![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17368 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.3.2-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 0x00000001f4d4c840 (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, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.graphics._graphics, chimerax.segment._segment (total: 51)
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{
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"procRole" : "Background",
"version" : 2,
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"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 151013,
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"build" : "24D81",
"releaseType" : "User"
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"captureTime" : "2025-04-14 18:26:37.5864 +0800",
"codeSigningMonitor" : 1,
"incident" : "C2A5E027-8427-4387-8767-41D40A896A26",
"pid" : 61378,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-11 08:54:32.1179 +0800",
"procStartAbsTime" : 20668030131845,
"procExitAbsTime" : 22950217102377,
"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":"707F7D5B-2303-5DE1-A1BE-64D13B59D433","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "7795A5D5-C886-C047-40D3-689BC2193327",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "1605ECC1-0BF2-443E-AA1D-70E2E5433AA3",
"wakeTime" : 41158,
"sleepWakeUUID" : "DC873EB4-1579-479E-AA78-079447B3F44F",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4375592599\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104ce4000-104ce8000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":61378},
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 4375592599\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104ce4000-104ce8000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"name" : "AppKit",
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"path" : "\/usr\/lib\/system\/libdispatch.dylib",
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"legacyInfo" : {
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"queue" : "com.apple.main-thread"
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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/youngsirashin/Downloads/initial_model.mrc
Opened initial_model.mrc as #1, grid size 64,64,64, pixel 4, shown at level
0.0254, step 1, values float32
> lighting simple
> lighting soft
> lighting simple
> volume #1 level 0.02485
> set bgColor white
> lighting soft
> open /Users/youngsirashin/Downloads/emd_15854.mrc
Opened emd_15854.mrc as #2, grid size 384,384,384, pixel 0.729, shown at level
0.000594, step 2, values float32
> volume #2 step 1
> hide #!2 models
> volume #1 level 0.02458
> volume #1 level 0.02292
> show #!2 models
> hide #!1 models
> volume #2 level 0.001891
> show #!1 models
> hide #!2 models
> open /Users/youngsirashin/Downloads/run_class001.mrc
Opened run_class001.mrc as #3, grid size 64,64,64, pixel 4, shown at level
0.0302, step 1, values float32
> hide #!1 models
> volume #3 level 0.02956
> show #!2 models
> select add #2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-12.898,0,1,0,-130.22,0,0,1,-7.6949
> select subtract #2
Nothing selected
> volume #3 level 0.02203
> volume #2 level 0.001557
> volume #3 level 0.02826
> show #!1 models
> hide #!3 models
> open /Users/youngsirashin/Downloads/initial_model_alignO.mrc
Opened initial_model_alignO.mrc as #4, grid size 64,64,64, pixel 4, shown at
level 0.0258, step 1, values float32
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.0268
> select add #1
2 models selected
> view matrix models #1,1,0,0,22.617,0,1,0,-109.18,0,0,1,2.6329
> select subtract #1
Nothing selected
> show #!2 models
> select add #2
2 models selected
> view matrix models #2,1,0,0,-18.959,0,1,0,-240.87,0,0,1,-2.5992
> hide #!2 models
> show #!2 models
> select subtract #2
Nothing selected
> select add #4
2 models selected
> view matrix models #4,1,0,0,0.55392,0,1,0,9.0909,0,0,1,-0.10672
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.98456,0.16421,-0.060672,-10.707,-0.1638,0.98642,0.011819,30.282,0.061789,-0.0016991,0.99809,-7.5544
> select subtract #4
Nothing selected
> volume #4 level 0.02087
> volume #1 level 0.02302
> volume #4 level 0.02497
> close #4
> close
> open /Users/youngsirashin/Downloads/emd_15854.mrc
Opened emd_15854.mrc as #1, grid size 384,384,384, pixel 0.729, shown at level
0.000594, step 2, values float32
> open /Users/youngsirashin/Downloads/emd_15854_alignO.mrc
Opened emd_15854_alignO.mrc as #2, grid size 384,384,384, pixel 0.729, shown
at level 0.000594, step 2, values float32
> volume #2 step 1
> volume #1 step 1
> volume #1 level 0.001729
> volume #2 level 0.002026
> volume #1 level 0.002431
> close
> open
> /Users/youngsirashin/Downloads/riboSPA/ribosome_apo/cryosparc_P44_J165_map_sharp.mrc
Opened cryosparc_P44_J165_map_sharp.mrc as #1, grid size 448,448,448, pixel
0.96, shown at level 0.075, step 2, values float32
> volume #1 step 1
> ui tool show "Side View"
> lighting full
> volume #1 level 0.0329
> lighting simple
> lighting soft
> lighting full
> lighting soft
> close
> open
> /Users/youngsirashin/Downloads/riboSPA/ribosome_apo/cryosparc_P44_J164_008_volume_map.mrc
Opened cryosparc_P44_J164_008_volume_map.mrc as #1, grid size 448,448,448,
pixel 0.96, shown at level 0.0911, step 2, values float32
> volume showOutlineBox true
> set bgColor black
> open
> /Users/youngsirashin/Downloads/riboSPA/ribosome_apo/J164_008_volume_map_lowpass80.mrc
Opened J164_008_volume_map_lowpass80.mrc as #2, grid size 448,448,448, pixel
0.96, shown at level 0.0533, step 2, values float32
> volume #2 step 1
> hide #!1 models
> volume #2 level 0.002946
> show #!1 models
> volume #2 level 0.005993
> volume #2 level 0.005558
> select add #2
2 models selected
> transparency sel 50
> ui tool show "Map Eraser"
> select add #3
3 models selected
> hide #!2 models
> volume #1 step 1
> select subtract #2
1 model selected
> show #!2 models
> hide #!1 models
> volume erase #2 center 210.36,245.17,197.94 radius 60 outside true
Opened J164_008_volume_map_lowpass80.mrc copy as #4, grid size 448,448,448,
pixel 0.96, shown at step 1, values float32
> select subtract #3
Nothing selected
> select add #4
2 models selected
> hide #3 models
> transparency sel 0
> volume #4 level 0.006367
> volume #4 level 0.001793
> color #4 #ff2f92ff models
> color #4 #941751ff models
> show #!1 models
> select subtract #4
Nothing selected
> hide #!1 models
> transparency #4.1 50
> show #!1 models
> color #4 #941751ff models
> color #4 #94175196 models
> color #4 #73fcd6ff models
> color #4 #00fdffff models
> color #4 #76d6ffff models
> color #4 #ffd479ff models
> color #4 #ff8ad8ff models
> color #4 #ff85ffff models
> color #4 #ff85ff8a models
> color #4 #ff85ff70 models
> volume #4 level 0.01185
> volume #4 level 0.0006379
> hide #!1 models
> select add #4
2 models selected
> save
> /Users/youngsirashin/Downloads/riboSPA/ribosome_apo/focus_mask_APEsite.mrc
> models #4
> volume sel showOutlineBox true
> volume sel showOutlineBox false
> volume sel showOutlineBox true
> select subtract #4
Nothing selected
> show #!1 models
> hide #!4 models
> open /Users/youngsirashin/Downloads/cryosparc_P44_J170_mask.mrc
Opened cryosparc_P44_J170_mask.mrc as #5, grid size 448,448,448, pixel 0.96,
shown at level 1, step 2, values float32
> volume #5 step 1
> volume #5 level 0.5323
> transparency #1.1#5.1 50
> transparency #1.1#5.1 0
> select add #5
2 models selected
> transparency sel 50
> volume #5 level 0.2662
> select subtract #5
Nothing selected
> hide #!5 models
> hide #!1 models
> open
> /Users/youngsirashin/Downloads/cryosparc_P44_J171_class_00_00100_volume.mrc
Opened cryosparc_P44_J171_class_00_00100_volume.mrc as #6, grid size
160,160,160, pixel 2.69, shown at level 0.439, step 1, values float32
> open
> /Users/youngsirashin/Downloads/cryosparc_P44_J171_class_01_00100_volume.mrc
Opened cryosparc_P44_J171_class_01_00100_volume.mrc as #7, grid size
160,160,160, pixel 2.69, shown at level 0.428, step 1, values float32
> open
> /Users/youngsirashin/Downloads/cryosparc_P44_J171_class_02_00100_volume.mrc
Opened cryosparc_P44_J171_class_02_00100_volume.mrc as #8, grid size
160,160,160, pixel 2.69, shown at level 0.432, step 1, values float32
> open
> /Users/youngsirashin/Downloads/cryosparc_P44_J171_class_03_00100_volume.mrc
Opened cryosparc_P44_J171_class_03_00100_volume.mrc as #9, grid size
160,160,160, pixel 2.69, shown at level 0.42, step 1, values float32
> open
> /Users/youngsirashin/Downloads/cryosparc_P44_J171_class_04_00100_volume.mrc
Opened cryosparc_P44_J171_class_04_00100_volume.mrc as #10, grid size
160,160,160, pixel 2.69, shown at level 0.407, step 1, values float32
> open
> /Users/youngsirashin/Downloads/cryosparc_P44_J171_class_05_00100_volume.mrc
Opened cryosparc_P44_J171_class_05_00100_volume.mrc as #11, grid size
160,160,160, pixel 2.69, shown at level 0.431, step 1, values float32
> select add #7
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,-26.647,0,1,0,-283.81,0,0,1,-42.313
> select subtract #7
Nothing selected
> select add #8
2 models selected
> view matrix models #8,1,0,0,-54.39,0,1,0,-580.29,0,0,1,-87.302
> select subtract #8
Nothing selected
> select add #9
2 models selected
> view matrix models #9,1,0,0,38.992,0,1,0,48.956,0,0,1,-281.38
> select subtract #9
Nothing selected
> select add #10
2 models selected
> view matrix models #10,1,0,0,10.754,0,1,0,-243.08,0,0,1,-318.05
> select subtract #10
Nothing selected
> select add #11
2 models selected
> view matrix models #11,1,0,0,-17.002,0,1,0,-544.31,0,0,1,-367.38
> select subtract #11
Nothing selected
> volume #6 level 0.2244
> volume #7 level 0.2061
> ui tool show "Side View"
> hide #!6 models
> hide #!7 models
> volume #8 level 0.1411
> hide #!8 models
> show #!8 models
> hide #!8 models
> volume #9 level 0.115
> volume #9 level 0.1912
> hide #!9 models
> volume #10 level 0.1715
> volume #10 level 0.2384
> hide #!10 models
> show #!10 models
> volume #10 level 0.2009
> hide #!10 models
> show #!10 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!1 models
> hide #!1 models
> volume #10 level 0.3054
> hide #!10 models
> volume #11 level 0.1488
> volume #11 level 0.319
> volume #11 level 0.2933
> hide #!11 models
> show #!6 models
> hide #!6 models
> show #!8 models
> volume #8 level 0.2593
> show #!7 models
> close
> open
> /Users/youngsirashin/Downloads/cryosparc_P44_J171_class_03_00100_volume.mrc
Opened cryosparc_P44_J171_class_03_00100_volume.mrc as #1, grid size
160,160,160, pixel 2.69, shown at level 0.42, step 1, values float32
> open
> /Users/youngsirashin/Downloads/cryosparc_P44_J171_class_02_00100_volume.mrc
Opened cryosparc_P44_J171_class_02_00100_volume.mrc as #2, grid size
160,160,160, pixel 2.69, shown at level 0.432, step 1, values float32
> open
> /Users/youngsirashin/Downloads/cryosparc_P44_J171_class_04_00100_volume.mrc
Opened cryosparc_P44_J171_class_04_00100_volume.mrc as #3, grid size
160,160,160, pixel 2.69, shown at level 0.407, step 1, values float32
> open
> /Users/youngsirashin/Downloads/cryosparc_P44_J171_class_01_00100_volume.mrc
Opened cryosparc_P44_J171_class_01_00100_volume.mrc as #4, grid size
160,160,160, pixel 2.69, shown at level 0.428, step 1, values float32
> open
> /Users/youngsirashin/Downloads/cryosparc_P44_J171_class_05_00100_volume.mrc
Opened cryosparc_P44_J171_class_05_00100_volume.mrc as #5, grid size
160,160,160, pixel 2.69, shown at level 0.431, step 1, values float32
> open
> /Users/youngsirashin/Downloads/cryosparc_P44_J171_class_00_00100_volume.mrc
Opened cryosparc_P44_J171_class_00_00100_volume.mrc as #6, grid size
160,160,160, pixel 2.69, shown at level 0.439, step 1, values float32
> volume #1 level 0.2576
> volume #2 level 0.2752
> volume #3 level 0.2304
> volume #4 level 0.185
> volume #5 level 0.1745
> volume #6 level 0.1031
> volume #6 level 0.1689
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> open
> /Users/youngsirashin/Downloads/riboSPA/ribosome_apo/cryosparc_P44_J164_008_volume_map.mrc
Opened cryosparc_P44_J164_008_volume_map.mrc as #7, grid size 448,448,448,
pixel 0.96, shown at level 0.0911, step 2, values float32
> show #!4 models
> hide #!4 models
> hide #8 models
> hide #!7 models
> show #!7 models
> show #!5 models
> hide #!5 models
> show #!5 models
> volume #5 level 0.3094
> volume #7 step 1
> volume #7 level 0.08068
> hide #!7 models
> show #!7 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!6 models
> volume #6 level 0.2937
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!7 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> volume #4 level 0.2692
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!3 models
> show #!2 models
> show #!6 models
> hide #!6 models
> volume #2 level 0.2561
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!1 models
> show #!2 models
> show #!6 models
> show #!5 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!5 models
> hide #!6 models
> hide #!2 models
> show #!2 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> hide #!2 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> open /Users/youngsirashin/Downloads/riboSPA/emd_3751.mrc
Opened emd_3751.mrc as #9, grid size 216,216,216, pixel 1.39, shown at level
0.151, step 1, values float32
> hide #!6 models
> hide #!9 models
> show #!9 models
> volume #9 level 0.08301
> show #!7 models
> select add #9
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.34124,-0.49906,0.79655,144.92,-0.019405,0.85097,0.52485,-63.772,-0.93978,0.16364,-0.30007,339.98
> view matrix models
> #9,-0.12873,-0.060573,-0.98983,350.74,-0.69096,0.72144,0.045709,140.85,0.71134,0.68982,-0.13472,-21.729
> view matrix models
> #9,-0.11099,-0.020267,-0.99362,342.31,-0.76307,0.64227,0.072135,159.78,0.63671,0.76621,-0.086749,-30.836
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.11099,-0.020267,-0.99362,349.99,-0.76307,0.64227,0.072135,229.3,0.63671,0.76621,-0.086749,-9.1469
> view matrix models
> #9,-0.11099,-0.020267,-0.99362,394.12,-0.76307,0.64227,0.072135,230.79,0.63671,0.76621,-0.086749,-1.7261
> view matrix models
> #9,-0.11099,-0.020267,-0.99362,396.04,-0.76307,0.64227,0.072135,223.09,0.63671,0.76621,-0.086749,-4.4746
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.12192,-0.024454,-0.99224,398.12,-0.76261,0.64216,0.077875,222.05,0.63527,0.76618,-0.096938,-2.4982
> view matrix models
> #9,-0.11952,-0.018612,-0.99266,396.9,-0.786,0.61261,0.083149,229.37,0.60657,0.79016,-0.087848,-3.5316
> view matrix models
> #9,-0.12182,-0.018238,-0.99238,397.14,-0.7862,0.61206,0.08526,229.12,0.60585,0.7906,-0.0889,-3.3106
> select subtract #9
Nothing selected
> volume #7 level 0.07204
> hide #!7 models
> show #8 models
> hide #8 models
> show #!6 models
> show #!5 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #8 models
> hide #8 models
> show #!7 models
> hide #!7 models
> show #8 models
> hide #8 models
> show #!6 models
> hide #!6 models
> hide #!9 models
> show #!7 models
> show #!6 models
> hide #!6 models
> hide #!7 models
> open /Users/youngsirashin/Downloads/cryosparc_P44_J172_component_0.mrc
Opened cryosparc_P44_J172_component_0.mrc as #10, grid size 448,448,448, pixel
0.96, shown at level 3.29e-07, step 2, values float32
> open /Users/youngsirashin/Downloads/cryosparc_P44_J172_component_2.mrc
Opened cryosparc_P44_J172_component_2.mrc as #11, grid size 448,448,448, pixel
0.96, shown at level 1.54e-05, step 2, values float32
> open /Users/youngsirashin/Downloads/cryosparc_P44_J172_component_1.mrc
Opened cryosparc_P44_J172_component_1.mrc as #12, grid size 448,448,448, pixel
0.96, shown at level 2.1e-05, step 2, values float32
> hide #!10 models
> hide #!11 models
> volume #10 step 1
> volume #11 step 1
> volume #12 step 1
> volume #12 level 2.102e-05
> hide #!12 models
> show #!10 models
> volume #10 level 3.292e-07
> volume #10 level 6.039e-05
> volume #10 level 0.0001405
> volume #10 level 0.0002205
> volume #10 level 0.0002406
> volume #10 level 0.0003006
> volume #10 level 0.0003206
> volume #10 level 0.0003607
> volume #10 level 0.0004007
> show #!7 models
> volume #10 level 0.001302
> volume #10 level 0.001101
> hide #!10 models
> show #!11 models
> volume #11 level 0.001299
> volume #11 level 0.0009942
> hide #!11 models
> show #!12 models
> volume #12 level 0.0008108
> volume #12 level 0.001315
> hide #!7 models
> show #!11 models
> show #!10 models
> close #11
> hide #!12 models
> show #!12 models
> select add #12
2 models selected
> close #12
> select add #10
2 models selected
> close #10
> open /Users/youngsirashin/Downloads/cryosparc_P44_J173_cluster_000.mrc
Opened cryosparc_P44_J173_cluster_000.mrc as #10, grid size 448,448,448, pixel
0.96, shown at level 0.0762, step 2, values float32
> open /Users/youngsirashin/Downloads/cryosparc_P44_J173_cluster_001.mrc
Opened cryosparc_P44_J173_cluster_001.mrc as #11, grid size 448,448,448, pixel
0.96, shown at level 0.0806, step 2, values float32
> open /Users/youngsirashin/Downloads/cryosparc_P44_J173_cluster_002.mrc
Opened cryosparc_P44_J173_cluster_002.mrc as #12, grid size 448,448,448, pixel
0.96, shown at level 0.0743, step 2, values float32
> volume #12 step 1
> volume #11 step 1
> volume #10 step 1
> volume #10 level 0.03733
> volume #11 level 0.03799
> volume #11 level 0.03835
> volume #12 level 0.03154
> hide #!12 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!11 models
> show #!12 models
> show #!11 models
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!10 models
> show #!12 models
> show #!10 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> volume #12 level 0.04262
> volume #10 level 0.04739
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> volume #11 level 0.04716
> volume #11 level 0.05773
> hide #!12 models
> show #!10 models
> hide #!11 models
> hide #!10 models
> show #!11 models
> show #!10 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> volume #10 level 0.04357
> hide #!11 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> hide #!10 models
> show #!5 models
> show #!6 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #6 level 0.1863
> volume #5 level 0.1649
> volume #6 level 0.1585
> volume #5 level 0.1263
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> open
> /Users/youngsirashin/Downloads/riboSPA/ribosome_apo/cryosparc_P44_J164_008_volume_map.mrc
Opened cryosparc_P44_J164_008_volume_map.mrc as #13, grid size 448,448,448,
pixel 0.96, shown at level 0.0911, step 2, values float32
> close
> open
> /Users/youngsirashin/Downloads/riboSPA/ribosome_apo/cryosparc_P44_J164_008_volume_map.mrc
Opened cryosparc_P44_J164_008_volume_map.mrc as #1, grid size 448,448,448,
pixel 0.96, shown at level 0.0911, step 2, values float32
> volume #1 step 1
> open
> /Users/youngsirashin/Downloads/riboSPA/ribosome_apo/J164_008_volume_map_lowpass80.mrc
Opened J164_008_volume_map_lowpass80.mrc as #3, grid size 448,448,448, pixel
0.96, shown at level 0.0533, step 2, values float32
> hide #2 models
> volume #3 step 1
> volume #3 level 0.01499
> volume #3 level 0.01571
> hide #!3 models
> volume #1 level 0.06083
> close
> open
> /Users/youngsirashin/Downloads/riboSPA/ribosome_apo/cryosparc_P44_J164_008_volume_map.mrc
Opened cryosparc_P44_J164_008_volume_map.mrc as #1, grid size 448,448,448,
pixel 0.96, shown at level 0.0911, step 2, values float32
> volume #1 step 1
> set bgColor white
> volume gaussian #1 sDev 2
Opened cryosparc_P44_J164_008_volume_map.mrc gaussian as #2, grid size
448,448,448, pixel 0.96, shown at step 1, values float32
> ui tool show "Show Volume Menu"
> show #!1 models
> hide #!1 models
> volume #2 level 0.0123
> volume #2 level 0.004692
> set bgColor black
> lighting full
> lighting soft
> volume #2 level 0.02142
> select add #2
2 models selected
> close #2
> volume gaussian #1 sDev 4
Opened cryosparc_P44_J164_008_volume_map.mrc gaussian as #2, grid size
448,448,448, pixel 0.96, shown at step 1, values float32
> volume #2 level 0.01259
> volume #2 level 0.004538
> volume #2 level 0.01528
> volume #2 level 0.01832
> toolshed show
> volume #2 level 0.004896
> volume #2 level 0.02656
> volume #2 level 0.01206
> volume #2 level 0.00418
> volume #2 level 0.01206
> volume #2 level 0.01313
> volume #2 level 0.01152
> ui tool show "Segment Map"
Segmenting cryosparc_P44_J164_008_volume_map.mrc gaussian, density threshold
0.011520
Only showing 5 of 209 regions.
Showing 5 of 209 region surfaces
479 watershed regions, grouped to 209 regions
Showing cryosparc_P44_J164_008_volume_map gaussian.seg - 209 regions, 5
surfaces
> select add #3
6 models selected
> close #3
Segmenting cryosparc_P44_J164_008_volume_map.mrc gaussian, density threshold
0.011520
Only showing 20 of 209 regions.
Showing 20 of 209 region surfaces
479 watershed regions, grouped to 209 regions
Showing cryosparc_P44_J164_008_volume_map gaussian.seg - 209 regions, 20
surfaces
> select add #3
21 models selected
> close
> open
> /Users/youngsirashin/Downloads/riboSPA/ribosome_apo/cryosparc_P44_J164_008_volume_map.mrc
Opened cryosparc_P44_J164_008_volume_map.mrc as #1, grid size 448,448,448,
pixel 0.96, shown at level 0.0911, step 2, values float32
> volume gaussian #1 sDev 2
Opened cryosparc_P44_J164_008_volume_map.mrc gaussian as #2, grid size
448,448,448, pixel 0.96, shown at step 1, values float32
> volume #1 step 1
> volume #2 level 0.02218
> volume #2 level 0.01306
> volume #2 level 0.02244
Segmenting cryosparc_P44_J164_008_volume_map.mrc, density threshold 0.091059
Only showing 50 of 524 regions.
Showing 50 of 524 region surfaces
22484 watershed regions, grouped to 524 regions
Showing cryosparc_P44_J164_008_volume_map.seg - 524 regions, 50 surfaces
> select add #3
51 models selected
> close #3
Segmenting cryosparc_P44_J164_008_volume_map.mrc gaussian, density threshold
0.022438
Only showing 50 of 376 regions.
Showing 50 of 376 region surfaces
3623 watershed regions, grouped to 376 regions
Showing cryosparc_P44_J164_008_volume_map gaussian.seg - 376 regions, 50
surfaces
> select add #3
51 models selected
> select subtract #3
Nothing selected
> select add #3
51 models selected
> hide #!2 models
> select subtract #3
Nothing selected
> select add #3
51 models selected
> hide #!3 models
> show #!3 models
> select subtract #3
Nothing selected
> select add #3
51 models selected
> select add #3.1
51 models selected
> select subtract #3
Nothing selected
> select add #3
51 models selected
> close #3
Segmenting cryosparc_P44_J164_008_volume_map.mrc gaussian, density threshold
0.022438
Only showing 50 of 376 regions.
Showing 50 of 376 region surfaces
3623 watershed regions, grouped to 376 regions
Showing cryosparc_P44_J164_008_volume_map gaussian.seg - 376 regions, 50
surfaces
Ungrouped to 474 regions, but did not show all surfaces, see Options
> select add #3
97 models selected
> hide #!3 models
> show #!3 models
> select subtract #3
Nothing selected
> close #3
Segmenting cryosparc_P44_J164_008_volume_map.mrc gaussian, density threshold
0.022438
Showing 376 region surfaces
3623 watershed regions, grouped to 376 regions
Showing cryosparc_P44_J164_008_volume_map gaussian.seg - 376 regions, 376
surfaces
> select #3.258
1 model selected
> select #3.10
1 model selected
> select #3.176
1 model selected
> select #3.20
1 model selected
> select #3.258
1 model selected
> select #3.20
1 model selected
> select #3.258
1 model selected
Deleted 1 regions
> select #3.10
1 model selected
Deleted 1 regions
> select #3.4
1 model selected
Deleted 1 regions
> select #3.44
1 model selected
Deleted 1 regions
> select #3.346
1 model selected
Deleted 1 regions
> select #3.227
1 model selected
> select add #3.243
2 models selected
> select add #3.169
3 models selected
> select add #3.208
4 models selected
> select add #3.238
5 models selected
> select add #3.177
6 models selected
> select subtract #3.177
5 models selected
> select add #3.196
6 models selected
> select add #3.177
7 models selected
> select add #3.365
8 models selected
> select add #3.147
9 models selected
> select add #3.206
10 models selected
> select add #3.244
11 models selected
> select add #3.304
12 models selected
> select add #3.161
13 models selected
> select add #3.273
14 models selected
> select add #3.5
15 models selected
> select add #3.320
16 models selected
> select add #3.164
17 models selected
> select add #3.27
18 models selected
> select add #3.134
19 models selected
> select subtract #3.27
18 models selected
> select add #3.65
19 models selected
> select add #3.39
20 models selected
> select add #3.355
21 models selected
> select add #3.316
22 models selected
> select add #3.55
23 models selected
> select add #3.213
24 models selected
> select add #3.117
25 models selected
> select add #3.309
26 models selected
> select add #3.284
27 models selected
> select add #3.76
28 models selected
> select add #3.293
29 models selected
> select add #3.9
30 models selected
> select add #3.324
31 models selected
> select add #3.118
32 models selected
Deleted 32 regions
> select add #3.88
1 model selected
> select subtract #3.88
Nothing selected
> select add #3.88
1 model selected
> select subtract #3.88
Nothing selected
> select add #3.88
1 model selected
> select add #3.247
2 models selected
Drag select of 4447, 52 of 29916 triangles, 5026, 49 of 23148 triangles, 1867,
44 of 20852 triangles, 4814, 19 of 18468 triangles, 4432, 56 of 18752
triangles, 5481, 56 of 19480 triangles, 5294, 38 of 18424 triangles, 4923, 40
of 14772 triangles
> select subtract #3.88
7 models selected
> select add #3.190
8 models selected
> select add #3.247
9 models selected
> select add #3.2
10 models selected
> select add #3.172
11 models selected
> select add #3.168
12 models selected
> select add #3.139
13 models selected
> select add #3.84
14 models selected
> select add #3.154
15 models selected
> select add #3.152
16 models selected
> select add #3.27
17 models selected
> select add #3.178
18 models selected
> select subtract #3.178
17 models selected
> select add #3.255
18 models selected
> select add #3.370
19 models selected
> select add #3.275
20 models selected
> select add #3.20
21 models selected
> select subtract #3.20
20 models selected
> select add #3.18
21 models selected
> select add #3.20
22 models selected
> select add #3.115
23 models selected
> select add #3.178
24 models selected
Deleted 24 regions
> select add #3.88
1 model selected
> select add #3.212
2 models selected
Drag select of 5415, 472 of 43396 triangles, 5446, 17 of 34812 triangles,
5484, 554 of 38004 triangles, 5374, 201 of 30076 triangles, 5520, 286 of 26736
triangles, 5458, 424 of 29496 triangles, 5418, 464 of 27368 triangles, 5493,
88 of 28660 triangles, 5220, 225 of 20416 triangles, 5056, 382 of 20900
triangles, 5194, 626 of 18456 triangles, 5392, 236 of 20520 triangles, 5492,
209 of 18512 triangles, 5473, 230 of 16380 triangles
> select add #3.6
17 models selected
> select add #3.298
18 models selected
> select add #3.173
19 models selected
> select add #3.349
20 models selected
> select subtract #3.88
19 models selected
> select subtract #3.212
18 models selected
> select add #3.88
19 models selected
> select add #3.132
20 models selected
> select add #3.212
21 models selected
> select subtract #3.212
20 models selected
> select add #3.62
21 models selected
> select add #3.339
22 models selected
> select add #3.294
23 models selected
> select add #3.129
24 models selected
> select add #3.82
25 models selected
> select add #3.47
26 models selected
> select add #3.282
27 models selected
> select add #3.111
28 models selected
> select add #3.237
29 models selected
> select add #3.125
30 models selected
> select add #3.317
31 models selected
> select add #3.114
32 models selected
> select add #3.192
33 models selected
> select add #3.197
34 models selected
Deleted 34 regions
> select add #3.372
1 model selected
> select add #3.212
2 models selected
> select add #3.325
3 models selected
> select add #3.214
4 models selected
> select add #3.327
5 models selected
> select add #3.333
6 models selected
> select add #3.163
7 models selected
> select add #3.332
8 models selected
> select add #3.104
9 models selected
> select add #3.59
10 models selected
> select add #3.313
11 models selected
> select add #3.103
12 models selected
> select subtract #3.103
11 models selected
> select add #3.97
12 models selected
> select add #3.124
13 models selected
> select add #3.167
14 models selected
> select add #3.103
15 models selected
> select add #3.56
16 models selected
> select add #3.265
17 models selected
> select add #3.329
18 models selected
> select add #3.360
19 models selected
> select add #3.363
20 models selected
Deleted 20 regions
> select add #3.359
1 model selected
> select add #3.269
2 models selected
> select add #3.199
3 models selected
> select add #3.318
4 models selected
> select add #3.261
5 models selected
> select add #3.40
6 models selected
> select add #3.187
7 models selected
> select add #3.83
8 models selected
> select subtract #3.83
7 models selected
> select add #3.201
8 models selected
> select add #3.110
9 models selected
> select add #3.312
10 models selected
> select add #3.83
11 models selected
> select add #3.209
12 models selected
> select add #3.375
13 models selected
> select add #3.57
14 models selected
> select add #3.300
15 models selected
> select add #3.123
16 models selected
> select add #3.60
17 models selected
> select add #3.8
18 models selected
> select add #3.153
19 models selected
Deleted 19 regions
> select add #3.23
1 model selected
> select add #3.26
2 models selected
> select add #3.85
3 models selected
> select add #3.51
4 models selected
> select add #3.366
5 models selected
> select subtract #3.366
4 models selected
> select subtract #3.51
3 models selected
> select add #3.194
4 models selected
> select add #3.366
5 models selected
> select add #3.51
6 models selected
> select subtract #3.366
5 models selected
Deleted 5 regions
> select add #3.16
1 model selected
> select add #3.48
2 models selected
> select add #3.74
3 models selected
> select subtract #3.74
2 models selected
> select add #3.45
3 models selected
> select add #3.157
4 models selected
> select add #3.74
5 models selected
> select add #3.175
6 models selected
> select add #3.119
7 models selected
> select add #3.107
8 models selected
> select subtract #3.107
7 models selected
> select add #3.49
8 models selected
> select add #3.274
9 models selected
> select add #3.267
10 models selected
> select subtract #3.74
9 models selected
> select add #3.19
10 models selected
> select add #3.28
11 models selected
> select add #3.222
12 models selected
Deleted 12 regions
> select add #3.366
1 model selected
> select add #3.335
2 models selected
> select add #3.210
3 models selected
> select add #3.74
4 models selected
> select add #3.34
5 models selected
> select add #3.81
6 models selected
> select subtract #3.81
5 models selected
> select add #3.259
6 models selected
> select add #3.182
7 models selected
> select add #3.81
8 models selected
> select add #3.180
9 models selected
Drag select of 5309, 297 of 20268 triangles, 5110, 538 of 17268 triangles,
5519, 659 of 18824 triangles, 4518, 319 of 9524 triangles, 4148, 382 of 6552
triangles
> select add #3.143
15 models selected
> select subtract #3.182
14 models selected
> select add #3.220
15 models selected
> select subtract #3.143
14 models selected
> select add #3.182
15 models selected
> select add #3.53
16 models selected
> select add #3.292
17 models selected
> select add #3.32
18 models selected
> select add #3.160
19 models selected
Deleted 19 regions
> select add #3.174
1 model selected
> select add #3.107
2 models selected
> select add #3.283
3 models selected
> select add #3.70
4 models selected
> select add #3.270
5 models selected
> select add #3.362
6 models selected
> select add #3.108
7 models selected
> select add #3.343
8 models selected
> select add #3.58
9 models selected
> select add #3.101
10 models selected
> select subtract #3.101
9 models selected
> select add #3.376
10 models selected
> select add #3.143
11 models selected
> select add #3.101
12 models selected
> select add #3.321
13 models selected
> select add #3.127
14 models selected
> select add #3.334
15 models selected
> select add #3.146
16 models selected
> select add #3.249
17 models selected
Deleted 17 regions
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select add #3.92
1 model selected
> select add #3.264
2 models selected
> select subtract #3.264
1 model selected
> select add #3.302
2 models selected
> select add #3.219
3 models selected
> select subtract #3.219
2 models selected
> select add #3.287
3 models selected
> select add #3.204
4 models selected
> select add #3.189
5 models selected
> select add #3.246
6 models selected
> select add #3.262
7 models selected
Deleted 7 regions
> select add #3.106
1 model selected
> select add #3.289
2 models selected
> select add #3.140
3 models selected
> select add #3.186
4 models selected
> select add #3.203
5 models selected
> select add #3.281
6 models selected
> select add #3.361
7 models selected
> select add #3.95
8 models selected
> select add #3.264
9 models selected
> select subtract #3.264
8 models selected
> select add #3.102
9 models selected
> select add #3.219
10 models selected
> select add #3.264
11 models selected
Deleted 11 regions
> select add #3.277
1 model selected
Drag select of 4480, 67 of 10748 triangles
> select add #3.374
3 models selected
> select add #3.285
4 models selected
> select add #3.191
5 models selected
> select add #3.245
6 models selected
> select add #3.121
7 models selected
> select subtract #3.121
6 models selected
> select add #3.242
7 models selected
> select add #3.121
8 models selected
> select add #3.252
9 models selected
> select add #3.155
10 models selected
> select add #3.357
11 models selected
> select add #3.322
12 models selected
> select add #3.344
13 models selected
Deleted 13 regions
> show #!2 models
> select add #3.73
1 model selected
> select add #3.122
2 models selected
> select add #3.368
3 models selected
Deleted 3 regions
> select add #3.21
1 model selected
> select add #3.276
2 models selected
> select add #3.240
3 models selected
> select subtract #3.276
2 models selected
> select add #3.276
3 models selected
Deleted 3 regions
> hide #!2 models
> select add #3.11
1 model selected
> select subtract #3.11
Nothing selected
> select add #3.89
1 model selected
> select add #3.323
2 models selected
> select add #3.11
3 models selected
> select subtract #3.11
2 models selected
> select add #3.11
3 models selected
Drag select of 5479, 1311 of 49812 triangles, 5514, 1369 of 36824 triangles,
5483, 1291 of 27784 triangles, 5018, 596 of 22840 triangles, 5533, 1054 of
24712 triangles, 5451, 1180 of 21976 triangles, 5036, 2149 of 17492 triangles,
5356, 1569 of 14624 triangles, 5280, 197 of 18532 triangles, 4503, 1144 of
13200 triangles, 5237, 603 of 13980 triangles, 5131, 995 of 13380 triangles,
4470, 1030 of 10172 triangles, 4962, 716 of 9252 triangles
> select add #3.162
15 models selected
> select add #3.319
16 models selected
Drag select of 5479, 13940 of 49812 triangles, 5483, 2718 of 27784 triangles,
5399, 6320 of 30332 triangles, 5376, 7382 of 26024 triangles, 5508, 15272 of
28628 triangles, 5421, 540 of 25984 triangles, 5385, 690 of 22136 triangles,
5527, 5100 of 20352 triangles, 5424, 513 of 19680 triangles, 5494, 3194 of
18212 triangles, 5381, 6879 of 20668 triangles, 5512, 11573 of 19596
triangles, 5208, 8577 of 17228 triangles, 5474, 809 of 17748 triangles, 4625,
22 of 15532 triangles, 5024, 2398 of 17620 triangles, 5442, 360 of 15164
triangles, 5344, 7726 of 16176 triangles, 5177, 11986 of 15972 triangles,
5107, 701 of 14964 triangles, 5280, 4138 of 18532 triangles, 3936, 61 of 13252
triangles, 5137, 9255 of 11632 triangles, 5131, 1736 of 13380 triangles, 5172,
8912 of 12500 triangles
Drag select of 5479, 24823 of 49812 triangles, 5531, 27950 of 40656 triangles,
5422, 15700 of 31512 triangles, 5185, 16396 of 32136 triangles, 5483, 17910 of
27784 triangles, 5449, 9316 of 25640 triangles, 5445, 24477 of 27788
triangles, 5399, 23855 of 30332 triangles, 5155, 5425, 354 of 25684 triangles,
5376, 19392 of 26024 triangles, 5508, 27434 of 28628 triangles, 5421, 5386,
16012 of 25084 triangles, 5342, 3436 of 26924 triangles, 5018, 11391 of 22840
triangles, 5266, 5038, 21152 of 21764 triangles, 5521, 7262 of 19888
triangles, 5491, 2792 of 25916 triangles, 5439, 14552 of 18904 triangles,
5325, 4959 of 23668 triangles, 5451, 1651 of 21976 triangles, 5527, 19926 of
20352 triangles, 5424, 5494, 18144 of 18212 triangles, 5381, 10822 of 20668
triangles, 5139, 17669 of 17844 triangles, 5512, 18661 of 19596 triangles,
5036, 286 of 17492 triangles, 5208, 5474, 15703 of 17748 triangles, 4625,
11710 of 15532 triangles, 4501, 3164 of 15732 triangles, 5085, 16113 of 17340
triangles, 4980, 6966 of 16800 triangles, 5024, 5442, 1756 of 15164 triangles,
5344, 9586 of 16176 triangles, 5177, 10115 of 15972 triangles, 5107, 12942 of
14964 triangles, 5280, 13321 of 18532 triangles, 3936, 10570 of 13252
triangles, 5398, 14800 of 14912 triangles, 3798, 4639, 10781 of 12388
triangles, 5137, 1352 of 11632 triangles, 5131, 1754 of 13380 triangles, 5172,
10553 of 12500 triangles, 5375, 9987 of 11060 triangles, 5480, 5979 of 9588
triangles, 4410, 4944, 5328, 8212 of 8960 triangles, 4091, 5495 of 6448
triangles, 4949, 5394 of 5488 triangles, 831, 2692 of 4820 triangles
Drag select of 5479, 30103 of 49812 triangles, 5185, 1252 of 32136 triangles,
5483, 189 of 27784 triangles, 5399, 2710 of 30332 triangles, 5376, 25313 of
26024 triangles, 5508, 27117 of 28628 triangles, 5421, 5385, 285 of 22136
triangles, 5527, 13486 of 20352 triangles, 5424, 7552 of 19680 triangles,
5494, 4534 of 18212 triangles, 5381, 14289 of 20668 triangles, 5512, 8831 of
19596 triangles, 5208, 16698 of 17228 triangles, 4625, 12251 of 15532
triangles, 5024, 3085 of 17620 triangles, 5344, 3781 of 16176 triangles, 5177,
9589 of 15972 triangles, 5107, 768 of 14964 triangles, 5280, 4020 of 18532
triangles, 3936, 12807 of 13252 triangles, 5357, 560 of 11340 triangles, 5137,
6833 of 11632 triangles, 5131, 9249 of 13380 triangles, 5172, 10290 of 12500
triangles, 5375, 554 of 11060 triangles, 5328
Drag select of 5479, 42775 of 49812 triangles, 5185, 762 of 32136 triangles,
5483, 8082 of 27784 triangles, 5399, 7166 of 30332 triangles, 5376, 5508,
22689 of 28628 triangles, 5421, 5385, 4524 of 22136 triangles, 5527, 13676 of
20352 triangles, 5424, 54 of 19680 triangles, 5494, 1293 of 18212 triangles,
5381, 19120 of 20668 triangles, 5512, 16341 of 19596 triangles, 5208, 5474,
2969 of 17748 triangles, 4625, 5024, 5693 of 17620 triangles, 5442, 481 of
15164 triangles, 5344, 9321 of 16176 triangles, 5177, 14022 of 15972
triangles, 5280, 11583 of 18532 triangles, 3936, 4503, 1604 of 13200
triangles, 5357, 4390 of 11340 triangles, 5137, 11201 of 11632 triangles,
5131, 12557 of 13380 triangles, 5172, 11434 of 12500 triangles, 5375, 2959 of
11060 triangles, 5328
Drag select of 5479, 34643 of 49812 triangles, 5185, 199 of 32136 triangles,
5483, 2348 of 27784 triangles, 5399, 4798 of 30332 triangles, 5376, 25862 of
26024 triangles, 5508, 24237 of 28628 triangles, 5421, 23471 of 25984
triangles, 5385, 1213 of 22136 triangles, 5527, 13457 of 20352 triangles,
5424, 2092 of 19680 triangles, 5494, 1830 of 18212 triangles, 5381, 16263 of
20668 triangles, 5512, 11008 of 19596 triangles, 5208, 5474, 223 of 17748
triangles, 4625, 12994 of 15532 triangles, 5024, 4131 of 17620 triangles,
5344, 5585 of 16176 triangles, 5177, 11386 of 15972 triangles, 5280, 6177 of
18532 triangles, 3936, 5357, 1668 of 11340 triangles, 5137, 8753 of 11632
triangles, 5131, 10475 of 13380 triangles, 5172, 11900 of 12500 triangles,
5375, 1497 of 11060 triangles, 5328, 7986 of 8960 triangles
Deleted 29 regions
> show #!2 models
> select #3.113
1 model selected
Deleted 1 regions
> select #3.341
1 model selected
Deleted 1 regions
> select #3.142
1 model selected
Deleted 1 regions
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select add #3.367
1 model selected
> select add #3.348
2 models selected
> select add #3.100
3 models selected
> select add #3.260
4 models selected
> select add #3.224
5 models selected
> select add #3.356
6 models selected
> select add #3.77
7 models selected
Deleted 7 regions
> show #!2 models
> hide #!2 models
> select #3.295
1 model selected
Deleted 1 regions
> select #3.151
1 model selected
Drag select of 5475, 5382, 5417, 5432, 5531, 5384, 5361, 5518, 5369, 5436,
5448, 5120, 5410, 5510, 5412, 33265 of 36052 triangles, 5514, 36746 of 36824
triangles, 5422, 5490, 5380, 5472, 5497, 5441, 5277, 5457, 5037, 5330, 5411,
5449, 5023, 4411, 5155, 5425, 5447, 5116, 5496, 5032, 23125 of 27304
triangles, 5405, 5464, 5423, 5488, 5456, 5454, 5386, 5342, 4969, 5018, 5393,
5489, 5310, 5038, 5521, 5491, 5439, 5533, 5341, 5325, 5451, 5186, 5478, 5403,
5241, 423, 5164, 5139, 4682, 5036, 5017, 4496, 238, 4501, 5085, 3760, 4980,
4871, 5535, 5020, 5034, 5187, 5258, 5471, 5154, 5356, 5430, 4578, 5148, 3852,
5211, 5259, 4242, 17, 4538, 3798, 4052, 4554, 5237, 10560 of 13980 triangles,
4639, 4630, 4668, 4930, 5296, 4968, 4654, 4470, 788, 5365, 4842, 1154, 5076,
4962, 7116 of 9252 triangles, 4737, 4949, 831
Drag select of 5475, 5382, 5417, 5432, 5531, 5384, 5361, 5518, 5369, 5436,
5448, 5120, 5410, 5510, 5412, 36025 of 36052 triangles, 5514, 5422, 5490,
5380, 5472, 5497, 5441, 5277, 5457, 5037, 5330, 5411, 5449, 5023, 4411, 5155,
5425, 5447, 5116, 5496, 5032, 24605 of 27304 triangles, 5405, 5464, 5423,
5488, 5456, 5454, 5386, 5342, 4969, 5018, 5393, 5489, 5310, 5038, 5521, 5491,
5439, 5533, 5341, 5325, 5451, 5186, 5478, 5403, 5241, 423, 5164, 5139, 4682,
5036, 5017, 4496, 238, 4501, 5085, 3760, 4980, 4871, 5535, 5020, 5034, 5187,
5258, 5471, 5154, 5356, 5430, 4578, 5148, 3852, 5211, 5259, 4242, 17, 4538,
3798, 4052, 4554, 5237, 13945 of 13980 triangles, 4639, 4630, 4668, 4930,
5296, 4968, 4654, 4470, 788, 5365, 4842, 1154, 5076, 4962, 4737, 4949, 831
> select subtract #3.291
111 models selected
> select add #3.291
112 models selected
Drag select of 5475, 5382, 5417, 5432, 5531, 5384, 5361, 5518, 5369, 5436,
5448, 5120, 5410, 5510, 5412, 5514, 5422, 5490, 5380, 5472, 5497, 5441, 5277,
5457, 5037, 5330, 5411, 5449, 5023, 4411, 5155, 5425, 5447, 5116, 5496, 5032,
5405, 5464, 5423, 5488, 5456, 5454, 5386, 5342, 4969, 5018, 5393, 5489, 5310,
5038, 5521, 5491, 5439, 5533, 5341, 5325, 5451, 5186, 5478, 5403, 5241, 423,
5164, 5139, 4682, 5036, 5017, 4496, 238, 4501, 5085, 3760, 4980, 4871, 5535,
5020, 5034, 5187, 5258, 5471, 5154, 5356, 5430, 4578, 5148, 3852, 5211, 5259,
4242, 17, 4538, 3798, 4052, 4554, 5237, 4639, 4630, 4668, 4930, 5296, 4968,
4654, 4470, 788, 5365, 4842, 1154, 5076, 4962, 4737, 4949, 831
> select clear
Drag select of 5475, 5382, 5417, 5432, 5531, 5384, 5361, 5518, 5369, 5436,
5448, 5120, 5410, 5510, 5412, 5514, 5422, 5490, 5380, 5472, 5497, 5441, 5277,
5457, 5037, 5330, 5411, 5449, 5023, 4411, 5155, 5425, 5447, 5116, 5496, 5032,
5405, 5464, 5423, 5488, 5456, 5454, 5386, 5342, 4969, 5018, 5393, 5489, 5310,
5038, 5521, 5491, 5439, 5533, 5341, 5325, 5451, 5186, 5478, 5403, 5241, 423,
5164, 5139, 4682, 5036, 5017, 4496, 238, 4501, 5085, 3760, 4980, 4871, 5535,
5020, 5034, 5187, 5258, 5471, 5154, 5356, 5430, 4578, 5148, 3852, 5211, 5259,
4242, 17, 4538, 3798, 4052, 4554, 5237, 4639, 4630, 4668, 4930, 5296, 4968,
4654, 4470, 788, 5365, 4842, 1154, 5076, 4962, 4737, 4949, 831
> select clear
Drag select of 5475, 5382, 5417, 5432, 5531, 5384, 5361, 5518, 5369, 5436,
5448, 5120, 5410, 5510, 5412, 5514, 5422, 5490, 5380, 5472, 5497, 5441, 5277,
5457, 5037, 5330, 5411, 5449, 5023, 4411, 5155, 5425, 5447, 5116, 5496, 5032,
5405, 5464, 5423, 5488, 5456, 5454, 5386, 5342, 4969, 5018, 5393, 5489, 5310,
5038, 5521, 5491, 5439, 5533, 5341, 5325, 5451, 5186, 5478, 5403, 5241, 423,
5164, 5139, 4682, 5036, 5017, 4496, 238, 4501, 5085, 3760, 4980, 4871, 5535,
5020, 5034, 5187, 5258, 5471, 5154, 5356, 5430, 4578, 5148, 3852, 5211, 5259,
4242, 17, 4538, 3798, 4052, 4554, 5237, 4639, 4630, 4668, 4930, 5296, 4968,
4654, 4470, 788, 5365, 4842, 1154, 5076, 4962, 4737, 4949, 831
Drag select of 5475, 5382, 5417, 5432, 5531, 5384, 5361, 5518, 5369, 5436,
5448, 5120, 5410, 5510, 5412, 5514, 5422, 5490, 5380, 5472, 5497, 5441, 5277,
5457, 5037, 5330, 5411, 5449, 5023, 4411, 5155, 5425, 5447, 5116, 5496, 5032,
5405, 5464, 5423, 5488, 5456, 5454, 5386, 5342, 4969, 5018, 5393, 5489, 5310,
5038, 5521, 5491, 5439, 5533, 5341, 5325, 5451, 5186, 5478, 5403, 5241, 423,
5164, 5139, 4682, 5036, 5017, 4496, 238, 4501, 5085, 3760, 4980, 4871, 5535,
5020, 5034, 5187, 5258, 5471, 5154, 5356, 5430, 4578, 5148, 3852, 5211, 5259,
4242, 17, 4538, 3798, 8793 of 11152 triangles, 4052, 4554, 5237, 4639, 4630,
4668, 4930, 5296, 4968, 4654, 4470, 788, 5365, 4842, 1154, 5076, 4962, 4737,
4949, 831
Drag select of 5475, 5382, 5417, 5432, 5531, 5384, 5361, 5518, 5369, 5436,
5448, 5120, 5410, 5510, 5412, 5514, 5422, 5490, 5380, 5472, 5497, 5441, 5277,
5457, 5037, 5330, 5411, 5449, 5023, 4411, 5155, 5425, 5447, 5116, 5496, 5032,
5405, 5464, 5423, 5488, 5456, 5454, 5386, 5342, 4969, 5018, 5393, 5489, 5310,
5038, 5521, 5491, 5439, 5533, 5341, 5325, 5451, 5186, 5478, 5403, 5241, 423,
5164, 5139, 4682, 5036, 5017, 4496, 238, 4501, 5085, 3760, 4980, 4871, 5535,
5020, 5034, 5187, 5258, 5471, 5154, 5356, 5430, 4578, 5148, 3852, 5211, 5259,
4242, 17, 4538, 3798, 4052, 4554, 5237, 4639, 4630, 4668, 4930, 5296, 4968,
4654, 4470, 788, 5365, 4842, 1154, 5076, 4962, 4737, 4949, 831
> select add #3.1
112 models selected
> select add #3
113 models selected
> select subtract #3
Nothing selected
> select add #3
113 models selected
> select subtract #3.1
112 models selected
> select subtract #3
Nothing selected
> select add #3
113 models selected
> select subtract #3
Nothing selected
Drag select of 5475, 5382, 5417, 5432, 5531, 5384, 5361, 5518, 5369, 5436,
5448, 5120, 5410, 5510, 5412, 5514, 5422, 5490, 5380, 5472, 5497, 5441, 5277,
5457, 5037, 5330, 5411, 5449, 5023, 4411, 5155, 5425, 5447, 5116, 5496, 5032,
5405, 5464, 5423, 5488, 5456, 5454, 5386, 5342, 4969, 5018, 5393, 5489, 5310,
5038, 5521, 5491, 5439, 5533, 5341, 5325, 5451, 5186, 5478, 5403, 5241, 423,
5164, 5139, 4682, 5036, 5017, 4496, 238, 4501, 5085, 3760, 4980, 4871, 5535,
5020, 5034, 5187, 5258, 5471, 5154, 5356, 5430, 4578, 5148, 3852, 5211, 5259,
4242, 17, 4538, 3798, 4052, 4554, 5237, 4639, 4630, 4668, 4930, 5296, 4968,
4654, 4470, 788, 5365, 4842, 1154, 5076, 4962, 4737, 4949, 831
Drag select of 5475, 5382, 5417, 5432, 5531, 5384, 5361, 5518, 5369, 5436,
5448, 5120, 5410, 5510, 5412, 5514, 5422, 5490, 5380, 5472, 5497, 5441, 5277,
5457, 5037, 5330, 5411, 5449, 5023, 4411, 5155, 5425, 5447, 5116, 5496, 5032,
26141 of 27304 triangles, 5405, 5464, 5423, 5488, 5456, 5454, 5386, 5342,
4969, 5018, 5393, 5489, 5310, 5038, 5521, 5491, 5439, 5533, 5341, 5325, 5451,
5186, 5478, 5403, 5241, 423, 5164, 5139, 4682, 5036, 5017, 4496, 238, 4501,
5085, 3760, 4980, 4871, 5535, 5020, 5034, 5187, 5258, 5471, 5154, 5356, 5430,
4578, 5148, 3852, 5211, 5259, 4242, 17, 4538, 3798, 4052, 4554, 5237, 4639,
4630, 4668, 4930, 5296, 4968, 4654, 4470, 788, 5365, 4842, 1154, 5076, 4962,
4737, 4949, 831
Drag select of 5475, 5382, 5417, 5432, 5531, 5384, 5361, 5518, 5369, 5436,
5448, 5120, 5410, 5510, 5412, 5514, 5422, 5490, 5380, 5472, 5497, 5441, 5277,
5457, 5037, 5330, 5411, 5449, 5023, 4411, 5155, 5425, 5447, 5116, 5496, 5032,
5405, 5464, 5423, 5488, 5456, 5454, 5386, 5342, 4969, 5018, 5393, 5489, 5310,
5038, 5521, 5491, 5439, 5533, 5341, 5325, 5451, 5186, 5478, 5403, 5241, 423,
5164, 5139, 4682, 5036, 5017, 4496, 238, 4501, 5085, 3760, 4980, 4871, 5535,
5020, 5034, 5187, 5258, 5471, 5154, 5356, 5430, 4578, 5148, 3852, 5211, 5259,
4242, 17, 4538, 3798, 4052, 4554, 5237, 4639, 4630, 4668, 4930, 5296, 4968,
4654, 4470, 788, 5365, 4842, 1154, 5076, 4962, 4737, 4949, 831
Saving 112 regions to mrc file...
Opened mask_small_unit.mrc as #4, grid size 189,255,150, pixel 0.96, shown at
step 1, values float32
Wrote mask_small_unit.mrc
> select add #3
113 models selected
> hide #!3 models
> select subtract #3
Nothing selected
> volume #4 level 0.02302
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> select add #4
2 models selected
> transparency sel 50
> volume resample #4 onGrid #1
Opened mask_small_unit.mrc resampled as #5, grid size 448,448,448, pixel 0.96,
shown at step 1, values float32
> select subtract #4
Nothing selected
> select add #5
2 models selected
> transparency sel 50
> volume sel showOutlineBox true
> save
> /Users/youngsirashin/Downloads/riboSPA/ribosome_apo/mask_small_unit_resample.mrc
> models #5
> close #4
> close
> open
> /Users/youngsirashin/Downloads/riboSPA/ribosome_apo/mask_small_unit_resample.mrc
Opened mask_small_unit_resample.mrc as #1, grid size 448,448,448, pixel 0.96,
shown at level 0.0417, step 2, values float32
> volume #1 step 1
> volume showOutlineBox true
> open
> /Users/youngsirashin/Downloads/riboSPA/ribosome_apo/cryosparc_P44_J164_008_volume_map.mrc
Opened cryosparc_P44_J164_008_volume_map.mrc as #2, grid size 448,448,448,
pixel 0.96, shown at level 0.0911, step 2, values float32
> volume #2 step 1
> volume showOutlineBox false
> volume showOutlineBox true
> volume showOutlineBox false
> volume showOutlineBox true
> select add #1
2 models selected
> transparency sel 50
> volume #2 level 0.07827
> volume #1 level 0.02388
> volume #1 level 0.02242
> volume #1 level 0.02222
> select subtract #1
Nothing selected
> hide #!1 models
> open /Users/youngsirashin/Downloads/cryosparc_P44_J175_mask.mrc
Opened cryosparc_P44_J175_mask.mrc as #3, grid size 448,448,448, pixel 0.96,
shown at level 1, step 2, values float32
> volume #3 step 1
> volume #3 level 0.3832
> transparency #2.1#3.1 50
> transparency #2.1#3.1 0
> select add #3
2 models selected
> transparency sel 50
> volume #3 level 0.4851
> volume #2 level 0.02401
> volume #2 level 0.08649
> volume #2 level 0.05525
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.02905
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select subtract #3
Nothing selected
> hide #!3 models
> hide #!2 models
> hide #!1 models
> close #3
> close
> open
> /Users/youngsirashin/Downloads/cryosparc_P44_J176_00118_volume_series/J176_class_00_00118_volume.mrc
Opened J176_class_00_00118_volume.mrc as #1, grid size 96,96,96, pixel 4.48,
shown at level 0.803, step 1, values float32
> open
> /Users/youngsirashin/Downloads/cryosparc_P44_J176_00118_volume_series/J176_class_04_00118_volume.mrc
Opened J176_class_04_00118_volume.mrc as #2, grid size 96,96,96, pixel 4.48,
shown at level 0.809, step 1, values float32
> open
> /Users/youngsirashin/Downloads/cryosparc_P44_J176_00118_volume_series/J176_class_03_00118_volume.mrc
Opened J176_class_03_00118_volume.mrc as #3, grid size 96,96,96, pixel 4.48,
shown at level 0.842, step 1, values float32
> open
> /Users/youngsirashin/Downloads/cryosparc_P44_J176_00118_volume_series/J176_class_02_00118_volume.mrc
Opened J176_class_02_00118_volume.mrc as #4, grid size 96,96,96, pixel 4.48,
shown at level 0.905, step 1, values float32
> open
> /Users/youngsirashin/Downloads/cryosparc_P44_J176_00118_volume_series/J176_class_01_00118_volume.mrc
Opened J176_class_01_00118_volume.mrc as #5, grid size 96,96,96, pixel 4.48,
shown at level 0.806, step 1, values float32
> volume #1 level 0.1639
> volume #2 level 0.2066
> volume #3 level 0.2246
> volume #4 level 0.2709
> volume #5 level 0.1972
> hide #!1 models
> hide #!4 models
> hide #!5 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!4 models
> hide #!3 models
> show #!1 models
> show #!2 models
> show #!5 models
> hide #!5 models
> hide #!2 models
> hide #!1 models
> show #!4 models
> show #!3 models
> ui tool show "Side View"
> 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 #!1 models
> show #!2 models
> show #!5 models
> hide #!5 models
> hide #!2 models
> hide #!1 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> show #!3 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> show #!2 models
> show #!5 models
> show #!3 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> hide #!5 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!3 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> show #!4 models
> hide #!4 models
> show #!3 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!2 models
> hide #!5 models
> volume #2 level 0.333
> volume #1 level 0.3759
> volume #3 level 0.3533
> volume #4 level 0.5629
> volume #5 level 0.4875
> volume #2 level 0.4561
> volume #3 level 0.492
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> volume #1 level 0.2422
> hide #!1 models
> open /Users/youngsirashin/Downloads/cryosparc_P44_J179_007_volume_map.mrc
Opened cryosparc_P44_J179_007_volume_map.mrc as #6, grid size 448,448,448,
pixel 0.96, shown at level 0.0866, step 2, values float32
> open /Users/youngsirashin/Downloads/cryosparc_P44_J177_003_volume_map.mrc
Opened cryosparc_P44_J177_003_volume_map.mrc as #7, grid size 448,448,448,
pixel 0.96, shown at level 0.0884, step 2, values float32
> volume #6 step 1
> volume #7 step 1
> hide #!6 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> show #!6 models
> hide #!7 models
> volume #6 level 0.07941
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!6 models
> show #!7 models
> hide #!6 models
> hide #!7 models
> show #!7 models
> show #!6 models
> hide #!7 models
> volume #6 level 0.1094
> show #!7 models
> hide #!6 models
> volume #7 level 0.122
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> show #!6 models
> select add #6
2 models selected
> select add #7
4 models selected
> close #6
> select subtract #7
Nothing selected
> select add #7
2 models selected
> close #7
===== 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
> open /Users/youngsirashin/Downloads/cryosparc_P44_J182_006_volume_map.mrc
Opened cryosparc_P44_J182_006_volume_map.mrc as #1, grid size 448,448,448,
pixel 0.96, shown at level 0.0876, step 2, values float32
> open /Users/youngsirashin/Downloads/cryosparc_P44_J183_005_volume_map.mrc
Opened cryosparc_P44_J183_005_volume_map.mrc as #2, grid size 448,448,448,
pixel 0.96, shown at level 0.0894, step 2, values float32
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: Z11C000BPCH/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 28 days, 11 hours
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
annotated-types: 0.7.0
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-ArtiaX: 0.6.0
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
geomdl: 5.3.1
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
pandas: 2.2.3
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
pyarrow: 19.0.1
pycollada: 0.8
pydantic: 2.11.3
pydantic_core: 2.33.1
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
starfile: 0.5.12
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-inspection: 0.4.0
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 6 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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