![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 months ago
Closed 2 months ago
#18744 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.7.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001fbe38f80 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.surface._surface, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.segment._segment (total: 61)
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{
"uptime" : 1000000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac15,12",
"coalitionID" : 134596,
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"build" : "23H311",
"releaseType" : "User"
},
"captureTime" : "2025-09-08 18:16:51.8385 +0200",
"codeSigningMonitor" : 1,
"incident" : "7CAB024F-1CF9-4C3F-B515-44C0436B0200",
"pid" : 31040,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-09-08 11:27:46.6451 +0200",
"procStartAbsTime" : 24321313596345,
"procExitAbsTime" : 24910397321549,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"69AEABDF-0D7D-515C-A41F-DCC45B0C895F","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "3E8A3289-E23E-F62C-606A-0ADCE74B70CA",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 31039,
"sleepWakeUUID" : "57B099B1-72F9-47F6-A515-CFF84CD8EB0B",
"sip" : "enabled",
"vmRegionInfo" : "0x3f49bcbd0d18 is not in any region. Bytes after previous region: 69104895331609 Bytes before following region: 35967184597736\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000bf49bcbd0d18","rawCodes":[1,210323420024088],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000bf49bcbd0d18 -> 0x00003f49bcbd0d18 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":31040},
"vmregioninfo" : "0x3f49bcbd0d18 is not in any region. Bytes after previous region: 69104895331609 Bytes before following region: 35967184597736\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/dario.guerrini/Downloads/MISKYD_Rec8m6A_SAH_3Dclass_iteration2_NoDyn2.cxs
> format session
Opened cryosparc_P174_J49_class_06_00180_volume.mrc as #2, grid size
200,200,200, pixel 1.44, shown at level 0.111, step 1, values float32
Opened cryosparc_P174_J49_class_03_00180_volume.mrc as #3, grid size
200,200,200, pixel 1.44, shown at level 0.11, step 1, values float32
Opened cryosparc_P174_J73_class_00_00120_volume.mrc as #4.1, grid size
200,200,200, pixel 1.44, shown at level 0.171, step 1, values float32
Opened cryosparc_P174_J73_class_02_00120_volume.mrc as #4.2, grid size
200,200,200, pixel 1.44, shown at level 0.182, step 1, values float32
opened ChimeraX session
> close #4
> open
> /Users/dario.guerrini/Downloads/cryosparc_P174_J74_class_01_00236_volume.mrc
> /Users/dario.guerrini/Downloads/cryosparc_P174_J74_class_04_00236_volume.mrc
> /Users/dario.guerrini/Downloads/cryosparc_P174_J74_class_03_00236_volume.mrc
Opened cryosparc_P174_J74_class_01_00236_volume.mrc as #4.1, grid size
200,200,200, pixel 1.44, shown at level 0.117, step 1, values float32
Opened cryosparc_P174_J74_class_04_00236_volume.mrc as #4.2, grid size
200,200,200, pixel 1.44, shown at level 0.112, step 1, values float32
Opened cryosparc_P174_J74_class_03_00236_volume.mrc as #4.3, grid size
200,200,200, pixel 1.44, shown at level 0.115, step 1, values float32
> volume #4.1 color #b2b2b28d
> volume #4.2 color #ffffb28c
> volume #4.3 color #b2ffff8c
> ui tool show "Fit in Map"
> fitmap #4.1 inMap #2
Fit map cryosparc_P174_J74_class_01_00236_volume.mrc in map
cryosparc_P174_J49_class_06_00180_volume.mrc using 79976 points
correlation = 0.9514, correlation about mean = 0.8435, overlap = 7223
steps = 52, shift = 0.504, angle = 0.694 degrees
Position of cryosparc_P174_J74_class_01_00236_volume.mrc (#4.1) relative to
cryosparc_P174_J49_class_06_00180_volume.mrc (#2) coordinates:
Matrix rotation and translation
0.99998244 0.00233926 -0.00544541 0.44202800
-0.00239663 0.99994143 -0.01055390 1.33783186
0.00542040 0.01056676 0.99992948 -2.31186933
Axis 0.87205744 -0.44864171 -0.19554141
Axis point 0.00000000 215.30030246 135.65602470
Rotation angle (degrees) 0.69385019
Shift along axis 0.23733284
> fitmap #4.2 inMap #2
Fit map cryosparc_P174_J74_class_04_00236_volume.mrc in map
cryosparc_P174_J49_class_06_00180_volume.mrc using 79964 points
correlation = 0.9904, correlation about mean = 0.9654, overlap = 7949
steps = 60, shift = 0.438, angle = 0.665 degrees
Position of cryosparc_P174_J74_class_04_00236_volume.mrc (#4.2) relative to
cryosparc_P174_J49_class_06_00180_volume.mrc (#2) coordinates:
Matrix rotation and translation
0.99999165 0.00155841 -0.00377893 0.37033779
-0.00159937 0.99993973 -0.01086171 1.33043530
0.00376178 0.01086766 0.99993387 -2.14237938
Axis 0.93595077 -0.32480147 -0.13601532
Axis point 0.00000000 195.33282668 127.56142300
Rotation angle (degrees) 0.66511475
Shift along axis 0.20588701
> fitmap #4.3 inMap #2
Fit map cryosparc_P174_J74_class_03_00236_volume.mrc in map
cryosparc_P174_J49_class_06_00180_volume.mrc using 79952 points
correlation = 0.9465, correlation about mean = 0.8278, overlap = 7272
steps = 52, shift = 0.478, angle = 0.68 degrees
Position of cryosparc_P174_J74_class_03_00236_volume.mrc (#4.3) relative to
cryosparc_P174_J49_class_06_00180_volume.mrc (#2) coordinates:
Matrix rotation and translation
0.99999168 0.00218338 -0.00344524 0.24636145
-0.00222163 0.99993551 -0.01113767 1.42918406
0.00342070 0.01114523 0.99993204 -2.11567561
Axis 0.93905164 -0.28934580 -0.18563680
Axis point 0.00000000 187.12988212 132.70651978
Rotation angle (degrees) 0.67980616
Shift along axis 0.21056497
> show #!1 models
> volume #4.1 level 0.1382
> volume #4.1 color #f7b2b28d
> volume #4.1 color #f7b2a48d
> volume #4.1 color #f7ada48d
> volume #4.1 color #f7ad748d
> volume #4.1 color #f7ad748c
> lighting simple
> lighting soft
> hide #!1 models
> ui mousemode right pivot
> ui mousemode right translate
> volume #4.2 level 0.187
> show #!1 models
> volume #4.2 level 0.1676
> volume #4.2 level 0.3085
> volume #4.2 level 0.2312
> volume #4.2 level 0.1455
> hide #!1 models
> save "/Users/dario.guerrini/OneDrive -
> Htechnopole/MISKYD_Rec8m6A_SAH_3Dclass_iteration2_withDyn2.cxs"
> open /Users/dario.guerrini/Library/CloudStorage/OneDrive-
> Htechnopole/MISKYD_Rec8m6A_SAH_3Dclass_iteration2_NoDyn2.cxs
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "ClipCap" returned None
opened ChimeraX session
> close #4
> open /Users/dario.guerrini/Library/CloudStorage/OneDrive-
> Htechnopole/MISKYD_Rec8m6A_SAH_3Dclass_iteration2_NoDyn2.cxs
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "ClipCap" returned None
opened ChimeraX session
> open /Users/dario.guerrini/Library/CloudStorage/OneDrive-
> Htechnopole/MISKYD_Rec8m6A_SAH_3Dclass_iteration2_withDyn2.cxs
Opened cryosparc_P174_J49_class_06_00180_volume.mrc as #2, grid size
200,200,200, pixel 1.44, shown at level 0.111, step 1, values float32
Opened cryosparc_P174_J49_class_03_00180_volume.mrc as #3, grid size
200,200,200, pixel 1.44, shown at level 0.11, step 1, values float32
Opened cryosparc_P174_J74_class_01_00236_volume.mrc as #4.1, grid size
200,200,200, pixel 1.44, shown at level 0.138, step 1, values float32
Opened cryosparc_P174_J74_class_04_00236_volume.mrc as #4.2, grid size
200,200,200, pixel 1.44, shown at level 0.146, step 1, values float32
Opened cryosparc_P174_J74_class_03_00236_volume.mrc as #4.3, grid size
200,200,200, pixel 1.44, shown at level 0.115, step 1, values float32
opened ChimeraX session
> close #4
> open
> /Users/dario.guerrini/Downloads/cryosparc_P174_J73_class_00_00120_volume.mrc
> /Users/dario.guerrini/Downloads/cryosparc_P174_J73_class_02_00120_volume.mrc
Opened cryosparc_P174_J73_class_00_00120_volume.mrc as #4.1, grid size
200,200,200, pixel 1.44, shown at level 0.136, step 1, values float32
Opened cryosparc_P174_J73_class_02_00120_volume.mrc as #4.2, grid size
200,200,200, pixel 1.44, shown at level 0.106, step 1, values float32
> volume #4.1 level 0.1697
> volume #4.1 color #b2b2ff8c
> volume #4.2 color #ffb2ff8c
> ui tool show "Fit in Map"
> fitmap #4.1 inMap #2
Fit map cryosparc_P174_J73_class_00_00120_volume.mrc in map
cryosparc_P174_J49_class_06_00180_volume.mrc using 57412 points
correlation = 0.7921, correlation about mean = 0.4419, overlap = 3802
steps = 48, shift = 0.184, angle = 0.558 degrees
Position of cryosparc_P174_J73_class_00_00120_volume.mrc (#4.1) relative to
cryosparc_P174_J49_class_06_00180_volume.mrc (#2) coordinates:
Matrix rotation and translation
0.99995710 -0.00476100 -0.00794553 1.93969697
0.00473704 0.99998419 -0.00303113 -0.11206347
0.00795983 0.00299336 0.99996384 -1.65142557
Axis 0.30925801 -0.81647843 0.48756790
Axis point 201.62232437 0.00000000 247.46580998
Rotation angle (degrees) 0.55808238
Shift along axis -0.11381786
> fitmap #4.2 inMap #2
Fit map cryosparc_P174_J73_class_02_00120_volume.mrc in map
cryosparc_P174_J49_class_06_00180_volume.mrc using 79939 points
correlation = 0.902, correlation about mean = 0.743, overlap = 6908
steps = 44, shift = 0.145, angle = 0.343 degrees
Position of cryosparc_P174_J73_class_02_00120_volume.mrc (#4.2) relative to
cryosparc_P174_J49_class_06_00180_volume.mrc (#2) coordinates:
Matrix rotation and translation
0.99998210 -0.00068758 -0.00594444 0.98612381
0.00068779 0.99999976 0.00003360 -0.10401670
0.00594442 -0.00003769 0.99998233 -0.98496553
Axis -0.00595602 -0.99335717 0.11491758
Axis point 165.88326421 0.00000000 165.37470601
Rotation angle (degrees) 0.34287027
Shift along axis -0.01573749
> show #!3 models
> hide #!3 models
> show #!1 models
> volume #4.2 level 0.1903
> volume #4.1 level 0.1863
> volume #4.2 level 0.3547
> save "/Users/dario.guerrini/OneDrive -
> Htechnopole/MISKYD_Rec8m6A_SAH_3Dclass_iteration2_NoDyn2.cxs"
> close #4
> open /Users/dario.guerrini/Library/CloudStorage/OneDrive-
> Htechnopole/MISKYD_Rec8m6A_SAH_3Dclass_iteration2_withDyn2.cxs
Opened cryosparc_P174_J49_class_06_00180_volume.mrc as #2, grid size
200,200,200, pixel 1.44, shown at level 0.111, step 1, values float32
Opened cryosparc_P174_J49_class_03_00180_volume.mrc as #3, grid size
200,200,200, pixel 1.44, shown at level 0.11, step 1, values float32
Opened cryosparc_P174_J74_class_01_00236_volume.mrc as #4.1, grid size
200,200,200, pixel 1.44, shown at level 0.138, step 1, values float32
Opened cryosparc_P174_J74_class_04_00236_volume.mrc as #4.2, grid size
200,200,200, pixel 1.44, shown at level 0.146, step 1, values float32
Opened cryosparc_P174_J74_class_03_00236_volume.mrc as #4.3, grid size
200,200,200, pixel 1.44, shown at level 0.115, step 1, values float32
opened ChimeraX session
> open /Users/dario.guerrini/Library/CloudStorage/OneDrive-
> Htechnopole/MISKYD_Rec8m6A_SAH_3Dclass_iteration2_NoDyn2.cxs
Opened cryosparc_P174_J49_class_06_00180_volume.mrc as #2, grid size
200,200,200, pixel 1.44, shown at level 0.111, step 1, values float32
Opened cryosparc_P174_J49_class_03_00180_volume.mrc as #3, grid size
200,200,200, pixel 1.44, shown at level 0.11, step 1, values float32
Opened cryosparc_P174_J73_class_00_00120_volume.mrc as #4.1, grid size
200,200,200, pixel 1.44, shown at level 0.186, step 1, values float32
Opened cryosparc_P174_J73_class_02_00120_volume.mrc as #4.2, grid size
200,200,200, pixel 1.44, shown at level 0.355, step 1, values float32
opened ChimeraX session
> close #4
> open /Users/dario.guerrini/Downloads/cryosparc_P174_J64_map.mrc
Opened cryosparc_P174_J64_map.mrc as #4, grid size 384,384,384, pixel 0.748,
shown at level 0.043, step 2, values float32
> select #4
3 models selected
> color bfactor
21177 atoms, 2584 residues, atom bfactor range 15.5 to 334
> close #4
> color bychain
> show #!2 models
> hide #!2 models
> open /Users/dario.guerrini/Library/CloudStorage/OneDrive-
> Htechnopole/MISKYD_Rec8m6A_SAH_3Dclass_iteration2_withDyn2.cxs
Opened cryosparc_P174_J49_class_06_00180_volume.mrc as #2, grid size
200,200,200, pixel 1.44, shown at level 0.111, step 1, values float32
Opened cryosparc_P174_J49_class_03_00180_volume.mrc as #3, grid size
200,200,200, pixel 1.44, shown at level 0.11, step 1, values float32
Opened cryosparc_P174_J74_class_01_00236_volume.mrc as #4.1, grid size
200,200,200, pixel 1.44, shown at level 0.138, step 1, values float32
Opened cryosparc_P174_J74_class_04_00236_volume.mrc as #4.2, grid size
200,200,200, pixel 1.44, shown at level 0.146, step 1, values float32
Opened cryosparc_P174_J74_class_03_00236_volume.mrc as #4.3, grid size
200,200,200, pixel 1.44, shown at level 0.115, step 1, values float32
opened ChimeraX session
> show #!1 models
> hide #!4.2 models
> show #!4.1 models
> hide #!1 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> show #!1 models
> hide #!4.3 models
> show #!4.3 models
> ui tool show "Side View"
> hide #!4.3 models
> volume #4.3 level 0.1835
> volume #4.3 level 0.1889
> volume #4.3 level 0.1835
> save "/Users/dario.guerrini/OneDrive -
> Htechnopole/MISKYD_Rec8m6A_SAH_3Dclass_iteration2_withDyn2.cxs"
> hide #!4 models
> hide #!1 models
> hide #!4.3 models
> show #!4.2 models
> lighting soft
> volume #4.2 color #ffffff8c
> volume #4.2 level 0.1868
> volume gaussian #4.2 sDev2
Expected a keyword
> volume gaussian #4.2 sDev 2
Opened cryosparc_P174_J74_class_04_00236_volume.mrc gaussian as #5, grid size
200,200,200, pixel 1.44, shown at step 1, values float32
> ui tool show "Segment Map"
Segmenting cryosparc_P174_J74_class_04_00236_volume.mrc gaussian, density
threshold 0.110138
Showing 27 region surfaces
496 watershed regions, grouped to 27 regions
Showing cryosparc_P174_J74_class_04_00236_volume gaussian.seg - 27 regions, 27
surfaces
> select #6.6
1 model selected
> select clear
> select #6.6
1 model selected
> undo
> select #6.6
1 model selected
> undo
> show #6.6 models
> show target m
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!4.1 models
> hide #!4.2 models
> hide #!4.3 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> select clear
> select #6.1
1 model selected
> select #6.5
1 model selected
> select #6.1
1 model selected
> select #6.5
1 model selected
Drag select of 755, 960 of 29284 triangles, 743, 123 of 27984 triangles, 750,
11730 of 21704 triangles, 751, 14432 of 23576 triangles, 748, 7702 of 22704
triangles, 758, 9649 of 16848 triangles, 746, 3595 of 15332 triangles, 753,
11031 of 17008 triangles, 740, 13997 of 15904 triangles, 756, 13029 of 15204
triangles, 752, 3229 of 14156 triangles, 745, 2711 of 10988 triangles, 696,
10309 of 10780 triangles, 741, 319 of 9776 triangles, 739, 1602 of 9276
triangles, 704, 239 of 7420 triangles, 757, 3291 of 6152 triangles, 738, 264
of 7180 triangles, 747, 22 of 7696 triangles, 744, 401 of 8064 triangles
> select #6.19
1 model selected
> select #6.26
1 model selected
Drag select of 742, 13197 of 17564 triangles, 712, 3220 of 9916 triangles,
749, 2720 of 8632 triangles, 719, 949 of 3556 triangles, 725, 330 of 3172
triangles
> select #6.6
1 model selected
Saving 1 regions to mrc file...
Opened Dyn2_mask.mrc as #7, grid size 27,35,27, pixel 1.44, shown at step 1,
values float32
Wrote Dyn2_mask.mrc
> select clear
Showing 27 region surfaces
> select #6.6
1 model selected
Drag select of 755, 743, 750, 751, 748, 742, 758, 746, 753, 740, 756, 752,
712, 749, 745, 696, 741, 732, 739, 704, 757, 738, 747, 744, 719, 725, 7
Dyn2_mask.mrc
Saving 26 regions to mrc file...
Opened yMTC_noDyn2_mask.mrc as #8, grid size 107,120,81, pixel 1.44, shown at
step 1, values float32
Wrote yMTC_noDyn2_mask.mrc
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select add #8
30 models selected
> select subtract #8
28 models selected
> select clear
> hide #!8 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> hide #6.1 models
> hide #6.2 models
> hide #6.3 models
> hide #6.4 models
> hide #6.5 models
> hide #6.7 models
> hide #6.8 models
> hide #6.9 models
> hide #6.10 models
> hide #6.11 models
> hide #6.13 models
> hide #6.14 models
> hide #6.12 models
> hide #6.27 models
> hide #6.26 models
> hide #6.25 models
> hide #6.24 models
> hide #6.23 models
> hide #6.22 models
> hide #6.21 models
> hide #6.20 models
> hide #6.19 models
> hide #6.18 models
> hide #6.17 models
> hide #6.16 models
> hide #6.15 models
> show #!8 models
> hide #!8 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> volume resample #4 onGrid #4.2
Opened cryosparc_P174_J74_class_01_00236_volume.mrc resampled as #9, grid size
200,200,200, pixel 1.44, shown at step 1, values float32
Opened cryosparc_P174_J74_class_04_00236_volume.mrc resampled as #10, grid
size 200,200,200, pixel 1.44, shown at step 1, values float32
Opened cryosparc_P174_J74_class_03_00236_volume.mrc resampled as #11, grid
size 200,200,200, pixel 1.44, shown at step 1, values float32
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> close #7-11
> close #6
> close #5
> show #!4.2 models
> volume gaussian #4.2 sDev 2
Opened cryosparc_P174_J74_class_04_00236_volume.mrc gaussian as #5, grid size
200,200,200, pixel 1.44, shown at step 1, values float32
Segmenting cryosparc_P174_J74_class_04_00236_volume.mrc gaussian, density
threshold 0.110138
Showing 27 region surfaces
496 watershed regions, grouped to 27 regions
Showing cryosparc_P174_J74_class_04_00236_volume gaussian.seg - 27 regions, 27
surfaces
Drag select of 740, 26601 of 29284 triangles, 739, 7835 of 27984 triangles,
752, 21613 of 21704 triangles, 747, 14852 of 23576 triangles, 753, 16956 of
22704 triangles, 744, 1406 of 17564 triangles, 757, 16195 of 16848 triangles,
755, 9451 of 15332 triangles, 750, 16184 of 17008 triangles, 745, 14683 of
15904 triangles, 748, 14335 of 15204 triangles, 738, 13583 of 14156 triangles,
715, 260 of 9916 triangles, 741, 3073 of 8632 triangles, 756, 9444 of 10988
triangles, 721, 9415 of 10780 triangles, 751, 4504 of 9776 triangles, 702,
1153 of 10280 triangles, 749, 7484 of 9276 triangles, 718, 4603 of 7420
triangles, 746, 6087 of 6152 triangles, 743, 3833 of 7180 triangles, 754, 4702
of 7696 triangles, 758, 5571 of 8064 triangles, 717, 224 of 3556 triangles,
695, 915 of 3172 triangles, 5 cryosparc_P174_J74_class_04_00236_volume.mrc
gaussian
> hide #!5 models
> select subtract #5
26 models selected
> clear sel
Unknown command: clear sel
> select clear
Drag select of 742
Saving 1 regions to mrc file...
Opened Dyn2.mrc as #7, grid size 27,35,27, pixel 1.44, shown at step 1, values
float32
Wrote Dyn2.mrc
Deleted 1 regions
> hide #!6 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!6 models
> select add #6
27 models selected
> select clear
> select add #6
27 models selected
Saving 26 regions to mrc file...
Opened yMTC_noDyn2.mrc as #8, grid size 107,120,81, pixel 1.44, shown at step
1, values float32
Wrote yMTC_noDyn2.mrc
> hide #!6 models
> show #!6 models
> select subtract #6
Nothing selected
> hide #!6 models
> hide #!8 models
> show #!7 models
> volume resample #7 onGrid #4.2
Opened Dyn2.mrc resampled as #9, grid size 200,200,200, pixel 1.44, shown at
step 1, values float32
> select #9
2 models selected
Please select one ore more regions to save to .mrc file
> hide #!4 models
Please select one ore more regions to save to .mrc file
> select clear]
Expected an objects specifier or a keyword
> select clear
Drag select of 9 Dyn2.mrc resampled
Please select one ore more regions to save to .mrc file
> hide #!9 models
> select subtract #9
Nothing selected
> show #!9 models
> select add #9
2 models selected
Cell requested for row 11 is out of bounds for table with 13 rows! Resizing
table model.
> save /Users/dario.guerrini/Library/CloudStorage/OneDrive-
> Htechnopole/Dyn2_mask_resampled.mrc models #9
> hide #!9 models
> select subtract #9
Nothing selected
> show #!8 models
> select add #8
2 models selected
> volume resample #8 onGrid #4.2
Opened yMTC_noDyn2.mrc resampled as #10, grid size 200,200,200, pixel 1.44,
shown at step 1, values float32
> save /Users/dario.guerrini/Library/CloudStorage/OneDrive-
> Htechnopole/yMTC_noDyn2_mask_resampled.mrc models #10
> open /Users/dario.guerrini/Downloads/cryosparc_P174_Dyn2_mask_resampled.mrc
Opened cryosparc_P174_Dyn2_mask_resampled.mrc as #11, grid size 200,200,200,
pixel 0.748, shown at level 9.7e-06, step 1, values float32
> close #11
> open /Users/dario.guerrini/Library/CloudStorage/OneDrive-
> Htechnopole/MISKYD_Rec8m6A_SAH_3Dclass_iteration2_NoDyn2.cxs
Opened cryosparc_P174_J49_class_06_00180_volume.mrc as #2, grid size
200,200,200, pixel 1.44, shown at level 0.111, step 1, values float32
Opened cryosparc_P174_J49_class_03_00180_volume.mrc as #3, grid size
200,200,200, pixel 1.44, shown at level 0.11, step 1, values float32
Opened cryosparc_P174_J73_class_00_00120_volume.mrc as #4.1, grid size
200,200,200, pixel 1.44, shown at level 0.186, step 1, values float32
Opened cryosparc_P174_J73_class_02_00120_volume.mrc as #4.2, grid size
200,200,200, pixel 1.44, shown at level 0.355, step 1, values float32
opened ChimeraX session
> hide #!4 models
> hide #!4.2 models
> show #!4.1 models
> show #!2 models
> hide #!1 models
> hide #!4 models
> hide #!4.1 models
> show #!4.1 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 #!4.1 models
> show #!4.1 models
> hide #!2 models
> show #!2 models
> volume #2 level 0.1081
> hide #!2 models
> show #!4.2 models
> volume #4.2 level 0.2057
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> volume #4.1 level 0.2096
> hide #!4 models
> show #!4 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> hide #!4.2 models
> show #!4.2 models
> show #!4.1 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> morph #4.1, #4.2 frames 50 method linear
Missing or invalid "structures" argument: only initial part "#4.1" of atom
specifier valid
> morph #4.1 #4.2 frames 50 method linear
Require at least 2 structures for morph
> morph #4.1, #4.2, frames 50 method linear
Missing or invalid "structures" argument: only initial part "#4.1" of atom
specifier valid
> morph #4.1, #4.2
Missing or invalid "structures" argument: only initial part "#4.1" of atom
specifier valid
>
Unknown command: vseries #4.1, #4.2, frames 50 method linear
>
Unknown command: vseries #4.1, #4.2, play frames 50
> morph #4.1, #4.2, play frames 50
Missing or invalid "structures" argument: only initial part "#4.1" of atom
specifier valid
> morph #2, #3
Missing or invalid "structures" argument: only initial part "#2" of atom
specifier valid
> morph #4.1,4.2
Require at least 2 structures for morph
> morph #4.1, 4.2 frames 50 method linear
Require at least 2 structures for morph
> morph #4.1 #4.2 frames 50 method linear
Require at least 2 structures for morph
> morph #4.1, #4.2 frames 50 method linear
Missing or invalid "structures" argument: only initial part "#4.1" of atom
specifier valid
> volume morph #4.1, #4.2 frames 50 method linear
Missing or invalid "volumes" argument: only initial part "#4.1" of atom
specifier valid
> volume morph #4.1,4.2 frames 50
volume morph requires 2 or more volumes, got 0
> volume morph #4.1, 4.2 frames 50
volume morph requires 2 or more volumes, got 0
> volume morph #4 frames 50
Map positions are not the same, cryosparc_P174_J73_class_02_00120_volume.mrc
#4.2 and cryosparc_P174_J73_class_00_00120_volume.mrc #4.1. Use the "volume
resample" command to make a copy of one map with the same grid as the other
map.
> volume morph #4 frames 50
Map positions are not the same, cryosparc_P174_J73_class_02_00120_volume.mrc
#4.2 and cryosparc_P174_J73_class_00_00120_volume.mrc #4.1. Use the "volume
resample" command to make a copy of one map with the same grid as the other
map.
> volume morph #4.1, #4.2
Missing or invalid "volumes" argument: only initial part "#4.1" of atom
specifier valid
> volume resample #4.1 onGrid #4.2
Opened cryosparc_P174_J73_class_00_00120_volume.mrc resampled as #5, grid size
200,200,200, pixel 1.44, shown at step 1, values float32
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> volume #5 color #99bfe58d
> volume #5 color #99bfe58c
> volume morph #5, #4.2
Missing or invalid "volumes" argument: only initial part "#5" of atom
specifier valid
> volume morph #5, #4.2
Missing or invalid "volumes" argument: only initial part "#5" of atom
specifier valid
> volume morph #5, #4.2
Missing or invalid "volumes" argument: only initial part "#5" of atom
specifier valid
> volume morph #5, 4.2
volume morph requires 2 or more volumes, got 1
> volume morph #5, #4.2
Missing or invalid "volumes" argument: only initial part "#5" of atom
specifier valid
===== 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 - 88.1
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac15,12
Model Number: Z1B8001FCT/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.140.19.700.2
OS Loader Version: 10151.140.19.700.2
Software:
System Software Overview:
System Version: macOS 14.7.2 (23H311)
Kernel Version: Darwin 23.6.0
Time since boot: 42 days, 44 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
HP Z27k G3:
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-locscalesurfer: 0.1.1
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
einops: 0.3.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
fsspec: 2025.5.1
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
mpmath: 1.3.0
mrcfile: 1.3.0
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: 1.24.4
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: 1.10.1
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
sympy: 1.14.0
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
timm: 0.4.12
tinyarray: 1.2.4
torch: 2.2.2
torchvision: 0.17.2
tornado: 6.4.2
tqdm: 4.66.6
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 , 2 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 , 2 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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