id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19112 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ 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) {""app_name"":""ChimeraX"",""timestamp"":""2025-10-12 10:51:44.00 -0400"",""app_version"":""1.8.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.6 (24G84)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""AD50BB20-611C-4D24-BA37-A7CBEDF640D9""} { ""uptime"" : 930000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac13,1"", ""coalitionID"" : 13033, ""osVersion"" : { ""train"" : ""macOS 15.6"", ""build"" : ""24G84"", ""releaseType"" : ""User"" }, ""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. 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#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 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 }}} " defect closed normal Window Toolkit duplicate all ChimeraX