.00363 degrees
Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative
to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates:
Matrix rotation and translation
-0.42417025 0.90558246 -0.00004143 107.24472659
0.90558245 0.42417025 0.00008541 -68.20089090
0.00009492 -0.00000129 -0.99999999 426.16706978
Axis -0.53657659 -0.84385162 -0.00003479
Axis point 75.29547795 0.00000000 213.08750754
Rotation angle (degrees) 179.99537094
Shift along axis -0.00840261
> fitmap #3 inMap #2
Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points
correlation = 0.7773, correlation about mean = 0.4363, overlap = 1.158e+04
steps = 44, shift = 0.016, angle = 0.00412 degrees
Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative
to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates:
Matrix rotation and translation
-0.42413018 0.90560122 -0.00006698 107.24002872
0.90560122 0.42413019 0.00003482 -68.18614701
0.00005994 -0.00004589 -0.99999999 426.19939305
Axis -0.53659523 -0.84383977 -0.00000732
Axis point 75.29020325 0.00000000 213.10238152
Rotation angle (degrees) 179.99569100
Shift along axis -0.00942393
> fitmap #3 inMap #2
Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points
correlation = 0.7773, correlation about mean = 0.4363, overlap = 1.157e+04
steps = 44, shift = 0.00344, angle = 0.0033 degrees
Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative
to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates:
Matrix rotation and translation
-0.42412314 0.90560452 -0.00006372 107.23622514
0.90560452 0.42412314 -0.00002210 -68.17686328
0.00000701 -0.00006708 -0.99999999 426.21518166
Axis -0.53659816 -0.84383791 0.00000741
Axis point 75.28971970 0.00000000 213.10862322
Rotation angle (degrees) 179.99759853
Shift along axis -0.00938304
> fitmap #3 inMap #2
Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points
correlation = 0.7768, correlation about mean = 0.4362, overlap = 1.159e+04
steps = 40, shift = 0.0182, angle = 0.00179 degrees
Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative
to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates:
Matrix rotation and translation
-0.42414966 0.90559210 -0.00006928 107.25092542
0.90559210 0.42414966 -0.00001300 -68.17191484
0.00001762 -0.00006825 -0.99999999 426.19881611
Axis -0.53658595 -0.84384567 0.00000859
Axis point 75.29359494 0.00000000 213.10069686
Rotation angle (degrees) 179.99704981
Shift along axis -0.01910210
> fitmap #3 inMap #2
Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points
correlation = 0.7769, correlation about mean = 0.4363, overlap = 1.159e+04
steps = 40, shift = 0.0101, angle = 0.00298 degrees
Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative
to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates:
Matrix rotation and translation
-0.42416360 0.90558557 -0.00008804 107.25194691
0.90558557 0.42416360 0.00003300 -68.19000892
0.00006723 -0.00006573 -0.99999999 426.18961038
Axis -0.53657974 -0.84384962 0.00000103
Axis point 75.29439134 0.00000000 213.09768660
Rotation angle (degrees) 179.99472882
Shift along axis -0.00666800
> fitmap #3 inMap #2
Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points
correlation = 0.777, correlation about mean = 0.4363, overlap = 1.159e+04
steps = 40, shift = 0.0123, angle = 0.0085 degrees
Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative
to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates:
Matrix rotation and translation
-0.42413291 0.90559995 0.00004920 107.21522113
0.90559995 0.42413291 0.00007821 -68.20736376
0.00004996 0.00007772 -0.99999999 426.16800583
Axis -0.53652100 -0.84388504 -0.00180371
Axis point 75.28982105 0.00000000 213.15691001
Rotation angle (degrees) 179.99997402
Shift along axis -0.73272608
> fitmap #3 inMap #2
Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points
correlation = 0.7765, correlation about mean = 0.4362, overlap = 1.161e+04
steps = 24, shift = 0.0212, angle = 0.00772 degrees
Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative
to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates:
Matrix rotation and translation
-0.42419484 0.90557094 -0.00006576 107.25563594
0.90557093 0.42419484 0.00009474 -68.20119474
0.00011369 -0.00001936 -0.99999999 426.16157095
Axis -0.53656523 -0.84385885 -0.00002983
Axis point 75.29716123 0.00000000 213.08536916
Rotation angle (degrees) 179.99390807
Shift along axis -0.01017496
> fitmap #3 inMap #2
Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map
301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points
correlation = 0.7774, correlation about mean = 0.4363, overlap = 1.157e+04
steps = 36, shift = 0.0233, angle = 0.00882 degrees
Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative
to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates:
Matrix rotation and translation
-0.42409073 0.90561970 -0.00008804 107.22896438
0.90561970 0.42409073 -0.00000517 -68.17397669
0.00003265 -0.00008193 -0.99999999 426.21410292
Axis -0.53661358 -0.84382810 0.00001466
Axis point 75.28230841 0.00000000 213.10873106
Rotation angle (degrees) 179.99590239
Shift along axis -0.00715236
[deleted to fit within ticket limits]
> color #1 #54164eff
> color #1 #671b60ff
> color #1 #7f2175ff
> color #1 #a02a94ff
> color #1 #c333b5ff
> color #1 #d036c0ff
> color #1 #ce36bfff
> color #1 #c533b6ff
> color #1 #b02ea3ff
> color #1 #8d2583ff
> color #1 #6a1c63ff
> color #1 #591752ff
> color #1 #52154cff
> color #1 #51154bff
> color #1 #53164dff
> color #1 #6a1c62ff
> color #1 #7b2072ff
> color #1 #98288dff
> color #1 #c032b2ff
> color #1 #c834baff
> color #1 #cf36bfff
> color #1 #3036bfff
> color #1 #3029bfff
> color #1 #30295dff
> color #1 #332c64ff
> color #1 #39316eff
> color #1 #3a3271ff
> color #1 #3c3374ff
> color #1 #3e3578ff
> color #1 #40377cff
> color #1 #41387eff
> color #1 #423880ff
> color #1 #443a84ff
> color #1 #443a85ff
> color #1 #453b86ff
> color #1 #453b87ff
> color #1 #463c88ff
> color #1 #473c89ff
> color #1 #473d8aff
> color #1 #483e8cff
> color #1 #493f8eff
> color #1 #4a3f90ff
> color #1 #4b4092ff
> color #1 #4d4296ff
> color #1 #4f4499ff
> color #1 #51459cff
> color #1 #5347a1ff
> color #1 #5548a4ff
> color #1 #5549a6ff
> color #1 #574ba9ff
> color #1 #584babff
> color #1 #594cacff
> color #1 #5a4dafff
> color #1 #5b4eb1ff
> color #1 #5c4eb2ff
> color #1 #5c4fb3ff
> color #1 #5d4fb4ff
> color #1 #5e50b6ff
> color #1 #5e51b7ff
> color #1 #6053bbff
> color #1 #6153bdff
> color #1 #6254beff
> color #1 #6355c0ff
> color #1 #6556c3ff
> color #1 #6557c4ff
> color #1 #6758c7ff
> color #1 #6758c8ff
> color #1 #6859caff
> color #1 #695accff
> color #1 #6a5acdff
> color #1 #6a5bceff
> color #1 #6a5bcfff
> color #1 #6b5cd0ff
> color #1 #6c5cd1ff
> color #1 #6c5dd2ff
> color #1 #6d5dd3ff
> color #1 #6d5dd4ff
> color #1 #6e5ed5ff
> color #1 #6e5ed6ff
> color #1 #6f5fd7ff
> color #1 #6f5fd8ff
> color #1 #7060d9ff
> color #1 #7060daff
> color #1 #7160daff
> color #1 #7161dbff
> color #1 #7261ddff
> color #1 #7262ddff
> color #1 #7262deff
> color #1 #7362dfff
> color #1 #7363e0ff
> color #1 #7463e1ff
> color #1 #7464e2ff
> color #1 #7564e3ff
> color #1 #7564e4ff
> color #1 #7665e4ff
> color #1 #7665e5ff
> color #1 #7766e7ff
> color #1 #7766e8ff
> color #1 #7867e9ff
> color #1 #7967eaff
> color #1 #7968ebff
> color #1 #7968ecff
> color #1 #7a68ecff
> color #1 #7a69edff
> color #1 #7b69eeff
> color #1 #7b69efff
> color #1 #7b6aefff
> color #1 #7c6af0ff
> color #1 #7c6af1ff
> color #1 #7d6bf3ff
> color #1 #7e6cf5ff
> color #1 #7f6df6ff
> color #1 #806df8ff
> color #1 #816efaff
> color #1 #826ffcff
> color #1 #826ffdff
> color #1 #8370feff
> color #1 #8370ffff
> select #7 /L
762 atoms, 780 bonds, 101 residues, 1 model selected
> ui windowfill toggle
> select #7 /L
762 atoms, 780 bonds, 101 residues, 1 model selected
> select up
21175 atoms, 21715 bonds, 2672 residues, 1 model selected
> select up
145807 atoms, 149542 bonds, 18287 residues, 18 models selected
> select up
145807 atoms, 149542 bonds, 18287 residues, 18 models selected
> select up
145807 atoms, 149542 bonds, 18287 residues, 18 models selected
> select clear
> hide #!1 models
> show #!7 models
> color zone #1 near #7 distance 5
> show #!1 models
> hide #!1 models
> color #!7 bychain
> color #7 /A,B,C,D,E,F gray
> color #7 /G,I,O,Q,M,J darkslategray
> color zone #1 near #7 distance 5
> show #!1 models
> color zone #1 near #7 distance 4.62
> color zone #1 near #7 distance 11.89
> color zone #1 near #7 distance 4.7
> color zone #1 near #7 distance 7.61
> color zone #1 near #7 distance 5
> hide #!1 models
> show #!1 models
> hide #!7 models
> color (:NAG, NAM, BMA) lavender
> color zone #1 near #7 distance 5
> ui tool show "Color Actions"
> color (:NAG, NAM, BMA) voilet
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color (:NAG, NAM, BMA) violet
> color zone #1 near #7 distance 5
> color (:NAG, NAM, BMA) lavender
> color zone #1 near #7 distance 5
> select ~sel & ##selected
Nothing selected
> color (:NAG, NAM, BMA) #E6E6FA
> color zone #1 near #7 distance 5
> select ~sel & ##selected
Nothing selected
> color (:NAG, NAM, BMA) violet
> color zone #1 near #7 distance 5
> color (:NAG, NAM, BMA) magenta
> color zone #1 near #7 distance 5
> color (:NAG, NAM, BMA) pink
> color zone #1 near #7 distance 5
> color (:NAG, NAM, BMA) lavender
> color zone #1 near #7 distance 5
> color (:NAG, NAM, BMA) magenta
> color zone #1 near #7 distance 5
> select ~sel & ##selected
Nothing selected
> color (:NAG, NAM, BMA) pink
> color zone #1 near #7 distance 5
> color #7 /H yellowgreen
> color #7 /H olivegreen
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #7 /H olive
> color #7 /H yellowgreen
> color #7 /L greenyellow
> color zone #1 near #7 distance 5
> color #7 /H olive
> color zone #1 near #7 distance 5
> color #7 /H green
> color zone #1 near #7 distance 5
> color #7 /H chartreuse
> color zone #1 near #7 distance 5
> color #7 /H green
> color #7 /L chartreuse
> color zone #1 near #7 distance 5
> color #7 /H green
> color zone #1 near #7 distance 5
> ui tool show "Side View"
> view name top
> view list
Named views: top
> view top
> lighting soft
> lighting full
> lighting soft
> lighting simple
> color zone #1 near #7 distance 5.09
> color zone #1 near #7 distance 6.11
> lighting soft
> lighting full
> set bgColor gray
> set bgColor #80808000
> set bgColor black
> set bgColor transparent
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting shadows false
> lighting shadows true
> set bgColor white
> set bgColor #ffffff00
> lighting simple
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> graphics silhouettes false
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 2
QPainter::translate: Painter not active
QPainter::setPen: Painter not active
QPainter::setBrush: Painter not active
QPainter::drawPoints: Painter not active
QPainter::end: Painter not active, aborted
QPainter::begin: Paint device returned engine == 0, type: 2
QPainter::translate: Painter not active
QPainter::setPen: Painter not active
QPainter::setBrush: Painter not active
QPainter::drawPoints: Painter not active
QPainter::end: Painter not active, aborted
Unsupported scale factor (0.000000) detected on Display0
> view name top
> show #!2 models
> hide #!1 models
> show #!8 models
> color zone #2 near #8 distance 6.2
> hide #!8 models
> show #!8 models
> volume #2 level 0.21
> hide #!8 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> view top
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!8 models
> select #8 /A,B,C,D,E,F
14085 atoms, 14370 bonds, 15 pseudobonds, 1740 residues, 2 models selected
> select #8
24630 atoms, 25167 bonds, 15 pseudobonds, 3123 residues, 2 models selected
> color sel bychain
> select clear
> select #8 /C
3656 atoms, 3733 bonds, 4 pseudobonds, 452 residues, 2 models selected
> select #8 /D
1039 atoms, 1057 bonds, 1 pseudobond, 128 residues, 2 models selected
> select #8 /E
3656 atoms, 3733 bonds, 4 pseudobonds, 452 residues, 2 models selected
> select #8 /F
1039 atoms, 1057 bonds, 1 pseudobond, 128 residues, 2 models selected
> select #8 /A,B,C,D,E,F
14085 atoms, 14370 bonds, 15 pseudobonds, 1740 residues, 2 models selected
> color #8 /A,B,C,D,E,F gray
> select clear
> color #8 /G,I,O,Q,M,J darkslategray
> select #8 /H
1022 atoms, 1050 bonds, 128 residues, 1 model selected
> select clear
> color #8 /A,B,C,D,E,F gray
> color #8 /G,I,O,Q,M,J darkslategray
> color (:NAG, NAM, BMA) pink
> color #8 /N,L,R teal
> color #8 /H,K,P navy
> color zone #2 near #8 distance 6.2
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!8 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> view list
Named views: top
> view top
> show #!2 models
> hide #!1 models
> view name front
> ui tool show Log
> view list
Named views: front, top
> view top
> save /Users/sphulera/Desktop/HVTN301/Map_session_042325.cxs
> ui tool show "Show Volume Menu"
> ui tool show "Volume Viewer"
> volume #2 level 0.215
> volume #2 level 0.216
> volume #2 level 0.217
> volume #2 level 0.218
> volume #2 level 0.219
> volume #2 level 0.22
> volume #2 level 0.225
> volume #1 level 0.225
> volume #2 level 0.22
> volume #2 level 0.221
> volume #2 level 0.222
> view front
> view top
> view name top
> view list
Named views: front, top
> view front
> view top
> ui tool show "Model Panel"
> show #!9 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> color #9 /A,B,C,D,E,F gray
> color #9 /G,I,O,Q,M,J darkslategray
> color (:NAG, NAM, BMA) pink
> color #9 /N,L,R maroon
> color #9 /H,K,P brown
> ui tool show "Color Actions"
> color #9 /H,K,P #9A6324
> color #9 /N,L,R #800000
> ui tool show "Color Zone"
> color zone #1 near #9 distance 1.03
> color zone #3 near #9 distance 6.2
> show #!3 models
> hide #!9 models
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!3 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!3 models
> show #!1 models
> hide #!2 models
> color zone #1 near #7 distance 1.03
> show #!7 models
> hide #!1 models
> color zone #1 near #7 distance 1.04
> color zone #1 near #7 distance 3.51
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!7 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> volume #3 level 0.22
> color #9 /H,K,P #800000
> color zone #3 near #9 distance 6.34
> color zone #3 near #9 distance 4.79
> color #9 /N,L,R #9A6324
> color zone #3 near #9 distance 4.79
> color #9 /H,K,P maroon
> color #9 /N,L,R brown
> color zone #3 near #9 distance 4.79
> color #9 /N,L,R #9A6324
> color zone #3 near #9 distance 4.79
> volume #3 level 0.225
> volume #3 level 0.229
> volume #3 level 0.23
> ui tool show "Hide Dust"
> surface dust #3 size 1.03
> surface dust #3 size 1.07
> surface dust #3 size 14.5
> show #!2 models
> hide #!3 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> view top
> view front
> show #!2 models
> hide #!3 models
> show #!1 models
> hide #!2 models
> ui tool show "Side View"
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> view name top
> show #!1 models
> hide #!3 models
> color #9 /H,K,P #800000
> color zone #3 near #9 distance 4.79
> show #!3 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!10 models
> color #10 /H,K,P purple
> color #10 /H,K,P lavender
> color #10 /H,K,P purple
> color #10 /N,L,R #dcbeff
> color zone #4 near #10 distance 6.2
> show #!4 models
> volume #4 level 0.08196
> volume #4 level 0.1
> volume #4 level 0.15
> hide #!10 models
> surface dust #4 size 10.3
> surface dust #4 size 10.05
> surface dust #4 size 20.62
> surface dust #4 size 21.28
> surface dust #4 size 115.02
> list view
Unknown command: list view
> view list
Named views: front, top
> view front
> view top
> view front
> view top
> volume #4 level 0.17
> volume #4 level 0.2
> surface dust #4 size 109.75
> surface dust #4 size 3.14
> surface dust #4 size 10
> surface dust #4 size 10.53
> surface dust #4 size 5.29
> save /Users/sphulera/Desktop/HVTN301/Map_session_042325.cxs
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #!11 models
> hide #!11 models
> hide #!5 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> show #!4 models
> show #!5 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!11 models
> hide #!5 models
> color #11 /A,B,C,D,E,F gray
> color #11 /G,I,O,Q,M,J darkslategray
> color (:NAG, NAM, BMA) pink
> color #11 /N,L,R lime
> color #11 /H,K,P green
> show #!1 models
> hide #!1 models
> color #11 /H,K,P blue
> color #11 /N,L,R cyan
> color zone #5 near #11 distance 5
> show #!5 models
> hide #!11 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!5 models
> show #!11 models
> hide #!2 models
> ui tool show "Color Actions"
> show #!1 models
> hide #!11 models
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> show #!5 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #!4 models
> hide #!5 models
> show #!3 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!3 models
> color #11 /N,L,R pink
> color zone #5 near #11 distance 5
> color #11 /N,L,R deeppink
> color zone #5 near #11 distance 5
> color #11 /H,K,P red
> color zone #5 near #11 distance 5
> color zone #5 near #11 distance 4.9
> color zone #5 near #11 distance 4.8
> color zone #5 near #11 distance 5
> color #11 /H,K,P #e6194B
> color zone #5 near #11 distance 5
> color #11 /N,L,R #fabed4
> color zone #5 near #11 distance 5
> color #11 /H,K,P orange
> color zone #5 near #11 distance 5
> color #11 /N,L,R apricot
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #11 /N,L,R #ffd8b1
> color zone #5 near #11 distance 5
> color #11 /H,K,P #f58231
> color zone #5 near #11 distance 5
> show #!2 models
> show #!1 models
> show #!4 models
> show #!3 models
> show #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!6 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!5 models
> hide #!4 models
> color #12 /A,B,C,D,E,F gray
> color #12 /G,I,O,Q,M,J darkslategray
> color (:NAG, NAM, BMA) pink
> color #12 /N,L,R yellow
> color #12 /H,K,P beige
> color zone #5 near #11 distance 5
> color zone #6 near #12 distance 6.2
> show #!6 models
> hide #!5 models
> color #12 /A,B,C,D,E,F gray
> color #12 /G,I,O,Q,M,J darkslategray
> color (:NAG, NAM, BMA) pink
> color #12 /N,L,R beige
> color #12 /H,K,P yellow
> color zone #6 near #12 distance 5
> save /Users/sphulera/Desktop/HVTN301/Map_session_042425.cxs
> ui tool show "Side View"
> view name front
> view name top
> hide #!6 models
> show #!1 models
> save /Users/sphulera/Desktop/HVTN301/map_figs/02_top.png width 704 height
> 850 supersample 3 transparentBackground true
> view name top
> save /Users/sphulera/Desktop/HVTN301/map_figs/02_top.png width 1822 height
> 850 supersample 3 transparentBackground true
> save /Users/sphulera/Desktop/HVTN301/map_figs/02_top.png width 2000 height
> 933 supersample 3
> save /Users/sphulera/Desktop/HVTN301/map_figs/02_top.png width 4287 height
> 2000 supersample 3 transparentBackground true
> ui tool show "Side View"
> save /Users/sphulera/Desktop/HVTN301/map_figs/02_top.png width 4287 height
> 2000 supersample 4
> ui tool show "Model Panel"
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> view name top
> ui tool show "Volume Viewer"
> volume #2 level 0.21
> volume #1 level 0.21
> volume #1 level 0.2
> volume #1 level 0.21
> ui tool show "Surface Zone"
> surface zone #1 nearAtoms #7 distance 7.71
> surface unzone #1
> ui tool show "Hide Dust"
> surface dust #1 size 6.2
> surface dust #1 size 10
> volume #1 level 0.2195
> volume #1 level 0.2272
> ui tool show "Color Zone"
> color zone #1 near #7 distance 1.03
> color zone #1 near #7 distance 1.05
> color zone #1 near #7 distance 1.22
> color zone #1 near #7 distance 1.18
> color zone #1 near #7 distance 5.99
> color zone #1 near #7 distance 5
> show #!2 models
> hide #!2 models
> save /Users/sphulera/Desktop/HVTN301/map_figs/02_top.png width 4287 height
> 2000 supersample 4 transparentBackground true
> show #!2 models
> hide #!1 models
> save /Users/sphulera/Desktop/HVTN301/map_figs/06_top.png width 4287 height
> 2000 supersample 4
> surface dust #2 size 10.3
> color zone #2 near #7 distance 6.2
> color zone #2 near #8 distance 6.2
> color zone #2 near #8 distance 6.27
> color zone #2 near #8 distance 5.48
> color zone #2 near #8 distance 5
> volume #2 level 0.215
> volume #2 level 0.216
> volume #2 level 0.218
> volume #2 level 0.22
> volume #2 level 0.225
> volume #2 level 0.224
> volume #2 level 0.223
> volume #2 level 0.222
> volume #2 level 0.221
> volume #2 level 0.2215
> volume #2 level 0.2216
> volume #2 level 0.2217
> volume #2 level 0.2218
> volume #2 level 0.2219
> volume #2 level 0.22
> volume #2 level 0.229
> volume #2 level 0.228
> volume #2 level 0.227
> volume #2 level 0.226
> volume #2 level 0.225
> volume #2 level 0.224
> volume #2 level 0.223
> volume #2 level 0.222
> volume #2 level 0.221
> volume #2 level 0.222
> save /Users/sphulera/Desktop/HVTN301/map_figs/06_top.png width 4287 height
> 2000 supersample 4
> view name top
> show #!3 models
> hide #!2 models
> volume #3 level 0.22
> volume #3 level 0.21
> volume #3 level 0.215
> volume #3 level 0.216
> save /Users/sphulera/Desktop/HVTN301/map_figs/46_top.png width 4287 height
> 2000 supersample 4
> show #!4 models
> hide #!3 models
> volume #4 level 0.1
> volume #4 level 0.15
> volume #4 level 0.17
> volume #4 level 0.18
> color zone #4 near #10 distance 6.2
> color zone #4 near #10 distance 5
> surface dust #4 size 10
> volume #4 level 0.19
> volume #4 level 0.2
> show #!10 models
> hide #!4 models
> show #!4 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> volume #4 level 0.21
> volume #4 level 0.215
> volume #4 color darkgrey
> color zone #4 near #10 distance 5
> volume #4 level 0.2
> save /Users/sphulera/Desktop/HVTN301/map_figs/48_top.png width 4287 height
> 2000 supersample 4
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> volume #5 level 0.2
> volume #5 level 0.21
> volume #5 level 0.212
> ui tool show "Side View"
> color zone #5 near #11 distance 5
> color zone #5 near #11 distance 5.1
> color zone #5 near #11 distance 5.2
> color zone #5 near #11 distance 5.3
> color zone #5 near #11 distance 5.4
> color zone #5 near #11 distance 5.5
> color zone #5 near #11 distance 5.6
> color zone #5 near #11 distance 5.7
> color zone #5 near #11 distance 5.8
> color zone #5 near #11 distance 5.9
> color zone #5 near #11 distance 6
> color zone #5 near #11 distance 6.1
> color zone #5 near #11 distance 6.2
> color zone #5 near #11 distance 6.3
> color zone #5 near #11 distance 6.32
> color zone #5 near #11 distance 6.76
> color zone #5 near #11 distance 12.55
> color zone #5 near #11 distance 5
> volume #5 color #ff9300
> color #11 /A,B,C,D,E,F gray
> color #11 /G,I,O,Q,M,J darkslategray
> color (:NAG, NAM, BMA) pink
> color #11 /N,L,R #ffd8b1
> color #11 /H,K,P #f58231
> color zone #5 near #11 distance 5
> save /Users/sphulera/Desktop/HVTN301/map_figs/56_top.png width 4369 height
> 2000 supersample 4 transparentBackground true
> hide #!5 models
> show #!2 models
> save /Users/sphulera/Desktop/HVTN301/map_figs/06_top.png width 4369 height
> 2000 supersample 4 transparentBackground true
> show #!3 models
> hide #!2 models
> save /Users/sphulera/Desktop/HVTN301/map_figs/46_top.png width 4369 height
> 2000 supersample 4 transparentBackground true
> show #!4 models
> hide #!3 models
> save /Users/sphulera/Desktop/HVTN301/map_figs/48_top.png width 4369 height
> 2000 supersample 4 transparentBackground true
> show #!5 models
> hide #!4 models
> show #!6 models
> hide #!5 models
> save /Users/sphulera/Desktop/HVTN301/map_figs/61_top.png width 4369 height
> 2000 supersample 4 transparentBackground true
> save /Users/sphulera/Desktop/HVTN301/Map_session_top_042425.cxs
> ui tool show Log
> view list
Named views: front, top
> view front
> show #!1 models
> hide #!6 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!5 models
> hide #!4 models
> color #11 /A,B,C,D,E,F gray
> color #11 /G,I,O,Q,M,J darkslategray
> color (:NAG, NAM, BMA) pink
> color #11 /N,L,R #ffd8b1
> color #11 /H,K,P #f58231
> color zone #5 near #11 distance 5
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> color #10 /A,B,C,D,E,F gray
> color #10 /G,I,O,Q,M,J darkslategray
> color (:NAG, NAM, BMA) pink
> color #10 /N,L,R #dcbeff
> color #10 /H,K,P #purple
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color zone #4 near #10 distance 5
> show #!3 models
> show #!2 models
> show #!1 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> view top
> hide #!5 models
> hide #!6 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> save /Users/sphulera/Desktop/HVTN301/map_figs/48_top.png width 4369 height
> 2000 supersample 4 transparentBackground true
> view front
> show #!1 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> view name front
===== 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 M3
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 Air
Model Identifier: Mac15,12
Model Number: Z1B600163LL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.101.1
OS Loader Version: 11881.101.1
Software:
System Software Overview:
System Version: macOS 15.4 (24E248)
Kernel Version: Darwin 24.4.0
Time since boot: 16 days, 2 hours, 34 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 Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG HDR 4K:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
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: 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
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
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
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 |
|---|---|
| Description: | modified (diff) |
| 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 |
The ChimeraX bug report panel explained what we know about this bug:
"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."
The ChimeraX daily build is using a newer version of Qt (6.8.2) that has not exhibited these multi-display Mac crashes so you may want to try it.
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Reported by Swastik