![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 weeks ago
Closed 4 weeks ago
#19112 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.6-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001f468e0c0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 59)
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{
"uptime" : 930000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac13,1",
"coalitionID" : 13033,
"osVersion" : {
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"build" : "24G84",
"releaseType" : "User"
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"captureTime" : "2025-10-12 10:51:43.0871 -0400",
"codeSigningMonitor" : 1,
"incident" : "AD50BB20-611C-4D24-BA37-A7CBEDF640D9",
"pid" : 29427,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-10-12 08:59:22.3513 -0400",
"procStartAbsTime" : 22214897104448,
"procExitAbsTime" : 22376671137401,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"F5319B2A-99FE-5DFC-A089-2820E639FE6C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "216F332D-5F24-FDDF-13EF-8C5782DCD983",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "24D8D3A7-C4F6-4C7F-A280-CCB2E8DEEDD6",
"sip" : "enabled",
"vmRegionInfo" : "0x2906450e9138 is not in any region. Bytes after previous region: 44625868788025 Bytes before following region: 60446211141320\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00002906450e9138","rawCodes":[1,45106905125176],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00002906450e9138"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":29427},
"vmregioninfo" : "0x2906450e9138 is not in any region. Bytes after previous region: 44625868788025 Bytes before following region: 60446211141320\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Application/Application
> Japan/To_Japan/To Osaka/Document/Work with
> Jenny/Presentations/HP_Movie/From-Lab-laptop/For-Osaka-Movie.cxs"
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Opened FlgV_monomer.mrc copy gaussian as #259.21, grid size 160,160,160, pixel
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Opened Cage_1unit.mrc copy as #85, grid size 240,240,240, pixel 2.1, shown at
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Opened Unknown_near_PflA.mrc copy as #25, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #26, grid size 240,240,240, pixel 2.1,
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Opened Unknown_near_PflA.mrc copy as #27, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #28, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #29, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #30, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #31, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #32, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #33, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #34, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #35, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #36, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #37, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Outer-ring-near-PL.mrc as #97, grid size 240,240,240, pixel 4.3, shown
at level 0.0141, step 1, values float32
Opened Hp-C1-4.296A-msk.mrc as #1, grid size 220,220,220, pixel 4.3, shown at
level 0.000693, step 1, values float32
Opened Top-middle.mrc as #7, grid size 240,240,240, pixel 2.1, shown at level
0.000178, step 1, values float32
Opened Top-middle.mrc copy as #8, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #9, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #10, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #11, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #12, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #13, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #14, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #15, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #17, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #18, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #19, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #38, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #39, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #40, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #41, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #42, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #43, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #44, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Log from Fri Oct 10 16:39:33 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shoichi/Desktop/For-Osaka.cxs
Opened 0838-bottom.mrc as #16, grid size 240,240,240, pixel 4.3, shown at
level 0.0144, step 1, values float32
Opened Disk.mrc gaussian as #312, grid size 250,250,250, pixel 4.3, shown at
level 0.0186, step 1, values float32
Opened IM-old-maps.mrc gaussian as #313, grid size 120,120,120, pixel 8.8,
shown at level 0.0702, step 1, values float32
Opened OM.mrc copy gaussian as #316, grid size 240,240,240, pixel 4.3, shown
at level 0.0323, step 1, values float32
Opened New_IM_Bottom2.mrc gaussian as #484, grid size 256,256,256, pixel 2.1,
shown at level 0.0072, step 1, values float32
Opened 0838-disk.mrc gaussian as #513, grid size 240,240,240, pixel 4.3, shown
at level 0.0153, step 1, values float32
Opened 0838-top.mrc gaussian as #514, grid size 240,240,240, pixel 4.3, shown
at level 0.00979, step 1, values float32
Opened FlgV_monomer.mrc gaussian as #259.1, grid size 160,160,160, pixel 4.2,
shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.2, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.3, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.4, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.5, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.6, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.7, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.8, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.9, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.10, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.11, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.12, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.13, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.14, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.15, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.16, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.17, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.18, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.19, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.20, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.21, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened Cage_1unit.mrc copy as #85, grid size 240,240,240, pixel 2.1, shown at
level 0.0446, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #20, grid size 240,240,240, pixel 2.1,
shown at level 0.15, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #21, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #22, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #23, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #24, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #25, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #26, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #28, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #29, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #30, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #31, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #32, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #33, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #34, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #35, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #36, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #37, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Outer-ring-near-PL.mrc as #97, grid size 240,240,240, pixel 4.3, shown
at level 0.0141, step 1, values float32
Opened Hp-C1-4.296A-msk.mrc as #1, grid size 220,220,220, pixel 4.3, shown at
level 0.000693, step 1, values float32
Opened Top-middle.mrc as #7, grid size 240,240,240, pixel 2.1, shown at level
0.000178, step 1, values float32
Opened Top-middle.mrc copy as #8, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #9, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #10, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #11, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #12, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #13, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #14, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #15, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #17, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #18, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #19, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #38, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #39, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #40, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #41, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #42, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #43, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #44, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Log from Tue Oct 7 16:41:24 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Poster/2025_MB/All-
> model_HP_for_Topcage_Poster.cxs"
Opened 0838-bottom.mrc as #16, grid size 240,240,240, pixel 4.3, shown at
level 0.0144, step 1, values float32
Opened Disk.mrc gaussian as #312, grid size 250,250,250, pixel 4.3, shown at
level 0.0186, step 1, values float32
Opened IM-old-maps.mrc gaussian as #313, grid size 120,120,120, pixel 8.8,
shown at level 0.0702, step 1, values float32
Opened OM.mrc copy gaussian as #316, grid size 240,240,240, pixel 4.3, shown
at level 0.0323, step 1, values float32
Opened New_IM_Bottom2.mrc gaussian as #484, grid size 256,256,256, pixel 2.1,
shown at level 0.0072, step 1, values float32
Opened 0838-disk.mrc gaussian as #513, grid size 240,240,240, pixel 4.3, shown
at level 0.0153, step 1, values float32
Opened 0838-top.mrc gaussian as #514, grid size 240,240,240, pixel 4.3, shown
at level 0.00979, step 1, values float32
Opened FlgV_monomer.mrc gaussian as #259.1, grid size 160,160,160, pixel 4.2,
shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.2, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.3, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.4, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.5, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.6, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.7, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.8, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.9, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.10, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.11, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.12, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.13, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.14, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.15, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.16, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.17, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.18, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.19, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.20, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.21, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened Cage_1unit.mrc copy as #85, grid size 240,240,240, pixel 2.1, shown at
level 0.0446, step 1, values float32
Opened Top-cage.mrc as #71, grid size 240,240,240, pixel 2.1, shown at level
0.143, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #20, grid size 240,240,240, pixel 2.1,
shown at level 0.15, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #21, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #22, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #23, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #24, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #25, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #26, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #28, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #29, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #30, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #31, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #32, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #33, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #34, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #35, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #36, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #37, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Top-cage.mrc copy as #58, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #59, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #73, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #74, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #75, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #76, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #77, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #78, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #79, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #80, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #81, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #82, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #83, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #84, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #86, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #122, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Outer-ring-near-PL.mrc as #97, grid size 240,240,240, pixel 4.3, shown
at level 0.0141, step 1, values float32
Opened Hp-C1-4.296A-msk.mrc as #1, grid size 220,220,220, pixel 4.3, shown at
level 0.000693, step 1, values float32
Opened Top-middle.mrc as #7, grid size 240,240,240, pixel 2.1, shown at level
0.000178, step 1, values float32
Opened Top-middle.mrc copy as #8, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #9, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #10, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #11, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #12, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #13, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #14, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #15, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #17, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #18, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #19, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #38, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #39, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #40, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #41, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #42, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #43, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Opened Top-middle.mrc copy as #44, grid size 240,240,240, pixel 2.1, shown at
level 0.000178, step 1, values float32
Log from Mon Sep 8 16:24:57 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shoichi/Desktop/All-model_HP_for_Topcage.cxs
Opened 0838-bottom.mrc as #16, grid size 240,240,240, pixel 4.3, shown at
level 0.0144, step 1, values float32
Opened Hpwt-L0.08-Global-Rod-no-MS.mrc as #113, grid size 240,240,240, pixel
4.3, shown at level 0.0151, step 1, values float32
Opened Disk.mrc gaussian as #312, grid size 250,250,250, pixel 4.3, shown at
level 0.0186, step 1, values float32
Opened IM-old-maps.mrc gaussian as #313, grid size 120,120,120, pixel 8.8,
shown at level 0.0702, step 1, values float32
Opened OM.mrc copy gaussian as #316, grid size 240,240,240, pixel 4.3, shown
at level 0.0323, step 1, values float32
Opened New_FliF.mrc gaussian as #479, grid size 256,256,256, pixel 2.1, shown
at level 0.0115, step 1, values float32
Opened New_FlhA.mrc gaussian as #481, grid size 256,256,256, pixel 2.1, shown
at level 0.00316, step 1, values float32
Opened PflBC13.mrc as #482, grid size 256,256,256, pixel 2.1, shown at level
0.00615, step 1, values float32
Opened New_IM_Bottom2.mrc as #483, grid size 256,256,256, pixel 2.1, shown at
level 0.0072, step 1, values float32
Opened New_IM_Bottom2.mrc gaussian as #484, grid size 256,256,256, pixel 2.1,
shown at level 0.0072, step 1, values float32
Opened PflB_C13.mrc as #507, grid size 256,256,256, pixel 2.1, shown at level
0.0015, step 1, values float32
Opened PflB_monomer.mrc as #508, grid size 256,256,256, pixel 2.1, shown at
level 0.00116, step 1, values float32
Opened Unknown-ring.mrc as #509, grid size 256,256,256, pixel 2.1, shown at
level 0.000608, step 1, values float32
Opened PflB_C13.mrc gaussian as #510, grid size 256,256,256, pixel 2.1, shown
at level 0.00108, step 1, values float32
Opened PflB_monomer.mrc gaussian as #511, grid size 256,256,256, pixel 2.1,
shown at level 0.000387, step 1, values float32
Opened Unknown-ring.mrc gaussian as #512, grid size 256,256,256, pixel 2.1,
shown at level 0.00109, step 1, values float32
Opened 0838-disk.mrc gaussian as #513, grid size 240,240,240, pixel 4.3, shown
at level 0.0153, step 1, values float32
Opened 0838-top.mrc gaussian as #514, grid size 240,240,240, pixel 4.3, shown
at level 0.00979, step 1, values float32
Opened FlgV_monomer.mrc gaussian as #259.1, grid size 160,160,160, pixel 4.2,
shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.2, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.3, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.4, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.5, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.6, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.7, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.8, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.9, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.10, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.11, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.12, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.13, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.14, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.15, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.16, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.17, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.18, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.19, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.20, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.21, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgY-with-joints.mrc as #93, grid size 220,220,220, pixel 4.3, shown at
level 2.81, step 1, values float32
Opened Cage_1unit.mrc copy as #85, grid size 240,240,240, pixel 2.1, shown at
level 0.0446, step 1, values float32
Opened FliL.mrc copy as #114, grid size 240,240,240, pixel 2.1, shown at level
0.0732, step 1, values float32
Opened PflA_new.mrc as #68, grid size 240,240,240, pixel 2.1, shown at level
0.162, step 1, values float32
Opened Unknown_near_PflA.mrc as #69, grid size 240,240,240, pixel 2.1, shown
at level 0.127, step 1, values float32
Opened PflB_new.mrc as #70, grid size 240,240,240, pixel 2.1, shown at level
0.0467, step 1, values float32
Opened Top-cage.mrc as #71, grid size 240,240,240, pixel 2.1, shown at level
0.143, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #20, grid size 240,240,240, pixel 2.1,
shown at level 0.15, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #21, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #22, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #23, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #24, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #25, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #26, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #28, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #29, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #30, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #31, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #32, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #33, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #34, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #35, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #36, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #37, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Top-cage.mrc copy as #58, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #59, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #73, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #74, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #75, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #76, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #77, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #78, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #79, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #80, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #81, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #82, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #83, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #84, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #86, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #121, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #122, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #123, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened volume sum as #144, grid size 642,583,278, pixel 2.1, shown at level
0.162, step 1, values float32
Opened FlgY-with-joints.mrc copy as #143, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened FlgY-with-joints.mrc copy as #145, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened 1x_Cage-units.mrc as #89, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened PilNO_PL-ring.mrc as #95, grid size 120,120,120, pixel 8.59, shown at
level 6.53e-05, step 1, values float32
Opened New_PL-ring.mrc as #96, grid size 240,240,240, pixel 4.3, shown at
level 0.0141, step 1, values float32
Opened Outer-ring-near-PL.mrc as #97, grid size 240,240,240, pixel 4.3, shown
at level 0.0141, step 1, values float32
Opened Hpwt-L0.08-Global-PL.mrc as #115, grid size 240,240,240, pixel 4.3,
shown at level 0.0148, step 1, values float32
Opened Hpwt-L0.08-rev.mrc as #142, grid size 240,240,240, pixel 4.3, shown at
level 0.0425, step 1, values float32
Opened New_PL-ring.mrc gaussian as #165, grid size 240,240,240, pixel 4.3,
shown at level 0.0105, step 1, values float32
Opened FlgY-with-joints.mrc copy as #173, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened Hp-C1-4.296A-msk.mrc as #174, grid size 220,220,220, pixel 4.3, shown
at level 0.0868, step 1, values float32
Opened Hp-C1-4.296A-msk.mrc as #1, grid size 220,220,220, pixel 4.3, shown at
level 0.000693, step 1, values float32
Log from Mon Sep 8 12:14:54 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shoichi/Desktop/Final-ver5_-10032024.cxs
Opened 0838-bottom.mrc as #16, grid size 240,240,240, pixel 4.3, shown at
level 0.0144, step 1, values float32
Opened Hpwt-L0.08-Global-Rod-no-MS.mrc as #113, grid size 240,240,240, pixel
4.3, shown at level 0.0151, step 1, values float32
Opened Disk.mrc gaussian as #312, grid size 250,250,250, pixel 4.3, shown at
level 0.0186, step 1, values float32
Opened IM-old-maps.mrc gaussian as #313, grid size 120,120,120, pixel 8.8,
shown at level 0.0702, step 1, values float32
Opened OM.mrc copy gaussian as #316, grid size 240,240,240, pixel 4.3, shown
at level 0.0323, step 1, values float32
Opened New_FliF.mrc gaussian as #479, grid size 256,256,256, pixel 2.1, shown
at level 0.0115, step 1, values float32
Opened New_FlhA.mrc gaussian as #481, grid size 256,256,256, pixel 2.1, shown
at level 0.00316, step 1, values float32
Opened PflBC13.mrc as #482, grid size 256,256,256, pixel 2.1, shown at level
0.00615, step 1, values float32
Opened New_IM_Bottom2.mrc as #483, grid size 256,256,256, pixel 2.1, shown at
level 0.0072, step 1, values float32
Opened New_IM_Bottom2.mrc gaussian as #484, grid size 256,256,256, pixel 2.1,
shown at level 0.0072, step 1, values float32
Opened PflB_C13.mrc as #507, grid size 256,256,256, pixel 2.1, shown at level
0.0015, step 1, values float32
Opened PflB_monomer.mrc as #508, grid size 256,256,256, pixel 2.1, shown at
level 0.00116, step 1, values float32
Opened Unknown-ring.mrc as #509, grid size 256,256,256, pixel 2.1, shown at
level 0.000608, step 1, values float32
Opened PflB_C13.mrc gaussian as #510, grid size 256,256,256, pixel 2.1, shown
at level 0.00108, step 1, values float32
Opened PflB_monomer.mrc gaussian as #511, grid size 256,256,256, pixel 2.1,
shown at level 0.000387, step 1, values float32
Opened Unknown-ring.mrc gaussian as #512, grid size 256,256,256, pixel 2.1,
shown at level 0.00109, step 1, values float32
Opened 0838-disk.mrc gaussian as #513, grid size 240,240,240, pixel 4.3, shown
at level 0.0153, step 1, values float32
Opened 0838-top.mrc gaussian as #514, grid size 240,240,240, pixel 4.3, shown
at level 0.00979, step 1, values float32
Opened FlgV_monomer.mrc gaussian as #259.1, grid size 160,160,160, pixel 4.2,
shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.2, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.3, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.4, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.5, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.6, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.7, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.8, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.9, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.10, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.11, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.12, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.13, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.14, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.15, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.16, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.17, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.18, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.19, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.20, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgV_monomer.mrc copy gaussian as #259.21, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32
Opened FlgY-with-joints.mrc as #93, grid size 220,220,220, pixel 4.3, shown at
level 2.81, step 1, values float32
Opened Cage_1unit.mrc copy as #85, grid size 240,240,240, pixel 2.1, shown at
level 0.0446, step 1, values float32
Opened FliL.mrc copy as #114, grid size 240,240,240, pixel 2.1, shown at level
0.0732, step 1, values float32
Opened PflA_new.mrc as #68, grid size 240,240,240, pixel 2.1, shown at level
0.162, step 1, values float32
Opened Unknown_near_PflA.mrc as #69, grid size 240,240,240, pixel 2.1, shown
at level 0.127, step 1, values float32
Opened PflB_new.mrc as #70, grid size 240,240,240, pixel 2.1, shown at level
0.0467, step 1, values float32
Opened Top-cage.mrc as #71, grid size 240,240,240, pixel 2.1, shown at level
0.143, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #20, grid size 240,240,240, pixel 2.1,
shown at level 0.15, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #21, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #22, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #23, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #24, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #25, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #26, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #28, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #29, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #30, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #31, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #32, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #33, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #34, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #35, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #36, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #37, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Top-cage.mrc copy as #58, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #59, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #73, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #74, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #75, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #76, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #77, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #78, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #79, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #80, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #81, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #82, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #83, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #84, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #86, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #121, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #122, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #123, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened volume sum as #144, grid size 642,583,278, pixel 2.1, shown at level
0.162, step 1, values float32
Opened FlgY-with-joints.mrc copy as #143, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened FlgY-with-joints.mrc copy as #145, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened 1x_Cage-units.mrc as #89, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened PilNO_PL-ring.mrc as #95, grid size 120,120,120, pixel 8.59, shown at
level 6.53e-05, step 1, values float32
Opened New_PL-ring.mrc as #96, grid size 240,240,240, pixel 4.3, shown at
level 0.0141, step 1, values float32
Opened Outer-ring-near-PL.mrc as #97, grid size 240,240,240, pixel 4.3, shown
at level 0.0141, step 1, values float32
Opened Hpwt-L0.08-Global-PL.mrc as #115, grid size 240,240,240, pixel 4.3,
shown at level 0.0148, step 1, values float32
Opened Hpwt-L0.08-rev.mrc as #142, grid size 240,240,240, pixel 4.3, shown at
level 0.0425, step 1, values float32
Opened New_PL-ring.mrc gaussian as #165, grid size 240,240,240, pixel 4.3,
shown at level 0.0105, step 1, values float32
Opened FlgY-with-joints.mrc copy as #173, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened Hp-C1-4.296A-msk.mrc as #174, grid size 220,220,220, pixel 4.3, shown
at level 0.0868, step 1, values float32
Opened Hp-C1-4.296A-msk.mrc as #1, grid size 220,220,220, pixel 4.3, shown at
level 0.000693, step 1, values float32
Log from Fri Oct 4 17:19:37 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Final-ver_side-
> view4top-09042024.cxs
Opened 0838-bottom.mrc as #16, grid size 240,240,240, pixel 4.3, shown at
level 0.0144, step 1, values float32
Opened Hpwt-L0.08-Global-Rod-no-MS.mrc as #113, grid size 240,240,240, pixel
4.3, shown at level 0.0151, step 1, values float32
Opened Single-MotA-truncated.mrc copy as #281, grid size 110,110,140, pixel
4.3,4.3,4.3, shown at level 0.00853, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #282, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #283, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #284, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #285, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #286, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #287, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #288, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #289, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #290, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #291, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #292, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #293, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #294, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #295, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #296, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #297, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #298, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Disk.mrc gaussian as #312, grid size 250,250,250, pixel 4.3, shown at
level 0.0186, step 1, values float32
Opened IM-old-maps.mrc gaussian as #313, grid size 120,120,120, pixel 8.8,
shown at level 0.0702, step 1, values float32
Opened OM.mrc copy gaussian as #316, grid size 240,240,240, pixel 4.3, shown
at level 0.0323, step 1, values float32
Opened Cage-bottom.mrc as #356, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #357, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #358, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #359, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #360, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #361, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #362, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #363, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #364, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #365, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #366, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #367, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #368, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #369, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #370, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #371, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #372, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #373, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened PilM-region.mrc gaussian as #377, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #378, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #379, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #380, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #381, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #382, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #383, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #384, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #385, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #386, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #387, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #388, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #389, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #390, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #391, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #415, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #416, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #417, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #418, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PflA.mrc as #424, grid size 160,160,200, pixel 4.3,4.3,4.3, shown at
level 0.00712, step 1, values float32
Opened PflA.mrc copy as #425, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #426, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #427, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #428, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #429, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #430, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #431, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #432, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #433, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #434, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #435, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #436, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #437, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #438, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #439, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #440, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #441, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened Cage_top.mrc as #442, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #443, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #444, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #445, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #446, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #447, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #448, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #449, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #450, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #451, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #452, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #453, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #454, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #455, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #456, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #457, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #458, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #459, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened MotB_PG.mrc as #460, grid size 160,160,200, pixel 4.3,4.3,4.3, shown at
level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #461, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #462, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #463, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #464, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #465, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #466, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #467, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #468, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #469, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #470, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #471, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #472, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #473, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #474, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #475, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #476, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #477, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened New_FliF.mrc gaussian as #479, grid size 256,256,256, pixel 2.1, shown
at level 0.0115, step 1, values float32
Opened New_FlhA.mrc gaussian as #481, grid size 256,256,256, pixel 2.1, shown
at level 0.00316, step 1, values float32
Opened PflBC13.mrc as #482, grid size 256,256,256, pixel 2.1, shown at level
0.00615, step 1, values float32
Opened New_IM_Bottom2.mrc as #483, grid size 256,256,256, pixel 2.1, shown at
level 0.0072, step 1, values float32
Opened New_IM_Bottom2.mrc gaussian as #484, grid size 256,256,256, pixel 2.1,
shown at level 0.0072, step 1, values float32
Opened PflB_C13.mrc as #507, grid size 256,256,256, pixel 2.1, shown at level
0.0015, step 1, values float32
Opened PflB_monomer.mrc as #508, grid size 256,256,256, pixel 2.1, shown at
level 0.00116, step 1, values float32
Opened Unknown-ring.mrc as #509, grid size 256,256,256, pixel 2.1, shown at
level 0.000608, step 1, values float32
Opened PflB_C13.mrc gaussian as #510, grid size 256,256,256, pixel 2.1, shown
at level 0.00108, step 1, values float32
Opened PflB_monomer.mrc gaussian as #511, grid size 256,256,256, pixel 2.1,
shown at level 0.000387, step 1, values float32
Opened Unknown-ring.mrc gaussian as #512, grid size 256,256,256, pixel 2.1,
shown at level 0.00109, step 1, values float32
Opened 0838-disk.mrc gaussian as #513, grid size 240,240,240, pixel 4.3, shown
at level 0.0153, step 1, values float32
Opened 0838-top.mrc gaussian as #514, grid size 240,240,240, pixel 4.3, shown
at level 0.00979, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.1, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.2, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.3, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.4, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.5, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.6, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.7, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.8, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.9, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.10, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.11, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.12, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.13, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.14, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.15, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.16, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.17, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
[deleted to fit within ticket limits]
> select add #25
41 models selected
> select add #26
42 models selected
> select add #20
43 models selected
> select add #21
44 models selected
> select add #22
45 models selected
> select subtract #20
42 models selected
> select subtract #21
39 models selected
> select subtract #22
36 models selected
> select subtract #23
33 models selected
> select subtract #24
30 models selected
> select subtract #26
27 models selected
> select subtract #25
24 models selected
> select add #27
25 models selected
> select add #28
26 models selected
> select add #29
27 models selected
> select add #30
28 models selected
> select add #31
29 models selected
> select subtract #32
26 models selected
> select subtract #33
23 models selected
> select add #34
24 models selected
> select add #35
25 models selected
> select add #36
26 models selected
> select add #37
27 models selected
> select subtract #27
24 models selected
> select subtract #28
21 models selected
> select subtract #29
18 models selected
> select subtract #30
15 models selected
> select subtract #31
12 models selected
> select subtract #37
9 models selected
> select subtract #36
6 models selected
> select subtract #35
3 models selected
> select subtract #34
Nothing selected
> color #20 #9292924d models
> hide #!1 models
> color #20-37 #9292924d models
> color #20 #7d7d7d4d models
> color #20 #7c7c7c4d models
> color #20 #7c7c7c40 models
> color #20-37 #7c7c7c40 models
> show #!16 models
> show #!52 models
> show #!53 models
> select add #52
114468 atoms, 116060 bonds, 18 pseudobonds, 15371 residues, 2 models selected
> select add #53
213710 atoms, 216576 bonds, 70 pseudobonds, 28761 residues, 81 models selected
> hide sel atoms
> select subtract #52
99242 atoms, 100516 bonds, 52 pseudobonds, 13390 residues, 131 models selected
> select subtract #53
129 models selected
> hide #!52 models
> hide #!53 models
> show #!52 models
> hide #!16 models
> show #!183 models
> show #!184 models
> show #!185 models
> show #!486 models
> show #!488 models
> show #!501 models
> show #!502 models
> show #!177 models
> hide #!177 models
> close #177
> show #!172 models
> show #!167 models
> show #!166 models
> hide #!166 models
> show #!169 models
> show #!165 models
> hide #!165 models
> show #!168 models
> show #!259 models
> show #!182 models
> view orient
> lighting soft
> save /Users/shoichi/Desktop/HP_Top_10032024.png supersample 2
> transparentBackground true
> show #!313 models
> hide #!502.6 models
> show #!502.6 models
> hide #!488.6 models
> hide #!488.7 models
> lighting simple
> show #!488.6 models
> show #!488.7 models
> hide #!488.14 models
> hide #!488.15 models
> hide #!488.16 models
> hide #!488.17 models
> hide #!488.18 models
> hide #!488.1 models
> hide #!488.2 models
> hide #!488.3 models
> hide #!488.4 models
> show #!488.4 models
> hide #!486.1 models
> hide #!486.2 models
> hide #!486.3 models
> hide #!486.4 models
> hide #!486.18 models
> hide #!486.17 models
> hide #!486.16 models
> hide #!486.15 models
> view SideP1
Expected an objects specifier or a view name or a keyword
> view Side P1
Expected an integer >= 1 or a keyword
> view Side
> hide #!502.15 models
> hide #!502.16 models
> hide #!502.17 models
> hide #!502.18 models
> hide #!502.1 models
> hide #!502.2 models
> hide #!502.3 models
> hide #!502.4 models
> hide #!501.1 models
> hide #!501.2 models
> hide #!501.3 models
> hide #!501.4 models
> show #!501.4 models
> hide #!501.18 models
> hide #!501.17 models
> hide #!501.16 models
> hide #!501.15 models
> turn x 90
[Repeated 2 time(s)]
> hide #!501.4 models
> turn x 90
> turn y 90
> hide #!502.14 models
> show #!502.4 models
> view Side
> turn x 45
> view Side
> turn x 40
> hide #!52 models
> lighting soft
[Repeated 1 time(s)]
> save /Users/shoichi/Desktop/HP_Tilt_10032024.png supersample 2
> transparentBackground true
[Repeated 1 time(s)]
> color #20 #7c7c7c1a models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color #20-37 #7c7c7c1a models
> save /Users/shoichi/Desktop/HP_Tilt_10032024.png supersample 2
> transparentBackground true
> color #20 #7c7c7c26 models
> color #20-37 #7c7c7c26 models
> save /Users/shoichi/Desktop/HP_Tilt_10032024.png supersample 2
> transparentBackground true
> hide #!313 models
> show #!52 models
> show #!501.15 models
> show #!502.1 models
> show #!502.2 models
> show #!502.3 models
> show #!502.14 models
> show #!502.15 models
> lighting simple
> show #!501.16 models
> show #!501.17 models
> show #!501.18 models
> show #!502.16 models
> show #!502.17 models
> show #!488.1 models
> show #!488.2 models
> show #!488.3 models
> show #!488.14 models
> show #!488.15 models
> show #!488.16 models
> show #!488.17 models
> show #!488.18 models
> show #!486.15 models
> show #!486.16 models
> show #!486.17 models
> show #!486.18 models
> show #!486.1 models
> show #!486.2 models
> show #!486.3 models
> show #!486.4 models
> show #!501.1 models
> show #!501.2 models
> show #!501.3 models
> show #!501.4 models
> show #!502.18 models
> view orient
> lighting soft
> save /Users/shoichi/Desktop/HP_Top_10032024.png supersample 2
> transparentBackground true
> view Side
> hide #!486.1 models
> hide #!486.2 models
> hide #!486.3 models
> show #!486.3 models
> hide #!486.3 models
> hide #!486.18 models
> hide #!486.17 models
> hide #!486.16 models
> lighting simple
> view Side
[Repeated 1 time(s)]
> hide #!486.4 models
> hide #!486.15 models
> hide #!488 models
> show #!488 models
> hide #!488.1 models
> hide #!488.2 models
> hide #!488.3 models
> hide #!488.17 models
> hide #!488.18 models
> hide #!488.15 models
> hide #!488.14 models
> hide #!488.16 models
> hide #!501.1 models
> hide #!501.2 models
> hide #!501.3 models
> hide #!501.4 models
> hide #!501.15 models
> hide #!501.16 models
> hide #!501.17 models
> hide #!501.18 models
> hide #!502.1 models
> hide #!502.2 models
> hide #!502.3 models
> hide #!502.14 models
> hide #!502.15 models
> hide #!502.16 models
> hide #!502.17 models
> hide #!502.18 models
> hide #!167.6 models
> hide #!167.5 models
> show #!167.5 models
> hide #!167.7 models
> hide #!167.8 models
> hide #!167.9 models
> hide #!167.10 models
> hide #!167.11 models
> hide #!167.12 models
> hide #!167.13 models
> show #!167.13 models
> hide #!168.6 models
> hide #!168.7 models
> hide #!168.8 models
> hide #!168.9 models
> hide #!168.10 models
> hide #!168.11 models
> hide #!168.12 models
> hide #!169.6 models
> hide #!169.7 models
> hide #!169.8 models
> hide #!169.9 models
> hide #!169.10 models
> show #!169.10 models
> hide #!169.11 models
> hide #!169.10 models
> hide #!169.12 models
> hide #!183.6 models
> show #!183.6 models
> hide #!183.10 models
> hide #!183.9 models
> hide #!183.8 models
> hide #!183.11 models
> hide #!183.12 models
> hide #!183.13 models
> hide #!184.29 models
> hide #!184.28 models
> hide #!184.27 models
> hide #!184.26 models
> hide #!184.10 models
> hide #!184.11 models
> hide #!184.12 models
> hide #!184.13 models
> hide #!184.14 models
> show #!184.14 models
> hide #!184.30 models
> hide #!184.9 models
> hide #!184.8 models
> hide #!185.44 models
> hide #!185.42 models
> show #!185.42 models
> hide #!185.1 models
> hide #!185.47 models
> hide #!185.48 models
> hide #!185.51 models
> hide #!185.52 models
> hide #!185.42 models
> show #!185.42 models
> hide #!185.13 models
> hide #!185.14 models
> view Side
> hide #!30 models
> hide #!31 models
> hide #!32 models
> hide #!33 models
> hide #!34 models
> hide #!35 models
> hide #!36 models
> hide #!29 models
> show #!16 models
> show #!53 models
> show #!58 models
> show #!59 models
> show #!65 models
> show #!67 models
> show #!71 models
> show #!74 models
> show #!73 models
> show #!75 models
> show #!76 models
> show #!77 models
> show #!78 models
> show #!79 models
> show #!80 models
> show #!123 models
> show #!122 models
> hide #!123 models
> show #!121 models
> hide #!121 models
> color #122 #b7916aff models
> show #!313 models
> show #!316 models
> show #!312 models
> show #!484 models
> show #!513 models
> show #!514 models
> show #!97 models
> lighting soft
> save /Users/shoichi/Desktop/HP_Side_10032024.png supersample 2
> transparentBackground true
> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Final-ver5_-10032024.cxs
> includeMaps true
——— End of log from Fri Oct 4 17:19:37 2024 ———
opened ChimeraX session
> lighting simple
> show #!29 models
> hide #!29 models
> show #!36 models
> show #!35 models
> show #!34 models
> show #!33 models
> show #!32 models
> show #!31 models
> show #!30 models
> show #!29 models
> hide #!29 models
> hide #!30 models
> hide #!31 models
> hide #!32 models
> hide #!34 models
> hide #!35 models
> hide #!52 models
> hide #!37 models
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Poster/2025_MB/HP_Cage_model.pdb"
Summary of feedback from opening /Volumes/Lab Backup/Jun Liu Lab
2025/Poster/2025_MB/HP_Cage_model.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 6 THR A 83 1 78
Start residue of secondary structure not found: HELIX 2 2 ASP A 93 CYS A 107 1
15
Start residue of secondary structure not found: HELIX 3 3 LEU A 136 TYR A 149
1 14
Start residue of secondary structure not found: SHEET 1 1 1 ALA A 110 LEU A
116 0
Start residue of secondary structure not found: SHEET 2 2 1 LYS A 124 ALA A
133 0
131 messages similar to the above omitted
Chain information for HP_Cage_model.pdb
---
Chain | Description
2.9/A 2.12/E | No description available
2.10/B 2.13/F | No description available
2.11/C 2.14/G | No description available
2.1/D 2.4/G | No description available
2.2/E 2.5/H | No description available
2.3/F 2.6/I | No description available
2.15/I 2.17/K | No description available
2.16/J 2.18/L | No description available
2.7/O 2.8/Q | No description available
Drag select of 214 residues
> select clear
[Repeated 1 time(s)]
> hide #2.6 models
> show #2.6 models
> select add #2.6
828 atoms, 835 bonds, 108 residues, 1 model selected
> hide #2.5 models
> show #2.5 models
> hide #2.5 models
> show #2.5 models
> select add #2.5
1401 atoms, 1421 bonds, 173 residues, 2 models selected
> hide #2.4 models
> show #2.4 models
> select add #2.4
3974 atoms, 4053 bonds, 486 residues, 3 models selected
> select add #2.3
4802 atoms, 4888 bonds, 594 residues, 4 models selected
> select add #2.2
5375 atoms, 5474 bonds, 659 residues, 5 models selected
> select add #2.1
7948 atoms, 8106 bonds, 972 residues, 6 models selected
> select subtract #2.1
5375 atoms, 5474 bonds, 659 residues, 5 models selected
> hide #2.1 models
> select subtract #2.2
4802 atoms, 4888 bonds, 594 residues, 4 models selected
> hide #2.2 models
> select subtract #2.3
3974 atoms, 4053 bonds, 486 residues, 3 models selected
> hide #2.3 models
> select add #2.7
4736 atoms, 4835 bonds, 572 residues, 4 models selected
> hide #2.7 models
> select add #2.8
5498 atoms, 5617 bonds, 658 residues, 5 models selected
> select add #2.9
6985 atoms, 7134 bonds, 837 residues, 6 models selected
> select add #2.10
8268 atoms, 8445 bonds, 994 residues, 7 models selected
> select add #2.11
10847 atoms, 11073 bonds, 1304 residues, 8 models selected
> show #2.7 models
> hide #2.7 models
> select subtract #2.7
10085 atoms, 10291 bonds, 1218 residues, 7 models selected
> select add #2.12
11572 atoms, 11808 bonds, 1397 residues, 8 models selected
> select add #2.13
12855 atoms, 13119 bonds, 1554 residues, 9 models selected
> select add #2.14
15434 atoms, 15747 bonds, 1864 residues, 10 models selected
> select add #2.15
16430 atoms, 16756 bonds, 1988 residues, 11 models selected
> select add #2.16
16661 atoms, 16990 bonds, 2018 residues, 12 models selected
> select add #2.17
17657 atoms, 17999 bonds, 2142 residues, 13 models selected
> close #2.7
> close #2.1-3
> combine #2
Remapping chain ID 'G' in HP_Cage_model.pdb #2.14 to 'J'
Remapping chain ID 'I' in HP_Cage_model.pdb #2.15 to 'K'
Remapping chain ID 'J' in HP_Cage_model.pdb #2.16 to 'L'
Remapping chain ID 'K' in HP_Cage_model.pdb #2.17 to 'M'
Remapping chain ID 'L' in HP_Cage_model.pdb #2.18 to 'N'
> hide #!2 models
> select add #2
17888 atoms, 18233 bonds, 2172 residues, 15 models selected
> hide #!488.4 models
> show #!488.4 models
> hide #!488.4 models
> show #!488.4 models
> combine #488.4
> hide #4 models
> show #4 models
> hide #!488.4 models
> hide #4 models
> show #4 models
> close #4
> show #487 models
> matchmaker #3 to #487
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PilNO_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#487)
with combination, chain A (#3), sequence alignment score = 923.6
RMSD between 36 pruned atom pairs is 1.311 angstroms; (across all 179 pairs:
5.544)
> close #485,487#486,488
> show #!82 models
> show #!86 models
> select subtract #2
Nothing selected
> select add #3
17888 atoms, 18233 bonds, 2172 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.98568,-0.098666,-0.13672,436.2,0.080939,-0.98825,0.12965,548.74,-0.1479,0.11673,0.98209,314.83
> view matrix models
> #3,-0.90936,-0.40897,-0.076248,491.93,0.39381,-0.90531,0.15916,454.44,-0.13412,0.1147,0.9843,312.03
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.90936,-0.40897,-0.076248,489.21,0.39381,-0.90531,0.15916,458.14,-0.13412,0.1147,0.9843,313.98
> show #!1 models
> hide #!1 models
> hide #!16 models
> hide #!16-514 models
> show #!1 models
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.97839,0.19722,0.062122,319.14,-0.20226,-0.97525,-0.089344,647.38,0.042964,-0.099977,0.99406,331.35
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.97839,0.19722,0.062122,305.93,-0.20226,-0.97525,-0.089344,682.4,0.042964,-0.099977,0.99406,330.22
> view matrix models
> #3,-0.97839,0.19722,0.062122,353.51,-0.20226,-0.97525,-0.089344,689.79,0.042964,-0.099977,0.99406,342.11
> view matrix models
> #3,-0.97839,0.19722,0.062122,344.61,-0.20226,-0.97525,-0.089344,708.99,0.042964,-0.099977,0.99406,337.95
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.97986,0.19701,0.032595,350.04,-0.19791,-0.97985,-0.027082,698.6,0.026603,-0.032988,0.9991,322.79
> ui tool show "Fit in Map"
> fitmap #3 inMap #16
Fit molecule combination (#3) to map 0838-bottom.mrc (#16) using 17888 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 17888, contour level = 0.01441
Position of combination (#3) relative to 0838-bottom.mrc (#16) coordinates:
Matrix rotation and translation
-0.97985882 0.19701334 0.03259504 325.57183750
-0.19791159 -0.97984569 -0.02708208 676.88455927
0.02660258 -0.03298755 0.99910166 93.52842138
Axis -0.01495002 0.01517023 -0.99977315
Axis point 195.91582755 322.97827102 0.00000000
Rotation angle (degrees) 168.60877152
Shift along axis -88.10601186
> fitmap #3 inMap #16
Fit molecule combination (#3) to map 0838-bottom.mrc (#16) using 17888 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 17888, contour level = 0.01441
Position of combination (#3) relative to 0838-bottom.mrc (#16) coordinates:
Matrix rotation and translation
-0.97985882 0.19701334 0.03259504 325.57183750
-0.19791159 -0.97984569 -0.02708208 676.88455927
0.02660258 -0.03298755 0.99910166 93.52842138
Axis -0.01495002 0.01517023 -0.99977315
Axis point 195.91582755 322.97827102 0.00000000
Rotation angle (degrees) 168.60877152
Shift along axis -88.10601186
> view matrix models
> #3,-0.98045,0.19594,0.01808,352.94,-0.19539,-0.98031,0.02867,688.62,0.023342,0.024577,0.99943,308.13
> select subtract #3
Nothing selected
> hide #!1 models
> save /Users/shoichi/Desktop/All-model_HP_for_Topcage.cxs includeMaps true
> show #!53 models
> hide #!53 models
> show #!52 models
> view orient
> sym #3 C18 copies true center #52
Made 18 copies for combination symmetry C18
> close #4
> split #3
Split combination (#3) into 14 models
Chain information for combination A #3.1
---
Chain | Description
A | No description available
Chain information for combination B #3.2
---
Chain | Description
B | No description available
Chain information for combination C #3.3
---
Chain | Description
C | No description available
Chain information for combination E #3.4
---
Chain | Description
E | No description available
Chain information for combination F #3.5
---
Chain | Description
F | No description available
Chain information for combination G #3.6
---
Chain | Description
G | No description available
Chain information for combination H #3.7
---
Chain | Description
H | No description available
Chain information for combination I #3.8
---
Chain | Description
I | No description available
Chain information for combination J #3.9
---
Chain | Description
J | No description available
Chain information for combination K #3.10
---
Chain | Description
K | No description available
Chain information for combination L #3.11
---
Chain | Description
L | No description available
Chain information for combination M #3.12
---
Chain | Description
M | No description available
Chain information for combination N #3.13
---
Chain | Description
N | No description available
Chain information for combination Q #3.14
---
Chain | Description
Q | No description available
> show #3.1 models
> show #3.2 models
> show #3.3 models
> show #3.4 models
> show #3.14 models
> show #3.13 models
> show #3.12 models
> show #3.11 models
> show #3.10 models
> show #3.9 models
> show #3.8 models
> show #3.7 models
> show #3.6 models
> show #3.5 models
> hide #!52 models
> select add #3.14
762 atoms, 782 bonds, 86 residues, 1 model selected
Drag select of 6 residues
> select add #3.7
573 atoms, 586 bonds, 65 residues, 1 model selected
> select add #3.8
1401 atoms, 1421 bonds, 173 residues, 2 models selected
> select subtract #3.8
573 atoms, 586 bonds, 65 residues, 1 model selected
> select add #3.6
3146 atoms, 3218 bonds, 378 residues, 2 models selected
> select subtract #3.7
2573 atoms, 2632 bonds, 313 residues, 1 model selected
> select subtract #3.6
Nothing selected
Drag select of 37 residues
> select add #3.12
996 atoms, 1009 bonds, 124 residues, 1 model selected
> select add #3.13
1227 atoms, 1243 bonds, 154 residues, 2 models selected
> select subtract #3.13
996 atoms, 1009 bonds, 124 residues, 1 model selected
> select add #3.11
1227 atoms, 1243 bonds, 154 residues, 2 models selected
> select subtract #3.11
996 atoms, 1009 bonds, 124 residues, 1 model selected
Drag select of 68 residues
> select add #3.10
1044 atoms, 1009 bonds, 129 residues, 2 models selected
> select add #3.12
2040 atoms, 2018 bonds, 253 residues, 3 models selected
> select add #3.4
3479 atoms, 3535 bonds, 427 residues, 3 models selected
> select subtract #3.4
1992 atoms, 2018 bonds, 248 residues, 2 models selected
> W16: color sel #1e46ffff models
Unknown command: W16: color sel #1e46ffff models
> color sel #1e46ffff models
> select clear
Drag select of 135 residues
> select add #3.3
3025 atoms, 2628 bonds, 365 residues, 2 models selected
> select add #3.9
5158 atoms, 5256 bonds, 620 residues, 2 models selected
> color sel #d4f9ffff models
> select clear
Drag select of 8 residues
Drag select of 12 residues
> select add #3.11
313 atoms, 234 bonds, 42 residues, 2 models selected
> select add #3.13
462 atoms, 468 bonds, 60 residues, 2 models selected
> color sel #7b80ffff models
> color sel #adffc1ff models
Drag select of 14 residues
Drag select of 6 residues
> select add #3.14
822 atoms, 782 bonds, 92 residues, 2 models selected
> select add #3.7
1335 atoms, 1368 bonds, 151 residues, 2 models selected
> color sel #adffc1ff models
> select clear
Drag select of 5 residues
> select add #3.2
1283 atoms, 1311 bonds, 157 residues, 1 model selected
> select add #3.4
2770 atoms, 2828 bonds, 336 residues, 2 models selected
> select subtract #3.4
1283 atoms, 1311 bonds, 157 residues, 1 model selected
> select add #3.4
2770 atoms, 2828 bonds, 336 residues, 2 models selected
> select subtract #3.4
1283 atoms, 1311 bonds, 157 residues, 1 model selected
> select add #3.6
3856 atoms, 3943 bonds, 470 residues, 2 models selected
> select subtract #3.6
1283 atoms, 1311 bonds, 157 residues, 1 model selected
> select add #3.8
2111 atoms, 2146 bonds, 265 residues, 2 models selected
> select subtract #3.8
1283 atoms, 1311 bonds, 157 residues, 1 model selected
> select add #3.1
2770 atoms, 2828 bonds, 336 residues, 2 models selected
> select subtract #3.1
1283 atoms, 1311 bonds, 157 residues, 1 model selected
> select add #3.3
3862 atoms, 3939 bonds, 467 residues, 2 models selected
> select subtract #3.3
1283 atoms, 1311 bonds, 157 residues, 1 model selected
> select add #3.4
2770 atoms, 2828 bonds, 336 residues, 2 models selected
> select subtract #3.4
1283 atoms, 1311 bonds, 157 residues, 1 model selected
> select add #3.5
2566 atoms, 2622 bonds, 314 residues, 2 models selected
> color sel #6bf7f8ff models
> color sel #0fb4fcff models
> select clear
> select add #3.3
2579 atoms, 2628 bonds, 310 residues, 1 model selected
> select add #3.1
4066 atoms, 4145 bonds, 489 residues, 2 models selected
> select subtract #3.3
1487 atoms, 1517 bonds, 179 residues, 1 model selected
> select add #3.6
4060 atoms, 4149 bonds, 492 residues, 2 models selected
> select subtract #3.6
1487 atoms, 1517 bonds, 179 residues, 1 model selected
> select add #3.4
2974 atoms, 3034 bonds, 358 residues, 2 models selected
> color sel #6bf7f8ff models
> select clear
[Repeated 1 time(s)]
> select add #3.3
2579 atoms, 2628 bonds, 310 residues, 1 model selected
> select subtract #3.3
Nothing selected
> select add #3.8
828 atoms, 835 bonds, 108 residues, 1 model selected
> color #3.8 #ecaae9ff
> color #3.8 #e49eecff
> color #3.8 #a237ecff
> lighting soft
[Repeated 1 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> color #3.8 #851decff
> color #3.8 #820fecff
> color #3.8 #780fecff
> select add #3.3
3407 atoms, 3463 bonds, 418 residues, 2 models selected
> select subtract #3.8
2579 atoms, 2628 bonds, 310 residues, 1 model selected
> select add #3.6
5152 atoms, 5260 bonds, 623 residues, 2 models selected
> select subtract #3.3
2573 atoms, 2632 bonds, 313 residues, 1 model selected
> color #3.6 #ecdfbcff
> color #3.6 #ecd4a8ff
> color #3.6 #ecc9a5ff
> color #3.6 #eccca2ff
> color sel #c49d5fff models
> select clear
> combine #3
> hide #!3 models
> show #!53 models
> hide #!53 models
> show #!52 models
> view orient
> sym #4 C18 copies true center #52
Made 18 copies for combination symmetry C18
> save /Users/shoichi/Desktop/All-model_HP_for_Topcage.cxs includeMaps true
——— End of log from Mon Sep 8 12:14:54 2025 ———
opened ChimeraX session
> show #!16 models
> show #!53 models
> lighting simple
> show #!65 models
> show #!67 models
> show #!97 models
> show #!167 models
> show #!168 models
> show #!169 models
> show #!172 models
> show #!182-185 models
> show #!259 models
> show #!312 models
> show #!313 models
> show #!316 models
> show #!484 models
> close #499-500#501-502
> show #!513 models
> show #!514 models
> view orient
> save /Users/shoichi/Desktop/All-model_HP_for_Topcage.cxs includeMaps true
> turn x 90
[Repeated 2 time(s)]
> turn y 90
> ui tool show "Volume Viewer"
> volume #97 region 0,0,0,239,239,239
> volume #513 region 0,0,0,239,239,239
> volume #514 region 0,0,0,239,239,239
> volume #484 region 0,0,0,239,239,239
> volume #316 region 0,0,0,239,239,239
> volume #313 region 0,0,0,239,239,239
> volume #312 region 0,0,0,239,239,239
> show #!58 models
> show #!59 models
> hide #!59 models
> hide #!58 models
> show #!58 models
> show #!59 models
> show #!71 models
> show #!73 models
> show #!74 models
> show #!75 models
> show #!75-84 models
> show #!86 models
> show #!122 models
> hide #!122 models
> show #!122 models
> save /Users/shoichi/Desktop/All-model_HP_for_Topcage.cxs includeMaps true
> close #60,64#61-63
> close #66
> close #68-70
> close #72
> show #!85 models
> close #87-96
> close #98-99#100,113-115,121
> close #123,142-145,165-166
> close #171#170
> close #176#173-175,178-179,181
> close #186-187
> close #479,481-483
> close #495-498,507-512
> hide #!85 models
> hide #!52 models
> hide #!1-514 models
> show #4 models
> show #!58 models
> show #!59 models
> show #!71 models
> show #!74 models
> show #!75 models
> show #!76 models
> show #!77 models
> show #!78 models
> hide #!71 models
> hide #!74 models
> hide #!75 models
> hide #!76 models
> hide #!78 models
> hide #!77 models
> show #!122 models
> show #!86 models
> show #!84 models
> hide #!122 models
> hide #!86 models
> show #!86 models
> hide #!84 models
> ui tool show "Segment Map"
Segmenting Top-cage.mrc copy, density threshold 0.143336
Showing 5 region surfaces
24 watershed regions, grouped to 5 regions
Showing Top-cage copy.seg - 5 regions, 5 surfaces
> hide #!59 models
> hide #!58 models
> select add #6
6 models selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,-120.34,0,1,0,36.834,0,0,1,78.752
> view matrix models #6,1,0,0,91.614,0,1,0,243.28,0,0,1,465.23
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.95062,0.095435,0.29531,81.316,-0.30194,0.50433,0.809,267.2,-0.071726,-0.85822,0.50825,529.81
> view matrix models
> #6,-0.7973,-0.27248,-0.53857,268.99,0.59101,-0.17133,-0.78826,275.13,0.12251,-0.94678,0.29765,522.8
> view matrix models
> #6,-0.84016,-0.34997,-0.41432,273.45,0.45421,-0.87149,-0.18492,306.39,-0.29636,-0.34355,0.89115,509.22
> select #6.2
1 model selected
> select add #6.1
2 models selected
Opened Top-cage_imasked as #7, grid size 240,240,240, pixel 2.1, shown at step
1, values float32
> hide #!6 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!86 models
> hide #!7 models
> show #!7 models
> save /Users/shoichi/Desktop/Top-middle.mrc models #7
> open /Users/shoichi/Desktop/Top-middle.mrc
Opened Top-middle.mrc as #8, grid size 240,240,240, pixel 2.1, shown at level
0.000178, step 1, values float32
> surface dust #7 size 21
> surface dust #8 size 21
> close #6
> select add #8
2 models selected
> show #!73 models
> hide #!73 models
> hide #4 models
> show #!5 models
> show #!58 models
> show #!59 models
> hide #!7 models
> hide #!58 models
> show #!71 models
> hide #!71 models
> show #!58 models
> hide #!58 models
> show #!71 models
> hide #!71 models
> show #!73 models
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,520.65,0,1,0,320.81,0,0,1,475.13
> view matrix models #8,1,0,0,612.82,0,1,0,209.49,0,0,1,487.47
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.52094,0.55507,-0.64847,636.41,-0.36097,0.83168,0.4219,239.24,0.77351,0.014295,0.63362,430.8
> view matrix models
> #8,0.25824,0.89945,-0.35257,640.94,-0.63916,0.43273,0.63579,273.28,0.72442,0.061167,0.68664,432.31
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.25824,0.89945,-0.35257,689.04,-0.63916,0.43273,0.63579,265.33,0.72442,0.061167,0.68664,488.19
> view matrix models
> #8,0.25824,0.89945,-0.35257,698.98,-0.63916,0.43273,0.63579,296.04,0.72442,0.061167,0.68664,489.61
> view matrix models
> #8,0.25824,0.89945,-0.35257,697.01,-0.63916,0.43273,0.63579,282.58,0.72442,0.061167,0.68664,476.53
> ui tool show "Fit in Map"
> fitmap #8 inMap #59
Fit map Top-middle.mrc in map Top-cage.mrc copy using 42001 points
correlation = 0.9994, correlation about mean = 0.9994, overlap = 5.943e+05
steps = 796, shift = 67.3, angle = 45.3 degrees
Position of Top-middle.mrc (#8) relative to Top-cage.mrc copy (#59)
coordinates:
Matrix rotation and translation
0.99998884 -0.00343469 -0.00324545 0.25009164
0.00342375 0.99998846 -0.00337128 -0.10368619
0.00325699 0.00336013 0.99998906 -0.34149610
Axis 0.58013923 -0.56040526 0.59108749
Axis point 30.30942820 72.48848021 0.00000000
Rotation angle (degrees) 0.33240608
Shift along axis 0.00134018
> fitmap #8 inMap #59
Fit map Top-middle.mrc in map Top-cage.mrc copy using 42001 points
correlation = 0.9992, correlation about mean = 0.9993, overlap = 5.942e+05
steps = 76, shift = 0.0659, angle = 0.0495 degrees
Position of Top-middle.mrc (#8) relative to Top-cage.mrc copy (#59)
coordinates:
Matrix rotation and translation
0.99998600 -0.00357231 -0.00390377 0.25095619
0.00355703 0.99998602 -0.00391329 -0.10232638
0.00391770 0.00389935 0.99998473 -0.41491489
Axis 0.59391535 -0.59458617 0.54197034
Axis point 104.09319997 0.00000000 66.19171392
Rotation angle (degrees) 0.37685080
Shift along axis -0.01498298
> select clear
> select add #5
321984 atoms, 328194 bonds, 39096 residues, 19 models selected
> show sel surfaces
> select clear
> show #!85 models
> select add #8
2 models selected
> view matrix models
> #8,0.52314,0.85132,-0.039735,437.32,-0.85156,0.52402,0.015766,243.15,0.034244,0.025589,0.99909,462.2
> close #7-8
> ui tool show "Segment Map"
Segmenting Cage_1unit.mrc copy, density threshold 0.044638
Showing 296 region surfaces
1367 watershed regions, grouped to 296 regions
Showing Cage_1unit copy.seg - 296 regions, 296 surfaces
> select add #6
297 models selected
> view matrix models #6,1,0,0,599.48,0,1,0,410.88,0,0,1,138.1
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.20217,0.97835,0.044155,584.5,-0.93341,-0.17885,-0.31106,389.01,-0.29643,-0.1041,0.94936,132.58
> view matrix models
> #6,-0.18964,0.97834,0.082966,584.74,-0.93863,-0.15584,-0.30772,388.82,-0.28812,-0.13623,0.94785,132.87
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.18964,0.97834,0.082966,660.67,-0.93863,-0.15584,-0.30772,457.34,-0.28812,-0.13623,0.94785,635.56
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.065345,0.98936,-0.12998,663.05,-0.9714,-0.033271,0.2351,459.33,0.22828,0.14163,0.96324,650.64
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.065345,0.98936,-0.12998,503.04,-0.9714,-0.033271,0.2351,474.09,0.22828,0.14163,0.96324,651.72
> show #!183 models
> hide #!6 models
> select subtract #6
Nothing selected
> open /Users/shoichi/Desktop/Top-middle.mrc
Opened Top-middle.mrc as #7, grid size 240,240,240, pixel 2.1, shown at level
0.000178, step 1, values float32
> select add #7
2 models selected
> surface dust #7 size 21
> view matrix models #7,1,0,0,243.57,0,1,0,415.82,0,0,1,122.75
> view matrix models #7,1,0,0,219.29,0,1,0,336.68,0,0,1,622.26
> view matrix models #7,1,0,0,288.54,0,1,0,296.38,0,0,1,591
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.041694,0.92425,0.37952,324.78,-0.99661,0.065421,-0.049832,408.76,-0.070886,-0.37615,0.92384,611.19
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.041694,0.92425,0.37952,478.43,-0.99661,0.065421,-0.049832,269.57,-0.070886,-0.37615,0.92384,552.45
> hide #!59 models
> hide #!73 models
> fitmap #7 inMap #85
Fit map Top-middle.mrc in map Cage_1unit.mrc copy using 42001 points
correlation = 0.9963, correlation about mean = 0.9965, overlap = 5.941e+05
steps = 432, shift = 24.6, angle = 27.5 degrees
Position of Top-middle.mrc (#7) relative to Cage_1unit.mrc copy (#85)
coordinates:
Matrix rotation and translation
0.99997772 0.00341867 -0.00573373 -0.11652290
-0.00351088 0.99986342 -0.01615023 0.52932007
0.00567774 0.01617000 0.99985315 -1.25326889
Axis 0.92425127 -0.32633009 -0.19816222
Axis point 0.00000000 78.18471709 31.46535518
Rotation angle (degrees) 1.00184177
Shift along axis -0.03207896
> fitmap #7 inMap #85
Fit map Top-middle.mrc in map Cage_1unit.mrc copy using 42001 points
correlation = 0.9961, correlation about mean = 0.9962, overlap = 5.937e+05
steps = 164, shift = 0.314, angle = 0.234 degrees
Position of Top-middle.mrc (#7) relative to Cage_1unit.mrc copy (#85)
coordinates:
Matrix rotation and translation
0.99996029 0.00738603 -0.00498719 -0.31489944
-0.00746846 0.99983237 -0.01671693 0.80537795
0.00486288 0.01675352 0.99984783 -1.21031389
Axis 0.88265209 -0.25975683 -0.39172908
Axis point 0.00000000 72.97625042 47.24306371
Rotation angle (degrees) 1.08640233
Shift along axis -0.01303393
> hide #!85 models
> show #!52 models
> view orient
> turn z 20 models #7 center #52
> volume copy #7
Opened Top-middle.mrc copy as #8, grid size 240,240,240, pixel 2.1, shown at
step 1, values float32
> volume #7 show
> turn z 20 models #7 center #52
> volume copy #7
Opened Top-middle.mrc copy as #9, grid size 240,240,240, pixel 2.1, shown at
step 1, values float32
> volume #7 show
> turn z 20 models #7 center #52
> volume copy #7
Opened Top-middle.mrc copy as #10, grid size 240,240,240, pixel 2.1, shown at
step 1, values float32
> volume #7 show
> turn z 20 models #7 center #52
> volume copy #7
Opened Top-middle.mrc copy as #11, grid size 240,240,240, pixel 2.1, shown at
step 1, values float32
> volume #7 show
> turn z 20 models #7 center #52
> volume copy #7
Opened Top-middle.mrc copy as #12, grid size 240,240,240, pixel 2.1, shown at
step 1, values float32
> volume #7 show
> turn z 20 models #7 center #52
> volume copy #7
Opened Top-middle.mrc copy as #13, grid size 240,240,240, pixel 2.1, shown at
step 1, values float32
> volume #7 show
> turn z 20 models #7 center #52
> volume copy #7
Opened Top-middle.mrc copy as #14, grid size 240,240,240, pixel 2.1, shown at
step 1, values float32
> volume #7 show
> turn z 20 models #7 center #52
> volume copy #7
Opened Top-middle.mrc copy as #15, grid size 240,240,240, pixel 2.1, shown at
step 1, values float32
> volume #7 show
> turn z 20 models #7 center #52
> volume copy #7
Opened Top-middle.mrc copy as #17, grid size 240,240,240, pixel 2.1, shown at
step 1, values float32
> volume #7 show
> turn z 20 models #7 center #52
> volume copy #7
Opened Top-middle.mrc copy as #18, grid size 240,240,240, pixel 2.1, shown at
step 1, values float32
> volume #7 show
> turn z 20 models #7 center #52
> volume copy #7
Opened Top-middle.mrc copy as #19, grid size 240,240,240, pixel 2.1, shown at
step 1, values float32
> volume #7 show
> turn z 20 models #7 center #52
> volume copy #7
Opened Top-middle.mrc copy as #38, grid size 240,240,240, pixel 2.1, shown at
step 1, values float32
> volume #7 show
> turn z 20 models #7 center #52
> volume copy #7
Opened Top-middle.mrc copy as #39, grid size 240,240,240, pixel 2.1, shown at
step 1, values float32
> volume #7 show
> turn z 20 models #7 center #52
> volume copy #7
Opened Top-middle.mrc copy as #40, grid size 240,240,240, pixel 2.1, shown at
step 1, values float32
> volume #7 show
> turn z 20 models #7 center #52
> volume copy #7
Opened Top-middle.mrc copy as #41, grid size 240,240,240, pixel 2.1, shown at
step 1, values float32
> volume #7 show
> turn z 20 models #7 center #52
> volume copy #7
Opened Top-middle.mrc copy as #42, grid size 240,240,240, pixel 2.1, shown at
step 1, values float32
> volume #7 show
> surface dust #7 size 21
[Repeated 1 time(s)]
> turn z 20 models #7 center #52
> volume copy #7
Opened Top-middle.mrc copy as #43, grid size 240,240,240, pixel 2.1, shown at
step 1, values float32
> volume #7 show
> surface dust #7-25 size 58.49
> surface dust #7-43 size 58.49
> color #38 #5e5e5e4c models
> hide #!43 models
> show #!43 models
> surface dust #7-43 size 58.49
> hide #!8 models
> show #!8 models
> turn z 20 models #7 center #52
> volume copy #7
Opened Top-middle.mrc copy as #44, grid size 240,240,240, pixel 2.1, shown at
step 1, values float32
> volume #7 show
> surface dust #7-44 size 58.49
> color #39 #5e5e5e4c models
> color #38-44 #5e5e5e4c models
> color #7-15 #5e5e5e4c models
> color #17-19 #5e5e5e4c models
> show #!183.8 models
> show #!183.9 models
> show #!183.10 models
> show #!183.11 models
> show #!183.12 models
> show #!183.13 models
> show #!167 models
> show #!167.6 models
> show #!167.7 models
> show #!167.8 models
> show #!167.9 models
> show #!167.10 models
> show #!167.11 models
> show #!167.12 models
> show #!168 models
> show #!168.6 models
> show #!168.7 models
> show #!168.8 models
> show #!168.9 models
> show #!168.10 models
> show #!168.11 models
> show #!168.12 models
> color #168 #bfb986ff models
> show #!169 models
> color #169 #bfa315ff models
> color #169 #bfaf00ff models
> color #169 #d5c300ff models
> select clear
> show #!169.6 models
> show #!169.7 models
> show #!169.8 models
> show #!169.9 models
> show #!169.10 models
> show #!169.11 models
> show #!169.12 models
> show #!184 models
> show #!184.8 models
> show #!184.9 models
> show #!184.10 models
> show #!184.11 models
> show #!184.12 models
> show #!184.13 models
> show #!184.26 models
> show #!184.27 models
> show #!184.28 models
> show #!184.29 models
> show #!184.30 models
> show #!185 models
> show #!185.1 models
> show #!185.13 models
> show #!185.14 models
> show #!185.44 models
> show #!185.47 models
> show #!185.48 models
> show #!185.51 models
> show #!185.52 models
> show #!182 models
> save /Users/shoichi/Desktop/All-model_HP_for_Topcage_Poster.cxs includeMaps
> true
> color #184 #ff0002ff models
> view orient
> show #!172 models
> show #!259 models
> ui tool show "Side View"
> lighting soft
> save /Users/shoichi/Desktop/Poster-model-top.png supersample 2
> transparentBackground true
> lighting soft
> lighting simple
> turn x 90
[Repeated 10 time(s)]
> show #!312 models
> show #!312-514 models
> show #!53 models
> show #!65 models
> show #!67 models
> turn y -10
[Repeated 9 time(s)]
> color #313 #9ebfabff models
> color #316 #9ebfabff models
> lighting soft
> color #313 #acd1bfff models
> color #313 #9ebfabff models
> color #313 #929292ff models
> color #313 #424242ff models
> color #313 #9ebfabff models
> color #313 #9dbfabff models
> color #313 #8fae9bff models
> color #313 #8fad9bff models
> color #313 #6a8174ff models
> color #313 #70887aff models
> color #316 #70887aff models
> turn z -0.1
[Repeated 1 time(s)]
> color #38 #5e5e5e00 models
> color #38 #5e5e5e99 models
> color #38-44 #5e5e5e99 models
> color #7-15 #5e5e5e99 models
> color #17-19 #5e5e5e99 models
> save /Users/shoichi/Desktop/Poster-model-side.png supersample 2
> transparentBackground true
> turn x 45
> lighting simple
> turn x -45
> turn x -90
> select add #312
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #312,0.99997,0.0080447,2.7675e-05,-4.32,-0.0080447,0.99997,4.7651e-06,4.3326,-2.7635e-05,-4.9876e-06,1,0.017513
> view matrix models
> #312,0.99934,0.036194,0.00012482,-19.163,-0.036194,0.99934,1.9686e-05,19.768,-0.00012402,-2.4191e-05,1,0.079569
> select clear
> turn x 90
> lighting soft
> save /Users/shoichi/Desktop/All-model_HP_for_Topcage_Poster.cxs includeMaps
> true
> save /Users/shoichi/Desktop/Poster-model-side.png supersample 2
> transparentBackground true
> hide #!316 models
> hide #!312 models
> hide #!514 models
> hide #!513 models
> hide #!65 models
> hide #!52 models
> hide #!53 models
> turn x 40
> hide #!313 models
> hide #!484 models
> save /Users/shoichi/Desktop/Poster-model-tilt40a.png supersample 2
> transparentBackground true
> show #!316 models
> hide #!316 models
> show #!313 models
> hide #!313 models
> show #!484 models
> show #!313 models
> color #484 #70887aff models
> save /Users/shoichi/Desktop/Poster-model-tilt40b.png supersample 2
> transparentBackground true
> save /Users/shoichi/Desktop/All-model_HP_for_Topcage_Poster.cxs includeMaps
> true
——— End of log from Mon Sep 8 16:24:57 2025 ———
opened ChimeraX session
Showing Cage_1unit copy.seg - 296 regions, 296 surfaces
> lighting simple
> hide #!6 models
> show #!16 models
> show #!22 models
> hide #!22 models
> show #!52 models
> show #!53 models
> show #!65 models
> show #!97 models
> close #71,73-84
> close #58-59
> close #86
> close #122
> show #!513 models
> show #!514 models
> show #!316 models
> show #!312 models
> view orient
> turn x 90
[Repeated 6 time(s)]
> turn y 20
[Repeated 48 time(s)]
> save /Users/shoichi/Desktop/For-Osaka.cxs includeMaps true
——— End of log from Tue Oct 7 16:41:24 2025 ———
opened ChimeraX session
Showing Cage_1unit copy.seg - 296 regions, 296 surfaces
> close #6
> hide #!5.7 models
> show #!5.7 models
> hide #!5.6 models
> hide #!5.7 models
> hide #!5.8 models
> hide #!5.9 models
> hide #!5.10 models
> hide #!5.11 models
> hide #!5.12 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!8 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!17 models
> select add #183.2
6829 atoms, 6972 bonds, 843 residues, 1 model selected
> select subtract #183.2
1 model selected
> hide #!183.3 models
> hide #!183.4 models
> show #!183.3 models
> hide #!183.3 models
> hide #!183.2 models
> hide #!183.1 models
> hide #!183.18 models
> hide #!183.17 models
> hide #!183.16 models
> show #!183.1 models
> show #!183.2 models
> show #!183.3 models
> show #!183.4 models
> show #!183.16 models
> show #!183.17 models
> show #!183.18 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> show #!12 models
> show #!13 models
> show #!14 models
> show #!15 models
> show #!17 models
> show #!5.6 models
> show #!5.7 models
> show #!5.8 models
> show #!5.9 models
> show #!5.10 models
> show #!5.11 models
> show #!5.12 models
> crossfade
> hide
> #!5.6#!5.7#!5.8#!5.9#!5.10#!5.11#!5.12#!8#!9#!10#!11#!12#!13#!14#!15#!17#!183.1#!183.2#!183.3#!183.4#!183.16#!183.17#!183.18
> models
> wait 50
> view name P50
> save /Users/shoichi/Desktop/For-Osaka-Movie.cxs includeMaps true
——— End of log from Fri Oct 10 16:39:33 2025 ———
opened ChimeraX session
> show #!5.6 models
> show #!5.7 models
> show #!5.8 models
> show #!5.9 models
> show #!5.10 models
> show #!5.11 models
> show #!5.12 models
> crossfade
> hide #!5.5#!5.6#!5.7#!5.8#!5.9#!5.10#!5.11#!5.12 models
> wait 60
> crossfade
> hide #!185.38#!185.37 models
> wait 60
> show #!185.37 models
> show #!185.38 models
> view P1
> view P2
> ui tool show "Side View"
> turn y 90
> volume #316 region 120,0,0,239,239,239
> turn y 90
> volume #316 region 0,120,0,239,239,239
> turn y 90
> volume #316 region 120,0,0,239,239,239
> turn y 90
> volume #313 region 0,60,0,120,120,120
> volume #313 region 60,0,0,120,120,120
> volume #316 region 0,0,0,239,239,239
> volume #316 region 0,120,0,239,239,239
> volume #316 region 120,0,0,239,239,239
> volume #484 region 120,0,0,239,239,239
> volume #316#513#514#16 region 120,0,0,239,239,239
> volume #316#513#514#16#312 region 120,0,0,239,239,239
> show #!5.5 models
> hide #!5.5 models
> select add #5.5
17888 atoms, 18233 bonds, 2172 residues, 1 model selected
> select add #5.12
35776 atoms, 36466 bonds, 4344 residues, 16 models selected
> show #!5.5 models
> show #!5.6 models
> show #!5.7 models
> show #!5.8 models
> show #!5.9 models
> show #!5.10 models
> show #!5.11 models
> show #!5.12 models
> hide #!5.4 models
> show #!5.4 models
> hide #!5.14 models
> show #!5.14 models
> hide #!5.17 models
> hide #!5.16 models
> hide #!5.15 models
> hide #!5.14 models
> hide #!5.18 models
> hide #!5.1 models
> hide #!5.2 models
> hide #!5.3 models
> hide #!167.4 models
> select clear
> show #!167.4 models
> hide #!167.18 models
> show #!167.18 models
> hide #!167.13 models
> show #!167.13 models
> hide #!167.12 models
> hide #!167.11 models
> hide #!167.10 models
> hide #!167.9 models
> hide #!167.8 models
> hide #!167.7 models
> hide #!167.6 models
> hide #!168.11 models
> show #!168.11 models
> hide #!168.11 models
> hide #!168.10 models
> hide #!168.12 models
> hide #!168.9 models
> hide #!168.8 models
> hide #!168.7 models
> hide #!168.6 models
> hide #!169.6 models
> hide #!169.7 models
> show #!169.6 models
> hide #!169.6 models
> hide #!169.8 models
> hide #!169.9 models
> hide #!169.10 models
> hide #!169.11 models
> hide #!169.12 models
> show #!183.1 models
> show #!183.2 models
> show #!183.3 models
> show #!183.4 models
> hide #!183.5 models
> show #!183.5 models
> hide #!183.6 models
> show #!183.6 models
> hide #!183.7 models
> show #!183.7 models
> hide #!183.7 models
> hide #!183.8 models
> hide #!183.9 models
> hide #!183.10 models
> hide #!183.11 models
> show #!183.16 models
> show #!183.17 models
> show #!183.18 models
> hide #!183.12 models
> hide #!183.13 models
> hide #!184.10 models
> hide #!184.11 models
> hide #!184.12 models
> hide #!184.13 models
> hide #!184.14 models
> hide #!184.15 models
> show #!184.15 models
> hide #!184.8 models
> hide #!184.1 models
> hide #!184.25 models
> hide #!184.7 models
> view name P1
> hide #!38 models
> hide #!39 models
> hide #!40 models
> hide #!41 models
> hide #!42 models
> hide #!43 models
> hide #!44 models
> hide #!52 models
> hide #!19 models
> hide #!18 models
> hide #!7 models
> show #!184.7 models
> hide #!184.26 models
> hide #!184.27 models
> hide #!184.28 models
> hide #!184.29 models
> hide #!184.30 models
> hide #!184.24 models
> show #!184.24 models
> hide #!184.31 models
> show #!184.31 models
> hide #!184.9 models
> hide #!185.44 models
> hide #!185.42 models
> show #!185.42 models
> hide #!185.47 models
> hide #!185.48 models
> hide #!185.51 models
> hide #!185.52 models
> hide #!185.1 models
> hide #!185.3 models
> show #!185.3 models
> hide #!185.13 models
> hide #!185.14 models
> hide #!185.17 models
> hide #!185.18 models
> view P1
> show #!52 models
> ui tool show "Side View"
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac13,1
Model Number: Z14J000E1LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6 (24G84)
Kernel Version: Darwin 24.6.0
Time since boot: 10 days, 19 hours, 1 minute
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Q24i-10:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
ASUS PA279:
Resolution: 6016 x 3384
UI Looks like: 3008 x 1692 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 4 weeks ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 4 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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