![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#16990 closed defect (duplicate)
Crash moving window between screens
| 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-15.3.1-x86_64-i386-64bit
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 0x00007ff858abcb00 (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, chimerax.surface._surface, 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.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, psutil._psutil_osx, psutil._psutil_posix, chimerax.segment._segment, lxml._elementpath, lxml.etree, chimerax.graphics._graphics, PIL._imagingmath (total: 57)
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{
"uptime" : 350000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 28856,
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"build" : "24D70",
"releaseType" : "User"
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"captureTime" : "2025-02-28 17:30:31.3854 +0000",
"codeSigningMonitor" : 0,
"incident" : "D710C6B9-A8CC-4CFB-9DBF-7234B5EF32C9",
"pid" : 73716,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-28 13:34:26.2126 +0000",
"procStartAbsTime" : 340250626418983,
"procExitAbsTime" : 354415438617733,
"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":"5FC18D3C-1898-50CA-92F1-24E40C066179","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "22AFD314-FBF5-45F4-A151-6BB76F846F16",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bootSessionUUID" : "8E8F0CDF-D54B-4FF3-ADAB-7455928495CF",
"wakeTime" : 20605,
"bridgeVersion" : {"build":"22P3051","train":"9.3"},
"sleepWakeUUID" : "64E6D44E-6BC5-4548-B49F-90D8EA88AE53",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4414275584\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1071c8000-1071cc000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x000000000000000d, 0x0000000000000000","rawCodes":[13,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"UNKNOWN_0xD at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":73716},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4414275584\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1071c8000-1071cc000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/cvetkom/Documents/chimera_sessions/20250228_post_polish_mix.cxs
Opened cryosparc_P17_J1528_010_volume_map.mrc as #1, grid size 588,588,588,
pixel 0.95, shown at level 0.0982, step 1, values float32
Opened J1741_class_00_00075_volume.mrc as #2, grid size 240,240,240, pixel
2.33, shown at level 0.296, step 1, values float32
Opened J1741_class_01_00075_volume.mrc as #3, grid size 240,240,240, pixel
2.33, shown at level 0.335, step 1, values float32
Opened J1741_class_02_00075_volume.mrc as #4, grid size 240,240,240, pixel
2.33, shown at level 0.377, step 1, values float32
Opened J1741_class_03_00075_volume.mrc as #5, grid size 240,240,240, pixel
2.33, shown at level 0.317, step 1, values float32
Opened J1741_class_04_00075_volume.mrc as #6, grid size 240,240,240, pixel
2.33, shown at level 0.466, step 1, values float32
Opened J1741_class_05_00075_volume.mrc as #7, grid size 240,240,240, pixel
2.33, shown at level 0.36, step 1, values float32
Opened J1741_class_06_00075_volume.mrc as #8, grid size 240,240,240, pixel
2.33, shown at level 0.295, step 1, values float32
Opened J1741_class_07_00075_volume.mrc as #9, grid size 240,240,240, pixel
2.33, shown at level 0.696, step 1, values float32
Opened J1745_class_00_00094_volume.mrc as #10, grid size 192,192,192, pixel
2.91, shown at level 0.451, step 1, values float32
Opened J1745_class_01_00094_volume.mrc as #11, grid size 192,192,192, pixel
2.91, shown at level 0.428, step 1, values float32
Opened J1745_class_02_00094_volume.mrc as #12, grid size 192,192,192, pixel
2.91, shown at level 0.526, step 1, values float32
Opened J1745_class_03_00094_volume.mrc as #13, grid size 192,192,192, pixel
2.91, shown at level 0.652, step 1, values float32
Opened J1745_class_04_00094_volume.mrc as #14, grid size 192,192,192, pixel
2.91, shown at level 15.3, step 1, values float32
Opened J1745_class_05_00094_volume.mrc as #15, grid size 192,192,192, pixel
2.91, shown at level 5.97, step 1, values float32
Opened cryosparc_P17_J1549_007_volume_map.mrc as #16, grid size 588,588,588,
pixel 0.95, shown at level 0.1, step 1, values float32
Opened J1757_class_00_00039_volume.mrc as #17, grid size 120,120,120, pixel
4.65, shown at level 0.238, step 1, values float32
Opened J1757_class_01_00039_volume.mrc as #18, grid size 120,120,120, pixel
4.65, shown at level 0.232, step 1, values float32
Opened J1757_class_02_00039_volume.mrc as #19, grid size 120,120,120, pixel
4.65, shown at level 0.283, step 1, values float32
Opened J1757_class_03_00039_volume.mrc as #20, grid size 120,120,120, pixel
4.65, shown at level 0.348, step 1, values float32
Opened J1757_class_04_00039_volume.mrc as #21, grid size 120,120,120, pixel
4.65, shown at level 0.221, step 1, values float32
Opened J1757_class_05_00039_volume.mrc as #22, grid size 120,120,120, pixel
4.65, shown at level 0.341, step 1, values float32
Opened J1757_class_06_00039_volume.mrc as #23, grid size 120,120,120, pixel
4.65, shown at level 0.176, step 1, values float32
Opened J1757_class_07_00039_volume.mrc as #24, grid size 120,120,120, pixel
4.65, shown at level 0.311, step 1, values float32
Opened J1567_class_00_00061_volume.mrc as #25, grid size 120,120,120, pixel
4.65, shown at level 0.377, step 1, values float32
Opened J1567_class_01_00061_volume.mrc as #26, grid size 120,120,120, pixel
4.65, shown at level 0.297, step 1, values float32
Opened J1567_class_02_00061_volume.mrc as #27, grid size 120,120,120, pixel
4.65, shown at level 0.186, step 1, values float32
Opened J1567_class_03_00061_volume.mrc as #28, grid size 120,120,120, pixel
4.65, shown at level 0.33, step 1, values float32
Opened J1567_class_04_00061_volume.mrc as #29, grid size 120,120,120, pixel
4.65, shown at level 0.403, step 1, values float32
Opened cryosparc_P17_J1757_volume_map_consensus.mrc as #30, grid size
120,120,120, pixel 4.65, shown at level 0.168, step 1, values float32
Opened volume sum as #31, grid size 120,120,120, pixel 4.65, shown at level
0.5, step 1, values float32
Opened cryosparc_P17_J1757_volume_map_NCP_for_mask.mrc as #34, grid size
120,120,120, pixel 4.65, shown at level 0.5, step 1, values float32
Opened cryosparc_P17_J1765_mask.mrc as #33, grid size 120,120,120, pixel 4.65,
shown at level 1, step 1, values float32
Opened run_it025_class001.mrc as #35, grid size 520,520,520, pixel 0.95, shown
at level 0.00223, step 1, values float32
Opened run_it025_class002.mrc as #36, grid size 520,520,520, pixel 0.95, shown
at level 0.00226, step 1, values float32
Opened run_it025_class003.mrc as #37, grid size 520,520,520, pixel 0.95, shown
at level 0.00248, step 1, values float32
Opened run_it025_class004.mrc as #38, grid size 520,520,520, pixel 0.95, shown
at level 0.0031, step 1, values float32
Opened run_it025_class001.mrc as #39, grid size 520,520,520, pixel 0.95, shown
at level 0.00395, step 1, values float32
Opened run_it025_class002.mrc as #40, grid size 520,520,520, pixel 0.95, shown
at level 0.0021, step 1, values float32
Opened run_it025_class003.mrc as #41, grid size 520,520,520, pixel 0.95, shown
at level 0.00258, step 1, values float32
Opened run_it025_class004.mrc as #42, grid size 520,520,520, pixel 0.95, shown
at level 0.00269, step 1, values float32
Opened run_it025_class005.mrc as #43, grid size 520,520,520, pixel 0.95, shown
at level 0.0027, step 1, values float32
Opened run_it025_class006.mrc as #44, grid size 520,520,520, pixel 0.95, shown
at level 0.00228, step 1, values float32
Opened run_it025_class001.mrc as #45, grid size 520,520,520, pixel 0.95, shown
at level 0.00293, step 1, values float32
Opened run_it025_class002.mrc as #46, grid size 520,520,520, pixel 0.95, shown
at level 0.00275, step 1, values float32
Opened run_it025_class003.mrc as #47, grid size 520,520,520, pixel 0.95, shown
at level 0.00243, step 1, values float32
Opened run_it025_class004.mrc as #48, grid size 520,520,520, pixel 0.95, shown
at level 0.00254, step 1, values float32
Opened run_it025_class005.mrc as #49, grid size 520,520,520, pixel 0.95, shown
at level 0.00296, step 1, values float32
Opened run_it025_class002.mrc as #50, grid size 520,520,520, pixel 0.95, shown
at level 0.00199, step 1, values float32
Opened run_it025_class006.mrc as #51, grid size 520,520,520, pixel 0.95, shown
at level 0.00268, step 1, values float32
Opened run_it025_class001.mrc as #52, grid size 520,520,520, pixel 0.95, shown
at level 0.00209, step 1, values float32
Opened run_it025_class004.mrc as #53, grid size 520,520,520, pixel 0.95, shown
at level 0.00208, step 1, values float32
Opened run_it025_class002.mrc as #54, grid size 520,520,520, pixel 0.95, shown
at level 0.00153, step 1, values float32
Opened cryosparc_P17_J1626_009_volume_map.mrc as #55, grid size 588,588,588,
pixel 0.95, shown at level 0.0718, step 1, values float32
Opened cryosparc_P17_J1598_volume_map.mrc as #56, grid size 520,520,520, pixel
0.95, shown at level 0.0358, step 1, values float32
Opened cryosparc_P17_J1600_mask.mrc as #57, grid size 520,520,520, pixel 0.95,
shown at level 0.799, step 1, values float32
Opened cryosparc_P17_J1762_008_volume_map.mrc as #58, grid size 588,588,588,
pixel 0.95, shown at level 0.078, step 1, values float32
Opened cryosparc_P17_J1759_008_volume_map.mrc as #59, grid size 588,588,588,
pixel 0.95, shown at level 0.12, step 1, values float32
Opened cryosparc_P17_J1760_007_volume_map.mrc as #60, grid size 588,588,588,
pixel 0.95, shown at level 0.13, step 1, values float32
Opened cryosparc_P17_J1761_008_volume_map.mrc as #61, grid size 588,588,588,
pixel 0.95, shown at level 0.14, step 1, values float32
Opened cryosparc_P17_J1748_008_volume_map.mrc as #62, grid size 588,588,588,
pixel 0.95, shown at level 0.09, step 1, values float32
Opened cryosparc_P17_J1749_007_volume_map.mrc as #63, grid size 588,588,588,
pixel 0.95, shown at level 0.09, step 1, values float32
Log from Fri Feb 28 11:55:25 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/cvetkom/Documents/chimera_sessions/20250227_ATPase_DNA_grip.cxs
Opened cryosparc_P17_J1528_010_volume_map.mrc as #1, grid size 588,588,588,
pixel 0.95, shown at level 0.0982, step 1, values float32
Opened J1741_class_00_00075_volume.mrc as #2, grid size 240,240,240, pixel
2.33, shown at level 0.296, step 1, values float32
Opened J1741_class_01_00075_volume.mrc as #3, grid size 240,240,240, pixel
2.33, shown at level 0.335, step 1, values float32
Opened J1741_class_02_00075_volume.mrc as #4, grid size 240,240,240, pixel
2.33, shown at level 0.377, step 1, values float32
Opened J1741_class_03_00075_volume.mrc as #5, grid size 240,240,240, pixel
2.33, shown at level 0.317, step 1, values float32
Opened J1741_class_04_00075_volume.mrc as #6, grid size 240,240,240, pixel
2.33, shown at level 0.466, step 1, values float32
Opened J1741_class_05_00075_volume.mrc as #7, grid size 240,240,240, pixel
2.33, shown at level 0.36, step 1, values float32
Opened J1741_class_06_00075_volume.mrc as #8, grid size 240,240,240, pixel
2.33, shown at level 0.295, step 1, values float32
Opened J1741_class_07_00075_volume.mrc as #9, grid size 240,240,240, pixel
2.33, shown at level 0.696, step 1, values float32
Opened J1745_class_00_00094_volume.mrc as #10, grid size 192,192,192, pixel
2.91, shown at level 0.451, step 1, values float32
Opened J1745_class_01_00094_volume.mrc as #11, grid size 192,192,192, pixel
2.91, shown at level 0.428, step 1, values float32
Opened J1745_class_02_00094_volume.mrc as #12, grid size 192,192,192, pixel
2.91, shown at level 0.526, step 1, values float32
Opened J1745_class_03_00094_volume.mrc as #13, grid size 192,192,192, pixel
2.91, shown at level 0.652, step 1, values float32
Opened J1745_class_04_00094_volume.mrc as #14, grid size 192,192,192, pixel
2.91, shown at level 15.3, step 1, values float32
Opened J1745_class_05_00094_volume.mrc as #15, grid size 192,192,192, pixel
2.91, shown at level 5.97, step 1, values float32
Log from Thu Feb 27 16:32:14 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/cvetkom/Documents/chimera_sessions/20250227_ATPase_DNA_grip.cxs
Opened cryosparc_P17_J1528_010_volume_map.mrc as #1, grid size 588,588,588,
pixel 0.95, shown at level 0.0982, step 1, values float32
Opened J1741_class_00_00075_volume.mrc as #2, grid size 240,240,240, pixel
2.33, shown at level 0.296, step 1, values float32
Opened J1741_class_01_00075_volume.mrc as #3, grid size 240,240,240, pixel
2.33, shown at level 0.335, step 1, values float32
Opened J1741_class_02_00075_volume.mrc as #4, grid size 240,240,240, pixel
2.33, shown at level 0.0857, step 1, values float32
Opened J1741_class_03_00075_volume.mrc as #5, grid size 240,240,240, pixel
2.33, shown at level 0.0673, step 1, values float32
Opened J1741_class_04_00075_volume.mrc as #6, grid size 240,240,240, pixel
2.33, shown at level 0.0974, step 1, values float32
Opened J1741_class_05_00075_volume.mrc as #7, grid size 240,240,240, pixel
2.33, shown at level 0.0705, step 1, values float32
Opened J1741_class_06_00075_volume.mrc as #8, grid size 240,240,240, pixel
2.33, shown at level 0.0727, step 1, values float32
Opened J1741_class_07_00075_volume.mrc as #9, grid size 240,240,240, pixel
2.33, shown at level 0.13, step 1, values float32
Opened J1745_class_00_00094_volume.mrc as #10, grid size 192,192,192, pixel
2.91, shown at level 0.103, step 1, values float32
Opened J1745_class_01_00094_volume.mrc as #11, grid size 192,192,192, pixel
2.91, shown at level 0.0878, step 1, values float32
Opened J1745_class_02_00094_volume.mrc as #12, grid size 192,192,192, pixel
2.91, shown at level 0.0973, step 1, values float32
Opened J1745_class_03_00094_volume.mrc as #13, grid size 192,192,192, pixel
2.91, shown at level 0.107, step 1, values float32
Opened J1745_class_04_00094_volume.mrc as #14, grid size 192,192,192, pixel
2.91, shown at level 13.4, step 1, values float32
Opened J1745_class_05_00094_volume.mrc as #15, grid size 192,192,192, pixel
2.91, shown at level 5.97, step 1, values float32
Log from Thu Feb 27 15:22:49 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class001.mrc
Opened Cl3D_j581_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
1.9, shown at level 0.0158, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class002.mrc
Opened Cl3D_j581_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
1.9, shown at level 0.0166, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class003.mrc
Opened Cl3D_j581_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class004.mrc
Opened Cl3D_j581_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
1.9, shown at level 0.0131, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class005.mrc
Opened Cl3D_j581_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class006.mrc
Opened Cl3D_j581_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class007.mrc
Opened Cl3D_j581_run_it025_class007.mrc as #7, grid size 294,294,294, pixel
1.9, shown at level 0.018, step 2, values float32
> tile
7 models tiled
> tile 7
Expected a models specifier or a keyword
> volume all step 1
> set bgColor white
> lighting soft
> lighting simple
> volume #1 level 0.01308
> volume #2 level 0.01493
> volume #2 level 0.0143
> volume #3 level 0.01453
> volume #4 level 0.01256
> volume #5 level 0.01323
> volume #6 level 0.01418
> save /Users/cvetkom/Desktop/image3.png supersample 3
> close #1-7
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1528_010_volume_map.mrc
Opened cryosparc_P17_J1528_010_volume_map.mrc as #1, grid size 588,588,588,
pixel 0.95, shown at level 0.0454, step 4, values float32
> volume #1 step 1
> volume #1 level 0.0845
> volume #1 level 0.1119
> volume #1 level 0.09818
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_00_00075_volume.mrc
Opened J1741_class_00_00075_volume.mrc as #2, grid size 240,240,240, pixel
2.33, shown at level 0.064, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_01_00075_volume.mrc
Opened J1741_class_01_00075_volume.mrc as #3, grid size 240,240,240, pixel
2.33, shown at level 0.0741, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_02_00075_volume.mrc
Opened J1741_class_02_00075_volume.mrc as #4, grid size 240,240,240, pixel
2.33, shown at level 0.0857, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_03_00075_volume.mrc
Opened J1741_class_03_00075_volume.mrc as #5, grid size 240,240,240, pixel
2.33, shown at level 0.0673, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_04_00075_volume.mrc
Opened J1741_class_04_00075_volume.mrc as #6, grid size 240,240,240, pixel
2.33, shown at level 0.0974, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_05_00075_volume.mrc
Opened J1741_class_05_00075_volume.mrc as #7, grid size 240,240,240, pixel
2.33, shown at level 0.0705, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_06_00075_volume.mrc
Opened J1741_class_06_00075_volume.mrc as #8, grid size 240,240,240, pixel
2.33, shown at level 0.0727, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_07_00075_volume.mrc
Opened J1741_class_07_00075_volume.mrc as #9, grid size 240,240,240, pixel
2.33, shown at level 0.13, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_00_00094_volume.mrc
Opened J1745_class_00_00094_volume.mrc as #10, grid size 192,192,192, pixel
2.91, shown at level 0.103, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_01_00094_volume.mrc
Opened J1745_class_01_00094_volume.mrc as #11, grid size 192,192,192, pixel
2.91, shown at level 0.0878, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_02_00094_volume.mrc
Opened J1745_class_02_00094_volume.mrc as #12, grid size 192,192,192, pixel
2.91, shown at level 0.0973, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_03_00094_volume.mrc
Opened J1745_class_03_00094_volume.mrc as #13, grid size 192,192,192, pixel
2.91, shown at level 0.107, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_04_00094_volume.mrc
Opened J1745_class_04_00094_volume.mrc as #14, grid size 192,192,192, pixel
2.91, shown at level 13.4, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_05_00094_volume.mrc
Opened J1745_class_05_00094_volume.mrc as #15, grid size 192,192,192, pixel
2.91, shown at level 5.97, step 1, values float32
> volume all step 1
> hide #!15 models
> hide #!14 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!5 models
> hide #!6 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> hide #!3 models
> show #!2 models
> volume #2 level 0.2493
> lighting soft
> lighting simple
> set bgColor black
> set bgColor transparent
> volume #2 level 0.2963
> volume #3 level 0.3843
> ui mousemode right zoom
> volume #3 level 0.3973
> volume #3 level 0.3348
> show #!2 models
> hide #!3 models
> save /Users/cvetkom/Documents/chimera_sessions/20250227_ATPase_DNA_grip.cxs
——— End of log from Thu Feb 27 15:22:49 2025 ———
opened ChimeraX session
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> volume #4 level 0.387
> volume #4 level 0.3774
> volume #5 level 0.3801
> volume #5 level 0.2856
> volume #5 level 0.3318
> volume #5 level 0.3486
> volume #6 level 0.418
> lighting soft
> lighting simple
> volume #6 level 0.4659
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> 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 #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> hide #!6 models
> show #!7 models
> volume #7 level 0.3604
> volume #8 level 0.2682
> volume #8 level 0.2344
> volume #8 level 0.2947
> volume #9 level 0.6956
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!5 models
> volume #5 level 0.2877
> volume #5 level 0.3171
> volume #10 level 0.4639
> volume #10 level 0.4515
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!10 models
> show #!11 models
> volume #11 level 0.4281
> volume #12 level 0.526
> volume #13 level 0.6189
> volume #13 level 0.6518
> volume #14 level 15.29
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!6 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> ui mousemode right zoom
> save /Users/cvetkom/Documents/chimera_sessions/20250227_ATPase_DNA_grip.cxs
——— End of log from Thu Feb 27 16:32:14 2025 ———
opened ChimeraX session
> hide #!6 models
> show #!6 models
> show #!2 models
> hide #!6 models
> show #!3 models
> hide #!2 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!3 models
> hide #!3 models
> show #!6 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!13 models
> show #!14 models
> show #!15 models
> hide #!15 models
> hide #!14 models
> hide #!13 models
> show #!13 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> 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
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!13 models
> show #!10 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!4 models
> show #!4 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!3 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> hide #!3 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1549_007_volume_map.mrc
Opened cryosparc_P17_J1549_007_volume_map.mrc as #16, grid size 588,588,588,
pixel 0.95, shown at level 0.0482, step 4, values float32
> volume #16 step 1
> volume #16 level 0.1686
> volume #16 level 0.1246
> volume #16 level 0.1093
> volume #16 level 0.1055
> volume #16 level 0.1
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_00_00039_volume.mrc
Opened J1757_class_00_00039_volume.mrc as #17, grid size 120,120,120, pixel
4.65, shown at level 0.123, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_01_00039_volume.mrc
Opened J1757_class_01_00039_volume.mrc as #18, grid size 120,120,120, pixel
4.65, shown at level 0.116, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_02_00039_volume.mrc
Opened J1757_class_02_00039_volume.mrc as #19, grid size 120,120,120, pixel
4.65, shown at level 0.113, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_03_00039_volume.mrc
Opened J1757_class_03_00039_volume.mrc as #20, grid size 120,120,120, pixel
4.65, shown at level 0.108, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_04_00039_volume.mrc
Opened J1757_class_04_00039_volume.mrc as #21, grid size 120,120,120, pixel
4.65, shown at level 0.105, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_05_00039_volume.mrc
Opened J1757_class_05_00039_volume.mrc as #22, grid size 120,120,120, pixel
4.65, shown at level 0.112, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_06_00039_volume.mrc
Opened J1757_class_06_00039_volume.mrc as #23, grid size 120,120,120, pixel
4.65, shown at level 0.107, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_07_00039_volume.mrc
Opened J1757_class_07_00039_volume.mrc as #24, grid size 120,120,120, pixel
4.65, shown at level 0.113, step 1, values float32
> hide #!18 models
> hide #!19 models
> hide #!20 models
> hide #!21 models
> hide #!22 models
> hide #!23 models
> hide #!24 models
> volume #17 level 0.1994
> volume #17 level 0.2377
> volume #18 level 0.2399
> volume #18 level 0.2839
> volume #18 level 0.2324
> volume #19 level 0.2826
> show #!17 models
> hide #!17 models
> volume #20 level 0.348
> volume #21 level 0.2206
> volume #22 level 0.3406
> volume #23 level 0.1761
> volume #24 level 0.3109
> show #!21 models
> hide #!21 models
> show #!20 models
> hide #!20 models
> hide #!24 models
> show #!22 models
> show #!23 models
> hide #!22 models
> show #!22 models
> show #!24 models
> hide #!23 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!20 models
> hide #!20 models
> show #!19 models
> show #!18 models
> show #!20 models
> show #!21 models
> show #!17 models
> hide #!22 models
> show #!22 models
> hide #!16 models
> show #!16 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> hide #!19 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #!21 models
> hide #!20 models
> hide #!24 models
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1567_00061_volume_series/J1567_class_00_00061_volume.mrc
Opened J1567_class_00_00061_volume.mrc as #25, grid size 120,120,120, pixel
4.65, shown at level 0.103, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1567_00061_volume_series/J1567_class_01_00061_volume.mrc
Opened J1567_class_01_00061_volume.mrc as #26, grid size 120,120,120, pixel
4.65, shown at level 0.107, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1567_00061_volume_series/J1567_class_02_00061_volume.mrc
Opened J1567_class_02_00061_volume.mrc as #27, grid size 120,120,120, pixel
4.65, shown at level 0.105, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1567_00061_volume_series/J1567_class_03_00061_volume.mrc
Opened J1567_class_03_00061_volume.mrc as #28, grid size 120,120,120, pixel
4.65, shown at level 0.116, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1567_00061_volume_series/J1567_class_04_00061_volume.mrc
Opened J1567_class_04_00061_volume.mrc as #29, grid size 120,120,120, pixel
4.65, shown at level 0.103, step 1, values float32
> hide #!22 models
> hide #!26 models
> hide #!27 models
> hide #!28 models
> hide #!29 models
> volume #25 level 0.2732
> volume #25 level 0.3769
> show #!26 models
> hide #!25 models
> volume #26 level 0.2965
> show #!25 models
> hide #!25 models
> hide #!26 models
> show #!27 models
> volume #27 level 0.1864
> volume #28 level 0.3188
> volume #28 level 0.3298
> volume #29 level 0.319
> volume #29 level 0.3859
> volume #29 level 0.4027
> open /Users/cvetkom/Downloads/cryosparc_P17_J1757_volume_map_consensus.mrc
Opened cryosparc_P17_J1757_volume_map_consensus.mrc as #30, grid size
120,120,120, pixel 4.65, shown at level 0.136, step 1, values float32
> hide #!29 models
> hide #!16 models
> show #!16 models
> volume #30 level 0.1682
> show #!17 models
> show #!18 models
> show #!19 models
> show #!20 models
> show #!21 models
> show #!22 models
> show #!23 models
> hide #!22 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> hide #!21 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!24 models
> hide #!24 models
> show #!24 models
> show #!23 models
> hide #!23 models
> show #!22 models
> show #!21 models
> hide #!22 models
> show #!22 models
> hide #!21 models
> show #!21 models
> show #!20 models
> show #!19 models
> show #!18 models
> show #!17 models
> volume add #17,18,19,20,21,22
Opened volume sum as #31, grid size 120,120,120, pixel 4.65, shown at step 1,
values float32
> hide #!24 models
> volume #31 level 0.5557
> volume #31 level 0.5367
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!20 models
> hide #!20 models
> show #!21 models
> hide #!21 models
> show #!22 models
> hide #!22 models
> show #!23 models
> hide #!23 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> volume add #17,18,19,20,21,22
Opened volume sum as #32, grid size 120,120,120, pixel 4.65, shown at step 1,
values float32
> close #32
> close #31
> show #!24 models
> hide #!24 models
> show #!24 models
> show #!23 models
> hide #!23 models
> show #!22 models
> show #!21 models
> hide #!21 models
> show #!21 models
> show #!20 models
> show #!19 models
> show #!18 models
> show #!17 models
> volume add #17,18,19,20,21,22,24
Opened volume sum as #31, grid size 120,120,120, pixel 4.65, shown at step 1,
values float32
> volume #31 level 0.585
> volume #31 level 0.5
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!23 models
> hide #!23 models
> show #!24 models
> show #!22 models
> show #!21 models
> show #!20 models
> show #!19 models
> show #!18 models
> show #!17 models
> hide #!24 models
> show #!24 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!21 models
> hide #!22 models
> hide #!20 models
> hide #!24 models
> hide #!16 models
> ui tool show "Segment Map"
Segmenting volume sum, density threshold 0.500000
Showing 17 region surfaces
75 watershed regions, grouped to 17 regions
Showing volume sum.seg - 17 regions, 17 surfaces
> select #32.1
1 model selected
Ungrouped to 2 regions
> select #32.18
1 model selected
Ungrouped to 2 regions
> select #32.1
1 model selected
Ungrouped to 2 regions
> select #32.18
1 model selected
Ungrouped to 2 regions
> select #32.1
1 model selected
Ungrouped to 2 regions
> select #32.23
1 model selected
Ungrouped to 2 regions
> select #32.1
1 model selected
Ungrouped to 2 regions
> select #32.18
1 model selected
Ungrouped to 2 regions
> select #32.1
1 model selected
Ungrouped to 2 regions
> select #32.18
1 model selected
Ungrouped to 2 regions
> select #32.28
1 model selected
Ungrouped to 2 regions
> select #32.18
1 model selected
Ungrouped to 0 regions
> select #32.18
1 model selected
Ungrouped to 0 regions
> select #32.20
1 model selected
Ungrouped to 2 regions
> select #32.28
1 model selected
Ungrouped to 2 regions
> select #32.25
1 model selected
Ungrouped to 2 regions
> show #!17 models
> show #!18 models
> show #!19 models
> hide #!19 models
> hide #!18 models
> hide #!17 models
> show #!16 models
> select #32.28
1 model selected
Ungrouped to 2 regions
> select #32.33
1 model selected
Ungrouped to 0 regions
> select #32.33
1 model selected
Ungrouped to 0 regions
> select #32.1
1 model selected
> select add #32.27
2 models selected
> select add #32.22
3 models selected
> select add #32.21
4 models selected
> select add #32.19
5 models selected
> select add #32.25
6 models selected
> select add #32.26
7 models selected
Grouped 7 regions
> select add #32.29
2 models selected
> select add #32.18
3 models selected
Grouped 3 regions
> hide #!31 models
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!32 models
> show #!32 models
> hide #!29 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!24 models
> show #!23 models
> hide #!23 models
> show #!22 models
> hide #!22 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!20 models
> hide #!20 models
> show #!19 models
> hide #!32 models
> show #!32 models
> hide #!19 models
> show #!18 models
> hide #!18 models
> show #!17 models
> hide #!17 models
Showing 24 region surfaces
> select #32.20
1 model selected
Ungrouped to 2 regions
> select #32.1
1 model selected
> select add #32.19
2 models selected
Grouped 2 regions
Opened volume sum_imasked as #33, grid size 120,120,120, pixel 4.65, shown at
step 1, values float32
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!33 models
> hide #!16 models
> show #!24 models
> show #!23 models
> hide #!23 models
> show #!22 models
> show #!21 models
> show #!20 models
> show #!19 models
> show #!18 models
> show #!17 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!24 models
> hide #!22 models
> hide #!21 models
> hide #!20 models
> hide #!19 models
> hide #!18 models
> hide #!17 models
Showing 24 region surfaces
> select #32.1
1 model selected
Ungrouped to 2 regions
> select #32.20
1 model selected
Ungrouped to 3 regions
> select #32.21
1 model selected
Ungrouped to 0 regions
> select #32.21
1 model selected
Ungrouped to 0 regions
> select #32.1
1 model selected
Ungrouped to 7 regions
> select #32.20
1 model selected
> select #32.21
1 model selected
Ungrouped to 0 regions
> select #32.20
1 model selected
Ungrouped to 2 regions
> select #32.1
1 model selected
Ungrouped to 2 regions
> select #32.20
1 model selected
Ungrouped to 2 regions
> select #32.37
1 model selected
Ungrouped to 0 regions
> select #32.37
1 model selected
Ungrouped to 0 regions
> select #32.21
1 model selected
Ungrouped to 0 regions
> hide #!32 models
> show #!33 models
> ui mousemode right "map eraser"
> volume erase #33 center 232.01,334.59,191.4 radius 158.31
> show #!16 models
> ui tool show "Map Filter"
> volume gaussian #33 sDev 1.21
Opened volume sum_imasked gaussian as #34, grid size 120,120,120, pixel 4.65,
shown at step 1, values float32
> close #34
> volume gaussian #33 sDev 2
Opened volume sum_imasked gaussian as #34, grid size 120,120,120, pixel 4.65,
shown at step 1, values float32
> close #33
> volume #34 level 0.5
> ui mousemode right zoom
> save
> /Users/cvetkom/Downloads/cryosparc_P17_J1757_volume_map_NCP_for_mask.mrc
> models #34
> open /Users/cvetkom/Downloads/cryosparc_P17_J1765_mask.mrc
Opened cryosparc_P17_J1765_mask.mrc as #33, grid size 120,120,120, pixel 4.65,
shown at level 1, step 1, values float32
> volume #33 level 1
> volume #33 color #ffffb27d
> volume #33 level 0.5139
> volume #33 level 1
> hide #!34 models
> hide #!33 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!20 models
> hide #!20 models
> show #!21 models
> hide #!21 models
> show #!22 models
> hide #!22 models
> show #!23 models
> hide #!23 models
> show #!24 models
> hide #!24 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1479/run_it025_class001.mrc
Opened run_it025_class001.mrc as #35, grid size 520,520,520, pixel 0.95, shown
at level 0.000296, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1479/run_it025_class002.mrc
Opened run_it025_class002.mrc as #36, grid size 520,520,520, pixel 0.95, shown
at level 0.000188, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1479/run_it025_class003.mrc
Opened run_it025_class003.mrc as #37, grid size 520,520,520, pixel 0.95, shown
at level 0.000293, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1479/run_it025_class004.mrc
Opened run_it025_class004.mrc as #38, grid size 520,520,520, pixel 0.95, shown
at level 0.000144, step 4, values float32
> hide #!16 models
> hide #!23 models
> volume all step 1
> volume #35 level 0.00175
> volume #35 level 0.001985
> volume #36 level 0.001419
> volume #36 level 0.002258
> volume #35 level 0.002231
> volume #37 level 0.001461
> volume #37 level 0.002052
> volume #38 level 0.003347
> volume #38 level 0.003643
> volume #38 level 0.003021
> volume #38 level 0.002881
> volume #38 level 0.003099
> volume #37 level 0.002479
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class001.mrc
Opened run_it025_class001.mrc as #39, grid size 520,520,520, pixel 0.95, shown
at level 0.000136, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class002.mrc
Opened run_it025_class002.mrc as #40, grid size 520,520,520, pixel 0.95, shown
at level 0.000382, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class003.mrc
Opened run_it025_class003.mrc as #41, grid size 520,520,520, pixel 0.95, shown
at level 0.000168, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class004.mrc
Opened run_it025_class004.mrc as #42, grid size 520,520,520, pixel 0.95, shown
at level 0.000171, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class005.mrc
Opened run_it025_class005.mrc as #43, grid size 520,520,520, pixel 0.95, shown
at level 0.000178, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class006.mrc
Opened run_it025_class006.mrc as #44, grid size 520,520,520, pixel 0.95, shown
at level 0.000256, step 4, values float32
> volume all step 1
> volume #39 level 0.003951
> volume #40 level 0.002104
> volume #41 level 0.000915
> volume #41 level 0.002577
> volume #42 level 0.002549
> volume #42 level 0.00269
> volume #43 level 0.001448
> volume #43 level 0.002702
> volume #44 level 0.002278
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1488/run_it025_class001.mrc
Opened run_it025_class001.mrc as #45, grid size 520,520,520, pixel 0.95, shown
at level 0.00022, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1488/run_it025_class002.mrc
Opened run_it025_class002.mrc as #46, grid size 520,520,520, pixel 0.95, shown
at level 0.000144, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1488/run_it025_class003.mrc
Opened run_it025_class003.mrc as #47, grid size 520,520,520, pixel 0.95, shown
at level 0.000205, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1488/run_it025_class004.mrc
Opened run_it025_class004.mrc as #48, grid size 520,520,520, pixel 0.95, shown
at level 0.00024, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1488/run_it025_class005.mrc
Opened run_it025_class005.mrc as #49, grid size 520,520,520, pixel 0.95, shown
at level 0.000309, step 4, values float32
> volume all step 1
> volume #45 level 0.002525
> volume #45 level 0.002927
> volume #46 level 0.002752
> volume #47 level 0.002429
> volume #48 level 0.002541
> volume #49 level 0.002957
> show #!49 models
> hide #!49 models
> show #!48 models
> hide #!48 models
> show #!47 models
> hide #!47 models
> show #!49 models
> hide #!49 models
> volume #46 level 0.002752
> hide #!36 models
> show #!36 models
> show #!38 models
> hide #!36 models
> hide #!38 models
> show #!36 models
> hide #!36 models
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1476/run_it025_class002.mrc
Opened run_it025_class002.mrc as #50, grid size 520,520,520, pixel 0.95, shown
at level 0.000201, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1476/run_it025_class006.mrc
Opened run_it025_class006.mrc as #51, grid size 520,520,520, pixel 0.95, shown
at level 0.000132, step 4, values float32
> volume all step 1
> volume #50 level 0.002655
> volume #50 level 0.002444
> volume #51 level 0.002852
> volume #50 level 0.001989
> volume #51 level 0.002679
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1475/run_it025_class001.mrc
Opened run_it025_class001.mrc as #52, grid size 520,520,520, pixel 0.95, shown
at level 0.000198, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1475/run_it025_class004.mrc
Opened run_it025_class004.mrc as #53, grid size 520,520,520, pixel 0.95, shown
at level 0.00011, step 4, values float32
> volume all step 1
> volume #52 level 0.00258
> volume #52 level 0.002524
> volume #53 level 0.002425
> volume #52 level 0.002093
> volume #53 level 0.002078
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1474/run_it025_class002.mrc
Opened run_it025_class002.mrc as #54, grid size 520,520,520, pixel 0.95, shown
at level 0.00018, step 4, values float32
> volume all step 1
> volume #54 level 0.002427
> volume #54 level 0.001525
> open /Users/cvetkom/Downloads/cryosparc_P17_J1626_009_volume_map.mrc
Opened cryosparc_P17_J1626_009_volume_map.mrc as #55, grid size 588,588,588,
pixel 0.95, shown at level 0.0688, step 4, values float32
> volume #55 step 1
> lighting soft
> volume #55 level 0.07079
> volume #55 level 0.09629
> volume #55 level 0.07181
> hide #!55 models
> show #!36 models
> lighting simple
[Repeated 1 time(s)]
> show #!42 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> hide #!42 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J1598_volume_map.mrc
Opened cryosparc_P17_J1598_volume_map.mrc as #56, grid size 520,520,520, pixel
0.95, shown at level 0.00289, step 4, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J1600_mask.mrc
Opened cryosparc_P17_J1600_mask.mrc as #57, grid size 520,520,520, pixel 0.95,
shown at level 0.799, step 4, values float32
> hide #!56 models
> show #!56 models
> volume #56 level 0.03581
> volume #56 step 1
> volume #57 color #ffb2ff82
> volume #57 step 1
> open /Users/cvetkom/Downloads/cryosparc_P17_J1762_008_volume_map.mrc
Opened cryosparc_P17_J1762_008_volume_map.mrc as #58, grid size 588,588,588,
pixel 0.95, shown at level 0.061, step 4, values float32
> volume #58 step 1
> volume #58 level 0.09631
> volume #58 level 0.07799
> lighting soft
> open /Users/cvetkom/Downloads/cryosparc_P17_J1759_008_volume_map.mrc
Opened cryosparc_P17_J1759_008_volume_map.mrc as #59, grid size 588,588,588,
pixel 0.95, shown at level 0.0499, step 4, values float32
> hide #!58 models
> volume #59 step 1
> volume #59 level 0.1244
> lighting simple
> volume #59 level 0.1026
> ui tool show "Side View"
> volume #59 level 0.1135
> lighting soft
> lighting full
> lighting simple
> open /Users/cvetkom/Downloads/cryosparc_P17_J1760_007_volume_map.mrc
Opened cryosparc_P17_J1760_007_volume_map.mrc as #60, grid size 588,588,588,
pixel 0.95, shown at level 0.047, step 4, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J1761_008_volume_map.mrc
Opened cryosparc_P17_J1761_008_volume_map.mrc as #61, grid size 588,588,588,
pixel 0.95, shown at level 0.0467, step 4, values float32
> volume #60 step 1
> volume #61 step 1
> volume #60 level 0.1558
> volume #60 level 0.1281
> volume #61 level 0.1442
> open /Users/cvetkom/Downloads/cryosparc_P17_J1748_008_volume_map.mrc
Opened cryosparc_P17_J1748_008_volume_map.mrc as #62, grid size 588,588,588,
pixel 0.95, shown at level 0.0485, step 4, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J1749_007_volume_map.mrc
Opened cryosparc_P17_J1749_007_volume_map.mrc as #63, grid size 588,588,588,
pixel 0.95, shown at level 0.048, step 4, values float32
> volume #62 step 2
> volume #62 step 1
> volume #63 step 1
> volume #62 level 0.1539
> volume #63 level 0.1446
> volume #62 color darkgrey
[Repeated 1 time(s)]
> volume #62 color #929292
> volume #62 color darkgrey
> volume #62 color #929292
> volume #60 level 0.13
> volume #62 level 0.13
> volume #62 level 0.135
> volume #62 level 0.14
> volume #61 level 0.14
> volume #63 level 0.14
> show #!59 models
> hide #!62 models
> volume #59 color #009193
> volume #59 level 0.13
> volume #59 level 0.12
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> hide #!59 models
> show #!62 models
> show #!63 models
> hide #!62 models
> show #!62 models
> hide #!63 models
> hide #!62 models
> show #!59 models
> show #!62 models
> hide #!62 models
> show #!63 models
> hide #!59 models
> show #!59 models
> hide #!63 models
> show #!63 models
> hide #!63 models
> hide #!59 models
> show #!60 models
> show #!62 models
> hide #!62 models
> show #!61 models
> hide #!61 models
> show #!61 models
> hide #!60 models
> show #!60 models
> hide #!61 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!60 models
> show #!60 models
> hide #!60 models
> hide #!62 models
> show #!61 models
> show #!63 models
> hide #!63 models
> show #!63 models
> hide #!63 models
> show #!63 models
> hide #!63 models
> show #!63 models
> hide #!63 models
> show #!63 models
> hide #!63 models
> hide #!61 models
> show #!62 models
> volume #63 level 0.1
> volume #63 level 0.06
> volume #63 level 0.08
> volume #63 level 0.085
> volume #63 level 0.09
> volume #62 level 0.09
> show #!63 models
> hide #!62 models
> show #!62 models
> hide #!63 models
> show #!63 models
> hide #!63 models
> show #!63 models
> hide #!63 models
> show #!63 models
> hide #!63 models
> hide #!62 models
> show #!62 models
> show #!63 models
> save /Users/cvetkom/Documents/chimera_sessions/20250228_post_polish_mix.cxs
——— End of log from Fri Feb 28 11:55:25 2025 ———
opened ChimeraX session
Showing volume sum.seg - 36 regions, 36 surfaces
> ui tool show "Side View"
> view
> hide #!32 models
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1773_00025_volume_series/J1773_class_00_00025_volume.mrc
Opened J1773_class_00_00025_volume.mrc as #64, grid size 240,240,240, pixel
2.33, shown at level 0.044, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1773_00025_volume_series/J1773_class_01_00025_volume.mrc
Opened J1773_class_01_00025_volume.mrc as #65, grid size 240,240,240, pixel
2.33, shown at level 0.0477, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1773_00025_volume_series/J1773_class_02_00025_volume.mrc
Opened J1773_class_02_00025_volume.mrc as #66, grid size 240,240,240, pixel
2.33, shown at level 0.0524, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1773_00025_volume_series/J1773_class_03_00025_volume.mrc
Opened J1773_class_03_00025_volume.mrc as #67, grid size 240,240,240, pixel
2.33, shown at level 0.0544, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1773_00025_volume_series/J1773_class_04_00025_volume.mrc
Opened J1773_class_04_00025_volume.mrc as #68, grid size 240,240,240, pixel
2.33, shown at level 0.0557, step 1, values float32
> volume #62 level 0.09192
> volume #64 level 0.04924
> volume #65 level 0.0645
> volume #67 level 0.06256
> volume #66 level 0.1228
> volume #66 level 0.1066
> volume #67 level 0.08881
> volume #68 level 0.1067
> volume #68 level 0.111
> volume #67 level 0.1008
> volume #67 level 0.1074
> volume #65 level 0.09522
> hide #!62 models
> show #!63 models
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1776_00024_volume_series/J1776_class_00_00024_volume.mrc
Opened J1776_class_00_00024_volume.mrc as #69, grid size 240,240,240, pixel
2.33, shown at level 0.0548, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1776_00024_volume_series/J1776_class_01_00024_volume.mrc
Opened J1776_class_01_00024_volume.mrc as #70, grid size 240,240,240, pixel
2.33, shown at level 0.0405, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1776_00024_volume_series/J1776_class_02_00024_volume.mrc
Opened J1776_class_02_00024_volume.mrc as #71, grid size 240,240,240, pixel
2.33, shown at level 0.0456, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1776_00024_volume_series/J1776_class_03_00024_volume.mrc
Opened J1776_class_03_00024_volume.mrc as #72, grid size 240,240,240, pixel
2.33, shown at level 0.0499, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1776_00024_volume_series/J1776_class_04_00024_volume.mrc
Opened J1776_class_04_00024_volume.mrc as #73, grid size 240,240,240, pixel
2.33, shown at level 0.0493, step 1, values float32
> volume #69 level 0.1114
> volume #69 level 0.115
> volume #70 level 0.1081
> volume #71 level 0.09332
> volume #72 level 0.1059
> volume #73 level 0.09531
> volume #73 level 0.09973
> volume #73 level 0.09807
> hide #!63 models
> show #!63 models
> hide #!63 models
> show #!16 models
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1766_00039_volume_series/J1766_class_00_00039_volume.mrc
Opened J1766_class_00_00039_volume.mrc as #74, grid size 120,120,120, pixel
4.65, shown at level 0.11, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1766_00039_volume_series/J1766_class_01_00039_volume.mrc
Opened J1766_class_01_00039_volume.mrc as #75, grid size 120,120,120, pixel
4.65, shown at level 0.121, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1766_00039_volume_series/J1766_class_02_00039_volume.mrc
Opened J1766_class_02_00039_volume.mrc as #76, grid size 120,120,120, pixel
4.65, shown at level 0.107, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1766_00039_volume_series/J1766_class_03_00039_volume.mrc
Opened J1766_class_03_00039_volume.mrc as #77, grid size 120,120,120, pixel
4.65, shown at level 0.0991, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1766_00039_volume_series/J1766_class_04_00039_volume.mrc
Opened J1766_class_04_00039_volume.mrc as #78, grid size 120,120,120, pixel
4.65, shown at level 0.0987, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1766_00039_volume_series/J1766_class_05_00039_volume.mrc
Opened J1766_class_05_00039_volume.mrc as #79, grid size 120,120,120, pixel
4.65, shown at level 0.105, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1766_00039_volume_series/J1766_class_06_00039_volume.mrc
Opened J1766_class_06_00039_volume.mrc as #80, grid size 120,120,120, pixel
4.65, shown at level 0.0997, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1766_00039_volume_series/J1766_class_07_00039_volume.mrc
Opened J1766_class_07_00039_volume.mrc as #81, grid size 120,120,120, pixel
4.65, shown at level 0.105, step 1, values float32
> hide #!74 models
> hide #!81 models
> show #!74 models
> volume #74 level 0.227
> volume #75 level 0.2227
> volume #75 level 0.2711
> volume #76 level 0.3119
> volume #77 level 0.3586
> volume #77 level 0.2851
> volume #78 level 0.2774
> volume #78 level 0.2938
> volume #79 level 0.3079
> volume #79 level 0.3271
> volume #80 level 0.3116
> volume #81 level 0.3244
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/cvetkom/Documents/chimera_sessions/20250228_post_polish_mix.cxs
Opened cryosparc_P17_J1528_010_volume_map.mrc as #1, grid size 588,588,588,
pixel 0.95, shown at level 0.0982, step 1, values float32
Opened J1741_class_00_00075_volume.mrc as #2, grid size 240,240,240, pixel
2.33, shown at level 0.296, step 1, values float32
Opened J1741_class_01_00075_volume.mrc as #3, grid size 240,240,240, pixel
2.33, shown at level 0.335, step 1, values float32
Opened J1741_class_02_00075_volume.mrc as #4, grid size 240,240,240, pixel
2.33, shown at level 0.377, step 1, values float32
Opened J1741_class_03_00075_volume.mrc as #5, grid size 240,240,240, pixel
2.33, shown at level 0.317, step 1, values float32
Opened J1741_class_04_00075_volume.mrc as #6, grid size 240,240,240, pixel
2.33, shown at level 0.466, step 1, values float32
Opened J1741_class_05_00075_volume.mrc as #7, grid size 240,240,240, pixel
2.33, shown at level 0.36, step 1, values float32
Opened J1741_class_06_00075_volume.mrc as #8, grid size 240,240,240, pixel
2.33, shown at level 0.295, step 1, values float32
Opened J1741_class_07_00075_volume.mrc as #9, grid size 240,240,240, pixel
2.33, shown at level 0.696, step 1, values float32
Opened J1745_class_00_00094_volume.mrc as #10, grid size 192,192,192, pixel
2.91, shown at level 0.451, step 1, values float32
Opened J1745_class_01_00094_volume.mrc as #11, grid size 192,192,192, pixel
2.91, shown at level 0.428, step 1, values float32
Opened J1745_class_02_00094_volume.mrc as #12, grid size 192,192,192, pixel
2.91, shown at level 0.526, step 1, values float32
Opened J1745_class_03_00094_volume.mrc as #13, grid size 192,192,192, pixel
2.91, shown at level 0.652, step 1, values float32
Opened J1745_class_04_00094_volume.mrc as #14, grid size 192,192,192, pixel
2.91, shown at level 15.3, step 1, values float32
Opened J1745_class_05_00094_volume.mrc as #15, grid size 192,192,192, pixel
2.91, shown at level 5.97, step 1, values float32
Opened cryosparc_P17_J1549_007_volume_map.mrc as #16, grid size 588,588,588,
pixel 0.95, shown at level 0.1, step 1, values float32
Opened J1757_class_00_00039_volume.mrc as #17, grid size 120,120,120, pixel
4.65, shown at level 0.238, step 1, values float32
Opened J1757_class_01_00039_volume.mrc as #18, grid size 120,120,120, pixel
4.65, shown at level 0.232, step 1, values float32
Opened J1757_class_02_00039_volume.mrc as #19, grid size 120,120,120, pixel
4.65, shown at level 0.283, step 1, values float32
Opened J1757_class_03_00039_volume.mrc as #20, grid size 120,120,120, pixel
4.65, shown at level 0.348, step 1, values float32
Opened J1757_class_04_00039_volume.mrc as #21, grid size 120,120,120, pixel
4.65, shown at level 0.221, step 1, values float32
Opened J1757_class_05_00039_volume.mrc as #22, grid size 120,120,120, pixel
4.65, shown at level 0.341, step 1, values float32
Opened J1757_class_06_00039_volume.mrc as #23, grid size 120,120,120, pixel
4.65, shown at level 0.176, step 1, values float32
Opened J1757_class_07_00039_volume.mrc as #24, grid size 120,120,120, pixel
4.65, shown at level 0.311, step 1, values float32
Opened J1567_class_00_00061_volume.mrc as #25, grid size 120,120,120, pixel
4.65, shown at level 0.377, step 1, values float32
Opened J1567_class_01_00061_volume.mrc as #26, grid size 120,120,120, pixel
4.65, shown at level 0.297, step 1, values float32
Opened J1567_class_02_00061_volume.mrc as #27, grid size 120,120,120, pixel
4.65, shown at level 0.186, step 1, values float32
Opened J1567_class_03_00061_volume.mrc as #28, grid size 120,120,120, pixel
4.65, shown at level 0.33, step 1, values float32
Opened J1567_class_04_00061_volume.mrc as #29, grid size 120,120,120, pixel
4.65, shown at level 0.403, step 1, values float32
Opened cryosparc_P17_J1757_volume_map_consensus.mrc as #30, grid size
120,120,120, pixel 4.65, shown at level 0.168, step 1, values float32
Opened volume sum as #31, grid size 120,120,120, pixel 4.65, shown at level
0.5, step 1, values float32
Opened cryosparc_P17_J1757_volume_map_NCP_for_mask.mrc as #34, grid size
120,120,120, pixel 4.65, shown at level 0.5, step 1, values float32
Opened cryosparc_P17_J1765_mask.mrc as #33, grid size 120,120,120, pixel 4.65,
shown at level 1, step 1, values float32
Opened run_it025_class001.mrc as #35, grid size 520,520,520, pixel 0.95, shown
at level 0.00223, step 1, values float32
Opened run_it025_class002.mrc as #36, grid size 520,520,520, pixel 0.95, shown
at level 0.00226, step 1, values float32
Opened run_it025_class003.mrc as #37, grid size 520,520,520, pixel 0.95, shown
at level 0.00248, step 1, values float32
Opened run_it025_class004.mrc as #38, grid size 520,520,520, pixel 0.95, shown
at level 0.0031, step 1, values float32
Opened run_it025_class001.mrc as #39, grid size 520,520,520, pixel 0.95, shown
at level 0.00395, step 1, values float32
Opened run_it025_class002.mrc as #40, grid size 520,520,520, pixel 0.95, shown
at level 0.0021, step 1, values float32
Opened run_it025_class003.mrc as #41, grid size 520,520,520, pixel 0.95, shown
at level 0.00258, step 1, values float32
Opened run_it025_class004.mrc as #42, grid size 520,520,520, pixel 0.95, shown
at level 0.00269, step 1, values float32
Opened run_it025_class005.mrc as #43, grid size 520,520,520, pixel 0.95, shown
at level 0.0027, step 1, values float32
Opened run_it025_class006.mrc as #44, grid size 520,520,520, pixel 0.95, shown
at level 0.00228, step 1, values float32
Opened run_it025_class001.mrc as #45, grid size 520,520,520, pixel 0.95, shown
at level 0.00293, step 1, values float32
Opened run_it025_class002.mrc as #46, grid size 520,520,520, pixel 0.95, shown
at level 0.00275, step 1, values float32
Opened run_it025_class003.mrc as #47, grid size 520,520,520, pixel 0.95, shown
at level 0.00243, step 1, values float32
Opened run_it025_class004.mrc as #48, grid size 520,520,520, pixel 0.95, shown
at level 0.00254, step 1, values float32
Opened run_it025_class005.mrc as #49, grid size 520,520,520, pixel 0.95, shown
at level 0.00296, step 1, values float32
Opened run_it025_class002.mrc as #50, grid size 520,520,520, pixel 0.95, shown
at level 0.00199, step 1, values float32
Opened run_it025_class006.mrc as #51, grid size 520,520,520, pixel 0.95, shown
at level 0.00268, step 1, values float32
Opened run_it025_class001.mrc as #52, grid size 520,520,520, pixel 0.95, shown
at level 0.00209, step 1, values float32
Opened run_it025_class004.mrc as #53, grid size 520,520,520, pixel 0.95, shown
at level 0.00208, step 1, values float32
Opened run_it025_class002.mrc as #54, grid size 520,520,520, pixel 0.95, shown
at level 0.00153, step 1, values float32
Opened cryosparc_P17_J1626_009_volume_map.mrc as #55, grid size 588,588,588,
pixel 0.95, shown at level 0.0718, step 1, values float32
Opened cryosparc_P17_J1598_volume_map.mrc as #56, grid size 520,520,520, pixel
0.95, shown at level 0.0358, step 1, values float32
Opened cryosparc_P17_J1600_mask.mrc as #57, grid size 520,520,520, pixel 0.95,
shown at level 0.799, step 1, values float32
Opened cryosparc_P17_J1762_008_volume_map.mrc as #58, grid size 588,588,588,
pixel 0.95, shown at level 0.078, step 1, values float32
Opened cryosparc_P17_J1759_008_volume_map.mrc as #59, grid size 588,588,588,
pixel 0.95, shown at level 0.12, step 1, values float32
Opened cryosparc_P17_J1760_007_volume_map.mrc as #60, grid size 588,588,588,
pixel 0.95, shown at level 0.13, step 1, values float32
Opened cryosparc_P17_J1761_008_volume_map.mrc as #61, grid size 588,588,588,
pixel 0.95, shown at level 0.14, step 1, values float32
Opened cryosparc_P17_J1748_008_volume_map.mrc as #62, grid size 588,588,588,
pixel 0.95, shown at level 0.09, step 1, values float32
Opened cryosparc_P17_J1749_007_volume_map.mrc as #63, grid size 588,588,588,
pixel 0.95, shown at level 0.09, step 1, values float32
Log from Fri Feb 28 11:55:25 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/cvetkom/Documents/chimera_sessions/20250227_ATPase_DNA_grip.cxs
Opened cryosparc_P17_J1528_010_volume_map.mrc as #1, grid size 588,588,588,
pixel 0.95, shown at level 0.0982, step 1, values float32
Opened J1741_class_00_00075_volume.mrc as #2, grid size 240,240,240, pixel
2.33, shown at level 0.296, step 1, values float32
Opened J1741_class_01_00075_volume.mrc as #3, grid size 240,240,240, pixel
2.33, shown at level 0.335, step 1, values float32
Opened J1741_class_02_00075_volume.mrc as #4, grid size 240,240,240, pixel
2.33, shown at level 0.377, step 1, values float32
Opened J1741_class_03_00075_volume.mrc as #5, grid size 240,240,240, pixel
2.33, shown at level 0.317, step 1, values float32
Opened J1741_class_04_00075_volume.mrc as #6, grid size 240,240,240, pixel
2.33, shown at level 0.466, step 1, values float32
Opened J1741_class_05_00075_volume.mrc as #7, grid size 240,240,240, pixel
2.33, shown at level 0.36, step 1, values float32
Opened J1741_class_06_00075_volume.mrc as #8, grid size 240,240,240, pixel
2.33, shown at level 0.295, step 1, values float32
Opened J1741_class_07_00075_volume.mrc as #9, grid size 240,240,240, pixel
2.33, shown at level 0.696, step 1, values float32
Opened J1745_class_00_00094_volume.mrc as #10, grid size 192,192,192, pixel
2.91, shown at level 0.451, step 1, values float32
Opened J1745_class_01_00094_volume.mrc as #11, grid size 192,192,192, pixel
2.91, shown at level 0.428, step 1, values float32
Opened J1745_class_02_00094_volume.mrc as #12, grid size 192,192,192, pixel
2.91, shown at level 0.526, step 1, values float32
Opened J1745_class_03_00094_volume.mrc as #13, grid size 192,192,192, pixel
2.91, shown at level 0.652, step 1, values float32
Opened J1745_class_04_00094_volume.mrc as #14, grid size 192,192,192, pixel
2.91, shown at level 15.3, step 1, values float32
Opened J1745_class_05_00094_volume.mrc as #15, grid size 192,192,192, pixel
2.91, shown at level 5.97, step 1, values float32
Log from Thu Feb 27 16:32:14 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/cvetkom/Documents/chimera_sessions/20250227_ATPase_DNA_grip.cxs
Opened cryosparc_P17_J1528_010_volume_map.mrc as #1, grid size 588,588,588,
pixel 0.95, shown at level 0.0982, step 1, values float32
Opened J1741_class_00_00075_volume.mrc as #2, grid size 240,240,240, pixel
2.33, shown at level 0.296, step 1, values float32
Opened J1741_class_01_00075_volume.mrc as #3, grid size 240,240,240, pixel
2.33, shown at level 0.335, step 1, values float32
Opened J1741_class_02_00075_volume.mrc as #4, grid size 240,240,240, pixel
2.33, shown at level 0.0857, step 1, values float32
Opened J1741_class_03_00075_volume.mrc as #5, grid size 240,240,240, pixel
2.33, shown at level 0.0673, step 1, values float32
Opened J1741_class_04_00075_volume.mrc as #6, grid size 240,240,240, pixel
2.33, shown at level 0.0974, step 1, values float32
Opened J1741_class_05_00075_volume.mrc as #7, grid size 240,240,240, pixel
2.33, shown at level 0.0705, step 1, values float32
Opened J1741_class_06_00075_volume.mrc as #8, grid size 240,240,240, pixel
2.33, shown at level 0.0727, step 1, values float32
Opened J1741_class_07_00075_volume.mrc as #9, grid size 240,240,240, pixel
2.33, shown at level 0.13, step 1, values float32
Opened J1745_class_00_00094_volume.mrc as #10, grid size 192,192,192, pixel
2.91, shown at level 0.103, step 1, values float32
Opened J1745_class_01_00094_volume.mrc as #11, grid size 192,192,192, pixel
2.91, shown at level 0.0878, step 1, values float32
Opened J1745_class_02_00094_volume.mrc as #12, grid size 192,192,192, pixel
2.91, shown at level 0.0973, step 1, values float32
Opened J1745_class_03_00094_volume.mrc as #13, grid size 192,192,192, pixel
2.91, shown at level 0.107, step 1, values float32
Opened J1745_class_04_00094_volume.mrc as #14, grid size 192,192,192, pixel
2.91, shown at level 13.4, step 1, values float32
Opened J1745_class_05_00094_volume.mrc as #15, grid size 192,192,192, pixel
2.91, shown at level 5.97, step 1, values float32
Log from Thu Feb 27 15:22:49 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class001.mrc
Opened Cl3D_j581_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
1.9, shown at level 0.0158, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class002.mrc
Opened Cl3D_j581_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
1.9, shown at level 0.0166, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class003.mrc
Opened Cl3D_j581_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
1.9, shown at level 0.0157, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class004.mrc
Opened Cl3D_j581_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
1.9, shown at level 0.0131, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class005.mrc
Opened Cl3D_j581_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
1.9, shown at level 0.013, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class006.mrc
Opened Cl3D_j581_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
1.9, shown at level 0.0154, step 2, values float32
> open
> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class007.mrc
Opened Cl3D_j581_run_it025_class007.mrc as #7, grid size 294,294,294, pixel
1.9, shown at level 0.018, step 2, values float32
> tile
7 models tiled
> tile 7
Expected a models specifier or a keyword
> volume all step 1
> set bgColor white
> lighting soft
> lighting simple
> volume #1 level 0.01308
> volume #2 level 0.01493
> volume #2 level 0.0143
> volume #3 level 0.01453
> volume #4 level 0.01256
> volume #5 level 0.01323
> volume #6 level 0.01418
> save /Users/cvetkom/Desktop/image3.png supersample 3
> close #1-7
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1528_010_volume_map.mrc
Opened cryosparc_P17_J1528_010_volume_map.mrc as #1, grid size 588,588,588,
pixel 0.95, shown at level 0.0454, step 4, values float32
> volume #1 step 1
> volume #1 level 0.0845
> volume #1 level 0.1119
> volume #1 level 0.09818
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_00_00075_volume.mrc
Opened J1741_class_00_00075_volume.mrc as #2, grid size 240,240,240, pixel
2.33, shown at level 0.064, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_01_00075_volume.mrc
Opened J1741_class_01_00075_volume.mrc as #3, grid size 240,240,240, pixel
2.33, shown at level 0.0741, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_02_00075_volume.mrc
Opened J1741_class_02_00075_volume.mrc as #4, grid size 240,240,240, pixel
2.33, shown at level 0.0857, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_03_00075_volume.mrc
Opened J1741_class_03_00075_volume.mrc as #5, grid size 240,240,240, pixel
2.33, shown at level 0.0673, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_04_00075_volume.mrc
Opened J1741_class_04_00075_volume.mrc as #6, grid size 240,240,240, pixel
2.33, shown at level 0.0974, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_05_00075_volume.mrc
Opened J1741_class_05_00075_volume.mrc as #7, grid size 240,240,240, pixel
2.33, shown at level 0.0705, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_06_00075_volume.mrc
Opened J1741_class_06_00075_volume.mrc as #8, grid size 240,240,240, pixel
2.33, shown at level 0.0727, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1741_00075_volume_series/J1741_class_07_00075_volume.mrc
Opened J1741_class_07_00075_volume.mrc as #9, grid size 240,240,240, pixel
2.33, shown at level 0.13, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_00_00094_volume.mrc
Opened J1745_class_00_00094_volume.mrc as #10, grid size 192,192,192, pixel
2.91, shown at level 0.103, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_01_00094_volume.mrc
Opened J1745_class_01_00094_volume.mrc as #11, grid size 192,192,192, pixel
2.91, shown at level 0.0878, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_02_00094_volume.mrc
Opened J1745_class_02_00094_volume.mrc as #12, grid size 192,192,192, pixel
2.91, shown at level 0.0973, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_03_00094_volume.mrc
Opened J1745_class_03_00094_volume.mrc as #13, grid size 192,192,192, pixel
2.91, shown at level 0.107, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_04_00094_volume.mrc
Opened J1745_class_04_00094_volume.mrc as #14, grid size 192,192,192, pixel
2.91, shown at level 13.4, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1745_00094_volume_series/J1745_class_05_00094_volume.mrc
Opened J1745_class_05_00094_volume.mrc as #15, grid size 192,192,192, pixel
2.91, shown at level 5.97, step 1, values float32
> volume all step 1
> hide #!15 models
> hide #!14 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!5 models
> hide #!6 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> hide #!3 models
> show #!2 models
> volume #2 level 0.2493
> lighting soft
> lighting simple
> set bgColor black
> set bgColor transparent
> volume #2 level 0.2963
> volume #3 level 0.3843
> ui mousemode right zoom
> volume #3 level 0.3973
> volume #3 level 0.3348
> show #!2 models
> hide #!3 models
> save /Users/cvetkom/Documents/chimera_sessions/20250227_ATPase_DNA_grip.cxs
——— End of log from Thu Feb 27 15:22:49 2025 ———
opened ChimeraX session
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> volume #4 level 0.387
> volume #4 level 0.3774
> volume #5 level 0.3801
> volume #5 level 0.2856
> volume #5 level 0.3318
> volume #5 level 0.3486
> volume #6 level 0.418
> lighting soft
> lighting simple
> volume #6 level 0.4659
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> 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 #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> hide #!6 models
> show #!7 models
> volume #7 level 0.3604
> volume #8 level 0.2682
> volume #8 level 0.2344
> volume #8 level 0.2947
> volume #9 level 0.6956
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!5 models
> volume #5 level 0.2877
> volume #5 level 0.3171
> volume #10 level 0.4639
> volume #10 level 0.4515
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!10 models
> show #!11 models
> volume #11 level 0.4281
> volume #12 level 0.526
> volume #13 level 0.6189
> volume #13 level 0.6518
> volume #14 level 15.29
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!6 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> ui mousemode right zoom
> save /Users/cvetkom/Documents/chimera_sessions/20250227_ATPase_DNA_grip.cxs
——— End of log from Thu Feb 27 16:32:14 2025 ———
opened ChimeraX session
> hide #!6 models
> show #!6 models
> show #!2 models
> hide #!6 models
> show #!3 models
> hide #!2 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!3 models
> hide #!3 models
> show #!6 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!13 models
> show #!14 models
> show #!15 models
> hide #!15 models
> hide #!14 models
> hide #!13 models
> show #!13 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> 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
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!13 models
> show #!10 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!4 models
> show #!4 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!3 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> hide #!3 models
> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1549_007_volume_map.mrc
Opened cryosparc_P17_J1549_007_volume_map.mrc as #16, grid size 588,588,588,
pixel 0.95, shown at level 0.0482, step 4, values float32
> volume #16 step 1
> volume #16 level 0.1686
> volume #16 level 0.1246
> volume #16 level 0.1093
> volume #16 level 0.1055
> volume #16 level 0.1
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_00_00039_volume.mrc
Opened J1757_class_00_00039_volume.mrc as #17, grid size 120,120,120, pixel
4.65, shown at level 0.123, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_01_00039_volume.mrc
Opened J1757_class_01_00039_volume.mrc as #18, grid size 120,120,120, pixel
4.65, shown at level 0.116, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_02_00039_volume.mrc
Opened J1757_class_02_00039_volume.mrc as #19, grid size 120,120,120, pixel
4.65, shown at level 0.113, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_03_00039_volume.mrc
Opened J1757_class_03_00039_volume.mrc as #20, grid size 120,120,120, pixel
4.65, shown at level 0.108, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_04_00039_volume.mrc
Opened J1757_class_04_00039_volume.mrc as #21, grid size 120,120,120, pixel
4.65, shown at level 0.105, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_05_00039_volume.mrc
Opened J1757_class_05_00039_volume.mrc as #22, grid size 120,120,120, pixel
4.65, shown at level 0.112, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_06_00039_volume.mrc
Opened J1757_class_06_00039_volume.mrc as #23, grid size 120,120,120, pixel
4.65, shown at level 0.107, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1757_00039_volume_series/J1757_class_07_00039_volume.mrc
Opened J1757_class_07_00039_volume.mrc as #24, grid size 120,120,120, pixel
4.65, shown at level 0.113, step 1, values float32
> hide #!18 models
> hide #!19 models
> hide #!20 models
> hide #!21 models
> hide #!22 models
> hide #!23 models
> hide #!24 models
> volume #17 level 0.1994
> volume #17 level 0.2377
> volume #18 level 0.2399
> volume #18 level 0.2839
> volume #18 level 0.2324
> volume #19 level 0.2826
> show #!17 models
> hide #!17 models
> volume #20 level 0.348
> volume #21 level 0.2206
> volume #22 level 0.3406
> volume #23 level 0.1761
> volume #24 level 0.3109
> show #!21 models
> hide #!21 models
> show #!20 models
> hide #!20 models
> hide #!24 models
> show #!22 models
> show #!23 models
> hide #!22 models
> show #!22 models
> show #!24 models
> hide #!23 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!20 models
> hide #!20 models
> show #!19 models
> show #!18 models
> show #!20 models
> show #!21 models
> show #!17 models
> hide #!22 models
> show #!22 models
> hide #!16 models
> show #!16 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> hide #!19 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #!21 models
> hide #!20 models
> hide #!24 models
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1567_00061_volume_series/J1567_class_00_00061_volume.mrc
Opened J1567_class_00_00061_volume.mrc as #25, grid size 120,120,120, pixel
4.65, shown at level 0.103, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1567_00061_volume_series/J1567_class_01_00061_volume.mrc
Opened J1567_class_01_00061_volume.mrc as #26, grid size 120,120,120, pixel
4.65, shown at level 0.107, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1567_00061_volume_series/J1567_class_02_00061_volume.mrc
Opened J1567_class_02_00061_volume.mrc as #27, grid size 120,120,120, pixel
4.65, shown at level 0.105, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1567_00061_volume_series/J1567_class_03_00061_volume.mrc
Opened J1567_class_03_00061_volume.mrc as #28, grid size 120,120,120, pixel
4.65, shown at level 0.116, step 1, values float32
> open
> /Users/cvetkom/Downloads/cryosparc_P17_J1567_00061_volume_series/J1567_class_04_00061_volume.mrc
Opened J1567_class_04_00061_volume.mrc as #29, grid size 120,120,120, pixel
4.65, shown at level 0.103, step 1, values float32
> hide #!22 models
> hide #!26 models
> hide #!27 models
> hide #!28 models
> hide #!29 models
> volume #25 level 0.2732
> volume #25 level 0.3769
> show #!26 models
> hide #!25 models
> volume #26 level 0.2965
> show #!25 models
> hide #!25 models
> hide #!26 models
> show #!27 models
> volume #27 level 0.1864
> volume #28 level 0.3188
> volume #28 level 0.3298
> volume #29 level 0.319
> volume #29 level 0.3859
> volume #29 level 0.4027
> open /Users/cvetkom/Downloads/cryosparc_P17_J1757_volume_map_consensus.mrc
Opened cryosparc_P17_J1757_volume_map_consensus.mrc as #30, grid size
120,120,120, pixel 4.65, shown at level 0.136, step 1, values float32
> hide #!29 models
> hide #!16 models
> show #!16 models
> volume #30 level 0.1682
> show #!17 models
> show #!18 models
> show #!19 models
> show #!20 models
> show #!21 models
> show #!22 models
> show #!23 models
> hide #!22 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> hide #!21 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!24 models
> hide #!24 models
> show #!24 models
> show #!23 models
> hide #!23 models
> show #!22 models
> show #!21 models
> hide #!22 models
> show #!22 models
> hide #!21 models
> show #!21 models
> show #!20 models
> show #!19 models
> show #!18 models
> show #!17 models
> volume add #17,18,19,20,21,22
Opened volume sum as #31, grid size 120,120,120, pixel 4.65, shown at step 1,
values float32
> hide #!24 models
> volume #31 level 0.5557
> volume #31 level 0.5367
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!20 models
> hide #!20 models
> show #!21 models
> hide #!21 models
> show #!22 models
> hide #!22 models
> show #!23 models
> hide #!23 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> volume add #17,18,19,20,21,22
Opened volume sum as #32, grid size 120,120,120, pixel 4.65, shown at step 1,
values float32
> close #32
> close #31
> show #!24 models
> hide #!24 models
> show #!24 models
> show #!23 models
> hide #!23 models
> show #!22 models
> show #!21 models
> hide #!21 models
> show #!21 models
> show #!20 models
> show #!19 models
> show #!18 models
> show #!17 models
> volume add #17,18,19,20,21,22,24
Opened volume sum as #31, grid size 120,120,120, pixel 4.65, shown at step 1,
values float32
> volume #31 level 0.585
> volume #31 level 0.5
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!23 models
> hide #!23 models
> show #!24 models
> show #!22 models
> show #!21 models
> show #!20 models
> show #!19 models
> show #!18 models
> show #!17 models
> hide #!24 models
> show #!24 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!21 models
> hide #!22 models
> hide #!20 models
> hide #!24 models
> hide #!16 models
> ui tool show "Segment Map"
Segmenting volume sum, density threshold 0.500000
Showing 17 region surfaces
75 watershed regions, grouped to 17 regions
Showing volume sum.seg - 17 regions, 17 surfaces
> select #32.1
1 model selected
Ungrouped to 2 regions
> select #32.18
1 model selected
Ungrouped to 2 regions
> select #32.1
1 model selected
Ungrouped to 2 regions
> select #32.18
1 model selected
Ungrouped to 2 regions
> select #32.1
1 model selected
Ungrouped to 2 regions
> select #32.23
1 model selected
Ungrouped to 2 regions
> select #32.1
1 model selected
Ungrouped to 2 regions
> select #32.18
1 model selected
Ungrouped to 2 regions
> select #32.1
1 model selected
Ungrouped to 2 regions
> select #32.18
1 model selected
Ungrouped to 2 regions
> select #32.28
1 model selected
Ungrouped to 2 regions
> select #32.18
1 model selected
Ungrouped to 0 regions
> select #32.18
1 model selected
Ungrouped to 0 regions
> select #32.20
1 model selected
Ungrouped to 2 regions
> select #32.28
1 model selected
Ungrouped to 2 regions
> select #32.25
1 model selected
Ungrouped to 2 regions
> show #!17 models
> show #!18 models
> show #!19 models
> hide #!19 models
> hide #!18 models
> hide #!17 models
> show #!16 models
> select #32.28
1 model selected
Ungrouped to 2 regions
> select #32.33
1 model selected
Ungrouped to 0 regions
> select #32.33
1 model selected
Ungrouped to 0 regions
> select #32.1
1 model selected
> select add #32.27
2 models selected
> select add #32.22
3 models selected
> select add #32.21
4 models selected
> select add #32.19
5 models selected
> select add #32.25
6 models selected
> select add #32.26
7 models selected
Grouped 7 regions
> select add #32.29
2 models selected
> select add #32.18
3 models selected
Grouped 3 regions
> hide #!31 models
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!32 models
> show #!32 models
> hide #!29 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!24 models
> show #!23 models
> hide #!23 models
> show #!22 models
> hide #!22 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!20 models
> hide #!20 models
> show #!19 models
> hide #!32 models
> show #!32 models
> hide #!19 models
> show #!18 models
> hide #!18 models
> show #!17 models
> hide #!17 models
Showing 24 region surfaces
> select #32.20
1 model selected
Ungrouped to 2 regions
> select #32.1
1 model selected
> select add #32.19
2 models selected
Grouped 2 regions
Opened volume sum_imasked as #33, grid size 120,120,120, pixel 4.65, shown at
step 1, values float32
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!33 models
> hide #!16 models
> show #!24 models
> show #!23 models
> hide #!23 models
> show #!22 models
> show #!21 models
> show #!20 models
> show #!19 models
> show #!18 models
> show #!17 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!24 models
> hide #!22 models
> hide #!21 models
> hide #!20 models
> hide #!19 models
> hide #!18 models
> hide #!17 models
Showing 24 region surfaces
> select #32.1
1 model selected
Ungrouped to 2 regions
> select #32.20
1 model selected
Ungrouped to 3 regions
> select #32.21
1 model selected
Ungrouped to 0 regions
> select #32.21
1 model selected
Ungrouped to 0 regions
> select #32.1
1 model selected
Ungrouped to 7 regions
> select #32.20
1 model selected
> select #32.21
1 model selected
Ungrouped to 0 regions
> select #32.20
1 model selected
Ungrouped to 2 regions
> select #32.1
1 model selected
Ungrouped to 2 regions
> select #32.20
1 model selected
Ungrouped to 2 regions
> select #32.37
1 model selected
Ungrouped to 0 regions
> select #32.37
1 model selected
Ungrouped to 0 regions
> select #32.21
1 model selected
Ungrouped to 0 regions
> hide #!32 models
> show #!33 models
> ui mousemode right "map eraser"
> volume erase #33 center 232.01,334.59,191.4 radius 158.31
> show #!16 models
> ui tool show "Map Filter"
> volume gaussian #33 sDev 1.21
Opened volume sum_imasked gaussian as #34, grid size 120,120,120, pixel 4.65,
shown at step 1, values float32
> close #34
> volume gaussian #33 sDev 2
Opened volume sum_imasked gaussian as #34, grid size 120,120,120, pixel 4.65,
shown at step 1, values float32
> close #33
> volume #34 level 0.5
> ui mousemode right zoom
> save
> /Users/cvetkom/Downloads/cryosparc_P17_J1757_volume_map_NCP_for_mask.mrc
> models #34
> open /Users/cvetkom/Downloads/cryosparc_P17_J1765_mask.mrc
Opened cryosparc_P17_J1765_mask.mrc as #33, grid size 120,120,120, pixel 4.65,
shown at level 1, step 1, values float32
> volume #33 level 1
> volume #33 color #ffffb27d
> volume #33 level 0.5139
> volume #33 level 1
> hide #!34 models
> hide #!33 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!20 models
> hide #!20 models
> show #!21 models
> hide #!21 models
> show #!22 models
> hide #!22 models
> show #!23 models
> hide #!23 models
> show #!24 models
> hide #!24 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1479/run_it025_class001.mrc
Opened run_it025_class001.mrc as #35, grid size 520,520,520, pixel 0.95, shown
at level 0.000296, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1479/run_it025_class002.mrc
Opened run_it025_class002.mrc as #36, grid size 520,520,520, pixel 0.95, shown
at level 0.000188, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1479/run_it025_class003.mrc
Opened run_it025_class003.mrc as #37, grid size 520,520,520, pixel 0.95, shown
at level 0.000293, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1479/run_it025_class004.mrc
Opened run_it025_class004.mrc as #38, grid size 520,520,520, pixel 0.95, shown
at level 0.000144, step 4, values float32
> hide #!16 models
> hide #!23 models
> volume all step 1
> volume #35 level 0.00175
> volume #35 level 0.001985
> volume #36 level 0.001419
> volume #36 level 0.002258
> volume #35 level 0.002231
> volume #37 level 0.001461
> volume #37 level 0.002052
> volume #38 level 0.003347
> volume #38 level 0.003643
> volume #38 level 0.003021
> volume #38 level 0.002881
> volume #38 level 0.003099
> volume #37 level 0.002479
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class001.mrc
Opened run_it025_class001.mrc as #39, grid size 520,520,520, pixel 0.95, shown
at level 0.000136, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class002.mrc
Opened run_it025_class002.mrc as #40, grid size 520,520,520, pixel 0.95, shown
at level 0.000382, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class003.mrc
Opened run_it025_class003.mrc as #41, grid size 520,520,520, pixel 0.95, shown
at level 0.000168, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class004.mrc
Opened run_it025_class004.mrc as #42, grid size 520,520,520, pixel 0.95, shown
at level 0.000171, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class005.mrc
Opened run_it025_class005.mrc as #43, grid size 520,520,520, pixel 0.95, shown
at level 0.000178, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1484/run_it025_class006.mrc
Opened run_it025_class006.mrc as #44, grid size 520,520,520, pixel 0.95, shown
at level 0.000256, step 4, values float32
> volume all step 1
> volume #39 level 0.003951
> volume #40 level 0.002104
> volume #41 level 0.000915
> volume #41 level 0.002577
> volume #42 level 0.002549
> volume #42 level 0.00269
> volume #43 level 0.001448
> volume #43 level 0.002702
> volume #44 level 0.002278
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1488/run_it025_class001.mrc
Opened run_it025_class001.mrc as #45, grid size 520,520,520, pixel 0.95, shown
at level 0.00022, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1488/run_it025_class002.mrc
Opened run_it025_class002.mrc as #46, grid size 520,520,520, pixel 0.95, shown
at level 0.000144, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1488/run_it025_class003.mrc
Opened run_it025_class003.mrc as #47, grid size 520,520,520, pixel 0.95, shown
at level 0.000205, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1488/run_it025_class004.mrc
Opened run_it025_class004.mrc as #48, grid size 520,520,520, pixel 0.95, shown
at level 0.00024, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1488/run_it025_class005.mrc
Opened run_it025_class005.mrc as #49, grid size 520,520,520, pixel 0.95, shown
at level 0.000309, step 4, values float32
> volume all step 1
> volume #45 level 0.002525
> volume #45 level 0.002927
> volume #46 level 0.002752
> volume #47 level 0.002429
> volume #48 level 0.002541
> volume #49 level 0.002957
> show #!49 models
> hide #!49 models
> show #!48 models
> hide #!48 models
> show #!47 models
> hide #!47 models
> show #!49 models
> hide #!49 models
> volume #46 level 0.002752
> hide #!36 models
> show #!36 models
> show #!38 models
> hide #!36 models
> hide #!38 models
> show #!36 models
> hide #!36 models
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1476/run_it025_class002.mrc
Opened run_it025_class002.mrc as #50, grid size 520,520,520, pixel 0.95, shown
at level 0.000201, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1476/run_it025_class006.mrc
Opened run_it025_class006.mrc as #51, grid size 520,520,520, pixel 0.95, shown
at level 0.000132, step 4, values float32
> volume all step 1
> volume #50 level 0.002655
> volume #50 level 0.002444
> volume #51 level 0.002852
> volume #50 level 0.001989
> volume #51 level 0.002679
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1475/run_it025_class001.mrc
Opened run_it025_class001.mrc as #52, grid size 520,520,520, pixel 0.95, shown
at level 0.000198, step 4, values float32
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1475/run_it025_class004.mrc
Opened run_it025_class004.mrc as #53, grid size 520,520,520, pixel 0.95, shown
at level 0.00011, step 4, values float32
> volume all step 1
> volume #52 level 0.00258
> volume #52 level 0.002524
> volume #53 level 0.002425
> volume #52 level 0.002093
> volume #53 level 0.002078
> open /Volumes/lab-
> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job1474/run_it025_class002.mrc
Opened run_it025_class002.mrc as #54, grid size 520,520,520, pixel 0.95, shown
at level 0.00018, step 4, values float32
> volume all step 1
> volume #54 level 0.002427
> volume #54 level 0.001525
> open /Users/cvetkom/Downloads/cryosparc_P17_J1626_009_volume_map.mrc
Opened cryosparc_P17_J1626_009_volume_map.mrc as #55, grid size 588,588,588,
pixel 0.95, shown at level 0.0688, step 4, values float32
> volume #55 step 1
> lighting soft
> volume #55 level 0.07079
> volume #55 level 0.09629
> volume #55 level 0.07181
> hide #!55 models
> show #!36 models
> lighting simple
[Repeated 1 time(s)]
> show #!42 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> hide #!42 models
> open /Users/cvetkom/Downloads/cryosparc_P17_J1598_volume_map.mrc
Opened cryosparc_P17_J1598_volume_map.mrc as #56, grid size 520,520,520, pixel
0.95, shown at level 0.00289, step 4, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J1600_mask.mrc
Opened cryosparc_P17_J1600_mask.mrc as #57, grid size 520,520,520, pixel 0.95,
shown at level 0.799, step 4, values float32
> hide #!56 models
> show #!56 models
> volume #56 level 0.03581
> volume #56 step 1
> volume #57 color #ffb2ff82
> volume #57 step 1
> open /Users/cvetkom/Downloads/cryosparc_P17_J1762_008_volume_map.mrc
Opened cryosparc_P17_J1762_008_volume_map.mrc as #58, grid size 588,588,588,
pixel 0.95, shown at level 0.061, step 4, values float32
> volume #58 step 1
> volume #58 level 0.09631
> volume #58 level 0.07799
> lighting soft
> open /Users/cvetkom/Downloads/cryosparc_P17_J1759_008_volume_map.mrc
Opened cryosparc_P17_J1759_008_volume_map.mrc as #59, grid size 588,588,588,
pixel 0.95, shown at level 0.0499, step 4, values float32
> hide #!58 models
> volume #59 step 1
> volume #59 level 0.1244
> lighting simple
> volume #59 level 0.1026
> ui tool show "Side View"
> volume #59 level 0.1135
> lighting soft
> lighting full
> lighting simple
> open /Users/cvetkom/Downloads/cryosparc_P17_J1760_007_volume_map.mrc
Opened cryosparc_P17_J1760_007_volume_map.mrc as #60, grid size 588,588,588,
pixel 0.95, shown at level 0.047, step 4, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J1761_008_volume_map.mrc
Opened cryosparc_P17_J1761_008_volume_map.mrc as #61, grid size 588,588,588,
pixel 0.95, shown at level 0.0467, step 4, values float32
> volume #60 step 1
> volume #61 step 1
> volume #60 level 0.1558
> volume #60 level 0.1281
> volume #61 level 0.1442
> open /Users/cvetkom/Downloads/cryosparc_P17_J1748_008_volume_map.mrc
Opened cryosparc_P17_J1748_008_volume_map.mrc as #62, grid size 588,588,588,
pixel 0.95, shown at level 0.0485, step 4, values float32
> open /Users/cvetkom/Downloads/cryosparc_P17_J1749_007_volume_map.mrc
Opened cryosparc_P17_J1749_007_volume_map.mrc as #63, grid size 588,588,588,
pixel 0.95, shown at level 0.048, step 4, values float32
> volume #62 step 2
> volume #62 step 1
> volume #63 step 1
> volume #62 level 0.1539
> volume #63 level 0.1446
> volume #62 color darkgrey
[Repeated 1 time(s)]
> volume #62 color #929292
> volume #62 color darkgrey
> volume #62 color #929292
> volume #60 level 0.13
> volume #62 level 0.13
> volume #62 level 0.135
> volume #62 level 0.14
> volume #61 level 0.14
> volume #63 level 0.14
> show #!59 models
> hide #!62 models
> volume #59 color #009193
> volume #59 level 0.13
> volume #59 level 0.12
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> hide #!59 models
> show #!62 models
> show #!63 models
> hide #!62 models
> show #!62 models
> hide #!63 models
> hide #!62 models
> show #!59 models
> show #!62 models
> hide #!62 models
> show #!63 models
> hide #!59 models
> show #!59 models
> hide #!63 models
> show #!63 models
> hide #!63 models
> hide #!59 models
> show #!60 models
> show #!62 models
> hide #!62 models
> show #!61 models
> hide #!61 models
> show #!61 models
> hide #!60 models
> show #!60 models
> hide #!61 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!60 models
> show #!60 models
> hide #!60 models
> hide #!62 models
> show #!61 models
> show #!63 models
> hide #!63 models
> show #!63 models
> hide #!63 models
> show #!63 models
> hide #!63 models
> show #!63 models
> hide #!63 models
> show #!63 models
> hide #!63 models
> hide #!61 models
> show #!62 models
> volume #63 level 0.1
> volume #63 level 0.06
> volume #63 level 0.08
> volume #63 level 0.085
> volume #63 level 0.09
> volume #62 level 0.09
> show #!63 models
> hide #!62 models
> show #!62 models
> hide #!63 models
> show #!63 models
> hide #!63 models
> show #!63 models
> hide #!63 models
> show #!63 models
> hide #!63 models
> hide #!62 models
> show #!62 models
> show #!63 models
> save /Users/cvetkom/Documents/chimera_sessions/20250228_post_polish_mix.cxs
——— End of log from Fri Feb 28 11:55:25 2025 ———
opened ChimeraX session
Showing volume sum.seg - 36 regions, 36 surfaces
OpenGL version: 4.1 ATI-6.1.13
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
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: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2069.80.3.0.0 (iBridge: 22.16.13051.0.0,0)
OS Loader Version: 582~3311
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 6 days, 8 hours, 28 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2415:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 7MT016923MAL
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 8 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
The crash report panel you used to report this bug explained what we know about it
"This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX."
The ChimeraX daily build now uses a newer Qt version 6.8.2 and we have not seen these Mac multi-display crashes in 6.8.2 yet, so it may be fixed. You can try the daily build if interested.