![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 months ago
Last modified 2 months ago
#19024 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.6-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
Thread 0x00000003168ab000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031589f000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000314893000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000313887000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031287b000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031186f000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000310863000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030f857000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030e84b000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030d83f000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030c833000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030b827000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030a81b000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x000000020a2220c0 (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, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, 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, chimerax.segment._segment (total: 60)
{"app_name":"ChimeraX","timestamp":"2025-09-29 00:48:47.00 -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":"3DFF73CF-CAB3-464F-96E1-BB5B914A8C18"}
{
"uptime" : 4300000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac13,1",
"coalitionID" : 13198,
"osVersion" : {
"train" : "macOS 15.6",
"build" : "24G84",
"releaseType" : "User"
},
"captureTime" : "2025-09-29 00:48:45.0676 -0400",
"codeSigningMonitor" : 1,
"incident" : "3DFF73CF-CAB3-464F-96E1-BB5B914A8C18",
"pid" : 8848,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-09-28 17:22:33.1110 -0400",
"procStartAbsTime" : 104623720205176,
"procExitAbsTime" : 105266245235486,
"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" : "C7B9956A-D635-442A-9D14-EA5F4A39739A",
"wakeTime" : 4381149,
"sleepWakeUUID" : "33DCD15E-AB4C-4937-83CB-3B0726637761",
"sip" : "enabled",
"vmRegionInfo" : "0x62d9cd21b5a8 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x0000e2d9cd21b5a8","rawCodes":[1,249425077319080],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000e2d9cd21b5a8 -> 0x000062d9cd21b5a8 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":8848},
"ktriageinfo" : "CL - (arg = 0x0) cluster_pagein past EOF\nAPFS - (arg = 0x3bcc001600200040) cluster_pagein() failed\nVM - (arg = 0x1900000016) Filesystem pagein returned an error in vnode_pagein\nVM - (arg = 0x0) Page has error bit set\nCL - (arg = 0x0) cluster_pagein past EOF\n",
"vmregioninfo" : "0x62d9cd21b5a8 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Manuscript/09262025/New Images/Composition-before-JMB-color.cxs"
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Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
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Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
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Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200,
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Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #180, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #181, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #182, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #185, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #186, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #187, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #188, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #189, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #190, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #191, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened Single-MotA-ring.mrc gaussian as #192, grid size 200,200,200, pixel
2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #193, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #194, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #195, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #196, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #199, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #200, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #202, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #203, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #204, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #206, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #207, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #208, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #214, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #215, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #219, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #220, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #221, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #222, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #223, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #224, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #225, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14,
shown at level 0.0112, step 1, values float32
Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel
2.14, shown at level 0.00974, step 1, values float32
Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at
level 0.157, step 1, values float32
Opened C-Vrings.mrc as #4, grid size 250,250,250, pixel 4.3, shown at level
0.0283, step 1, values float32
Opened 1unit_PflABCD.mrc as #5, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Log from Sat Sep 27 12:14:37 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/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Manuscript/09202025/Composition-with-color.cxs"
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137,
step 1, values float32
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
level 0.027, step 1, values float32
Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
step 1, values float32
Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at
level 0.0166, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #107, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #108, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #109, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #111, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #112, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #113, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #114, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #115, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #116, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #117, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #118, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #119, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #120, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #121, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #122, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #123, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #124, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #125, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #126, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #127, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #128, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #129, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #130, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #131, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #132, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #133, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #134, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #135, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #136, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #137, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #138, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #139, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #140, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #141, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #142, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #143, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #144, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #145, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #146, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #147, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #148, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #149, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #150, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #151, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #152, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #153, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #154, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #155, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #156, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #157, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #158, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #159, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #160, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #161, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #162, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #163, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #164, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #165, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #166, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #167, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #168, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #169, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #170, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #171, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #172, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #173, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #174, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #175, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #176, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #177, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #178, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #180, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #181, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #182, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #185, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #186, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #187, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #188, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #189, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #190, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #191, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened Single-MotA-ring.mrc gaussian as #192, grid size 200,200,200, pixel
2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #193, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #194, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #195, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #196, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #199, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #200, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #202, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #203, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #204, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #206, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #207, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #208, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #214, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #215, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #219, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #220, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #221, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #222, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #223, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #224, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #225, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14,
shown at level 0.0112, step 1, values float32
Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel
2.14, shown at level 0.00974, step 1, values float32
Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at
level 0.157, step 1, values float32
Opened C-Vrings.mrc as #4, grid size 250,250,250, pixel 4.3, shown at level
0.0283, step 1, values float32
Opened 1unit_PflABCD.mrc as #5, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Log from Sat Sep 20 19:10:23 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/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/09122025/For_Composition-
> maps/Building_Whole_Model_09102025_Backup.cxs"
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137,
step 1, values float32
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
level 0.027, step 1, values float32
Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
step 1, values float32
Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at
level 0.0166, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #107, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #108, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #109, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #111, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #112, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #113, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #114, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #115, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #116, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #117, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #118, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #119, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #120, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #121, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #122, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #123, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #124, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #125, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #126, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #127, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #128, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #129, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #130, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #131, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #132, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #133, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #134, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #135, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #136, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #137, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #138, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #139, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #140, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #141, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #142, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #143, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #144, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #145, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #146, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #147, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #148, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #149, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #150, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #151, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #152, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #153, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #154, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #155, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #156, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #157, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #158, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #159, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #160, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #161, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #162, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #163, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #164, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #165, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #166, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #167, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #168, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #169, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #170, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #171, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #172, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #173, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #174, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #175, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #176, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #177, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #178, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #180, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #181, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #182, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #185, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #186, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #187, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #188, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #189, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #190, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #191, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened Single-MotA-ring.mrc gaussian as #192, grid size 200,200,200, pixel
2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #193, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #194, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #195, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #196, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #199, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #200, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #202, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #203, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #204, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #206, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #207, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #208, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #214, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #215, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #219, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #220, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #221, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #222, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #223, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #224, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #225, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14,
shown at level 0.0112, step 1, values float32
Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel
2.14, shown at level 0.00974, step 1, values float32
Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at
level 0.157, step 1, values float32
Opened C-Vrings.mrc as #4, grid size 250,250,250, pixel 4.3, shown at level
0.0283, step 1, values float32
Opened 1unit_PflABCD.mrc as #5, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Log from Wed Sep 10 10:46:36 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shoichi/Desktop/For_Composition-
> maps/Building_Whole_Model_09102025.cxs
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137,
step 1, values float32
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
level 0.027, step 1, values float32
Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
step 1, values float32
Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at
level 0.0166, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #107, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #108, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #109, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #111, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #112, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #113, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #114, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #115, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #116, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #117, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #118, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #119, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #120, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #121, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #122, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #123, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #124, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #125, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #126, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #127, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #128, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #129, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #130, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #131, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #132, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #133, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #134, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #135, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #136, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #137, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #138, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #139, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #140, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #141, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #142, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #143, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #144, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #145, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #146, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #147, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #148, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #149, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #150, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #151, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #152, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #153, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #154, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #155, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #156, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #157, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #158, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #159, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #160, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #161, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #162, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #163, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #164, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #165, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #166, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #167, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #168, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #169, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #170, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #171, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #172, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #173, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #174, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #175, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #176, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #177, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #178, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #180, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #181, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #182, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #185, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #186, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #187, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #188, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #189, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #190, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #191, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened Single-MotA-ring.mrc gaussian as #192, grid size 200,200,200, pixel
2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #193, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #194, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #195, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #196, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #199, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #200, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #202, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #203, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #204, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #206, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #207, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #208, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #214, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #215, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #219, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #220, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #221, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #222, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #223, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #224, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #225, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14,
shown at level 0.0112, step 1, values float32
Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel
2.14, shown at level 0.00974, step 1, values float32
Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at
level 0.157, step 1, values float32
Opened C-Vrings.mrc as #4, grid size 250,250,250, pixel 4.3, shown at level
0.0283, step 1, values float32
Opened 1unit_PflABCD.mrc as #5, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Log from Wed Sep 10 10:14:24 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shoichi/Desktop/For_Composition-
> maps/Building_Whole_Model_09102025.cxs
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137,
step 1, values float32
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
level 0.027, step 1, values float32
Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
step 1, values float32
Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at
level 0.0166, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #107, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #108, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #109, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #111, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #112, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #113, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #114, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #115, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #116, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #117, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #118, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #119, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #120, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #121, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #122, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #123, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #124, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #125, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #126, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #127, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #128, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #129, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #130, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #131, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #132, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #133, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #134, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #135, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #136, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #137, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
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pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #199, grid size 200,200,200,
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200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
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Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel
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Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at
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Opened C-Vrings.mrc as #4, grid size 250,250,250, pixel 4.3, shown at level
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Log from Wed Sep 10 09:47:44 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/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/09092025/For_Composition-
> maps/Cleanup3_Building_Composition.cxs"
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Opened 1xMotBpg-09092025.mrc gaussian copy as #140, grid size 200,200,200,
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Opened 1xPflC.mrc gaussian copy as #162, grid size 200,200,200, pixel 2.14,
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Opened 1xPflC.mrc gaussian copy as #167, grid size 200,200,200, pixel 2.14,
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Opened 1xPflC.mrc gaussian copy as #168, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #169, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #170, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #171, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #172, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #173, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #174, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #175, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #176, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #177, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #178, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #180, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #181, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #182, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #185, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #186, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #187, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #188, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #189, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #190, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #191, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened Single-MotA-ring.mrc gaussian as #192, grid size 200,200,200, pixel
2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #193, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #194, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #195, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #196, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #199, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #200, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #202, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #203, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #204, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #206, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #207, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #208, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #214, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #215, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #219, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #220, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #221, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #222, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #223, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #224, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #225, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14,
shown at level 0.0112, step 1, values float32
Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel
2.14, shown at level 0.00974, step 1, values float32
Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at
level 0.157, step 1, values float32
Opened C-Vrings.mrc as #4, grid size 250,250,250, pixel 4.3, shown at level
0.0283, step 1, values float32
Log from Tue Sep 9 15:35:44 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shoichi/Desktop/For_Composition-
> maps/Cleanup_Building_Composition.cxs
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_rim.mrc as #2, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137,
step 1, values float32
Opened C-ring-stators.mrc as #77, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened C-Vring.mrc as #80, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
level 0.027, step 1, values float32
Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
step 1, values float32
Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at
level 0.0166, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #107, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #108, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #109, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #111, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #112, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #113, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #114, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #115, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #116, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #117, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #118, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #119, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #120, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #121, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #122, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #123, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #124, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #125, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #126, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #127, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #128, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #129, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #130, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #131, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #132, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #133, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #134, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #135, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #136, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #137, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #138, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #139, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #140, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #141, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #142, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #143, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #144, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #145, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #146, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #147, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #148, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #149, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #150, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #151, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #152, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #153, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #154, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #155, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #156, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #157, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #158, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #159, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #160, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #161, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #162, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #163, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #164, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #165, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #166, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #167, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #168, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #169, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #170, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #171, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #172, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #173, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #174, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #175, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #176, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #177, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #178, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #180, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #181, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #182, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #185, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #186, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #187, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #188, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #189, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #190, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #191, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened Single-MotA-ring.mrc gaussian as #192, grid size 200,200,200, pixel
2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #193, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #194, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #195, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #196, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #199, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #200, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #202, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #203, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #204, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #206, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #207, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #208, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #214, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #215, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #219, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #220, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #221, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #222, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #223, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #224, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #225, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14,
shown at level 0.0112, step 1, values float32
Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel
2.14, shown at level 0.00974, step 1, values float32
Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at
level 0.157, step 1, values float32
Log from Tue Sep 9 13:34:58 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shoichi/Desktop/For_Composition-maps/Building_Composition.cxs
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_rim.mrc as #2, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137,
step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #5, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #6, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #7, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #8, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #9, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #10, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #11, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #12, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #13, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #14, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #15, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #16, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #17, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #18, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #19, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #20, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc as #21, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #22, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #23, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #24, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #25, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #26, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #27, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #28, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #29, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #30, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #31, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #32, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #33, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #34, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #35, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #36, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #37, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #38, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #41, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #39, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #40, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #42, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #43, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #44, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #45, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #46, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #47, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #48, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #49, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #50, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #51, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #52, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #53, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #54, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #55, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #56, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL.mrc as #57, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc as #58, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #59, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #60, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #61, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #62, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #63, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #64, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #65, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #66, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #67, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #68, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #69, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #70, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #71, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #72, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #73, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #74, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #75, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened MS-ring.mrc as #76, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened E-ring.mrc gaussian as #78, grid size 250,250,250, pixel 4.3, shown at
level 0.114, step 1, values float32
Opened 1unit_rim.mrc gaussian as #4, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Basal_disk.mrc gaussian as #79, grid size 250,250,250, pixel 4.3, shown
at level 0.0595, step 1, values float32
Opened C-ring-stators.mrc as #77, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened C-Vring.mrc as #80, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened MotB.mrc as #81, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened PflC.mrc gaussian as #85, grid size 250,250,250, pixel 4.3, shown at
level 0.0439, step 1, values float32
Opened PflD.mrc as #86, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened PilM.mrc gaussian as #84, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
level 0.027, step 1, values float32
Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
step 1, values float32
Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at
level 0.0166, step 1, values float32
Opened C17-FlgY_New.mrc as #90, grid size 256,256,256, pixel 2.14, shown at
level 0.0212, step 1, values float32
Opened MS-ring_New.mrc as #91, grid size 256,256,256, pixel 2.14, shown at
level 0.0165, step 1, values float32
Opened Single_Cage_unit.mrc as #92, grid size 200,200,200, pixel 2.14, shown
at level 0.00159, step 1, values float32
Opened 1unit_PflABCD.mrc as #94, grid size 200,200,200, pixel 2.14, shown at
level 0.0064, step 1, values float32
Opened 1xMotBpg-09092025.mrc as #93, grid size 200,200,200, pixel 2.14, shown
at level 0.00231, step 1, values float32
Opened 1xPflD.mrc as #95, grid size 200,200,200, pixel 2.14, shown at level
0.00228, step 1, values float32
Opened 1xPflC.mrc as #96, grid size 200,200,200, pixel 2.14, shown at level
0.00265, step 1, values float32
Opened Single-MotA-ring.mrc as #97, grid size 200,200,200, pixel 2.14, shown
at level 0.00252, step 1, values float32
Opened 1xPflAB_region.mrc as #98, grid size 200,200,200, pixel 2.14, shown at
level 0.00102, step 1, values float32
Log from Tue Sep 9 11:45:50 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shoichi/Desktop/For_Composition-maps/Building_Composition.cxs
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_rim.mrc as #2, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137,
step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #5, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #6, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #7, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #8, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #9, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #10, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #11, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #12, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #13, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #14, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #15, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #16, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #17, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #18, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #19, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #20, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc as #21, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #22, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #23, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #24, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #25, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #26, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #27, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #28, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #29, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #30, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #31, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #32, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #33, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #34, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #35, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #36, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #37, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #38, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #41, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #39, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #40, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #42, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #43, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #44, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #45, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #46, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #47, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #48, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #49, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #50, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #51, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #52, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #53, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #54, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #55, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #56, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL.mrc as #57, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc as #58, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #59, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #60, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #61, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #62, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #63, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #64, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #65, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #66, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #67, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #68, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #69, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #70, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #71, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #72, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #73, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #74, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #75, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened MS-ring.mrc as #76, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened E-ring.mrc gaussian as #78, grid size 250,250,250, pixel 4.3, shown at
level 0.114, step 1, values float32
Opened 1unit_rim.mrc gaussian as #4, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Basal_disk.mrc gaussian as #79, grid size 250,250,250, pixel 4.3, shown
at level 0.0595, step 1, values float32
Opened C-ring-stators.mrc as #77, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened C-Vring.mrc as #80, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened MotB.mrc as #81, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened PflC.mrc gaussian as #85, grid size 250,250,250, pixel 4.3, shown at
level 0.0439, step 1, values float32
Opened PflD.mrc as #86, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened PilM.mrc gaussian as #84, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
level 0.027, step 1, values float32
Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
step 1, values float32
Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at
level 0.0166, step 1, values float32
Opened C17-FlgY_New.mrc as #90, grid size 256,256,256, pixel 2.14, shown at
level 0.0212, step 1, values float32
Opened MS-ring_New.mrc as #91, grid size 256,256,256, pixel 2.14, shown at
level 0.0165, step 1, values float32
Opened Single_Cage_unit.mrc as #92, grid size 200,200,200, pixel 2.14, shown
at level 0.00159, step 1, values float32
Opened Single_MotBpg_unit.mrc as #93, grid size 200,200,200, pixel 2.14, shown
at level 0.000906, step 1, values float32
Log from Tue Sep 9 10:34:35 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shoichi/Desktop/For_Composition-maps/Global_Segment_Fig1.cxs
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_rim.mrc as #2, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137,
step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #5, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #6, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #7, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #8, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #9, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #10, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #11, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #12, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #13, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #14, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #15, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #16, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #17, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #18, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #19, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #20, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc as #21, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #22, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #23, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #24, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #25, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #26, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #27, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #28, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #29, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #30, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #31, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #32, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #33, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #34, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #35, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #36, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #37, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #38, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #41, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #39, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #40, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #42, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #43, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #44, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #45, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #46, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #47, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #48, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #49, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #50, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #51, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #52, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #53, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #54, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #55, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #56, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL.mrc as #57, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc as #58, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #59, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #60, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #61, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #62, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #63, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #64, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #65, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #66, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #67, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #68, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #69, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #70, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #71, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #72, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #73, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #74, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #75, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened MS-ring.mrc as #76, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened E-ring.mrc gaussian as #78, grid size 250,250,250, pixel 4.3, shown at
level 0.114, step 1, values float32
Opened 1unit_rim.mrc gaussian as #4, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Basal_disk.mrc gaussian as #79, grid size 250,250,250, pixel 4.3, shown
at level 0.0595, step 1, values float32
Opened C-ring-stators.mrc as #77, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened C-Vring.mrc as #80, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened MotB.mrc as #81, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened PflC.mrc gaussian as #85, grid size 250,250,250, pixel 4.3, shown at
level 0.0439, step 1, values float32
Opened PflD.mrc as #86, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened PilM.mrc gaussian as #84, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
level 0.027, step 1, values float32
Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
step 1, values float32
Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at
level 0.0166, step 1, values float32
Log from Tue Sep 9 09:30:49 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/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/07252025/Original-map-deposit/Seg/Figure-1.cxs"
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_rim.mrc as #2, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137,
step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #5, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #6, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #7, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #8, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #9, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #10, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #11, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #12, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #13, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #14, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #15, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #16, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #17, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #18, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #19, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_rim.mrc gaussian copy as #20, grid size 250,250,250, pixel 4.3,
shown at level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc as #21, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #22, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #23, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #24, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #25, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #26, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #27, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #28, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #29, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #30, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #31, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #32, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #33, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #34, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #35, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #36, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #37, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened 1unit_PflA.mrc copy as #38, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #41, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #39, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #40, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #42, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #43, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #44, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #45, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #46, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #47, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #48, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #49, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #50, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #51, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #52, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #53, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #54, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #55, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL_out.mrc copy as #56, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened FliL.mrc as #57, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc as #58, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #59, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #60, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #61, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #62, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #63, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #64, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #65, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #66, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #67, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #68, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #69, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #70, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #71, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #72, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #73, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #74, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Cage-Mono-Good.mrc copy as #75, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened MS-ring.mrc as #76, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened E-ring.mrc gaussian as #78, grid size 250,250,250, pixel 4.3, shown at
level 0.114, step 1, values float32
Opened 1unit_rim.mrc gaussian as #4, grid size 250,250,250, pixel 4.3, shown
at level 0.0137, step 1, values float32
Opened Basal_disk.mrc gaussian as #79, grid size 250,250,250, pixel 4.3, shown
at level 0.0595, step 1, values float32
Opened C-ring-stators.mrc as #77, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened C-Vring.mrc as #80, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened MotB.mrc as #81, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened PflC.mrc gaussian as #85, grid size 250,250,250, pixel 4.3, shown at
level 0.0439, step 1, values float32
Opened PflD.mrc as #86, grid size 250,250,250, pixel 4.3, shown at level
0.0137, step 1, values float32
Opened PilM.mrc gaussian as #84, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
level 0.027, step 1, values float32
Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
step 1, values float32
Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at
level 0.0166, step 1, values float32
Log from Fri Jul 25 22:07:01 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/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/07252025/Original-map-deposit/Seg/Segmentation.cxs"
Opened L0.12-Wild-type_EMD_45507.mrc as #1, grid size 250,250,250, pixel 4.3,
shown at level 0.0107, step 1, values float32
Opened OM.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0107,
step 1, values float32
Opened L0.12-Wild-type_EMD_45507_imasked as #4, grid size 250,250,250, pixel
4.3, shown at level 0.0107, step 1, values float32
Opened Basal_disk.mrc as #5, grid size 250,250,250, pixel 4.3, shown at level
0.0107, step 1, values float32
Opened L0_imasked as #6, grid size 250,250,250, pixel 4.3, shown at level
0.0107, step 1, values float32
Opened LP-ring.mrc as #7, grid size 250,250,250, pixel 4.3, shown at level
0.0107, step 1, values float32
Opened L0_imasked_imasked as #8, grid size 250,250,250, pixel 4.3, shown at
level 0.0107, step 1, values float32
Opened PflC.mrc as #9, grid size 250,250,250, pixel 4.3, shown at level
0.0107, step 1, values float32
Opened L0_imasked_imasked_imasked as #10, grid size 250,250,250, pixel 4.3,
shown at level 0.0107, step 1, values float32
Opened PflD.mrc as #11, grid size 250,250,250, pixel 4.3, shown at level
0.0107, step 1, values float32
Opened L0_imasked_imasked_imasked_imasked as #12, grid size 250,250,250, pixel
4.3, shown at level 0.0107, step 1, values float32
Opened L0_imasked_imasked_imasked_imasked_imasked as #13, grid size
250,250,250, pixel 4.3, shown at level 0.0107, step 1, values float32
Opened L0_imasked_imasked_imasked_imasked_imasked_imasked as #14, grid size
250,250,250, pixel 4.3, shown at level 0.0107, step 1, values float32
Opened PilM.mrc as #15, grid size 250,250,250, pixel 4.3, shown at level
0.0107, step 1, values float32
Opened L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked as #16, grid
size 250,250,250, pixel 4.3, shown at level 0.0107, step 1, values float32
Opened Exp_ATP.mrc as #17, grid size 250,250,250, pixel 4.3, shown at level
0.0107, step 1, values float32
Opened L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#18, grid size 250,250,250, pixel 4.3, shown at level 0.0107, step 1, values
float32
Opened C-ring-stators.mrc as #19, grid size 250,250,250, pixel 4.3, shown at
level 0.0107, step 1, values float32
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#20, grid size 250,250,250, pixel 4.3, shown at level 0.0107, step 1, values
float32
Opened C-Vring.mrc as #21, grid size 250,250,250, pixel 4.3, shown at level
0.0107, step 1, values float32
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #22, grid size 250,250,250, pixel 4.3, shown at level 0.0107, step 1,
values float32
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #23, grid size 250,250,250, pixel 4.3, shown at level 0.0107, step 1,
values float32
Opened Cage-C17.mrc as #24, grid size 250,250,250, pixel 4.3, shown at level
0.0107, step 1, values float32
Opened Cage-Mono-Good.mrc as #25, grid size 250,250,250, pixel 4.3, shown at
level 0.0107, step 1, values float32
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #26, grid size 250,250,250, pixel 4.3, shown at level 0.0107, step 1,
values float32
Opened MotB.mrc as #27, grid size 250,250,250, pixel 4.3, shown at level
0.0107, step 1, values float32
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #28, grid size 250,250,250, pixel 4.3, shown at level 0.0107, step 1,
values float32
Log from Fri Jul 25 14:31:14 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shoichi/Desktop/Docking_models_07232025.cxs format session
Opened PflCD.mrc as #1, grid size 200,200,200, pixel 2.14, shown at level
0.00703, step 1, values float32
Opened Cage-PflAB.mrc as #2, grid size 200,200,200, pixel 2.14, shown at level
0.00703, step 1, values float32
Opened PflCD.mrc gaussian as #3, grid size 200,200,200, pixel 2.14, shown at
level 0.00136, step 1, values float32
Opened Cage-PflAB.mrc gaussian as #4, grid size 200,200,200, pixel 2.14, shown
at level 0.00131, step 1, values float32
Opened PflC-polished.mrc as #29, grid size 200,200,200, pixel 2.14, shown at
level 0.00703, step 1, values float32
Opened Cage-polished.mrc as #30, grid size 200,200,200, pixel 2.14, shown at
level 0.00703, step 1, values float32
Opened PflC-polished.mrc gaussian as #31, grid size 200,200,200, pixel 2.14,
shown at level 0.00135, step 1, values float32
Opened Cage-polished.mrc gaussian as #32, grid size 200,200,200, pixel 2.14,
shown at level 0.00135, step 1, values float32
Log from Wed Jul 23 17:25:02 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/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/PflCD_Docking_model_Fig3/REDO/Docking_models_07232025.cxs"
Opened PflCD.mrc as #1, grid size 200,200,200, pixel 2.14, shown at level
0.00703, step 1, values float32
Opened Cage-PflAB.mrc as #2, grid size 200,200,200, pixel 2.14, shown at level
0.00703, step 1, values float32
Opened PflCD.mrc gaussian as #3, grid size 200,200,200, pixel 2.14, shown at
level 0.00136, step 1, values float32
Opened Cage-PflAB.mrc gaussian as #4, grid size 200,200,200, pixel 2.14, shown
at level 0.00131, step 1, values float32
Log from Wed Jul 23 10:13:39 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/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/PflCD_Docking_model_Fig3/REDO/Docking_models.cxs"
Opened PflCD.mrc as #1, grid size 200,200,200, pixel 2.14, shown at level
0.00703, step 1, values float32
Opened Cage-PflAB.mrc as #2, grid size 200,200,200, pixel 2.14, shown at level
0.00703, step 1, values float32
Opened PflCD.mrc gaussian as #3, grid size 200,200,200, pixel 2.14, shown at
level 0.00136, step 1, values float32
Opened Cage-PflAB.mrc gaussian as #4, grid size 200,200,200, pixel 2.14, shown
at level 0.00131, step 1, values float32
Log from Tue Jul 22 22:37:33 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/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/07222025/CJSegment_no-mask/Segment-nomask.cxs"
Opened Rev-CJFlgYPlfAB-2.1A.mrc as #1, grid size 200,200,200, pixel 2.14,
shown at level 0.00711, step 1, values float32
Opened Rev-CJFlgYPlfAB-2.1A_imasked as #3, grid size 200,200,200, pixel 2.14,
shown at level 0.00711, step 1, values float32
Opened Rev-CJFlgYPlfAB-2_imasked as #4, grid size 200,200,200, pixel 2.14,
shown at level 0.00711, step 1, values float32
Opened PflC2.mrc as #5, grid size 200,200,200, pixel 2.14, shown at level
0.00711, step 1, values float32
Opened Rev-CJFlgYPlfAB-2_imasked_imasked as #6, grid size 200,200,200, pixel
2.14, shown at level 0.00711, step 1, values float32
Opened PflC1.mrc as #7, grid size 200,200,200, pixel 2.14, shown at level
0.00711, step 1, values float32
Opened Rev-CJFlgYPlfAB-2_imasked_imasked_imasked as #8, grid size 200,200,200,
pixel 2.14, shown at level 0.00711, step 1, values float32
Opened PflD.mrc as #9, grid size 200,200,200, pixel 2.14, shown at level
0.00711, step 1, values float32
Opened Rev-CJFlgYPlfAB-2_imasked_imasked_imasked_imasked as #10, grid size
200,200,200, pixel 2.14, shown at level 0.00711, step 1, values float32
Opened MotBpg.mrc as #11, grid size 200,200,200, pixel 2.14, shown at level
0.00711, step 1, values float32
Opened Rev-CJFlgYPlfAB-2_imasked_imasked_imasked_imasked_imasked as #12, grid
size 200,200,200, pixel 2.14, shown at level 0.00711, step 1, values float32
Opened PflA-FlgY.mrc as #13, grid size 200,200,200, pixel 2.14, shown at level
0.00711, step 1, values float32
Opened Rev-CJFlgYPlfAB-2_imasked_imasked_imasked_imasked_imasked_imasked as
#14, grid size 200,200,200, pixel 2.14, shown at level 0.00711, step 1, values
float32
Log from Tue Jul 22 14:40:48 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/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-PflCD/For_Cage_PflCD.cxs"
Opened 3xPflAB.mrc as #1, grid size 200,200,200, pixel 2.14, shown at level
0.0134, step 1, values float32
Opened 3xFliL.mrc as #2, grid size 200,200,200, pixel 2.14, shown at level
0.00115, step 1, values float32
Opened PflABY.mrc as #6, grid size 200,200,200, pixel 2.14, shown at level
0.00115, step 1, values float32
Opened PflABY.mrc gaussian as #7, grid size 200,200,200, pixel 2.14, shown at
level 0.00115, step 1, values float32
Opened PflABY_out_side-spokes.mrc gaussian as #11, grid size 200,200,200,
pixel 2.14, shown at level 0.00115, step 1, values float32
Opened Single-Spoke-ring.mrc as #14, grid size 200,200,200, pixel 2.14, shown
at level 0.00115, step 1, values float32
Opened Single-Spoke-ring.mrc gaussian as #9, grid size 200,200,200, pixel
2.14, shown at level 0.000387, step 1, values float32
Opened combination map 10 as #15, grid size 96,90,42, pixel 3.33, shown at
level 0.0635, step 1, values float32
Opened MS-ring.mrc as #16, grid size 200,200,200, pixel 2.14, shown at level
0.00124, step 1, values float32
Opened MS-ring.mrc gaussian as #17, grid size 200,200,200, pixel 2.14, shown
at level 0.00248, step 1, values float32
Opened PflC.mrc as #19, grid size 200,200,200, pixel 2.14, shown at level
0.00752, step 1, values float32
Opened PflD.mrc as #20, grid size 200,200,200, pixel 2.14, shown at level
0.00101, step 1, values float32
Opened Cages2.mrc as #21, grid size 200,200,200, pixel 2.14, shown at level
0.00187, step 1, values float32
Opened Rev-CJFlgYPlfAB-msk-2.1A.mrc as #22, grid size 200,200,200, pixel 2.14,
shown at level 0.00187, step 1, values float32
Opened Polished-PflCD.mrc as #29, grid size 200,200,200, pixel 2.14, shown at
level 0.00187, step 1, values float32
Opened Polished-PflCD.mrc gaussian as #26, grid size 200,200,200, pixel 2.14,
shown at level 0.00102, step 1, values float32
Opened Polished_Cage2.mrc as #28, grid size 200,200,200, pixel 2.14, shown at
level 0.00187, step 1, values float32
Opened Polished-IM2.mrc as #32, grid size 200,200,200, pixel 2.14, shown at
level 0.00146, step 1, values float32
Opened Polished_Cage2.mrc gaussian as #30, grid size 200,200,200, pixel 2.14,
shown at level 0.00184, step 1, values float32
Opened Polished-IM2.mrc gaussian as #31, grid size 200,200,200, pixel 2.14,
shown at level 0.000294, step 1, values float32
Opened Polished-PflCD_single.mrc as #33, grid size 200,200,200, pixel 2.14,
shown at level 0.00102, step 1, values float32
Opened Single-Cage.mrc as #34, grid size 200,200,200, pixel 2.14, shown at
level 0.00184, step 1, values float32
Opened Single-Cage-arch.mrc as #35, grid size 200,200,200, pixel 2.14, shown
at level 0.00184, step 1, values float32
Opened combination map 10 as #39, grid size 42,39,48, pixel 3.33, shown at
level 0.0506, step 1, values float32
Opened combination map 10 as #42, grid size 38,53,56, pixel 3.33, shown at
level 0.0458, step 1, values float32
Log from Sat Jul 12 20:19:26 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/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-PflCD/For_PflCD.cxs"
Opened 3xPflAB.mrc as #1, grid size 200,200,200, pixel 2.14, shown at level
0.0134, step 1, values float32
Opened 3xFliL.mrc as #2, grid size 200,200,200, pixel 2.14, shown at level
0.00115, step 1, values float32
Opened PflABY.mrc as #6, grid size 200,200,200, pixel 2.14, shown at level
0.00115, step 1, values float32
Opened PflABY.mrc gaussian as #7, grid size 200,200,200, pixel 2.14, shown at
level 0.00115, step 1, values float32
Opened PflABY_out_side-spokes.mrc gaussian as #11, grid size 200,200,200,
pixel 2.14, shown at level 0.00115, step 1, values float32
Opened Single-Spoke-ring.mrc as #14, grid size 200,200,200, pixel 2.14, shown
at level 0.00115, step 1, values float32
Opened Single-Spoke-ring.mrc gaussian as #9, grid size 200,200,200, pixel
2.14, shown at level 0.000387, step 1, values float32
Opened combination map 10 as #15, grid size 96,90,42, pixel 3.33, shown at
level 0.0635, step 1, values float32
Opened MS-ring.mrc as #16, grid size 200,200,200, pixel 2.14, shown at level
0.00124, step 1, values float32
Opened MS-ring.mrc gaussian as #17, grid size 200,200,200, pixel 2.14, shown
at level 0.00248, step 1, values float32
Opened PflC.mrc as #19, grid size 200,200,200, pixel 2.14, shown at level
0.00752, step 1, values float32
Opened PflD.mrc as #20, grid size 200,200,200, pixel 2.14, shown at level
0.00101, step 1, values float32
Opened Cages2.mrc as #21, grid size 200,200,200, pixel 2.14, shown at level
0.00187, step 1, values float32
Opened Rev-CJFlgYPlfAB-msk-2.1A.mrc as #22, grid size 200,200,200, pixel 2.14,
shown at level 0.00187, step 1, values float32
Opened Polished-PflCD.mrc as #29, grid size 200,200,200, pixel 2.14, shown at
level 0.00187, step 1, values float32
Opened Polished-PflCD.mrc gaussian as #26, grid size 200,200,200, pixel 2.14,
shown at level 0.00102, step 1, values float32
Opened Polished_Cage2.mrc as #28, grid size 200,200,200, pixel 2.14, shown at
level 0.00187, step 1, values float32
Opened Polished-IM2.mrc as #32, grid size 200,200,200, pixel 2.14, shown at
level 0.00146, step 1, values float32
Opened Polished_Cage2.mrc gaussian as #30, grid size 200,200,200, pixel 2.14,
shown at level 0.00184, step 1, values float32
Opened Polished-IM2.mrc gaussian as #31, grid size 200,200,200, pixel 2.14,
shown at level 0.000294, step 1, values float32
Opened Polished-PflCD_single.mrc as #33, grid size 200,200,200, pixel 2.14,
shown at level 0.00102, step 1, values float32
Opened Single-Cage.mrc as #34, grid size 200,200,200, pixel 2.14, shown at
level 0.00184, step 1, values float32
Opened Single-Cage-arch.mrc as #35, grid size 200,200,200, pixel 2.14, shown
at level 0.00184, step 1, values float32
Log from Fri Jul 11 22:22:46 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/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-PflCD/PflCD.cxs"
Opened 3xPflAB.mrc as #1, grid size 200,200,200, pixel 2.14, shown at level
0.0134, step 1, values float32
Opened 3xFliL.mrc as #2, grid size 200,200,200, pixel 2.14, shown at level
0.00115, step 1, values float32
Opened PflABY.mrc as #6, grid size 200,200,200, pixel 2.14, shown at level
0.00115, step 1, values float32
Opened PflABY.mrc gaussian as #7, grid size 200,200,200, pixel 2.14, shown at
level 0.00115, step 1, values float32
Opened PflABY_out_side-spokes.mrc gaussian as #11, grid size 200,200,200,
pixel 2.14, shown at level 0.00115, step 1, values float32
Opened Single-Spoke-ring.mrc as #14, grid size 200,200,200, pixel 2.14, shown
at level 0.00115, step 1, values float32
Opened Single-Spoke-ring.mrc gaussian as #9, grid size 200,200,200, pixel
2.14, shown at level 0.000387, step 1, values float32
Opened combination map 10 as #15, grid size 96,90,42, pixel 3.33, shown at
level 0.0635, step 1, values float32
Opened MS-ring.mrc as #16, grid size 200,200,200, pixel 2.14, shown at level
0.00124, step 1, values float32
Opened MS-ring.mrc gaussian as #17, grid size 200,200,200, pixel 2.14, shown
at level 0.00248, step 1, values float32
Opened PflC.mrc as #19, grid size 200,200,200, pixel 2.14, shown at level
0.00752, step 1, values float32
Opened PflD.mrc as #20, grid size 200,200,200, pixel 2.14, shown at level
0.00101, step 1, values float32
Opened Cages2.mrc as #21, grid size 200,200,200, pixel 2.14, shown at level
0.00187, step 1, values float32
Opened Rev-CJFlgYPlfAB-msk-2.1A.mrc as #22, grid size 200,200,200, pixel 2.14,
shown at level 0.00187, step 1, values float32
Log from Fri Jul 11 20:48:14 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/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-PflCD/For-PflD_PflC.cxs"
Opened 3xPflAB.mrc as #1, grid size 200,200,200, pixel 2.14, shown at level
0.0134, step 1, values float32
Opened 3xFliL.mrc as #2, grid size 200,200,200, pixel 2.14, shown at level
0.00115, step 1, values float32
Opened PflABY.mrc as #6, grid size 200,200,200, pixel 2.14, shown at level
0.00115, step 1, values float32
Opened PflABY.mrc gaussian as #7, grid size 200,200,200, pixel 2.14, shown at
level 0.00115, step 1, values float32
Opened PflABY_out_side-spokes.mrc gaussian as #11, grid size 200,200,200,
pixel 2.14, shown at level 0.00115, step 1, values float32
Opened Single-Spoke-ring.mrc as #14, grid size 200,200,200, pixel 2.14, shown
at level 0.00115, step 1, values float32
Opened Single-Spoke-ring.mrc gaussian as #9, grid size 200,200,200, pixel
2.14, shown at level 0.000387, step 1, values float32
Opened combination map 10 as #15, grid size 96,90,42, pixel 3.33, shown at
level 0.0635, step 1, values float32
Opened MS-ring.mrc as #16, grid size 200,200,200, pixel 2.14, shown at level
0.00124, step 1, values float32
Opened MS-ring.mrc gaussian as #17, grid size 200,200,200, pixel 2.14, shown
at level 0.00248, step 1, values float32
Opened PflC.mrc as #19, grid size 200,200,200, pixel 2.14, shown at level
0.00752, step 1, values float32
Opened PflD.mrc as #20, grid size 200,200,200, pixel 2.14, shown at level
0.00101, step 1, values float32
Opened Cages2.mrc as #21, grid size 200,200,200, pixel 2.14, shown at level
0.00187, step 1, values float32
Opened Rev-CJFlgYPlfAB-msk-2.1A.mrc as #22, grid size 200,200,200, pixel 2.14,
shown at level 0.00187, step 1, values float32
Log from Fri Jul 11 17:08:26 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/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-Chimera-PflAB/Resegment/Part3/Fitting_PflABY-JMB_07112025.cxs"
Opened 3xPflAB.mrc as #1, grid size 200,200,200, pixel 2.14, shown at level
0.0134, step 1, values float32
Opened 3xFliL.mrc as #2, grid size 200,200,200, pixel 2.14, shown at level
0.00115, step 1, values float32
Opened PflABY.mrc as #6, grid size 200,200,200, pixel 2.14, shown at level
0.00115, step 1, values float32
Opened PflABY.mrc gaussian as #7, grid size 200,200,200, pixel 2.14, shown at
level 0.00115, step 1, values float32
Opened PflABY_out_side-spokes.mrc gaussian as #11, grid size 200,200,200,
pixel 2.14, shown at level 0.00115, step 1, values float32
Opened Single-Spoke-ring.mrc as #14, grid size 200,200,200, pixel 2.14, shown
at level 0.00115, step 1, values float32
Opened Single-Spoke-ring.mrc gaussian as #9, grid size 200,200,200, pixel
2.14, shown at level 0.000387, step 1, values float32
Opened combination map 10 as #15, grid size 96,90,42, pixel 3.33, shown at
level 0.0635, step 1, values float32
Log from Fri Jul 11 12:46:52 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/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-Chimera-PflAB/Resegment/Docking_Jack_model.cxs"
Opened 3xPflAB.mrc as #1, grid size 200,200,200, pixel 2.14, shown at level
0.0134, step 1, values float32
Opened 3xFliL.mrc as #2, grid size 200,200,200, pixel 2.14, shown at level
0.00115, step 1, values float32
Log from Thu Jul 10 22:06:04 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/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/Start_Aug_2024/Local-ref-
> PflAB/Develop-model-Figure.cxs"
Opened IM.mrc as #1.1, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at
level 0.0246, step 1, values float32
Opened Cyt-components.mrc as #1.2, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at level 0.0159, step 1, values float32
Opened FliL.mrc as #1.3, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at
level 0.0029, step 1, values float32
Opened PflB-cage.mrc as #1.4, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened Cage.mrc as #1.5, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at
level 0.0029, step 1, values float32
Opened FlgY-PflA.mrc as #1.6, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened MS-ring.mrc as #1.7, grid size 220,250,200, pixel 2.15,2.15,2.15, shown
at level 0.0029, step 1, values float32
Opened Artifact3.mrc as #1.8, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened MotBpg.mrc as #1.9, grid size 220,250,200, pixel 2.15,2.15,2.15, shown
at level 0.0029, step 1, values float32
Opened Artifacts2.mrc as #1.10, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened PflC-PflD.mrc as #1.11, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened Basal-Disk.mrc as #1.12, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened OM.mrc as #1.13, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at
level 0.0029, step 1, values float32
Opened LP-ring.mrc as #1.14, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened Artifact1.mrc as #1.15, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened Rod.mrc as #1.16, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at
level 0.0029, step 1, values float32
Opened IM.mrc gaussian as #2, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened FliL.mrc gaussian as #4, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened PflB-cage.mrc gaussian as #5, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at level 0.0029, step 1, values float32
Opened Cage.mrc gaussian as #6, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened FlgY-PflA.mrc gaussian as #7, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at level 0.0216, step 1, values float32
Opened MS-ring.mrc gaussian as #8, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at level 0.0029, step 1, values float32
Opened MotBpg.mrc gaussian as #10, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at level 0.0029, step 1, values float32
Opened PflC-PflD.mrc gaussian as #12, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at level 0.0029, step 1, values float32
Opened Basal-Disk.mrc gaussian as #13, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at level 0.015, step 1, values float32
Opened LP-ring.mrc gaussian as #15, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at level 0.0029, step 1, values float32
Opened Rod.mrc gaussian as #17, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened 4x-FlgY-PflA.mrc as #23, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened 4x-FlgY-PflA.mrc gaussian as #32, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at level 0.00608, step 1, values float32
Opened IM.mrc gaussian as #24, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.00625, step 1, values float32
Opened 3xMotBpg.mrc gaussian as #21, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at level 0.000626, step 1, values float32
Log from Sat Aug 24 21:36:37 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/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/Develop-model-Figure.cxs
Opened IM.mrc as #1.1, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at
level 0.0246, step 1, values float32
Opened Cyt-components.mrc as #1.2, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at level 0.0159, step 1, values float32
Opened FliL.mrc as #1.3, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at
level 0.0029, step 1, values float32
Opened PflB-cage.mrc as #1.4, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened Cage.mrc as #1.5, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at
level 0.0029, step 1, values float32
Opened FlgY-PflA.mrc as #1.6, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened MS-ring.mrc as #1.7, grid size 220,250,200, pixel 2.15,2.15,2.15, shown
at level 0.0029, step 1, values float32
Opened Artifact3.mrc as #1.8, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened MotBpg.mrc as #1.9, grid size 220,250,200, pixel 2.15,2.15,2.15, shown
at level 0.0029, step 1, values float32
Opened Artifacts2.mrc as #1.10, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened PflC-PflD.mrc as #1.11, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened Basal-Disk.mrc as #1.12, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened OM.mrc as #1.13, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at
level 0.0029, step 1, values float32
Opened LP-ring.mrc as #1.14, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened Artifact1.mrc as #1.15, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened Rod.mrc as #1.16, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at
level 0.0029, step 1, values float32
Opened IM.mrc gaussian as #2, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened FliL.mrc gaussian as #4, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened PflB-cage.mrc gaussian as #5, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at level 0.0029, step 1, values float32
Opened Cage.mrc gaussian as #6, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Opened FlgY-PflA.mrc gaussian as #7, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at level 0.0216, step 1, values float32
Opened MS-ring.mrc gaussian as #8, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at level 0.0029, step 1, values float32
Opened MotBpg.mrc gaussian as #10, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at level 0.0029, step 1, values float32
Opened PflC-PflD.mrc gaussian as #12, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at level 0.0029, step 1, values float32
Opened Basal-Disk.mrc gaussian as #13, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at level 0.015, step 1, values float32
Opened LP-ring.mrc gaussian as #15, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at level 0.0029, step 1, values float32
Opened Rod.mrc gaussian as #17, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0029, step 1, values float32
Log from Sat Aug 24 18:41:04 2024 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
> open /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Segments/IM.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-
> chimera/cyc3/Segments/Artifacts-cyt.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Segments/PflB-
> cage.mrc /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-
> chimera/cyc3/Segments/FliLrings.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Segments/Cage.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Segments/FlgY-
> PflA.mrc /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-
> chimera/cyc3/Segments/MotBpg.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Segments/MS-
> ring.mrc /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-
> chimera/cyc3/Segments/Artifacts.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Segments/Rod.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Segments/LP-
> ring.mrc /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-
> chimera/cyc3/Segments/PflCD.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Segments/Basal-
> disk.mrc
Opened IM.mrc as #1.1, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at
level 0.0246, step 1, values float32
Opened Artifacts-cyt.mrc as #1.2, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0215, step 1, values float32
Opened PflB-cage.mrc as #1.3, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0223, step 1, values float32
Opened FliLrings.mrc as #1.4, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0214, step 1, values float32
Opened Cage.mrc as #1.5, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at
level 0.0213, step 1, values float32
Opened FlgY-PflA.mrc as #1.6, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0274, step 1, values float32
Opened MotBpg.mrc as #1.7, grid size 220,250,200, pixel 2.15,2.15,2.15, shown
at level 0.0214, step 1, values float32
Opened MS-ring.mrc as #1.8, grid size 220,250,200, pixel 2.15,2.15,2.15, shown
at level 0.0215, step 1, values float32
Opened Artifacts.mrc as #1.9, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0212, step 1, values float32
Opened Rod.mrc as #1.10, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at
level 0.0213, step 1, values float32
Opened LP-ring.mrc as #1.11, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0218, step 1, values float32
Opened PflCD.mrc as #1.12, grid size 220,250,200, pixel 2.15,2.15,2.15, shown
at level 0.0454, step 1, values float32
Opened Basal-disk.mrc as #1.13, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0247, step 1, values float32
> select add #1.2
2 models selected
> select subtract #1.2
Nothing selected
> hide #!1.2 models
> hide #!1.9 models
> volume #1.1 level 0.02218
> volume #1.2 level 0.0222
> volume #1.3 level 0.0222
> volume #1.4 level 0.0222
> volume #1.5 level 0.0222
> volume #1.6 level 0.0222
> volume #1.7 level 0.0222
> volume #1.8 level 0.0222
> volume #1.9 level 0.0222
> volume #1.10 level 0.0222
> volume #1.13 level 0.0222
> volume gaussian #1 sDev 3
Opened IM.mrc gaussian as #2, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at step 1, values float32
Opened Artifacts-cyt.mrc gaussian as #3, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened PflB-cage.mrc gaussian as #4, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened FliLrings.mrc gaussian as #5, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened Cage.mrc gaussian as #6, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at step 1, values float32
Opened FlgY-PflA.mrc gaussian as #7, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened MotBpg.mrc gaussian as #8, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at step 1, values float32
Opened MS-ring.mrc gaussian as #9, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened Artifacts.mrc gaussian as #10, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened Rod.mrc gaussian as #11, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at step 1, values float32
Opened LP-ring.mrc gaussian as #12, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened PflCD.mrc gaussian as #13, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at step 1, values float32
Opened Basal-disk.mrc gaussian as #14, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Cell requested for row 1 is out of bounds for table with 27 rows! Resizing
table model.
> close #2-14
> show #!1.1 models
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> show #!1.6 models
> show #!1.7 models
> show #!1.5 models
> volume gaussian #1 sDev 1.5
Opened IM.mrc gaussian as #2, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at step 1, values float32
Opened Artifacts-cyt.mrc gaussian as #3, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened PflB-cage.mrc gaussian as #4, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened FliLrings.mrc gaussian as #5, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened Cage.mrc gaussian as #6, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at step 1, values float32
Opened FlgY-PflA.mrc gaussian as #7, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened MotBpg.mrc gaussian as #8, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at step 1, values float32
Opened MS-ring.mrc gaussian as #9, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened Artifacts.mrc gaussian as #10, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened Rod.mrc gaussian as #11, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at step 1, values float32
Opened LP-ring.mrc gaussian as #12, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened PflCD.mrc gaussian as #13, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at step 1, values float32
Opened Basal-disk.mrc gaussian as #14, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Window position QRect(1940,817 575x728) outside any known screen, using
primary screen
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> surface dust #2 size 12.6
> show #!3 models
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/Test-model-local.cxs
> includeMaps true
> close session
> open /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Rev-CjpflAB-
> mask-L0.2.mrc
Opened Rev-CjpflAB-mask-L0.2.mrc as #1, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at level 0.0603, step 1, values float32
> volume #1 level 0.01305
> volume #1 level 0.009239
> volume #1 level 0.007334
> volume #1 level 0.003524
> ui tool show "Segment Map"
> volume #1 level 0.003143
Segmenting Rev-CjpflAB-mask-L0.2.mrc, density threshold 0.003143
Showing 581 region surfaces
31797 watershed regions, grouped to 581 regions
Showing Rev-CjpflAB-mask-L0.2.seg - 581 regions, 581 surfaces
> select #2.419
1 model selected
> select add #2.456
2 models selected
> select add #2.18
3 models selected
> select add #2.378
4 models selected
> hide #!1 models
> select add #2.439
5 models selected
> select add #2.1
6 models selected
> select add #2.16
7 models selected
> select add #2.29
8 models selected
> select add #2.404
9 models selected
Grouped 9 regions
> select #2.56
1 model selected
Ungrouped to 2 regions
> select #2.18
1 model selected
Ungrouped to 3 regions
> select #2.29
1 model selected
> select clear
> select #2.29
1 model selected
Showing 576 region surfaces
> select add #2.1
2 models selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Grouped 2 regions
> select #2.87
1 model selected
> select clear
> select #2.286
1 model selected
> select #2.87
1 model selected
Ungrouped to 10 regions
> select clear
> select #2.419
1 model selected
> select add #2.1
2 models selected
Opened Rev-CjpflAB-mask-L0.2_imasked as #3, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/Rod.mrc models #3
Opened Rev-CjpflAB-mask-L0.2_imasked as #4, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Segmenting Rev-CjpflAB-mask-L0.2_imasked, density threshold 0.003143
Showing 572 region surfaces
30650 watershed regions, grouped to 572 regions
Showing Rev-CjpflAB-mask-L0.seg - 572 regions, 572 surfaces
> hide #!4 models
> hide #!3 models
> show #!3 models
> select add #2.13
1 model selected
> select add #2.5
2 models selected
> select add #2.3
3 models selected
> select add #2.27
4 models selected
> select clear
> select #2.22
1 model selected
> select add #2.274
2 models selected
> select add #2.420
3 models selected
> select add #2.350
4 models selected
> select add #2.341
5 models selected
> select add #2.419
6 models selected
> select add #2.186
7 models selected
> select add #2.323
8 models selected
> select add #2.162
9 models selected
> select add #2.450
10 models selected
> select add #2.79
11 models selected
> select add #2.356
12 models selected
Grouped 12 regions
> hide #!3 models
Opened Rev-CjpflAB-mask-L0_imasked as #5, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/Artifact1.mrc models #5
Opened Rev-CjpflAB-mask-L0_imasked as #6, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Segmenting Rev-CjpflAB-mask-L0_imasked, density threshold 0.003143
Showing 559 region surfaces
29950 watershed regions, grouped to 559 regions
Showing Rev-CjpflAB-mask-L0_imasked.seg - 559 regions, 559 surfaces
> select #2.5
1 model selected
> select add #2.92
2 models selected
> select add #2.138
3 models selected
> select add #2.3
4 models selected
> select add #2.26
5 models selected
> select add #2.65
6 models selected
> select add #2.76
7 models selected
> select add #2.272
8 models selected
> select add #2.13
9 models selected
> hide #!5 models
> hide #!6 models
Grouped 9 regions
Opened Rev-CjpflAB-mask-L0_imasked_imasked as #7, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/LP-ring.mrc models #7
Opened Rev-CjpflAB-mask-L0_imasked_imasked as #8, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Segmenting Rev-CjpflAB-mask-L0_imasked_imasked, density threshold 0.003143
Showing 550 region surfaces
28997 watershed regions, grouped to 550 regions
Showing Rev-CjpflAB-mask-L0_imasked_imasked.seg - 550 regions, 550 surfaces
> hide #!7 models
> hide #!8 models
> select #2.31
1 model selected
> select add #2.422
2 models selected
> select add #2.162
3 models selected
> select add #2.149
4 models selected
> select add #2.307
5 models selected
> select add #2.358
6 models selected
> select add #2.43
7 models selected
> select add #2.360
8 models selected
> select add #2.323
9 models selected
> select add #2.401
10 models selected
> select add #2.467
11 models selected
> select add #2.409
12 models selected
> select add #2.42
13 models selected
> select add #2.429
14 models selected
> select add #2.475
15 models selected
> select subtract #2.42
14 models selected
> select add #2.443
15 models selected
> select add #2.392
16 models selected
> select add #2.320
17 models selected
> select add #2.396
18 models selected
> select add #2.479
19 models selected
> select add #2.349
20 models selected
> select add #2.329
21 models selected
> select add #2.460
22 models selected
> select add #2.435
23 models selected
> select subtract #2.435
22 models selected
> select add #2.421
23 models selected
> select add #2.456
24 models selected
> select add #2.435
25 models selected
> select add #2.457
26 models selected
> select add #2.465
27 models selected
> select add #2.445
28 models selected
> select add #2.373
29 models selected
> select add #2.322
30 models selected
> select add #2.351
31 models selected
> select add #2.372
32 models selected
> select add #2.464
33 models selected
Grouped 33 regions
Opened Rev-CjpflAB-mask-L0_imasked_imasked_imasked as #9, grid size
220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/OM.mrc models #9
Opened Rev-CjpflAB-mask-L0_imasked_imasked_imasked as #10, grid size
220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values float32
Segmenting Rev-CjpflAB-mask-L0_imasked_imasked_imasked, density threshold
0.003143
Showing 517 region surfaces
27609 watershed regions, grouped to 517 regions
Showing Rev-CjpflAB-mask-L0_imasked_imasked_imasked.seg - 517 regions, 517
surfaces
> hide #!9 models
> select #2.342
1 model selected
> select add #2.121
2 models selected
> select add #2.169
3 models selected
> select add #2.106
4 models selected
> select add #2.181
5 models selected
> select add #2.127
6 models selected
> select add #2.149
7 models selected
> select add #2.128
8 models selected
> select add #2.183
9 models selected
> select add #2.32
10 models selected
> select add #2.70
11 models selected
> select add #2.86
12 models selected
> select add #2.66
13 models selected
> select add #2.297
14 models selected
> select add #2.423
15 models selected
> select add #2.326
16 models selected
> select add #2.46
17 models selected
> select add #2.12
18 models selected
> select add #2.74
19 models selected
> select add #2.131
20 models selected
> select add #2.250
21 models selected
> select add #2.294
22 models selected
> select add #2.327
23 models selected
> select add #2.284
24 models selected
> select subtract #2.284
23 models selected
> select add #2.133
24 models selected
> select add #2.270
25 models selected
> select add #2.166
26 models selected
> select add #2.258
27 models selected
> select add #2.134
28 models selected
> select add #2.213
29 models selected
> select add #2.220
30 models selected
> select add #2.276
31 models selected
> select add #2.151
32 models selected
> select add #2.41
33 models selected
> select add #2.374
34 models selected
> select add #2.345
35 models selected
> select add #2.144
36 models selected
> select add #2.79
37 models selected
> select add #2.252
38 models selected
> select add #2.204
39 models selected
> select add #2.191
40 models selected
> select add #2.145
41 models selected
> select add #2.148
42 models selected
> select add #2.174
43 models selected
> select add #2.308
44 models selected
> select add #2.214
45 models selected
> select add #2.358
46 models selected
> select add #2.373
47 models selected
> select add #2.77
48 models selected
> select add #2.124
49 models selected
> select add #2.241
50 models selected
> select add #2.85
51 models selected
> select add #2.24
52 models selected
> select add #2.284
53 models selected
> select add #2.352
54 models selected
> select add #2.217
55 models selected
> select add #2.109
56 models selected
> select add #2.279
57 models selected
> select add #2.378
58 models selected
> select add #2.139
59 models selected
> select add #2.397
60 models selected
> select add #2.118
61 models selected
> select add #2.398
62 models selected
> select add #2.299
63 models selected
> select add #2.436
64 models selected
> select add #2.371
65 models selected
> select add #2.360
66 models selected
> select add #2.200
67 models selected
> select add #2.43
68 models selected
> select add #2.369
69 models selected
> select add #2.97
70 models selected
> select add #2.404
71 models selected
> select add #2.20
72 models selected
> select add #2.420
73 models selected
> select add #2.349
74 models selected
> select add #2.362
75 models selected
> select add #2.238
76 models selected
> select add #2.289
77 models selected
> select add #2.351
78 models selected
> select add #2.407
79 models selected
Grouped 79 regions
> hide #!10 models
> select add #2.430
2 models selected
Grouped 2 regions
Showing 438 region surfaces
> select #2.12
1 model selected
Opened Rev-CjpflAB-mask-L0_imasked_imasked_imasked_imasked as #11, grid size
220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/Basal-Disk.mrc models #11
Opened Rev-CjpflAB-mask-L0_imasked_imasked_imasked_imasked as #12, grid size
220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values float32
Segmenting Rev-CjpflAB-mask-L0_imasked_imasked_imasked_imasked, density
threshold 0.003143
Showing 437 region surfaces
22918 watershed regions, grouped to 437 regions
Showing Rev-CjpflAB-mask-L0_imasked_imasked_imasked_imasked.seg - 437 regions,
437 surfaces
> hide #!11 models
> hide #!12 models
> select #2.225
1 model selected
> select add #2.101
2 models selected
> select add #2.145
3 models selected
> select add #2.128
4 models selected
> select add #2.136
5 models selected
> select add #2.148
6 models selected
> select add #2.106
7 models selected
> select add #2.107
8 models selected
> select add #2.138
9 models selected
> select add #2.186
10 models selected
> select add #2.50
11 models selected
> select add #2.68
12 models selected
> select add #2.173
13 models selected
> select add #2.183
14 models selected
> select add #2.49
15 models selected
> select add #2.77
16 models selected
> select add #2.185
17 models selected
> select add #2.212
18 models selected
> select add #2.177
19 models selected
> select add #2.146
20 models selected
> select add #2.210
21 models selected
> select add #2.162
22 models selected
> select add #2.40
23 models selected
> select add #2.154
24 models selected
> select add #2.175
25 models selected
> select add #2.141
26 models selected
> select add #2.235
27 models selected
> select add #2.144
28 models selected
> select add #2.209
29 models selected
> select add #2.64
30 models selected
> select add #2.249
31 models selected
> select add #2.45
32 models selected
> select add #2.316
33 models selected
> select add #2.356
34 models selected
> select add #2.289
35 models selected
> select add #2.314
36 models selected
> select subtract #2.249
35 models selected
> select #2.225
1 model selected
> select add #2.101
2 models selected
> select add #2.145
3 models selected
> select add #2.128
4 models selected
> select add #2.136
5 models selected
> select add #2.148
6 models selected
> select add #2.106
7 models selected
> select add #2.107
8 models selected
> select add #2.138
9 models selected
Grouped 9 regions
> select add #2.176
2 models selected
> select add #2.178
3 models selected
> select add #2.194
4 models selected
> select add #2.175
5 models selected
> select add #2.177
6 models selected
> select add #2.183
7 models selected
> select add #2.186
8 models selected
> select add #2.173
9 models selected
Grouped 9 regions
> select add #2.49
2 models selected
> select add #2.50
3 models selected
> select add #2.146
4 models selected
> select add #2.210
5 models selected
> select add #2.209
6 models selected
> select add #2.144
7 models selected
> select add #2.235
8 models selected
> select add #2.141
9 models selected
> select add #2.198
10 models selected
> select add #2.142
11 models selected
> select add #2.119
12 models selected
> select subtract #2.119
11 models selected
> select add #2.147
12 models selected
> select clear
Showing 421 region surfaces
> select clear
> select add #2.141
1 model selected
> select add #2.142
2 models selected
> select add #2.147
3 models selected
> select add #2.118
4 models selected
> select add #2.28
5 models selected
> select add #2.146
6 models selected
> select add #2.49
7 models selected
> select add #2.50
8 models selected
> select add #2.68
9 models selected
Grouped 9 regions
> select #2.185
1 model selected
> select add #2.77
2 models selected
> select add #2.212
3 models selected
> select add #2.210
4 models selected
> select add #2.162
5 models selected
> select add #2.209
6 models selected
> select add #2.235
7 models selected
> select add #2.144
8 models selected
> select add #2.205
9 models selected
> select add #2.198
10 models selected
> select add #2.153
11 models selected
> select add #2.179
12 models selected
> select add #2.184
13 models selected
> select add #2.240
14 models selected
Grouped 14 regions
> select add #2.69
2 models selected
> select add #2.84
3 models selected
> select add #2.28
4 models selected
> select add #2.101
5 models selected
Grouped 5 regions
> select #2.65
1 model selected
> select add #2.76
2 models selected
> select add #2.39
3 models selected
> select add #2.204
4 models selected
> select add #2.73
5 models selected
> select add #2.43
6 models selected
> select add #2.72
7 models selected
> select add #2.45
8 models selected
> select add #2.64
9 models selected
> select add #2.40
10 models selected
> select add #2.154
11 models selected
Grouped 11 regions
> select add #2.292
2 models selected
> select add #2.350
3 models selected
> select add #2.300
4 models selected
> select add #2.271
5 models selected
> select add #2.346
6 models selected
> select add #2.243
7 models selected
> select add #2.166
8 models selected
> select add #2.325
9 models selected
> select add #2.316
10 models selected
> select add #2.356
11 models selected
> select add #2.289
12 models selected
> select add #2.314
13 models selected
Grouped 13 regions
Ungrouped to 13 regions
> select subtract #2.50
12 models selected
Grouped 12 regions
> select #2.50
1 model selected
> select add #2.349
2 models selected
> select add #2.28
3 models selected
Grouped 3 regions
> select add #2.267
2 models selected
> select add #2.252
3 models selected
> select add #2.260
4 models selected
> select add #2.249
5 models selected
Opened Rev-CjpflAB-mask-L0_imasked_imasked_imasked_imasked_imasked as #13,
grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/PflC-PflD.mrc models #13
Opened Rev-CjpflAB-mask-L0_imasked_imasked_imasked_imasked_imasked as #14,
grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values float32
Segmenting Rev-CjpflAB-mask-L0_imasked_imasked_imasked_imasked_imasked,
density threshold 0.003143
Showing 377 region surfaces
20568 watershed regions, grouped to 377 regions
Showing Rev-CjpflAB-mask-L0_imasked_imasked_imasked_imasked_imasked.seg - 377
regions, 377 surfaces
> hide #!13 models
> hide #!14 models
> select #2.133
1 model selected
> select add #2.267
2 models selected
> select add #2.257
3 models selected
> select add #2.231
4 models selected
> select add #2.190
5 models selected
> select add #2.163
6 models selected
> select add #2.247
7 models selected
> select add #2.285
8 models selected
> select add #2.234
9 models selected
Grouped 9 regions
> select add #2.258
2 models selected
> select add #2.307
3 models selected
Grouped 3 regions
> select #2.133
1 model selected
> select add #2.313
2 models selected
Grouped 2 regions
> select #2.133
1 model selected
> select add #2.296
2 models selected
Grouped 2 regions
> select add #2.320
2 models selected
Grouped 2 regions
Opened Rev-CjpflAB-mask-L0_imasked_imasked_imasked_imasked_imasked_imasked as
#15, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values
float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/Artifacts2.mrc models #15
Opened Rev-CjpflAB-mask-L0_imasked_imasked_imasked_imasked_imasked_imasked as
#16, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values
float32
Segmenting Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked, density threshold
0.003143
Showing 363 region surfaces
19942 watershed regions, grouped to 363 regions
Showing Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked.seg - 363 regions, 363
surfaces
> hide #!15 models
> hide #!16 models
Drag select of 26869, 8524 of 13900 triangles, 26883, 6666 of 8720 triangles,
26871, 2613 of 5312 triangles, 26856, 3553 of 4572 triangles, 26615, 3559 of
3928 triangles, 26885, 3805 of 4036 triangles, 26877, 2500 of 3532 triangles,
26878, 1482 of 2732 triangles, 22762, 26906, 1277 of 2324 triangles, 25872,
26879, 24548, 1346 of 1468 triangles, 26863, 440 of 2068 triangles, 26607,
22757, 19884, 25911, 26903, 648 of 728 triangles, 26310, 26880, 26900, 99 of
496 triangles, 26886, 160 of 524 triangles, 19814
Drag select of 19936, 19939
Drag select of 26737, 420 of 804 triangles
> select add #2.313
28 models selected
> select add #2.307
29 models selected
> select add #2.346
30 models selected
> select add #2.359
31 models selected
> select add #2.311
32 models selected
> select add #2.254
33 models selected
> select add #2.291
34 models selected
> select add #2.310
35 models selected
> select add #2.294
36 models selected
> select add #2.274
37 models selected
> select add #2.282
38 models selected
> select add #2.272
39 models selected
> select add #2.299
40 models selected
> select add #2.335
41 models selected
> select add #2.360
42 models selected
> select add #2.318
43 models selected
> select add #2.305
44 models selected
> select add #2.331
45 models selected
> select add #2.315
46 models selected
> select add #2.332
47 models selected
> select add #2.322
48 models selected
> select add #2.355
49 models selected
> select add #2.348
50 models selected
Grouped 50 regions
Opened Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked as #17, grid
size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values float32
Segmenting Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked, density
threshold 0.003143
Showing 315 region surfaces
19467 watershed regions, grouped to 315 regions
Showing Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg - 315
regions, 315 surfaces
> select #2.135
1 model selected
> select add #2.151
2 models selected
> select add #2.146
3 models selected
> select add #2.137
4 models selected
> select add #2.89
5 models selected
> hide #!17 models
Grouped 5 regions
Opened Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#18, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values
float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/MotBpg.mrc models #18
Opened Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#19, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values
float32
Segmenting Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.003143
Showing 310 region surfaces
19337 watershed regions, grouped to 310 regions
Showing Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg -
310 regions, 310 surfaces
> hide #!18 models
> hide #!19 models
> select #2.259
1 model selected
> select add #2.269
2 models selected
> select add #2.248
3 models selected
> select add #2.278
4 models selected
> select add #2.264
5 models selected
> select add #2.292
6 models selected
> select add #2.207
7 models selected
> select add #2.258
8 models selected
> select add #2.244
9 models selected
> select add #2.272
10 models selected
> select add #2.273
11 models selected
> select add #2.257
12 models selected
> select add #2.243
13 models selected
> select add #2.275
14 models selected
Grouped 14 regions
Opened Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #20, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values
float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/Artifact3.mrc models #20
Opened Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #21, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values
float32
Segmenting Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.003143
Showing 296 region surfaces
18845 watershed regions, grouped to 296 regions
Showing Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 296 regions, 296 surfaces
> hide #!20 models
> hide #!21 models
> select #2.95
1 model selected
> select add #2.116
2 models selected
> select add #2.141
3 models selected
Grouped 3 regions
> select #2.220
1 model selected
> select add #2.200
2 models selected
> select add #2.165
3 models selected
> select add #2.260
4 models selected
Grouped 4 regions
> select add #2.140
2 models selected
Grouped 2 regions
> select #2.109
1 model selected
> select add #2.168
2 models selected
> select add #2.116
3 models selected
Grouped 3 regions
> select add #2.83
2 models selected
Grouped 2 regions
> select add #2.93
2 models selected
> select add #2.155
3 models selected
> select add #2.124
4 models selected
Grouped 4 regions
> select add #2.95
2 models selected
Grouped 2 regions
> select add #2.218
2 models selected
> select add #2.199
3 models selected
> select add #2.157
4 models selected
> select add #2.254
5 models selected
> select add #2.148
6 models selected
Grouped 6 regions
> select add #2.222
2 models selected
> select add #2.215
3 models selected
> select add #2.127
4 models selected
> select add #2.98
5 models selected
Grouped 5 regions
> select add #2.228
2 models selected
> select add #2.110
3 models selected
> select add #2.135
4 models selected
Grouped 4 regions
> select #2.139
1 model selected
Ungrouped to 4 regions
> select #2.109
1 model selected
> select add #2.83
2 models selected
Grouped 2 regions
> select #2.93
1 model selected
Ungrouped to 15 regions
> select #2.127
1 model selected
> select add #2.140
2 models selected
> select add #2.83
3 models selected
Grouped 3 regions
> select #2.39
1 model selected
> select add #2.102
2 models selected
> select add #2.162
3 models selected
> select add #2.26
4 models selected
> select subtract #2.26
3 models selected
Ungrouped to 10 regions
Ungrouped to 75 regions
Ungrouped to 127 regions
> select #2.26
1 model selected
> select subtract #2.26
Nothing selected
Ungrouped to 376 regions
Ungrouped to 1634 regions
> select #2.1055
1 model selected
> select #2.1055
1 model selected
> select #2.1051
1 model selected
> select add #2.1056
2 models selected
> select add #2.1052
3 models selected
Ungrouped to 29 regions
> select #2.105
1 model selected
> select add #2.100
2 models selected
> select add #2.90
3 models selected
> select add #2.76
4 models selected
> select add #2.80
5 models selected
> select add #2.45
6 models selected
> select add #2.1055
7 models selected
> select add #2.115
8 models selected
> select subtract #2.115
7 models selected
> select #2.1055
1 model selected
Ungrouped to 9 regions
> select #2.2304
1 model selected
> select #2.1733
1 model selected
> select add #2.1731
2 models selected
> select add #2.1732
3 models selected
Grouped 3 regions
> select add #2.96
2 models selected
> select add #2.106
3 models selected
> select add #2.81
4 models selected
> select add #2.63
5 models selected
> select add #2.71
6 models selected
> select add #2.119
7 models selected
> select add #2.111
8 models selected
> select add #2.1735
9 models selected
> select add #2.1734
10 models selected
Grouped 10 regions
> select add #2.2304
2 models selected
> select add #2.1963
3 models selected
> select subtract #2.1963
2 models selected
> select add #2.1963
3 models selected
> select add #2.113
4 models selected
> select add #2.1965
5 models selected
> select add #2.2324
6 models selected
> select add #2.499
7 models selected
Grouped 7 regions
> select add #2.902
2 models selected
> select add #2.2306
3 models selected
> select add #2.901
4 models selected
> select add #2.900
5 models selected
Grouped 5 regions
> select add #2.122
2 models selected
> select add #2.427
3 models selected
> select add #2.428
4 models selected
> select subtract #2.428
3 models selected
> select subtract #2.427
2 models selected
> select add #2.378
3 models selected
> select add #2.347
4 models selected
> select add #2.382
5 models selected
> select add #2.466
6 models selected
> select add #2.473
7 models selected
> select add #2.228
8 models selected
Grouped 8 regions
> select add #2.427
2 models selected
> select add #2.428
3 models selected
> select add #2.429
4 models selected
> select add #2.336
5 models selected
> select add #2.379
6 models selected
> select add #2.384
7 models selected
> select add #2.360
8 models selected
> select add #2.133
9 models selected
> select add #2.132
10 models selected
> select add #2.1050
11 models selected
> select add #2.1053
12 models selected
> select subtract #2.1053
11 models selected
Grouped 11 regions
> select add #2.383
2 models selected
Grouped 2 regions
> select clear
> select #2.1053
1 model selected
Ungrouped to 15 regions
> select #2.137
1 model selected
> select add #2.134
2 models selected
> select add #2.63
3 models selected
Grouped 3 regions
> select add #2.112
2 models selected
> select #2.63
1 model selected
> select #2.63
1 model selected
> select add #2.112
2 models selected
> select add #2.117
3 models selected
> select add #2.45
4 models selected
> select add #2.76
5 models selected
> select add #2.80
6 models selected
> select add #2.105
7 models selected
> select add #2.97
8 models selected
> select subtract #2.97
7 models selected
> select add #2.100
8 models selected
> select add #2.90
9 models selected
Grouped 9 regions
> select add #2.101
2 models selected
> select clear
> select #2.101
1 model selected
Ungrouped to 2 regions
> select #2.63
1 model selected
> select add #2.76
2 models selected
> select add #2.92
3 models selected
Grouped 3 regions
> select add #2.45
2 models selected
Grouped 2 regions
> select add #2.108
2 models selected
> select add #2.366
3 models selected
> select add #2.420
4 models selected
> select add #2.318
5 models selected
> select add #2.355
6 models selected
> select add #2.422
7 models selected
> select add #2.421
8 models selected
> select add #2.413
9 models selected
> select add #2.475
10 models selected
> select add #2.414
11 models selected
Grouped 11 regions
> select add #2.354
2 models selected
> select add #2.400
3 models selected
> select add #2.469
4 models selected
Grouped 4 regions
> select add #2.476
2 models selected
> select add #2.401
3 models selected
Grouped 3 regions
> select add #2.402
2 models selected
> select add #2.346
3 models selected
> select add #2.477
4 models selected
> select add #2.222
5 models selected
> select add #2.403
6 models selected
> select add #2.305
7 models selected
Grouped 7 regions
> select add #2.371
2 models selected
> select add #2.474
3 models selected
> select add #2.391
4 models selected
> select add #2.303
5 models selected
> select add #2.482
6 models selected
> select add #2.464
7 models selected
> select add #2.478
8 models selected
> select add #2.480
9 models selected
Grouped 9 regions
> select add #2.416
2 models selected
> select add #2.387
3 models selected
> select add #2.404
4 models selected
> select add #2.405
5 models selected
> select add #2.479
6 models selected
> select add #2.373
7 models selected
Grouped 7 regions
> select add #2.406
2 models selected
Grouped 2 regions
> select add #2.415
2 models selected
> select add #2.372
3 models selected
Grouped 3 regions
> select add #2.299
2 models selected
> select subtract #2.299
1 model selected
Grouped 1 regions
> select #2.45
1 model selected
> select add #2.299
2 models selected
Grouped 2 regions
> select add #2.356
2 models selected
> select add #2.380
3 models selected
Grouped 3 regions
> select #2.83
1 model selected
> select clear
Showing 1942 region surfaces
> select #2.45
1 model selected
> select add #2.118
2 models selected
> select add #2.99
3 models selected
> select add #2.2098
4 models selected
> select add #2.2099
5 models selected
> select add #2.120
6 models selected
> select subtract #2.118
5 models selected
> select subtract #2.45
4 models selected
> select add #2.115
5 models selected
> select add #2.488
6 models selected
> select add #2.45
7 models selected
> select add #2.2307
8 models selected
> select add #2.2309
9 models selected
> select subtract #2.2307
8 models selected
Grouped 8 regions
> select add #2.118
2 models selected
> select add #2.2308
3 models selected
> select add #2.104
4 models selected
Grouped 4 regions
> select add #2.2307
2 models selected
> select subtract #2.2307
1 model selected
Grouped 1 regions
> select #2.2307
1 model selected
> select subtract #2.2307
Nothing selected
> select add #2.2307
1 model selected
> select add #2.45
2 models selected
Grouped 2 regions
> select add #2.1959
2 models selected
> select subtract #2.1959
1 model selected
> select clear
> select #2.45
1 model selected
> select #2.45
1 model selected
> select add #2.2305
2 models selected
> select add #2.2325
3 models selected
> select add #2.2326
4 models selected
> select add #2.1964
5 models selected
> select add #2.899
6 models selected
Grouped 6 regions
> select clear
> select #2.45
1 model selected
> select clear
> select #2.45
1 model selected
Grouped 1 regions
> select clear
> select #2.45
1 model selected
Ungrouped to 1 regions
Ungrouped to 6 regions
Ungrouped to 26 regions
Ungrouped to 76 regions
Ungrouped to 22 regions
Ungrouped to 24 regions
> select #2.355
1 model selected
Ungrouped to 3 regions
Ungrouped to 2 regions
Ungrouped to 1 regions
Ungrouped to 3 regions
> select #2.355
1 model selected
Ungrouped to 2 regions
Ungrouped to 7 regions
> select #2.401
1 model selected
Ungrouped to 9 regions
Ungrouped to 15 regions
> select clear
> select #2.478
1 model selected
Ungrouped to 3 regions
Ungrouped to 4 regions
> select #2.482
1 model selected
Ungrouped to 11 regions
Ungrouped to 7 regions
> select #2.515
1 model selected
Ungrouped to 9 regions
Ungrouped to 13 regions
> select #2.537
1 model selected
Ungrouped to 2 regions
Ungrouped to 11 regions
> select #2.519
1 model selected
Ungrouped to 8 regions
Ungrouped to 12 regions
> select #2.593
1 model selected
Ungrouped to 7 regions
Ungrouped to 69 regions
> select #2.673
1 model selected
> select #2.673
1 model selected
Ungrouped to 7 regions
Ungrouped to 0 regions
> select #2.573
1 model selected
> select add #2.571
2 models selected
> select add #2.596
3 models selected
> select clear
[Repeated 1 time(s)]Drag select of 15694, 14388, 16045, 16119, 16211, 15016,
16290, 16865, 15943, 14406, 15573, 15432, 15266, 15574, 16049, 16534, 14863,
15839, 15431, 15259, 15070, 14646, 16373, 16141, 15433, 15712, 15260, 15946,
15240, 15557, 16129, 15822, 15054, 16482, 15954, 15395, 16112, 16123, 15929,
14813, 14590, 14584, 14359, 15022, 14114, 15399, 16521, 14785, 16636, 16281,
15212, 15674, 14578, 15386, 15390, 13616, 12099, 14607, 14130, 11794, 15414,
15245, 15052, 15820, 15239, 14834, 14870, 15268, 14828, 16433, 16477, 15942,
15695, 15041, 15404, 15408, 15411, 15235, 11181, 11482, 14819, 15690, 12726,
12729, 11498, 10881, 13895, 12738, 11182, 12415, 12413, 12097, 14369, 13040,
14611, 14151, 19250, 10928, 14189, 19089, 19098, 19767, 23443, 23645, 23452,
24113, 24408, 24073, 24583, 13916, 14171, 13083, 12149, 19280, 20563, 12127,
19547, 19067, 12748, 17713, 16652, 18162, 18168, 18247, 17574, 17797, 17702,
17922, 17342, 16581, 16427, 16859, 16741, 16579, 16645, 16432, 16704, 16997,
16861, 17918, 17921, 17690, 16644, 16646, 16746, 17799, 17349, 21277, 18249,
17810, 17709, 18251, 18311, 17926, 18177, 18172, 18092, 16866, 17222, 16798,
18022, 18182, 17600, 17715, 17229, 17941, 17480, 16585, 16796, 16749, 25410,
17829, 18393, 18190, 17828, 17833, 18109, 17120, 17245, 17946, 18263, 17831,
17834, 17732, 18189, 17375, 17121, 16718, 22894, 16867, 16939, 16487, 16803,
17113, 16653, 16811, 16805, 16439, 16584, 16535, 16587, 16714, 16527, 16478,
16524, 16794, 16709, 16748, 16435, 16586, 24570, 24048, 23922, 13912 of 13984
triangles, 24655, 22984, 21069, 21011, 23263, 16227, 16138, 14395, 15058,
21667, 20987, 20972, 19207, 23293, 23216, 15821, 15228, 14155, 15945, 13656,
13653, 20073, 14393, 19003, 11533, 19965, 15251, 23275, 23197, 16139, 14637,
21830, 23091, 16542, 16596, 21433, 23963, 25401, 33304 of 33372 triangles,
16658, 21548, 23885, 21384, 21633, 21426, 19212, 23244, 16127, 16031, 21130,
16019, 21148, 16218, 15697, 15231, 14612, 14822, 21073, 21182, 23385, 23271,
16143, 14657, 14421, 21855, 23076, 23012, 23052, 23097, 16489, 16541, 16954,
16814, 16755
Grouped 286 regions
> select clear
Showing 1929 region surfaces
> select #2.45
1 model selected
Opened Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #22, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values
float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/MS-ring.mrc models #22
Opened Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #23, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values
float32
Segmenting Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.003143
Showing 290 region surfaces
18166 watershed regions, grouped to 290 regions
Showing Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 290 regions, 290 surfaces
> hide #!22 models
> hide #!23 models
> select #2.90
1 model selected
> select add #2.110
2 models selected
> select add #2.133
3 models selected
Grouped 3 regions
> select add #2.211
2 models selected
> select add #2.191
3 models selected
> select add #2.148
4 models selected
> select add #2.248
5 models selected
Drag select of 24474, 18 of 70876 triangles, 24048, 6 of 15928 triangles,
24459, 11 of 15700 triangles, 24074, 16 of 16680 triangles
> select add #2.148
8 models selected
Showing 288 region surfaces
> select #2.90
1 model selected
> select add #2.132
2 models selected
> select add #2.254
3 models selected
> select add #2.155
4 models selected
> select add #2.192
5 models selected
> select add #2.213
6 models selected
Grouped 6 regions
> select #2.211
1 model selected
> select add #2.191
2 models selected
> select add #2.148
3 models selected
> select add #2.248
4 models selected
> select add #2.139
5 models selected
Grouped 5 regions
> select #2.215
1 model selected
> select add #2.208
2 models selected
> select add #2.120
3 models selected
> select add #2.93
4 models selected
> select add #2.131
5 models selected
> select add #2.222
6 models selected
> select add #2.104
7 models selected
> select add #2.127
8 models selected
Grouped 8 regions
> select add #2.110
2 models selected
> select add #2.90
3 models selected
Grouped 3 regions
> select add #2.79
2 models selected
> select #2.79
1 model selected
> select add #2.159
2 models selected
> select add #2.103
3 models selected
> select add #2.88
4 models selected
> select add #2.146
5 models selected
> select add #2.117
6 models selected
Grouped 6 regions
> select add #2.90
2 models selected
> select add #2.53
3 models selected
> select add #2.201
4 models selected
> select add #2.168
5 models selected
> select add #2.156
6 models selected
> select add #2.219
7 models selected
Grouped 7 regions
Opened Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #24, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values
float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/FlgY-PflA.mrc models #24
Opened Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #25, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values
float32
Segmenting Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.003143
Showing 258 region surfaces
17247 watershed regions, grouped to 258 regions
Showing Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 258 regions, 258 surfaces
> hide #!24 models
> hide #!25 models
> select #2.45
1 model selected
> select #2.30
1 model selected
Ungrouped to 2 regions
> select #2.260
1 model selected
Ungrouped to 14 regions
> select subtract #2.269
13 models selected
> select #2.259
1 model selected
> select add #2.269
2 models selected
Grouped 2 regions
> select add #2.157
2 models selected
Grouped 2 regions
> select #2.26
1 model selected
Ungrouped to 2 regions
> select #2.260
1 model selected
> select add #2.157
2 models selected
Grouped 2 regions
> select #2.127
1 model selected
Ungrouped to 4 regions
> select #2.157
1 model selected
> select add #2.269
2 models selected
> select add #2.26
3 models selected
> select subtract #2.26
2 models selected
Grouped 2 regions
> select #2.26
1 model selected
> select add #2.127
2 models selected
> select clear
> select #2.127
1 model selected
Ungrouped to 2 regions
> select #2.269
1 model selected
Ungrouped to 9 regions
> select #2.280
1 model selected
> select add #2.157
2 models selected
> select add #2.127
3 models selected
> select subtract #2.157
2 models selected
Grouped 2 regions
> select add #2.157
2 models selected
Grouped 2 regions
> select add #2.282
2 models selected
> select add #2.277
3 models selected
> select add #2.26
4 models selected
Grouped 4 regions
> select #2.140
1 model selected
> select add #2.26
2 models selected
Grouped 2 regions
> select #2.162
1 model selected
> select add #2.26
2 models selected
Grouped 2 regions
> select #2.24
1 model selected
Ungrouped to 3 regions
> select #2.157
1 model selected
> select add #2.140
2 models selected
Grouped 2 regions
> select add #2.26
2 models selected
Grouped 2 regions
Opened Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #26, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values
float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/Cage.mrc models #26
Opened Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #27, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values
float32
Segmenting Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.003143
Showing 254 region surfaces
17052 watershed regions, grouped to 254 regions
Showing Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 254 regions, 254 surfaces
> hide #!26 models
> hide #!27 models
> select #2.81
1 model selected
> select #2.143
1 model selected
> select add #2.147
2 models selected
> select add #2.132
3 models selected
> select subtract #2.132
2 models selected
> select add #2.210
3 models selected
Grouped 3 regions
> select #2.81
1 model selected
> select add #2.67
2 models selected
> select add #2.75
3 models selected
> select add #2.72
4 models selected
> select add #2.143
5 models selected
> select add #2.175
6 models selected
Grouped 6 regions
> select #2.70
1 model selected
> select add #2.69
2 models selected
> select add #2.163
3 models selected
Ungrouped to 8 regions
Ungrouped to 28 regions
Ungrouped to 85 regions
Ungrouped to 41 regions
> select #2.67
1 model selected
> select add #2.334
2 models selected
> select add #2.333
3 models selected
> select add #2.335
4 models selected
Grouped 4 regions
> select #2.205
1 model selected
> select add #2.67
2 models selected
Grouped 2 regions
> select #2.132
1 model selected
Ungrouped to 10 regions
Ungrouped to 31 regions
> select #2.391
1 model selected
> select add #2.392
2 models selected
> select add #2.340
3 models selected
> select add #2.341
4 models selected
> select add #2.405
5 models selected
Grouped 5 regions
> select add #2.4
2 models selected
> select #2.205
1 model selected
> select #2.205
1 model selected
> select add #2.67
2 models selected
> select add #2.404
3 models selected
Grouped 3 regions
> select #2.67
1 model selected
Ungrouped to 3 regions
> select #2.294
1 model selected
> select add #2.205
2 models selected
Grouped 2 regions
> select #2.305
1 model selected
Ungrouped to 2 regions
> select #2.205
1 model selected
Ungrouped to 4 regions
> select #2.336
1 model selected
Ungrouped to 6 regions
> select #2.392
1 model selected
> select add #2.305
2 models selected
> select add #2.205
3 models selected
> select #2.205
1 model selected
> select #2.205
1 model selected
> select #2.283
1 model selected
> select add #2.284
2 models selected
> select add #2.205
3 models selected
> select subtract #2.205
2 models selected
> select add #2.305
3 models selected
> select add #2.392
4 models selected
> select add #2.205
5 models selected
> select add #2.5
6 models selected
> select add #2.362
7 models selected
> select subtract #2.362
6 models selected
> select #2.205
1 model selected
> select #2.5
1 model selected
> select add #2.205
2 models selected
> select #2.205
1 model selected
> select #2.5
1 model selected
Ungrouped to 4 regions
Ungrouped to 26 regions
> select #2.417
1 model selected
> select #2.205
1 model selected
> select add #2.417
2 models selected
> select add #2.421
3 models selected
Grouped 3 regions
> select #2.256
1 model selected
> select add #2.314
2 models selected
> select subtract #2.314
1 model selected
> select add #2.205
2 models selected
> select add #2.392
3 models selected
Grouped 3 regions
> select #2.340
1 model selected
> select #2.284
1 model selected
> select add #2.205
2 models selected
> select #2.39
1 model selected
> select #2.57
1 model selected
> select add #2.39
2 models selected
> select add #2.60
3 models selected
> select add #2.174
4 models selected
> select add #2.95
5 models selected
> select add #2.44
6 models selected
> select add #2.176
7 models selected
> select add #2.66
8 models selected
> select add #2.55
9 models selected
> select add #2.202
10 models selected
> select add #2.37
11 models selected
> select add #2.261
12 models selected
> select add #2.372
13 models selected
> select add #2.374
14 models selected
> select add #2.371
15 models selected
> select add #2.376
16 models selected
> select add #2.260
17 models selected
> select subtract #2.374
16 models selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #2.353
17 models selected
> select add #2.361
18 models selected
> select add #2.360
19 models selected
> select add #2.375
20 models selected
> select add #2.377
21 models selected
> select add #2.295
22 models selected
> select add #2.293
23 models selected
> select add #2.262
24 models selected
> select add #2.358
25 models selected
> select add #2.271
26 models selected
> select add #2.265
27 models selected
> select add #2.264
28 models selected
> select add #2.351
29 models selected
> select add #2.373
30 models selected
> select add #2.374
31 models selected
> select add #2.370
32 models selected
> select add #2.366
33 models selected
> select add #2.367
34 models selected
> select add #2.272
35 models selected
> select add #2.337
36 models selected
> select add #2.355
37 models selected
> select add #2.363
38 models selected
> select add #2.365
39 models selected
> select add #2.310
40 models selected
> select add #2.274
41 models selected
> select add #2.311
42 models selected
> select add #2.307
43 models selected
> select add #2.259
44 models selected
> select add #2.69
45 models selected
Grouped 45 regions
> select add #2.352
2 models selected
Grouped 2 regions
> select add #2.316
2 models selected
> select add #2.325
3 models selected
> select add #2.290
4 models selected
> select add #2.322
5 models selected
> select add #2.329
6 models selected
> select add #2.287
7 models selected
> select add #2.289
8 models selected
> select add #2.285
9 models selected
> select add #2.288
10 models selected
> select add #2.323
11 models selected
> select add #2.292
12 models selected
> select add #2.344
13 models selected
> select add #2.347
14 models selected
> select add #2.345
15 models selected
> select add #2.327
16 models selected
> select add #2.324
17 models selected
> select add #2.326
18 models selected
> select add #2.328
19 models selected
> select add #2.346
20 models selected
> select add #2.301
21 models selected
> select add #2.282
22 models selected
> select add #2.281
23 models selected
> select add #2.304
24 models selected
> select add #2.315
25 models selected
> select add #2.317
26 models selected
> select add #2.319
27 models selected
> select add #2.343
28 models selected
> select add #2.303
29 models selected
> select add #2.318
30 models selected
> select add #2.302
31 models selected
> select add #2.210
32 models selected
> select add #2.348
33 models selected
> select add #2.350
34 models selected
> select add #2.300
35 models selected
> select add #2.320
36 models selected
> select add #2.273
37 models selected
> select add #2.70
38 models selected
Grouped 38 regions
> select add #2.390
2 models selected
> select add #2.389
3 models selected
> select add #2.335
4 models selected
> select add #2.401
5 models selected
> select add #2.395
6 models selected
> select add #2.388
7 models selected
> select add #2.334
8 models selected
> select add #2.384
9 models selected
> select add #2.385
10 models selected
> select add #2.397
11 models selected
> select add #2.386
12 models selected
> select add #2.381
13 models selected
> select add #2.357
14 models selected
> select add #2.75
15 models selected
> select add #2.283
16 models selected
> select add #2.258
17 models selected
> select add #2.81
18 models selected
> select add #2.356
19 models selected
> select add #2.396
20 models selected
> select add #2.398
21 models selected
> select add #2.382
22 models selected
> select add #2.255
23 models selected
> select add #2.387
24 models selected
> select add #2.333
25 models selected
> select add #2.403
26 models selected
> select add #2.297
27 models selected
> select add #2.299
28 models selected
> select add #2.400
29 models selected
> select add #2.132
30 models selected
> select add #2.280
31 models selected
> select add #2.399
32 models selected
> select add #2.383
33 models selected
> select add #2.298
34 models selected
> select add #2.175
35 models selected
> select add #2.313
36 models selected
> select add #2.278
37 models selected
> select add #2.284
38 models selected
> select add #2.312
39 models selected
> select add #2.402
40 models selected
Grouped 40 regions
> select #2.68
1 model selected
Ungrouped to 3 regions
> select #2.55
1 model selected
> select add #2.39
2 models selected
> select #2.39
1 model selected
Ungrouped to 7 regions
> select #2.68
1 model selected
> select add #2.66
2 models selected
> select add #2.69
3 models selected
> select add #2.216
4 models selected
> select add #2.55
5 models selected
> select subtract #2.216
4 models selected
> select add #2.75
5 models selected
Showing 311 region surfaces
> select add #2.37
6 models selected
Grouped 6 regions
> select #2.44
1 model selected
Ungrouped to 3 regions
Ungrouped to 10 regions
> select #2.174
1 model selected
> select add #2.176
2 models selected
> select add #2.81
3 models selected
> select add #2.95
4 models selected
> select add #2.132
5 models selected
> select add #2.44
6 models selected
Grouped 6 regions
Showing 310 region surfaces
> select add #2.37
2 models selected
Grouped 2 regions
> view orient
> select clear
> select #2.37
1 model selected
> view sel
No displayed objects specified.
> ui tool show "Side View"
Opened Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #28, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values
float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/PflB-cage.mrc models #28
Opened Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #29, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values
float32
Segmenting Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.003143
Showing 238 region surfaces
16400 watershed regions, grouped to 238 regions
Showing Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 238 regions, 238 surfaces
> hide #!28 models
> hide #!29 models
> select #2.54
1 model selected
> select add #2.109
2 models selected
> select add #2.5
3 models selected
> select #2.5
1 model selected
Ungrouped to 4 regions
> select #2.239
1 model selected
Ungrouped to 10 regions
> select #2.246
1 model selected
> select add #2.250
2 models selected
> select add #2.54
3 models selected
> select add #2.109
4 models selected
Grouped 4 regions
> select #2.108
1 model selected
Ungrouped to 3 regions
> select #2.246
1 model selected
Ungrouped to 11 regions
> select #2.257
1 model selected
Ungrouped to 0 regions
> select #2.54
1 model selected
> select add #2.257
2 models selected
> select #2.54
1 model selected
> select add #2.57
2 models selected
> select add #2.117
3 models selected
Grouped 3 regions
> select #2.3
1 model selected
Ungrouped to 2 regions
> select #2.57
1 model selected
Ungrouped to 11 regions
> select #2.263
1 model selected
> select add #2.54
2 models selected
Grouped 2 regions
> select #2.239
1 model selected
Ungrouped to 10 regions
> select #2.277
1 model selected
Ungrouped to 3 regions
> select #2.279
1 model selected
> select add #2.239
2 models selected
> select add #2.54
3 models selected
Grouped 3 regions
> select #2.179
1 model selected
> select add #2.191
2 models selected
> select add #2.52
3 models selected
Grouped 3 regions
> select #2.4
1 model selected
Ungrouped to 2 regions
> select #2.191
1 model selected
Ungrouped to 23 regions
> select #2.294
1 model selected
> select add #2.52
2 models selected
> select subtract #2.52
1 model selected
Grouped 1 regions
> select add #2.280
2 models selected
> select add #2.52
3 models selected
Grouped 3 regions
> select #2.286
1 model selected
> select add #2.52
2 models selected
Grouped 2 regions
> select #2.282
1 model selected
Ungrouped to 4 regions
Ungrouped to 6 regions
Ungrouped to 0 regions
> select #2.52
1 model selected
> select add #2.286
2 models selected
> select add #2.191
3 models selected
> select subtract #2.286
2 models selected
Grouped 2 regions
> select add #2.54
2 models selected
Grouped 2 regions
> select add #2.63
2 models selected
> select #2.52
1 model selected
Opened Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #30, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values
float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/FliL.mrc models #30
Opened Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #31, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values
float32
Segmenting Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.003143
Showing 231 region surfaces
16015 watershed regions, grouped to 231 regions
Showing Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 231 regions, 231 surfaces
> hide #!30 models
> hide #!31 models
> select #2.14
1 model selected
> select add #2.36
2 models selected
> select add #2.169
3 models selected
> select add #2.67
4 models selected
> select add #2.78
5 models selected
> select add #2.159
6 models selected
> select add #2.156
7 models selected
> select add #2.37
8 models selected
> select add #2.60
9 models selected
> select add #2.199
10 models selected
> select add #2.88
11 models selected
> select add #2.151
12 models selected
> select subtract #2.151
11 models selected
> select add #2.134
12 models selected
> select add #2.151
13 models selected
> select add #2.135
14 models selected
> select add #2.196
15 models selected
> select add #2.174
16 models selected
> select add #2.2
17 models selected
> select subtract #2.2
16 models selected
Drag select of 20552, 20028, 21571, 21632, 21121, 244 of 292 triangles, 21566,
21499, 20373, 28 of 256 triangles, 16012, 15965
Drag select of 21694, 124 of 23904 triangles
> select subtract #2.93
26 models selected
> select add #2.193
27 models selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select subtract #2.193
26 models selected
Grouped 26 regions
> select #2.193
1 model selected
Ungrouped to 4 regions
> select clear
> select #2.36
1 model selected
> select add #2.14
2 models selected
> select subtract #2.14
1 model selected
> select add #2.14
2 models selected
Grouped 2 regions
> select #2.10
1 model selected
> select add #2.14
2 models selected
> select #2.2
1 model selected
> select add #2.10
2 models selected
Ungrouped to 6 regions
Ungrouped to 44 regions
> select #2.14
1 model selected
> select add #2.219
2 models selected
> select add #2.248
3 models selected
> select add #2.245
4 models selected
> select subtract #2.245
3 models selected
> select add #2.231
4 models selected
> select add #2.245
5 models selected
> select subtract #2.231
4 models selected
> select subtract #2.245
3 models selected
Opened Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #32, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values
float32
Segmenting Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.003143
Showing 205 region surfaces
15312 watershed regions, grouped to 205 regions
Showing Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 205 regions, 205 surfaces
> select add #2.99
1 model selected
> select add #2.87
2 models selected
> select add #2.122
3 models selected
> select add #2.127
4 models selected
> select add #2.142
5 models selected
> select add #2.156
6 models selected
> select add #2.124
7 models selected
> select add #2.67
8 models selected
> select add #2.114
9 models selected
> select add #2.49
10 models selected
> select add #2.107
11 models selected
> select add #2.128
12 models selected
> select add #2.157
13 models selected
> select add #2.175
14 models selected
> select add #2.126
15 models selected
> select add #2.133
16 models selected
> select add #2.144
17 models selected
> select add #2.131
18 models selected
> select add #2.136
19 models selected
> select add #2.161
20 models selected
> select add #2.105
21 models selected
> select add #2.162
22 models selected
> select add #2.165
23 models selected
> select add #2.154
24 models selected
> select add #2.85
25 models selected
> select add #2.84
26 models selected
> select add #2.120
27 models selected
> select add #2.94
28 models selected
> select add #2.130
29 models selected
> select add #2.163
30 models selected
> select add #2.21
31 models selected
> select add #2.18
32 models selected
> select add #2.174
33 models selected
> select add #2.17
34 models selected
> select add #2.11
35 models selected
> select add #2.14
36 models selected
> select add #2.12
37 models selected
> select add #2.115
38 models selected
> select add #2.132
39 models selected
> select add #2.159
40 models selected
> hide #!32 models
> select add #2.112
41 models selected
> select add #2.147
42 models selected
> select add #2.96
43 models selected
> select add #2.36
44 models selected
> select add #2.76
45 models selected
> select add #2.81
46 models selected
> select add #2.103
47 models selected
> select add #2.71
48 models selected
> select add #2.56
49 models selected
> select add #2.92
50 models selected
> select add #2.43
51 models selected
> select #2.99
1 model selected
> select #2.99
1 model selected
> select add #2.87
2 models selected
> select add #2.122
3 models selected
> select add #2.127
4 models selected
> select add #2.142
5 models selected
> select add #2.156
6 models selected
> select add #2.124
7 models selected
> select add #2.67
8 models selected
> select add #2.114
9 models selected
> select add #2.49
10 models selected
> select add #2.107
11 models selected
> select add #2.128
12 models selected
> select add #2.157
13 models selected
> select add #2.175
14 models selected
> select add #2.126
15 models selected
> select add #2.133
16 models selected
> select add #2.144
17 models selected
> select add #2.131
18 models selected
> select add #2.136
19 models selected
> select add #2.161
20 models selected
> select add #2.105
21 models selected
> select add #2.162
22 models selected
> select add #2.165
23 models selected
> select add #2.154
24 models selected
> select add #2.85
25 models selected
> select add #2.84
26 models selected
> select add #2.120
27 models selected
> select add #2.94
28 models selected
> select add #2.163
29 models selected
> select add #2.130
30 models selected
> select add #2.21
31 models selected
> select add #2.18
32 models selected
> select add #2.174
33 models selected
> select add #2.17
34 models selected
> select add #2.11
35 models selected
> select add #2.14
36 models selected
> select add #2.12
37 models selected
> select subtract #2.12
36 models selected
> select add #2.12
37 models selected
> select add #2.115
38 models selected
> select add #2.132
39 models selected
> select add #2.159
40 models selected
Grouped 40 regions
> select #2.11
1 model selected
> select #2.56
1 model selected
> select add #2.92
2 models selected
> select add #2.68
3 models selected
> select add #2.118
4 models selected
> select add #2.63
5 models selected
> select add #2.91
6 models selected
Grouped 6 regions
> select #2.184
1 model selected
> select add #2.103
2 models selected
> select add #2.198
3 models selected
> select add #2.185
4 models selected
> select add #2.197
5 models selected
> select add #2.195
6 models selected
> select add #2.76
7 models selected
> select add #2.112
8 models selected
> select add #2.147
9 models selected
> select add #2.96
10 models selected
> select add #2.12
11 models selected
Grouped 11 regions
> select #2.81
1 model selected
> select add #2.12
2 models selected
Showing 151 region surfaces
> select add #2.11
3 models selected
Grouped 3 regions
> select #2.43
1 model selected
> select add #2.31
2 models selected
Ungrouped to 4 regions
> select #2.12
1 model selected
> select add #2.18
2 models selected
> select subtract #2.18
1 model selected
> select #2.71
1 model selected
Ungrouped to 2 regions
Ungrouped to 18 regions
> select #2.99
1 model selected
> select add #2.103
2 models selected
> select add #2.94
3 models selected
> select add #2.68
4 models selected
> select add #2.43
5 models selected
> select add #2.91
6 models selected
> select add #2.63
7 models selected
> select add #2.92
8 models selected
> select add #2.87
9 models selected
> select add #2.85
10 models selected
> select add #2.67
11 models selected
> select subtract #2.67
10 models selected
> select add #2.56
11 models selected
> select add #2.84
12 models selected
> select add #2.49
13 models selected
> select add #2.71
14 models selected
> select add #2.12
15 models selected
> select add #2.67
16 models selected
> select add #2.81
17 models selected
Grouped 17 regions
> select #2.36
1 model selected
Ungrouped to 4 regions
> select #2.43
1 model selected
> select add #2.49
2 models selected
> select add #2.12
3 models selected
Grouped 3 regions
> select #2.39
1 model selected
> select add #2.41
2 models selected
Ungrouped to 4 regions
> select #2.36
1 model selected
> select add #2.56
2 models selected
Ungrouped to 15 regions
> select #2.39
1 model selected
> select add #2.41
2 models selected
> select add #2.68
3 models selected
> select add #2.94
4 models selected
> select add #2.85
5 models selected
> select add #2.91
6 models selected
> select add #2.87
7 models selected
> select add #2.84
8 models selected
> select add #2.12
9 models selected
Grouped 9 regions
> select #2.40
1 model selected
> select add #2.37
2 models selected
Ungrouped to 6 regions
Ungrouped to 39 regions
> select #2.142
1 model selected
> select subtract #2.142
Nothing selected
> select add #2.136
1 model selected
> select add #2.120
2 models selected
> select add #2.115
3 models selected
> select add #2.195
4 models selected
> select add #2.118
5 models selected
> select add #2.133
6 models selected
> select add #2.144
7 models selected
> select add #2.142
8 models selected
> select add #2.157
9 models selected
> select add #2.130
10 models selected
> select add #2.156
11 models selected
> select add #2.131
12 models selected
> select add #2.154
13 models selected
> select add #2.147
14 models selected
> select add #2.159
15 models selected
> select add #2.132
16 models selected
> select add #2.12
17 models selected
> select add #2.96
18 models selected
Grouped 18 regions
> select #2.18
1 model selected
> select #2.18
1 model selected
Ungrouped to 5 regions
> select #2.36
1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Showing 184 region surfaces
> select #2.11
1 model selected
> select add #2.12
2 models selected
> select add #2.36
3 models selected
> select add #2.199
4 models selected
> select add #2.190
5 models selected
> select add #2.196
6 models selected
> select add #2.200
7 models selected
> select add #2.187
8 models selected
> select add #2.191
9 models selected
> select add #2.201
10 models selected
Grouped 10 regions
> select add #2.194
2 models selected
Grouped 2 regions
> select #2.9
1 model selected
Ungrouped to 17 regions
Showing 190 region surfaces
> select #2.11
1 model selected
> select #2.120
1 model selected
> select add #2.36
2 models selected
> select add #2.96
3 models selected
> select add #2.11
4 models selected
Grouped 4 regions
> select add #2.193
2 models selected
> select add #2.188
3 models selected
Grouped 3 regions
> select #2.14
1 model selected
> select #2.17
1 model selected
Ungrouped to 5 regions
Ungrouped to 28 regions
> select #2.187
1 model selected
> select add #2.190
2 models selected
> select add #2.188
3 models selected
> select add #2.159
4 models selected
Grouped 4 regions
Showing 209 region surfaces
> select add #2.9
2 models selected
Grouped 2 regions
> select #2.45
1 model selected
Ungrouped to 2 regions
> select #2.36
1 model selected
> select #2.36
1 model selected
Ungrouped to 3 regions
Ungrouped to 16 regions
> select #2.36
1 model selected
> select add #2.219
2 models selected
Grouped 2 regions
> select #2.11
1 model selected
Ungrouped to 4 regions
Ungrouped to 24 regions
> select #2.36
1 model selected
> select add #2.229
2 models selected
> select add #2.228
3 models selected
> select add #2.230
4 models selected
Grouped 4 regions
Showing 243 region surfaces
> select add #2.9
2 models selected
Grouped 2 regions
> select clear
> select #2.175
1 model selected
> select add #2.174
2 models selected
> select add #2.20
3 models selected
Ungrouped to 22 regions
Ungrouped to 71 regions
> select #2.276
1 model selected
> select add #2.275
2 models selected
> select add #2.274
3 models selected
> select add #2.262
4 models selected
> select add #2.114
5 models selected
> select add #2.329
6 models selected
Grouped 6 regions
> select add #2.271
2 models selected
> select add #2.263
3 models selected
> select add #2.20
4 models selected
> select add #2.174
5 models selected
> select add #2.290
6 models selected
> select add #2.284
7 models selected
> select add #2.283
8 models selected
> select add #2.279
9 models selected
> select add #2.268
10 models selected
> select add #2.326
11 models selected
> select add #2.277
12 models selected
> select add #2.272
13 models selected
> select add #2.273
14 models selected
> select add #2.317
15 models selected
> select add #2.289
16 models selected
> select add #2.228
17 models selected
> select add #2.280
18 models selected
> select add #2.126
19 models selected
> select add #2.124
20 models selected
> select subtract #2.124
19 models selected
Grouped 19 regions
> select #2.124
1 model selected
Ungrouped to 10 regions
> select #2.126
1 model selected
> select add #2.20
2 models selected
Grouped 2 regions
> select add #2.118
2 models selected
Showing 304 region surfaces
> select add #2.9
3 models selected
Grouped 3 regions
Opened Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #33, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values
float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/Cyt-components.mrc models #33
Opened Rev-CjpflAB-
mask-L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #34, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at step 1, values
float32
> hide #!33 models
> hide #!2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/IM.mrc models #34
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/Segmentation2.cxs includeMaps true
> close session
> open /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/IM.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/Cyt-components.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/FliL.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/PflB-cage.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/Cage.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/FlgY-PflA.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/MS-ring.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/Artifact3.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/MotBpg.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/Artifacts2.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/PflC-PflD.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/Basal-Disk.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/OM.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/LP-ring.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/Artifact1.mrc
> /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/Rod.mrc
Opened IM.mrc as #1.1, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at
level 0.0246, step 1, values float32
Opened Cyt-components.mrc as #1.2, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at level 0.0159, step 1, values float32
Opened FliL.mrc as #1.3, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at
level 0.0029, step 1, values float32
Opened PflB-cage.mrc as #1.4, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0105, step 1, values float32
Opened Cage.mrc as #1.5, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at
level 0.00285, step 1, values float32
Opened FlgY-PflA.mrc as #1.6, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0231, step 1, values float32
Opened MS-ring.mrc as #1.7, grid size 220,250,200, pixel 2.15,2.15,2.15, shown
at level 0.00313, step 1, values float32
Opened Artifact3.mrc as #1.8, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0028, step 1, values float32
Opened MotBpg.mrc as #1.9, grid size 220,250,200, pixel 2.15,2.15,2.15, shown
at level 0.00284, step 1, values float32
Opened Artifacts2.mrc as #1.10, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.00286, step 1, values float32
Opened PflC-PflD.mrc as #1.11, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0453, step 1, values float32
Opened Basal-Disk.mrc as #1.12, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0237, step 1, values float32
Opened OM.mrc as #1.13, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at
level 0.00412, step 1, values float32
Opened LP-ring.mrc as #1.14, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.0134, step 1, values float32
Opened Artifact1.mrc as #1.15, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at level 0.00301, step 1, values float32
Opened Rod.mrc as #1.16, grid size 220,250,200, pixel 2.15,2.15,2.15, shown at
level 0.00577, step 1, values float32
> hide #!1.2 models
> hide #!1.8 models
> hide #!1.10 models
> hide #!1.12 models
> hide #!1.13 models
> hide #!1.14 models
> show #!1.14 models
> hide #!1.11 models
> show #!1.11 models
> hide #!1.5 models
> show #!1.5 models
> hide #!1.15 models
> show #!1.12 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #1.4 level 0.0029
> volume #1.5 level 0.0029
> volume #1.6 level 0.0029
> volume #1.7 level 0.0029
> volume #1.8 level 0.0029
> volume #1.9 level 0.0029
> volume #1.10 level 0.0029
> volume #1.11 level 0.0029
> volume #1.12 level 0.0029
> volume #1.13 level 0.0029
> volume #1.14 level 0.0029
> volume #1.15 level 0.0029
> volume #1.16 level 0.0029
> volume gaussian #1 sDev ２
Opened IM.mrc gaussian as #2, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at step 1, values float32
Opened Cyt-components.mrc gaussian as #3, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened FliL.mrc gaussian as #4, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at step 1, values float32
Opened PflB-cage.mrc gaussian as #5, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened Cage.mrc gaussian as #6, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at step 1, values float32
Opened FlgY-PflA.mrc gaussian as #7, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened MS-ring.mrc gaussian as #8, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened Artifact3.mrc gaussian as #9, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened MotBpg.mrc gaussian as #10, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened Artifacts2.mrc gaussian as #11, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened PflC-PflD.mrc gaussian as #12, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened Basal-Disk.mrc gaussian as #13, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened OM.mrc gaussian as #14, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at step 1, values float32
Opened LP-ring.mrc gaussian as #15, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened Artifact1.mrc gaussian as #16, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
Opened Rod.mrc gaussian as #17, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at step 1, values float32
> volume #2 level 0.0029
> volume #3 level 0.0029
> volume #4 level 0.0029
> volume #5 level 0.0029
> volume #6 level 0.0029
> volume #8 level 0.0029
> volume #9 level 0.0029
> volume #10 level 0.0029
> volume #11 level 0.0029
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #12 level 0.0029
> volume #13 level 0.0029
> volume #14 level 0.0029
> volume #15 level 0.0029
> volume #16 level 0.0029
> volume #17 level 0.0029
> volume #13 level 0.01497
> color #13 #727272ff models
> lighting soft
> set bgColor white
> color #12 #727272ff models
> color #6 #52cdd6ff models
> color #6 #4a9ed2ff models
> color #10 #905d12ff modelsmodels
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #10 #905d12ff models
> ui tool show "Surface Color"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> color radial #7.1 palette #ff0000:#ffffff:#0000ff
> color radial #7.1 palette #ff69f5:#ffffff:#ff1e17
> color radial #7.1 palette #ff69f5:#faceff:#ff1e17
[Repeated 1 time(s)]
> color radial #7.1 palette 229.5,#ff69f5:309.9,#faceff:590.3,#ff1e17
> color radial #7.1 palette 229.5,#f333ff:309.9,#faceff:590.3,#ff1e17
[Repeated 1 time(s)]
> color radial #7.1 palette 229.5,#f333ff:309.9,#fc73ff:590.3,#ff1e17
> color radial #7.1 palette 229.5,#f333ff:309.9,#fc73ff:490.3,#ff1e17
> color radial #7.1 palette 229.5,#f333ff:309.9,#eb21ff:490.3,#ff1e17
> color radial #7.1 palette 229.5,#f333ff:409.9,#eb21ff:490.3,#ff1e17
> color radial #7.1 palette 229.5,#f333ff:409.9,#ffa0fe:490.3,#ff1e17
> color radial #7.1 palette 229.5,#f333ff:359.9,#ffa0fe:490.3,#ff1e17
> color radial #7.1 palette 329.5,#f333ff:359.9,#ffa0fe:490.3,#ff1e17
> color #2 #bdbdbdff models
> color #4 #b7a359ff models
> color #5 magenta models
> hide #!5 models
> show #!5 models
> color #5 #ff77f7ff models
> color #5 #ff5eeaff models
> color #8 #5da36dff models
> color #15 #92aa93ff models
> color #17 #727272ff models
> color radial #5.1 palette #f333ff:#ffa0fe:#ff1e17
> color radial #5.1 palette 281.4,#ff40ff:450.7,#ff40ff:619.9,#797979
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color radial #5.1 palette #ff40ff:#ff40ff
> color radial #5.1 palette 281.4,#ff40ff:619.9,#797979
> key #ff40ff:281 #797979:620 showTool true
> ui mousemode right "color key"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> key #ff40ff:281 #797979:620 showTool true
[Repeated 1 time(s)]
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui dockable false "Surface Color"
Window position QRect(1224,1261 1291x284) outside any known screen, using
primary screen
> key #ff40ff:281 #797979:620 showTool true
> color single #5.1
[Repeated 1 time(s)]
> color radial #5.1 palette 281.4,#ff40ff:619.9,#797979
> color single #5.1
Fetching compressed palette hideTool from
https://www.colourlovers.com/api/palettes?keywords=hideTool&format=json&numResults=100
> key #ff40ff:281 #797979:620 hideTool true
Expected a keyword
> hide #18 models
> close #18
> ui mousemode right translate
> color #12 #72727259 models
> color #13 #72727259 models
> color #6 #72727259 models
> color #5 #72727259 models
> color #10 #72727259 models
> lighting full
> lighting soft
> color #4 #72727259 models
> color #7 #72727259 models
> close #9
> close #3
> close #11
> close #14
> close #16
> open /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/CJ_FlgV_ST/CJ-PflB-PflAnC17.pdb
Summary of feedback from opening
/Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
manuscript/Start_Aug_2024/CJ_FlgV_ST/CJ-PflB-PflAnC17.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA C 169 ASP C 182 1 14
Start residue of secondary structure not found: HELIX 2 2 TYR C 186 ARG C 199
1 14
Start residue of secondary structure not found: HELIX 3 3 THR C 206 TYR C 221
1 16
Start residue of secondary structure not found: HELIX 4 4 GLN C 230 THR C 246
1 17
Start residue of secondary structure not found: HELIX 5 5 PHE C 253 ALA C 266
1 14
607 messages similar to the above omitted
Chain information for CJ-PflB-PflAnC17.pdb
---
Chain | Description
3.1/A 3.2/A 3.3/A 3.4/A 3.5/A 3.6/A 3.7/A 3.8/A 3.9/A 3.10/A 3.11/A 3.12/A 3.13/A 3.14/A 3.15/A 3.16/A 3.17/A | No description available
3.1/C 3.2/C 3.3/C 3.4/C 3.5/C 3.6/C 3.7/C 3.8/C 3.9/C 3.10/C 3.11/C 3.12/C 3.13/C 3.14/C 3.15/C 3.16/C 3.17/C | No description available
> open /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/CJ_FlgV_ST/Cj-PflAc17.pdb
Chain information for Cj-PflAc17.pdb
---
Chain | Description
9.1/C 9.2/C 9.3/C 9.4/C 9.5/C 9.6/C 9.7/C 9.8/C 9.9/C 9.10/C 9.11/C 9.12/C 9.13/C 9.14/C 9.15/C 9.16/C 9.17/C | No description available
> open /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/CJ_FlgV_ST/Cj-FlgYc17.pdb
Summary of feedback from opening
/Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
manuscript/Start_Aug_2024/CJ_FlgV_ST/Cj-FlgYc17.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA C 169 ASP C 182 1 14
Start residue of secondary structure not found: HELIX 2 2 TYR C 186 ARG C 199
1 14
Start residue of secondary structure not found: HELIX 3 3 THR C 206 TYR C 221
1 16
Start residue of secondary structure not found: HELIX 4 4 GLN C 230 THR C 246
1 17
Start residue of secondary structure not found: HELIX 5 5 PHE C 253 ALA C 266
1 14
31 messages similar to the above omitted
Chain information for Cj-FlgYc17.pdb
---
Chain | Description
11.1/A 11.2/A 11.3/A 11.4/A 11.5/A 11.6/A 11.7/A 11.8/A 11.9/A 11.10/A 11.11/A 11.12/A 11.13/A 11.14/A 11.15/A 11.16/A 11.17/A 11.1/B 11.2/B 11.3/B 11.4/B 11.5/B 11.6/B 11.7/B 11.8/B 11.9/B 11.10/B 11.11/B 11.12/B 11.13/B 11.14/B 11.15/B 11.16/B 11.17/B | No description available
> select add #9
86207 atoms, 87652 bonds, 10557 residues, 18 models selected
> select add #11
128197 atoms, 129846 bonds, 15827 residues, 36 models selected
> select add #3
235875 atoms, 239445 bonds, 29206 residues, 54 models selected
> hide #!2 models
> hide #!4 models
> hide #!6 models
> hide #!8 models
> show #!8 models
> hide #!15 models
> hide #!17 models
> hide #!13 models
> hide #!12 models
> ui mousemode right "translate selected models"
> view matrix models
> #3,1,0,0,-542.96,0,1,0,-237.23,0,0,1,-106.9,#9,1,0,0,-542.96,0,1,0,-237.23,0,0,1,-106.9,#11,1,0,0,-542.96,0,1,0,-237.23,0,0,1,-106.9
> view matrix models
> #3,1,0,0,-544.56,0,1,0,-250.71,0,0,1,-326.13,#9,1,0,0,-544.56,0,1,0,-250.71,0,0,1,-326.13,#11,1,0,0,-544.56,0,1,0,-250.71,0,0,1,-326.13
> view matrix models
> #3,1,0,0,-531.61,0,1,0,-262.48,0,0,1,-325.48,#9,1,0,0,-531.61,0,1,0,-262.48,0,0,1,-325.48,#11,1,0,0,-531.61,0,1,0,-262.48,0,0,1,-325.48
> ui mousemode right "rotate selected models"
> view matrix models
> #3,1,-0.0014584,7.7162e-05,-530.87,0.0014584,1,2.6414e-06,-263.26,-7.7165e-05,-2.5288e-06,1,-325.44,#9,1,-0.0014584,7.7162e-05,-530.87,0.0014584,1,2.6414e-06,-263.26,-7.7165e-05,-2.5288e-06,1,-325.44,#11,1,-0.0014584,7.7162e-05,-530.87,0.0014584,1,2.6414e-06,-263.26,-7.7165e-05,-2.5288e-06,1,-325.44
> view matrix models
> #3,0.99997,0.0077913,-0.00041228,-535.55,-0.0077913,0.99997,-1.2204e-05,-258.27,0.00041217,1.5416e-05,1,-325.71,#9,0.99997,0.0077913,-0.00041228,-535.55,-0.0077913,0.99997,-1.2204e-05,-258.27,0.00041217,1.5416e-05,1,-325.71,#11,0.99997,0.0077913,-0.00041228,-535.55,-0.0077913,0.99997,-1.2204e-05,-258.27,0.00041217,1.5416e-05,1,-325.71
> view matrix models
> #3,0.99992,-0.012467,0.00065949,-525.24,0.012467,0.99992,2.6211e-05,-269.15,-0.00065977,-1.7986e-05,1,-325.12,#9,0.99992,-0.012467,0.00065949,-525.24,0.012467,0.99992,2.6211e-05,-269.15,-0.00065977,-1.7986e-05,1,-325.12,#11,0.99992,-0.012467,0.00065949,-525.24,0.012467,0.99992,2.6211e-05,-269.15,-0.00065977,-1.7986e-05,1,-325.12
> view orient
> turn x 90
[Repeated 2 time(s)]
> view matrix models
> #3,0.99992,-0.012467,0.00065949,-525.24,0.012446,0.99958,0.026169,-282.52,-0.00098547,-0.026159,0.99966,-310.77,#9,0.99992,-0.012467,0.00065949,-525.24,0.012446,0.99958,0.026169,-282.52,-0.00098547,-0.026159,0.99966,-310.77,#11,0.99992,-0.012467,0.00065949,-525.24,0.012446,0.99958,0.026169,-282.52,-0.00098547,-0.026159,0.99966,-310.77
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.99992,-0.012467,0.00065949,-526.09,0.012467,0.99992,2.6211e-05,-269.15,-0.00065977,-1.7986e-05,1,-308.76,#9,0.99992,-0.012467,0.00065949,-526.09,0.012467,0.99992,2.6211e-05,-269.15,-0.00065977,-1.7986e-05,1,-308.76,#11,0.99992,-0.012467,0.00065949,-526.09,0.012467,0.99992,2.6211e-05,-269.15,-0.00065977,-1.7986e-05,1,-308.76
> turn x 90
> view matrix models
> #3,0.99992,-0.012467,0.00065949,-523.3,0.012467,0.99992,2.6211e-05,-271.87,-0.00065977,-1.7986e-05,1,-308.76,#9,0.99992,-0.012467,0.00065949,-523.3,0.012467,0.99992,2.6211e-05,-271.87,-0.00065977,-1.7986e-05,1,-308.76,#11,0.99992,-0.012467,0.00065949,-523.3,0.012467,0.99992,2.6211e-05,-271.87,-0.00065977,-1.7986e-05,1,-308.76
> select subtract #3
128197 atoms, 129846 bonds, 15827 residues, 36 models selected
> select add #3.1
134531 atoms, 136293 bonds, 16614 residues, 37 models selected
> select subtract #3.1
128197 atoms, 129846 bonds, 15827 residues, 36 models selected
> select add #3.2
134531 atoms, 136293 bonds, 16614 residues, 37 models selected
> select subtract #3.2
128197 atoms, 129846 bonds, 15827 residues, 36 models selected
> select add #3.3
134531 atoms, 136293 bonds, 16614 residues, 37 models selected
> select subtract #3.3
128197 atoms, 129846 bonds, 15827 residues, 36 models selected
> select add #3.1
134531 atoms, 136293 bonds, 16614 residues, 37 models selected
> select subtract #3.1
128197 atoms, 129846 bonds, 15827 residues, 36 models selected
> select add #3.1
134531 atoms, 136293 bonds, 16614 residues, 37 models selected
> select add #3.17
140865 atoms, 142740 bonds, 17401 residues, 38 models selected
> select add #3.16
147199 atoms, 149187 bonds, 18188 residues, 39 models selected
> select add #3.15
153533 atoms, 155634 bonds, 18975 residues, 40 models selected
> select add #3.14
159867 atoms, 162081 bonds, 19762 residues, 41 models selected
> select subtract #3.14
153533 atoms, 155634 bonds, 18975 residues, 40 models selected
> select add #3.14
159867 atoms, 162081 bonds, 19762 residues, 41 models selected
> hide #!5 models
> hide #3.14 models
> show #3.14 models
> hide #3.14 models
> show #3.14 models
> select add #3.13
166201 atoms, 168528 bonds, 20549 residues, 42 models selected
> select subtract #3.13
159867 atoms, 162081 bonds, 19762 residues, 41 models selected
> hide sel cartoons
> show sel cartoons
> select subtract #9
73660 atoms, 74429 bonds, 9205 residues, 23 models selected
> select subtract #11
31670 atoms, 32235 bonds, 3935 residues, 5 models selected
> hide sel cartoons
> show sel cartoons
> select add #7
31670 atoms, 32235 bonds, 3935 residues, 7 models selected
> select subtract #7
31670 atoms, 32235 bonds, 3935 residues, 5 models selected
> select add #7
31670 atoms, 32235 bonds, 3935 residues, 7 models selected
> select subtract #7
31670 atoms, 32235 bonds, 3935 residues, 5 models selected
> select add #7
31670 atoms, 32235 bonds, 3935 residues, 7 models selected
> select subtract #7
31670 atoms, 32235 bonds, 3935 residues, 5 models selected
Cell requested for row 41 is out of bounds for table with 49 rows! Resizing
table model.
> select add #9.1
36741 atoms, 37391 bonds, 4556 residues, 6 models selected
> select add #9.2
41812 atoms, 42547 bonds, 5177 residues, 7 models selected
> select add #9.17
46883 atoms, 47703 bonds, 5798 residues, 8 models selected
> select add #9.16
51954 atoms, 52859 bonds, 6419 residues, 9 models selected
> select add #9.15
57025 atoms, 58015 bonds, 7040 residues, 10 models selected
> select add #9.14
62096 atoms, 63171 bonds, 7661 residues, 11 models selected
> select add #9.3
67167 atoms, 68327 bonds, 8282 residues, 12 models selected
> select add #11.1
69637 atoms, 70809 bonds, 8592 residues, 13 models selected
> select add #11.2
72107 atoms, 73291 bonds, 8902 residues, 14 models selected
> select add #11.3
74577 atoms, 75773 bonds, 9212 residues, 15 models selected
> select add #11.17
77047 atoms, 78255 bonds, 9522 residues, 16 models selected
> select add #11.16
79517 atoms, 80737 bonds, 9832 residues, 17 models selected
> select add #11.15
81987 atoms, 83219 bonds, 10142 residues, 18 models selected
> select add #11.14
84457 atoms, 85701 bonds, 10452 residues, 19 models selected
> hide sel cartoons
> show sel cartoons
> select add #3.2
90791 atoms, 92148 bonds, 11239 residues, 20 models selected
> select add #3.13
97125 atoms, 98595 bonds, 12026 residues, 21 models selected
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/PDB-extract-from-Jack/FlgY-PflA-
> PflB.pdb selectedOnly true
> open /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/PDB-extract-from-Jack/FlgY-PflA-
> PflB.pdb
Summary of feedback from opening
/Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
manuscript/Start_Aug_2024/Local-ref-PflAB/PDB-extract-from-Jack/FlgY-PflA-
PflB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ARG A 109 LEU A 122 1 14
Start residue of secondary structure not found: HELIX 2 2 VAL A 126 MET A 153
1 28
Start residue of secondary structure not found: HELIX 3 3 PHE A 158 ALA A 170
1 13
Start residue of secondary structure not found: HELIX 4 4 GLN A 175 LYS A 188
1 14
Start residue of secondary structure not found: HELIX 5 5 LYS A 192 TYR A 205
1 14
821 messages similar to the above omitted
Chain information for FlgY-PflA-PflB.pdb
---
Chain | Description
14.1/A 14.2/A 14.3/A 14.4/A 14.5/A 14.6/A 14.7/A | No description available
14.15/A 14.16/A 14.17/A 14.18/A 14.19/A 14.20/A 14.21/A 14.15/B 14.16/B 14.17/B 14.18/B 14.19/B 14.20/B 14.21/B | No description available
14.1/C 14.2/C 14.3/C 14.4/C 14.5/C 14.6/C 14.7/C | No description available
14.8/C 14.9/C 14.10/C 14.11/C 14.12/C 14.13/C 14.14/C | No description available
> select add #3
160465 atoms, 163065 bonds, 19896 residues, 32 models selected
> hide #!3 models
> select subtract #3
52787 atoms, 53466 bonds, 6517 residues, 14 models selected
> select add #9
103497 atoms, 105026 bonds, 12727 residues, 25 models selected
> select subtract #9
17290 atoms, 17374 bonds, 2170 residues, 7 models selected
> hide #!9 models
> select add #11
41990 atoms, 42194 bonds, 5270 residues, 18 models selected
> select subtract #11
Nothing selected
> hide #!11 models
> select add #14
97125 atoms, 98595 bonds, 12026 residues, 22 models selected
> combine #14 modelId #15 name FlgY-PflA-PflB-comp
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.2 to 'B'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.2 to 'D'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.3 to 'E'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.3 to 'F'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.4 to 'G'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.4 to 'H'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.5 to 'I'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.5 to 'J'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.6 to 'K'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.6 to 'L'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.7 to 'M'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.7 to 'N'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.8 to 'O'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.9 to 'P'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.10 to 'Q'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.11 to 'R'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.12 to 'S'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.13 to 'T'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.14 to 'U'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.15 to 'V'
Remapping chain ID 'B' in FlgY-PflA-PflB.pdb #14.15 to 'W'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.16 to 'X'
Remapping chain ID 'B' in FlgY-PflA-PflB.pdb #14.16 to 'Y'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.17 to 'Z'
Remapping chain ID 'B' in FlgY-PflA-PflB.pdb #14.17 to 'a'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.18 to 'b'
Remapping chain ID 'B' in FlgY-PflA-PflB.pdb #14.18 to 'c'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.19 to 'd'
Remapping chain ID 'B' in FlgY-PflA-PflB.pdb #14.19 to 'e'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.20 to 'f'
Remapping chain ID 'B' in FlgY-PflA-PflB.pdb #14.20 to 'g'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.21 to 'h'
Remapping chain ID 'B' in FlgY-PflA-PflB.pdb #14.21 to 'i'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 169, in combine_cmd
session.models.add([combination])
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 756, in add
p = self._parent_for_added_model(model, parent, root_model = root_model)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 825, in _parent_for_added_model
raise ValueError('Tried to add model %s with the same id as another model %s'
ValueError: Tried to add model FlgY-PflA-PflB-comp #15 with the same id as
another model LP-ring.mrc gaussian #15
ValueError: Tried to add model FlgY-PflA-PflB-comp #15 with the same id as
another model LP-ring.mrc gaussian #15
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 825, in _parent_for_added_model
raise ValueError('Tried to add model %s with the same id as another model %s'
See log for complete Python traceback.
> combine #14 modelId #16 name FlgY-PflA-PflB-comp
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.2 to 'B'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.2 to 'D'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.3 to 'E'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.3 to 'F'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.4 to 'G'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.4 to 'H'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.5 to 'I'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.5 to 'J'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.6 to 'K'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.6 to 'L'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.7 to 'M'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.7 to 'N'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.8 to 'O'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.9 to 'P'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.10 to 'Q'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.11 to 'R'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.12 to 'S'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.13 to 'T'
Remapping chain ID 'C' in FlgY-PflA-PflB.pdb #14.14 to 'U'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.15 to 'V'
Remapping chain ID 'B' in FlgY-PflA-PflB.pdb #14.15 to 'W'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.16 to 'X'
Remapping chain ID 'B' in FlgY-PflA-PflB.pdb #14.16 to 'Y'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.17 to 'Z'
Remapping chain ID 'B' in FlgY-PflA-PflB.pdb #14.17 to 'a'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.18 to 'b'
Remapping chain ID 'B' in FlgY-PflA-PflB.pdb #14.18 to 'c'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.19 to 'd'
Remapping chain ID 'B' in FlgY-PflA-PflB.pdb #14.19 to 'e'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.20 to 'f'
Remapping chain ID 'B' in FlgY-PflA-PflB.pdb #14.20 to 'g'
Remapping chain ID 'A' in FlgY-PflA-PflB.pdb #14.21 to 'h'
Remapping chain ID 'B' in FlgY-PflA-PflB.pdb #14.21 to 'i'
> select subtract #14
Nothing selected
> hide #!14 models
> select add #16
97125 atoms, 98595 bonds, 12026 residues, 1 model selected
> ui tool show "Fit in Map"
> hide #!7 models
> show #!7 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #16 inMap #7
Fit molecule FlgY-PflA-PflB-comp (#16) to map FlgY-PflA.mrc gaussian (#7)
using 97125 atoms
average map value = 0.02173, steps = 76
shifted from previous position = 10.6
rotated from previous position = 2.68 degrees
atoms outside contour = 62067, contour level = 0.021605
Position of FlgY-PflA-PflB-comp (#16) relative to FlgY-PflA.mrc gaussian (#7)
coordinates:
Matrix rotation and translation
0.99890813 -0.04632273 -0.00606159 12.03955752
0.04632964 0.99892570 0.00100467 -4.85386975
0.00600854 -0.00128440 0.99998112 -10.34904122
Axis -0.02449159 -0.12914303 0.99132348
Axis point 138.26968799 251.39821636 0.00000000
Rotation angle (degrees) 2.67850189
Shift along axis -9.92727198
> fitmap #16 inMap #7
Fit molecule FlgY-PflA-PflB-comp (#16) to map FlgY-PflA.mrc gaussian (#7)
using 97125 atoms
average map value = 0.02173, steps = 40
shifted from previous position = 0.0317
rotated from previous position = 0.00436 degrees
atoms outside contour = 62067, contour level = 0.021605
Position of FlgY-PflA-PflB-comp (#16) relative to FlgY-PflA.mrc gaussian (#7)
coordinates:
Matrix rotation and translation
0.99890639 -0.04636086 -0.00605837 12.04749501
0.04636737 0.99892401 0.00093864 -4.85138056
0.00600834 -0.00121852 0.99998121 -10.39765652
Axis -0.02306257 -0.12900753 0.99137540
Axis point 138.18039759 251.64926912 0.00000000
Rotation angle (degrees) 2.68055621
Shift along axis -9.95996242
> fitmap #16 inMap #7
Fit molecule FlgY-PflA-PflB-comp (#16) to map FlgY-PflA.mrc gaussian (#7)
using 97125 atoms
average map value = 0.02173, steps = 44
shifted from previous position = 0.00727
rotated from previous position = 0.00299 degrees
atoms outside contour = 62063, contour level = 0.021605
Position of FlgY-PflA-PflB-comp (#16) relative to FlgY-PflA.mrc gaussian (#7)
coordinates:
Matrix rotation and translation
0.99890454 -0.04640439 -0.00602977 12.05565586
0.04641086 0.99892200 0.00093720 -4.85263354
0.00597978 -0.00121602 0.99998138 -10.39368692
Axis -0.02300119 -0.12828821 0.99147016
Axis point 137.93292863 251.60266362 0.00000000
Rotation angle (degrees) 2.68281694
Shift along axis -9.95978923
> select subtract #16
Nothing selected
> open /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/Hp_FliF.pdb
Summary of feedback from opening
/Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
manuscript/Start_Aug_2024/Local-ref-PflAB/Hp_FliF.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 78 1 77
Start residue of secondary structure not found: HELIX 2 2 LEU A 79 ILE A 81 1
3
Start residue of secondary structure not found: HELIX 3 3 LYS A 107 LEU A 118
1 12
Start residue of secondary structure not found: HELIX 4 4 ASN A 119 MET A 121
1 3
Start residue of secondary structure not found: HELIX 5 5 GLU A 154 ILE A 156
1 3
5 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
13 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 87 ILE A 93 0
Start residue of secondary structure not found: SHEET 2 2 1 SER A 97 THR A 104
0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 124 PRO A
131 0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 137 PHE A
144 0
Start residue of secondary structure not found: SHEET 5 5 1 ALA B 110 LEU B
116 0
Start residue of secondary structure not found: SHEET 6 6 1 LYS B 124 ALA B
133 0
1143 messages similar to the above omitted
Chain information for Hp_FliF.pdb
---
Chain | Description
18.1/A 18.2/A 18.3/A 18.4/A 18.5/A 18.6/A 18.7/A 18.8/A 18.9/A 18.10/A 18.11/A 18.12/A 18.13/A 18.14/A 18.15/A 18.16/A 18.17/A 18.18/A 18.19/A 18.20/A 18.21/A | No description available
18.22/A 18.23/A 18.24/A 18.25/A 18.26/A 18.27/A 18.28/A 18.29/A 18.30/A 18.31/A 18.32/A 18.33/A 18.34/A 18.35/A 18.36/A 18.37/A 18.38/A 18.39/A 18.40/A 18.41/A 18.42/A | No description available
18.43/A 18.44/A 18.45/A 18.46/A 18.47/A 18.48/A 18.49/A 18.50/A 18.51/A 18.52/A 18.53/A 18.54/A 18.55/A 18.56/A 18.57/A 18.58/A 18.59/A 18.60/A 18.61/A 18.62/A 18.63/A 18.64/A 18.65/A 18.66/A 18.67/A 18.68/A 18.69/A 18.70/A 18.71/A 18.72/A 18.73/A 18.74/A 18.75/A 18.76/A 18.77/A 18.78/A 18.79/A 18.80/A 18.81/A | No description available
> select add #18
112125 atoms, 113781 bonds, 39 pseudobonds, 14157 residues, 121 models
selected
> view matrix models #18,1,0,0,-412.46,0,1,0,-284.19,0,0,1,80.619
> view matrix models #18,1,0,0,-500.78,0,1,0,-408.54,0,0,1,-217.91
> view matrix models #18,1,0,0,-525.11,0,1,0,-308.76,0,0,1,-172.07
> view matrix models #18,1,0,0,-528.84,0,1,0,-264.67,0,0,1,-290.37
> view matrix models #18,1,0,0,-526.71,0,1,0,-269.57,0,0,1,-290.29
> view matrix models #18,1,0,0,-526.04,0,1,0,-271.65,0,0,1,-309.49
> combine #18 modelId #19 name Hp-FliF-comp
Remapping chain ID 'A' in Hp_FliF.pdb #18.2 to 'B'
Remapping chain ID 'A' in Hp_FliF.pdb #18.3 to 'C'
Remapping chain ID 'A' in Hp_FliF.pdb #18.4 to 'D'
Remapping chain ID 'A' in Hp_FliF.pdb #18.5 to 'E'
Remapping chain ID 'A' in Hp_FliF.pdb #18.6 to 'F'
Remapping chain ID 'A' in Hp_FliF.pdb #18.7 to 'G'
Remapping chain ID 'A' in Hp_FliF.pdb #18.8 to 'H'
Remapping chain ID 'A' in Hp_FliF.pdb #18.9 to 'I'
Remapping chain ID 'A' in Hp_FliF.pdb #18.10 to 'J'
Remapping chain ID 'A' in Hp_FliF.pdb #18.11 to 'K'
Remapping chain ID 'A' in Hp_FliF.pdb #18.12 to 'L'
Remapping chain ID 'A' in Hp_FliF.pdb #18.13 to 'M'
Remapping chain ID 'A' in Hp_FliF.pdb #18.14 to 'N'
Remapping chain ID 'A' in Hp_FliF.pdb #18.15 to 'O'
Remapping chain ID 'A' in Hp_FliF.pdb #18.16 to 'P'
Remapping chain ID 'A' in Hp_FliF.pdb #18.17 to 'Q'
Remapping chain ID 'A' in Hp_FliF.pdb #18.18 to 'R'
Remapping chain ID 'A' in Hp_FliF.pdb #18.19 to 'S'
Remapping chain ID 'A' in Hp_FliF.pdb #18.20 to 'T'
Remapping chain ID 'A' in Hp_FliF.pdb #18.21 to 'U'
Remapping chain ID 'A' in Hp_FliF.pdb #18.22 to 'V'
Remapping chain ID 'A' in Hp_FliF.pdb #18.23 to 'W'
Remapping chain ID 'A' in Hp_FliF.pdb #18.24 to 'X'
Remapping chain ID 'A' in Hp_FliF.pdb #18.25 to 'Y'
Remapping chain ID 'A' in Hp_FliF.pdb #18.26 to 'Z'
Remapping chain ID 'A' in Hp_FliF.pdb #18.27 to 'a'
Remapping chain ID 'A' in Hp_FliF.pdb #18.28 to 'b'
Remapping chain ID 'A' in Hp_FliF.pdb #18.29 to 'c'
Remapping chain ID 'A' in Hp_FliF.pdb #18.30 to 'd'
Remapping chain ID 'A' in Hp_FliF.pdb #18.31 to 'e'
Remapping chain ID 'A' in Hp_FliF.pdb #18.32 to 'f'
Remapping chain ID 'A' in Hp_FliF.pdb #18.33 to 'g'
Remapping chain ID 'A' in Hp_FliF.pdb #18.34 to 'h'
Remapping chain ID 'A' in Hp_FliF.pdb #18.35 to 'i'
Remapping chain ID 'A' in Hp_FliF.pdb #18.36 to 'j'
Remapping chain ID 'A' in Hp_FliF.pdb #18.37 to 'k'
Remapping chain ID 'A' in Hp_FliF.pdb #18.38 to 'l'
Remapping chain ID 'A' in Hp_FliF.pdb #18.39 to 'm'
Remapping chain ID 'A' in Hp_FliF.pdb #18.40 to 'n'
Remapping chain ID 'A' in Hp_FliF.pdb #18.41 to 'o'
Remapping chain ID 'A' in Hp_FliF.pdb #18.42 to 'p'
Remapping chain ID 'A' in Hp_FliF.pdb #18.43 to 'q'
Remapping chain ID 'A' in Hp_FliF.pdb #18.44 to 'r'
Remapping chain ID 'A' in Hp_FliF.pdb #18.45 to 's'
Remapping chain ID 'A' in Hp_FliF.pdb #18.46 to 't'
Remapping chain ID 'A' in Hp_FliF.pdb #18.47 to 'u'
Remapping chain ID 'A' in Hp_FliF.pdb #18.48 to 'v'
Remapping chain ID 'A' in Hp_FliF.pdb #18.49 to 'w'
Remapping chain ID 'A' in Hp_FliF.pdb #18.50 to 'x'
Remapping chain ID 'A' in Hp_FliF.pdb #18.51 to 'y'
Remapping chain ID 'A' in Hp_FliF.pdb #18.52 to 'z'
Remapping chain ID 'A' in Hp_FliF.pdb #18.53 to '1'
Remapping chain ID 'A' in Hp_FliF.pdb #18.54 to '2'
Remapping chain ID 'A' in Hp_FliF.pdb #18.55 to '3'
Remapping chain ID 'A' in Hp_FliF.pdb #18.56 to '4'
Remapping chain ID 'A' in Hp_FliF.pdb #18.57 to '5'
Remapping chain ID 'A' in Hp_FliF.pdb #18.58 to '6'
Remapping chain ID 'A' in Hp_FliF.pdb #18.59 to '7'
Remapping chain ID 'A' in Hp_FliF.pdb #18.60 to '8'
Remapping chain ID 'A' in Hp_FliF.pdb #18.61 to '9'
Remapping chain ID 'A' in Hp_FliF.pdb #18.62 to '0'
Remapping chain ID 'A' in Hp_FliF.pdb #18.63 to 'AA'
Remapping chain ID 'A' in Hp_FliF.pdb #18.64 to 'AB'
Remapping chain ID 'A' in Hp_FliF.pdb #18.65 to 'AC'
Remapping chain ID 'A' in Hp_FliF.pdb #18.66 to 'AD'
Remapping chain ID 'A' in Hp_FliF.pdb #18.67 to 'AE'
Remapping chain ID 'A' in Hp_FliF.pdb #18.68 to 'AF'
Remapping chain ID 'A' in Hp_FliF.pdb #18.69 to 'AG'
Remapping chain ID 'A' in Hp_FliF.pdb #18.70 to 'AH'
Remapping chain ID 'A' in Hp_FliF.pdb #18.71 to 'AI'
Remapping chain ID 'A' in Hp_FliF.pdb #18.72 to 'AJ'
Remapping chain ID 'A' in Hp_FliF.pdb #18.73 to 'AK'
Remapping chain ID 'A' in Hp_FliF.pdb #18.74 to 'AL'
Remapping chain ID 'A' in Hp_FliF.pdb #18.75 to 'AM'
Remapping chain ID 'A' in Hp_FliF.pdb #18.76 to 'AN'
Remapping chain ID 'A' in Hp_FliF.pdb #18.77 to 'AO'
Remapping chain ID 'A' in Hp_FliF.pdb #18.78 to 'AP'
Remapping chain ID 'A' in Hp_FliF.pdb #18.79 to 'AQ'
Remapping chain ID 'A' in Hp_FliF.pdb #18.80 to 'AR'
Remapping chain ID 'A' in Hp_FliF.pdb #18.81 to 'AS'
> select subtract #18
Nothing selected
> hide #!18 models
> close #18
> fitmap #19 inMap #8
Fit molecule Hp-FliF-comp (#19) to map MS-ring.mrc gaussian (#8) using 112125
atoms
average map value = 0.01124, steps = 240
shifted from previous position = 6.7
rotated from previous position = 5.76 degrees
atoms outside contour = 79659, contour level = 0.0029
Position of Hp-FliF-comp (#19) relative to MS-ring.mrc gaussian (#8)
coordinates:
Matrix rotation and translation
0.99494987 -0.08808776 -0.04811753 -453.04926146
0.08819268 0.99610343 0.00005766 -318.27166417
0.04792495 -0.00430098 0.99884168 -326.11066539
Axis -0.02170712 -0.47831516 0.87791993
Axis point 4043.75615626 -5405.60252129 0.00000000
Rotation angle (degrees) 5.76201189
Shift along axis -124.23049728
> fitmap #19 inMap #8
Fit molecule Hp-FliF-comp (#19) to map MS-ring.mrc gaussian (#8) using 112125
atoms
average map value = 0.01124, steps = 44
shifted from previous position = 0.0187
rotated from previous position = 0.115 degrees
atoms outside contour = 79648, contour level = 0.0029
Position of Hp-FliF-comp (#19) relative to MS-ring.mrc gaussian (#8)
coordinates:
Matrix rotation and translation
0.99477266 -0.09007936 -0.04809439 -451.89435525
0.09018680 0.99592486 0.00006420 -319.22900610
0.04789261 -0.00440134 0.99884279 -326.04112326
Axis -0.02186016 -0.46988510 0.88245687
Axis point 3967.21079221 -5277.86678279 0.00000000
Rotation angle (degrees) 5.86234530
Shift along axis -127.83779472
> fitmap #19 inMap #8
Fit molecule Hp-FliF-comp (#19) to map MS-ring.mrc gaussian (#8) using 112125
atoms
average map value = 0.01125, steps = 40
shifted from previous position = 0.0156
rotated from previous position = 0.0564 degrees
atoms outside contour = 79654, contour level = 0.0029
Position of Hp-FliF-comp (#19) relative to MS-ring.mrc gaussian (#8)
coordinates:
Matrix rotation and translation
0.99468143 -0.09105658 -0.04814093 -451.31123222
0.09116550 0.99583575 0.00006715 -319.70117678
0.04793435 -0.00445559 0.99884055 -326.02873784
Axis -0.02194993 -0.46627609 0.88436690
Axis point 3930.10921638 -5217.12001004 0.00000000
Rotation angle (degrees) 5.91333413
Shift along axis -129.35375721
> fitmap #19 inMap #8
Fit molecule Hp-FliF-comp (#19) to map MS-ring.mrc gaussian (#8) using 112125
atoms
average map value = 0.01125, steps = 48
shifted from previous position = 0.0121
rotated from previous position = 0.0167 degrees
atoms outside contour = 79655, contour level = 0.0029
Position of Hp-FliF-comp (#19) relative to MS-ring.mrc gaussian (#8)
coordinates:
Matrix rotation and translation
0.99465592 -0.09134481 -0.04812207 -451.14593579
0.09145477 0.99580923 0.00008361 -319.84811212
0.04791277 -0.00448416 0.99884146 -326.01348203
Axis -0.02211556 -0.46496714 0.88505167
Axis point 3919.20566949 -5199.66103898 0.00000000
Rotation angle (degrees) 5.92753566
Shift along axis -129.84257200
> show #!5 models
> show #!4 models
> open /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/CJ_FlgV_ST/Cj-FliLringC17.pdb
Chain information for Cj-FliLringC17.pdb
---
Chain | Description
18.11/? 18.12/? 18.13/? 18.14/? 18.15/? 18.16/? 18.17/? 18.18/? 18.19/? 18.20/? | No description available
18.1/B 18.2/B 18.3/B 18.4/B 18.5/B 18.6/B 18.7/B 18.8/B 18.9/B 18.10/B | No description available
> select add #19
112125 atoms, 113781 bonds, 39 pseudobonds, 14157 residues, 2 models selected
> select subtract #19
Nothing selected
> select add #18
9850 atoms, 9950 bonds, 1220 residues, 21 models selected
> view matrix models #18,1,0,0,-563.06,0,1,0,-280.22,0,0,1,-81.971
> view matrix models #18,1,0,0,-548.17,0,1,0,-365.12,0,0,1,-224.09
> view matrix models #18,1,0,0,-584.16,0,1,0,-178.03,0,0,1,-299.62
> view matrix models #18,1,0,0,-529.26,0,1,0,-247.21,0,0,1,-290.01
> hide #!19 models
> hide #16 models
> hide #!10 models
> hide #!8 models
> hide #!7 models
> hide #!5 models
> view matrix models #18,1,0,0,-535.14,0,1,0,-254.76,0,0,1,-314.65
> view matrix models #18,1,0,0,-525.73,0,1,0,-256.3,0,0,1,-316.03
> combine #18 modelId #20 name Cj-FliL
Remapping chain ID 'B' in Cj-FliLringC17.pdb #18.2 to 'C'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #18.3 to 'D'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #18.4 to 'E'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #18.5 to 'F'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #18.6 to 'G'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #18.7 to 'H'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #18.8 to 'I'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #18.9 to 'J'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #18.10 to 'K'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #18.11 to 'A'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #18.12 to 'L'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #18.13 to 'M'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #18.14 to 'N'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #18.15 to 'O'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #18.16 to 'P'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #18.17 to 'Q'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #18.18 to 'R'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #18.19 to 'S'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #18.20 to 'T'
> select subtract #18
Nothing selected
> hide #!18 models
> select add #20
9850 atoms, 9950 bonds, 1220 residues, 1 model selected
> fitmap #20 inMap #4
Fit molecule Cj-FliL (#20) to map FliL.mrc gaussian (#4) using 9850 atoms
average map value = 0.01285, steps = 124
shifted from previous position = 7.8
rotated from previous position = 27.4 degrees
atoms outside contour = 4114, contour level = 0.0029
Position of Cj-FliL (#20) relative to FliL.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.94102639 0.01215047 0.33811493 -645.76339539
-0.12192253 0.94438907 0.30539185 -270.36425430
-0.31560139 -0.32860561 0.89017645 158.93123829
Axis -0.68877240 0.71019490 -0.14565639
Axis point 101.55935502 0.00000000 1459.84234590
Rotation angle (degrees) 27.40241934
Shift along axis 229.62333998
> fitmap #20 inMap #4
Fit molecule Cj-FliL (#20) to map FliL.mrc gaussian (#4) using 9850 atoms
average map value = 0.01285, steps = 48
shifted from previous position = 0.0435
rotated from previous position = 0.0183 degrees
atoms outside contour = 4116, contour level = 0.0029
Position of Cj-FliL (#20) relative to FliL.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.94110316 0.01231967 0.33789505 -645.83093702
-0.12195683 0.94443396 0.30523928 -270.31144458
-0.31535911 -0.32847026 0.89031226 158.62213340
Axis -0.68883142 0.71007609 -0.14595626
Axis point 101.31864999 0.00000000 1460.57780476
Rotation angle (degrees) 27.38638790
Shift along axis 229.77505253
> open /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/CJ_FlgV_ST/Cj-FliLringC17.pdb
Summary of feedback from opening
/Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
manuscript/Start_Aug_2024/CJ_FlgV_ST/Cj-FliLringC17.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA C 169 ASP C 182 1 14
Start residue of secondary structure not found: HELIX 2 2 TYR C 186 ARG C 199
1 14
Start residue of secondary structure not found: HELIX 3 3 THR C 206 TYR C 221
1 16
Start residue of secondary structure not found: HELIX 4 4 GLN C 230 THR C 246
1 17
Start residue of secondary structure not found: HELIX 5 5 PHE C 253 ALA C 266
1 14
715 messages similar to the above omitted
Chain information for Cj-FliLringC17.pdb
---
Chain | Description
21.11/? 21.12/? 21.13/? 21.14/? 21.15/? 21.16/? 21.17/? 21.18/? 21.19/? 21.20/? | No description available
21.1/B 21.2/B 21.3/B 21.4/B 21.5/B 21.6/B 21.7/B 21.8/B 21.9/B 21.10/B | No description available
> select subtract #20
Nothing selected
> hide #20 models
> close #18
> combine #21 modelId #18 name Cj-FliL
Remapping chain ID 'B' in Cj-FliLringC17.pdb #21.2 to 'C'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #21.3 to 'D'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #21.4 to 'E'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #21.5 to 'F'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #21.6 to 'G'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #21.7 to 'H'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #21.8 to 'I'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #21.9 to 'J'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #21.10 to 'K'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #21.11 to 'A'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #21.12 to 'L'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #21.13 to 'M'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #21.14 to 'N'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #21.15 to 'O'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #21.16 to 'P'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #21.17 to 'Q'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #21.18 to 'R'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #21.19 to 'S'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #21.20 to 'T'
> select add #18
9850 atoms, 9950 bonds, 1220 residues, 1 model selected
> view matrix models #18,1,0,0,-17.715,0,1,0,-133.96,0,0,1,18.357
> view matrix models #18,1,0,0,-40.442,0,1,0,-341.63,0,0,1,-243.52
> show #20 models
> view matrix models #18,1,0,0,-266.44,0,1,0,-386.31,0,0,1,-485.51
> view matrix models #18,1,0,0,-462.06,0,1,0,-235.61,0,0,1,-433.25
> view matrix models #18,1,0,0,-509.52,0,1,0,-172.96,0,0,1,-466.54
> view matrix models #18,1,0,0,-514.97,0,1,0,-145.22,0,0,1,-326.99
> view matrix models #18,1,0,0,-530.51,0,1,0,-147.06,0,0,1,-334.39
> fitmap #18 inMap #4
Fit molecule Cj-FliL (#18) to map FliL.mrc gaussian (#4) using 9850 atoms
average map value = 0.01222, steps = 128
shifted from previous position = 15.9
rotated from previous position = 27.1 degrees
atoms outside contour = 4262, contour level = 0.0029
Position of Cj-FliL (#18) relative to FliL.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.97347543 0.11182108 0.19960370 -668.52021332
-0.18250281 0.90566474 0.38270629 -124.05180923
-0.13797941 -0.40898340 0.90205003 43.97468080
Axis -0.87037687 0.37113598 -0.32357716
Axis point 0.00000000 303.50292607 904.78157801
Rotation angle (degrees) 27.05187769
Shift along axis 521.59524082
> fitmap #18 inMap #4
Fit molecule Cj-FliL (#18) to map FliL.mrc gaussian (#4) using 9850 atoms
average map value = 0.01222, steps = 44
shifted from previous position = 0.0133
rotated from previous position = 0.0193 degrees
atoms outside contour = 4260, contour level = 0.0029
Position of Cj-FliL (#18) relative to FliL.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.97344914 0.11187129 0.19970373 -668.56847363
-0.18254518 0.90578463 0.38240223 -123.94269269
-0.13810874 -0.40870407 0.90215684 43.90161217
Axis -0.87011101 0.37154849 -0.32381870
Axis point 0.00000000 303.77005735 905.61942679
Rotation angle (degrees) 27.03925105
Shift along axis 521.46190660
> fitmap #18 inMap #4
Fit molecule Cj-FliL (#18) to map FliL.mrc gaussian (#4) using 9850 atoms
average map value = 0.01222, steps = 28
shifted from previous position = 0.0119
rotated from previous position = 0.00767 degrees
atoms outside contour = 4259, contour level = 0.0029
Position of Cj-FliL (#18) relative to FliL.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.97343461 0.11195548 0.19972740 -668.60903994
-0.18264464 0.90573382 0.38247508 -123.87978882
-0.13807968 -0.40879362 0.90212071 43.93733564
Axis -0.87009939 0.37146136 -0.32394986
Axis point 0.00000000 303.98954245 905.30120865
Rotation angle (degrees) 27.04564469
Shift along axis 521.50626848
> fitmap #18 inMap #4
Fit molecule Cj-FliL (#18) to map FliL.mrc gaussian (#4) using 9850 atoms
average map value = 0.01222, steps = 40
shifted from previous position = 0.0241
rotated from previous position = 0.0219 degrees
atoms outside contour = 4263, contour level = 0.0029
Position of Cj-FliL (#18) relative to FliL.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.97346986 0.11182028 0.19963131 -668.52957119
-0.18253076 0.90561199 0.38281777 -124.05437106
-0.13798172 -0.40910041 0.90199662 44.05927998
Axis -0.87041873 0.37107962 -0.32352920
Axis point 0.00000000 303.52185212 904.51087593
Rotation angle (degrees) 27.05891488
Shift along axis 521.61214860
> combine #21 modelId #22 name Cj-FliL
Remapping chain ID 'B' in Cj-FliLringC17.pdb #21.2 to 'C'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #21.3 to 'D'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #21.4 to 'E'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #21.5 to 'F'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #21.6 to 'G'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #21.7 to 'H'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #21.8 to 'I'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #21.9 to 'J'
Remapping chain ID 'B' in Cj-FliLringC17.pdb #21.10 to 'K'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #21.11 to 'A'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #21.12 to 'L'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #21.13 to 'M'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #21.14 to 'N'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #21.15 to 'O'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #21.16 to 'P'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #21.17 to 'Q'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #21.18 to 'R'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #21.19 to 'S'
Remapping chain ID ' ' in Cj-FliLringC17.pdb #21.20 to 'T'
> close #21
> select add #22
19700 atoms, 19900 bonds, 2440 residues, 2 models selected
> select subtract #18
9850 atoms, 9950 bonds, 1220 residues, 1 model selected
> view matrix models #22,1,0,0,11.87,0,1,0,-455.3,0,0,1,-341.08
> view matrix models #22,1,0,0,-507.9,0,1,0,-338.33,0,0,1,-160.15
> view matrix models #22,1,0,0,-568.6,0,1,0,-385.42,0,0,1,-312.91
> view matrix models #22,1,0,0,-557.67,0,1,0,-367.42,0,0,1,-315.9
> fitmap #22 inMap #4
Fit molecule Cj-FliL (#22) to map FliL.mrc gaussian (#4) using 9850 atoms
average map value = 0.01111, steps = 152
shifted from previous position = 8
rotated from previous position = 30.2 degrees
atoms outside contour = 4331, contour level = 0.0029
Position of Cj-FliL (#22) relative to FliL.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.88960038 0.01753559 0.45640296 -691.78157037
-0.12269540 0.97170740 0.20181816 -343.47684430
-0.43995113 -0.23553606 0.86658281 228.11215813
Axis -0.43424014 0.88997180 -0.13923251
Axis point 33.94104032 0.00000000 1559.18250017
Rotation angle (degrees) 30.23751103
Shift along axis -37.04601017
> fitmap #22 inMap #4
Fit molecule Cj-FliL (#22) to map FliL.mrc gaussian (#4) using 9850 atoms
average map value = 0.01111, steps = 44
shifted from previous position = 0.0322
rotated from previous position = 0.0603 degrees
atoms outside contour = 4334, contour level = 0.0029
Position of Cj-FliL (#22) relative to FliL.mrc gaussian (#4) coordinates:
Matrix rotation and translation
0.88948500 0.01849848 0.45658979 -692.23623286
-0.12373404 0.97160376 0.20168296 -342.51158062
-0.43989353 -0.23588967 0.86651587 228.26163190
Axis -0.43424554 0.88966690 -0.14115105
Axis point 34.18728538 0.00000000 1558.93754237
Rotation angle (degrees) 30.25377436
Shift along axis -36.34008748
> select subtract #22
Nothing selected
> show #!19 models
> show #16 models
> show #!5 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!1.6 models
> hide #!1.6 models
> show #!1.6 models
> hide #!1.6 models
> ui tool show Segmentations
> ui view fourup
> segmentations mouseModes false
Mouse bindings not saved; ignoring 'mouseModes false'
> ui view fourup
> undo
> segmentations mouseModes false
Mouse bindings not saved; ignoring 'mouseModes false'
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> close #24
> close #23
> close #21
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Error in sys.excepthook:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 334, in ehook
self.session.ui.thread_safe(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 516, in report_exception
self.bug(err_msg.replace("\n", "
"), is_html=True)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 394, in bug
self._log(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 572, in _log
if log.log(*args):
^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 342, in log
self.session.ui.thread_safe(f)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 341, in
f = lambda self=self, msg=dlg_msg: self.show_error_message(msg, bug=bug)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 262, in show_error_message
ed.showMessage(msg)
SystemError: returned a result with an exception set
Original exception was:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Error in sys.excepthook:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 334, in ehook
self.session.ui.thread_safe(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 516, in report_exception
self.bug(err_msg.replace("\n", "
"), is_html=True)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 394, in bug
self._log(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 572, in _log
if log.log(*args):
^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 342, in log
self.session.ui.thread_safe(f)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 341, in
f = lambda self=self, msg=dlg_msg: self.show_error_message(msg, bug=bug)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 262, in show_error_message
ed.showMessage(msg)
SystemError: returned a result with an exception set
Original exception was:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Error in sys.excepthook:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 334, in ehook
self.session.ui.thread_safe(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 516, in report_exception
self.bug(err_msg.replace("\n", "
"), is_html=True)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 394, in bug
self._log(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 572, in _log
if log.log(*args):
^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 342, in log
self.session.ui.thread_safe(f)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 341, in
f = lambda self=self, msg=dlg_msg: self.show_error_message(msg, bug=bug)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 262, in show_error_message
ed.showMessage(msg)
SystemError: returned a result with an exception set
Original exception was:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Error in sys.excepthook:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 334, in ehook
self.session.ui.thread_safe(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 516, in report_exception
self.bug(err_msg.replace("\n", "
"), is_html=True)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 394, in bug
self._log(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 572, in _log
if log.log(*args):
^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 342, in log
self.session.ui.thread_safe(f)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 341, in
f = lambda self=self, msg=dlg_msg: self.show_error_message(msg, bug=bug)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 262, in show_error_message
ed.showMessage(msg)
SystemError: returned a result with an exception set
Original exception was:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Error in sys.excepthook:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 334, in ehook
self.session.ui.thread_safe(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 516, in report_exception
self.bug(err_msg.replace("\n", "
"), is_html=True)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 394, in bug
self._log(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 572, in _log
if log.log(*args):
^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 342, in log
self.session.ui.thread_safe(f)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 341, in
f = lambda self=self, msg=dlg_msg: self.show_error_message(msg, bug=bug)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 262, in show_error_message
ed.showMessage(msg)
SystemError: returned a result with an exception set
Original exception was:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Error in sys.excepthook:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 334, in ehook
self.session.ui.thread_safe(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 516, in report_exception
self.bug(err_msg.replace("\n", "
"), is_html=True)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 394, in bug
self._log(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 572, in _log
if log.log(*args):
^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 342, in log
self.session.ui.thread_safe(f)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 341, in
f = lambda self=self, msg=dlg_msg: self.show_error_message(msg, bug=bug)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 262, in show_error_message
ed.showMessage(msg)
SystemError: returned a result with an exception set
Original exception was:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Error in sys.excepthook:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 334, in ehook
self.session.ui.thread_safe(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 516, in report_exception
self.bug(err_msg.replace("\n", "
"), is_html=True)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 394, in bug
self._log(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 572, in _log
if log.log(*args):
^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 342, in log
self.session.ui.thread_safe(f)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 341, in
f = lambda self=self, msg=dlg_msg: self.show_error_message(msg, bug=bug)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 262, in show_error_message
ed.showMessage(msg)
SystemError: returned a result with an exception set
Original exception was:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Error in sys.excepthook:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 334, in ehook
self.session.ui.thread_safe(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 516, in report_exception
self.bug(err_msg.replace("\n", "
"), is_html=True)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 394, in bug
self._log(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 572, in _log
if log.log(*args):
^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 342, in log
self.session.ui.thread_safe(f)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 341, in
f = lambda self=self, msg=dlg_msg: self.show_error_message(msg, bug=bug)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 262, in show_error_message
ed.showMessage(msg)
SystemError: returned a result with an exception set
Original exception was:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Error in sys.excepthook:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 334, in ehook
self.session.ui.thread_safe(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 516, in report_exception
self.bug(err_msg.replace("\n", "
"), is_html=True)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 394, in bug
self._log(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 572, in _log
if log.log(*args):
^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 342, in log
self.session.ui.thread_safe(f)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 341, in
f = lambda self=self, msg=dlg_msg: self.show_error_message(msg, bug=bug)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 262, in show_error_message
ed.showMessage(msg)
SystemError: returned a result with an exception set
Original exception was:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
Error in sys.excepthook:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 334, in ehook
self.session.ui.thread_safe(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 516, in report_exception
self.bug(err_msg.replace("\n", "
"), is_html=True)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 394, in bug
self._log(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 572, in _log
if log.log(*args):
^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 342, in log
self.session.ui.thread_safe(f)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 341, in
f = lambda self=self, msg=dlg_msg: self.show_error_message(msg, bug=bug)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 262, in show_error_message
ed.showMessage(msg)
SystemError: returned a result with an exception set
Original exception was:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> close #
Expected a models specifier or a keyword
> close #
Expected a models specifier or a keyword
close #
......^
Expected a models specifier or a keyword
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/logging.py", line 40, in
log_equivalent_command
command.run(command_text, log_only=True)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3175, in run
raise UserError(self._error)
chimerax.core.errors.UserError: Expected a models specifier or a keyword
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2138, in close_map_cb
log_equivalent_command(v.session, 'close #%s' % v.id_string)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/logging.py", line 42, in
log_equivalent_command
session.logger.info(str(err))
^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'logger'
AttributeError: 'NoneType' object has no attribute 'logger'
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/logging.py", line 42, in
log_equivalent_command
session.logger.info(str(err))
^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
Error in sys.excepthook:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 334, in ehook
self.session.ui.thread_safe(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 516, in report_exception
self.bug(err_msg.replace("\n", "
"), is_html=True)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 394, in bug
self._log(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 572, in _log
if log.log(*args):
^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 342, in log
self.session.ui.thread_safe(f)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 341, in
f = lambda self=self, msg=dlg_msg: self.show_error_message(msg, bug=bug)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 262, in show_error_message
ed.showMessage(msg)
SystemError: returned a result with an exception set
Original exception was:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1139, in
mouseStoppedMoving
level = self.drawingParentVolume().data.matrix()[
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'data'
Error in sys.excepthook:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an exception
set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
SystemError: returned a result with an
exception set
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 334, in ehook
self.session.ui.thread_safe(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 516, in report_exception
self.bug(err_msg.replace("\n", "
"), is_html=True)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 394, in bug
self._log(
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 572, in _log
if log.log(*args):
^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 342, in log
self.session.ui.thread_safe(f)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 341, in
f = lambda self=self, msg=dlg_msg: self.show_error_message(msg, bug=bug)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 262, in show_error_message
ed.showMessage(msg)
SystemError: returned a result with an exception set
Original exception was:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1139, in
mouseStoppedMoving
level = self.drawingParentVolume().data.matrix()[
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'data'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1127, in
mouseStoppedMoving
level = self.drawingParentVolume().data.matrix()[
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'data'
AttributeError: 'NoneType' object has no attribute 'data'
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1127, in
mouseStoppedMoving
level = self.drawingParentVolume().data.matrix()[
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
RuntimeError: Tried to get the position of deleted drawing "sagittal
segmentation cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 894, in event
self.enterEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 918, in enterEvent
self.segmentation_tool.make_puck_visible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 810, in
make_puck_visible
self.segmentation_cursors[axis].display = True
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1164, in
mouseMoveEvent
self.moveSegmentationPuck(x, y, record_seg=False)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1090, in
moveSegmentationPuck
old_origin = self.segmentation_tool.segmentation_cursors[self.axis].origin
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/graphics/cylinder.py", line 77, in origin
return self.position.origin()
^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
RuntimeError: Tried to get the position of deleted drawing "axial segmentation
cursor"
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 896, in event
self.leaveEvent()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 923, in leaveEvent
self.segmentation_tool.make_puck_invisible(self.axis)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/segmentations.py", line 814, in
make_puck_invisible
self.segmentation_cursors[axis].display = False
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 345, in _set_display
Drawing.set_display(self, display)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 392, in set_display
dp = self.display_positions
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 406, in get_display_positions
dp = ones((len(self._positions),), bool)
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/Develop-model-Figure.cxs
> includeMaps true
——— End of log from Sat Aug 24 18:41:04 2024 ———
opened ChimeraX session
> ui tool show "Segment Map"
> hide #!1.6 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Segmenting FlgY-PflA.mrc, density threshold 0.002900
Only showing 60 of 1053 regions.
Showing 60 of 1053 region surfaces
46616 watershed regions, grouped to 1053 regions
Showing FlgY-PflA.seg - 1053 regions, 60 surfaces
> hide #!4 models
> hide #!5 models
> hide #!7 models
> hide #16 models
> hide #18 models
> hide #!19 models
> hide #20 models
> hide #!21 models
> hide #22 models
> show #!2 models
> hide #!2 models
Segmenting FlgY-PflA.mrc, density threshold 0.002900
Only showing 60 of 1053 regions.
Showing 60 of 1053 region surfaces
46616 watershed regions, grouped to 1053 regions
Showing FlgY-PflA.seg - 1053 regions, 60 surfaces
> select #21.1
1 model selected
> select add #21.25
2 models selected
> select add #21.22
3 models selected
> select add #21.19
4 models selected
> select add #21.28
5 models selected
> select add #21.5
6 models selected
> select add #21.16
7 models selected
> select add #21.15
8 models selected
> select add #21.14
9 models selected
Grouped 9 regions
> select add #21.11
2 models selected
> select add #21.8
3 models selected
> select add #21.30
4 models selected
> select add #21.18
5 models selected
> select add #21.23
6 models selected
> select add #21.26
7 models selected
> select add #21.9
8 models selected
> select add #21.4
9 models selected
Grouped 9 regions
> select add #21.31
2 models selected
> select add #21.20
3 models selected
> select add #21.24
4 models selected
> select add #21.27
5 models selected
> select add #21.6
6 models selected
> select add #21.2
7 models selected
Grouped 7 regions
Ungrouped to 7 regions
> select subtract #21.6
6 models selected
> select subtract #21.2
5 models selected
> select subtract #21.4
4 models selected
> select add #21.37
5 models selected
Grouped 5 regions
Ungrouped to 5 regions
> select #21.8
1 model selected
> select add #21.2
2 models selected
> select add #21.6
3 models selected
> select add #21.4
4 models selected
> select add #21.11
5 models selected
Grouped 5 regions
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Opened FlgY-PflA_imasked as #23, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/4x-FlgY-PflA.mrc models #23
> hide #!1 models
> select add #21
41 models selected
> hide #!21 models
> select subtract #21
Nothing selected
> show #22 models
> show #20 models
> show #18 models
> show #16 models
> volume gaussian #23 sDev 1.5
Opened 4x-FlgY-PflA.mrc gaussian as #24, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
> color #24 #72727259 models
> open /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/PDB-
> files/fold_2024_08_24_18_52_cj_pilno/fold_2024_08_24_18_52_cj_pilno_model_0.cif
Chain information for fold_2024_08_24_18_52_cj_pilno_model_0.cif #25
---
Chain | Description
A | .
B | .
> hide #16 models
> hide #18 models
> hide #20 models
> hide #22 models
> hide #!24 models
> show #!6 models
> select add #25
3000 atoms, 3051 bonds, 364 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #25,1,0,0,54.542,0,1,0,107.69,0,0,1,187.71
> view matrix models #25,1,0,0,315.46,0,1,0,99.412,0,0,1,177.4
> show #!23 models
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.92497,-0.25489,-0.2819,309.98,-0.073904,0.60695,-0.7913,88.864,0.37279,0.75276,0.54257,186
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.92497,-0.25489,-0.2819,323.18,-0.073904,0.60695,-0.7913,59.794,0.37279,0.75276,0.54257,154.07
> view matrix models
> #25,0.92497,-0.25489,-0.2819,315.02,-0.073904,0.60695,-0.7913,50.859,0.37279,0.75276,0.54257,155.86
> view matrix models
> #25,0.92497,-0.25489,-0.2819,313.66,-0.073904,0.60695,-0.7913,52.673,0.37279,0.75276,0.54257,159.19
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #25 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#25) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.01786, steps = 568
shifted from previous position = 6.42
rotated from previous position = 18.5 degrees
atoms outside contour = 1398, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#25) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.93069891 0.01078518 -0.36562716 312.00547894
-0.24907478 0.75071594 -0.61187199 52.38438399
0.26788298 0.66053710 0.70137682 165.28070412
Axis 0.88058898 -0.43842979 -0.17983982
Axis point 0.00000000 -168.92693268 313.54903096
Rotation angle (degrees) 46.25929668
Shift along axis 222.05766187
> fitmap #25 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#25) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.01786, steps = 48
shifted from previous position = 0.0347
rotated from previous position = 0.68 degrees
atoms outside contour = 1400, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#25) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.92708453 0.01757937 -0.37443990 312.02395524
-0.25911489 0.75187863 -0.60624912 52.39103307
0.27087588 0.65906714 0.70161012 165.31032924
Axis 0.87439758 -0.44594586 -0.19120974
Axis point 0.00000000 -170.71746548 316.54258510
Rotation angle (degrees) 46.34719667
Shift along axis 217.86048186
> open /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/PDB-
> files/fold_2024_08_24_18_52_cj_pilno/fold_2024_08_24_18_52_cj_pilno_model_0.cif
Chain information for fold_2024_08_24_18_52_cj_pilno_model_0.cif #26
---
Chain | Description
A | .
B | .
> select subtract #25
Nothing selected
> select add #26
3000 atoms, 3051 bonds, 364 residues, 1 model selected
> select subtract #26
Nothing selected
> select add #26
3000 atoms, 3051 bonds, 364 residues, 1 model selected
> open /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/PDB-
> files/fold_2024_08_24_18_52_cj_pilno/fold_2024_08_24_18_52_cj_pilno_model_0.cif
Chain information for fold_2024_08_24_18_52_cj_pilno_model_0.cif #27
---
Chain | Description
A | .
B | .
> open /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/PDB-
> files/fold_2024_08_24_18_52_cj_pilno/fold_2024_08_24_18_52_cj_pilno_model_0.cif
Chain information for fold_2024_08_24_18_52_cj_pilno_model_0.cif #28
---
Chain | Description
A | .
B | .
> open /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/PDB-
> files/fold_2024_08_24_18_52_cj_pilno/fold_2024_08_24_18_52_cj_pilno_model_0.cif
Chain information for fold_2024_08_24_18_52_cj_pilno_model_0.cif #29
---
Chain | Description
A | .
B | .
> open /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/PDB-
> files/fold_2024_08_24_18_52_cj_pilno/fold_2024_08_24_18_52_cj_pilno_model_0.cif
Chain information for fold_2024_08_24_18_52_cj_pilno_model_0.cif #30
---
Chain | Description
A | .
B | .
> open /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/PDB-
> files/fold_2024_08_24_18_52_cj_pilno/fold_2024_08_24_18_52_cj_pilno_model_0.cif
Chain information for fold_2024_08_24_18_52_cj_pilno_model_0.cif #31
---
Chain | Description
A | .
B | .
> select add #27
6000 atoms, 6102 bonds, 728 residues, 2 models selected
> select add #28
9000 atoms, 9153 bonds, 1092 residues, 3 models selected
> select add #29
12000 atoms, 12204 bonds, 1456 residues, 4 models selected
> select add #30
15000 atoms, 15255 bonds, 1820 residues, 5 models selected
> select add #31
18000 atoms, 18306 bonds, 2184 residues, 6 models selected
> view matrix models
> #26,1,0,0,88.1,0,1,0,244.56,0,0,1,-3.9196,#27,1,0,0,88.1,0,1,0,244.56,0,0,1,-3.9196,#28,1,0,0,88.1,0,1,0,244.56,0,0,1,-3.9196,#29,1,0,0,88.1,0,1,0,244.56,0,0,1,-3.9196,#30,1,0,0,88.1,0,1,0,244.56,0,0,1,-3.9196,#31,1,0,0,88.1,0,1,0,244.56,0,0,1,-3.9196
> view matrix models
> #26,1,0,0,151.79,0,1,0,186.89,0,0,1,231.34,#27,1,0,0,151.79,0,1,0,186.89,0,0,1,231.34,#28,1,0,0,151.79,0,1,0,186.89,0,0,1,231.34,#29,1,0,0,151.79,0,1,0,186.89,0,0,1,231.34,#30,1,0,0,151.79,0,1,0,186.89,0,0,1,231.34,#31,1,0,0,151.79,0,1,0,186.89,0,0,1,231.34
> view matrix models
> #26,1,0,0,362.26,0,1,0,196.53,0,0,1,161.39,#27,1,0,0,362.26,0,1,0,196.53,0,0,1,161.39,#28,1,0,0,362.26,0,1,0,196.53,0,0,1,161.39,#29,1,0,0,362.26,0,1,0,196.53,0,0,1,161.39,#30,1,0,0,362.26,0,1,0,196.53,0,0,1,161.39,#31,1,0,0,362.26,0,1,0,196.53,0,0,1,161.39
> view matrix models
> #26,1,0,0,353.03,0,1,0,179.71,0,0,1,162.21,#27,1,0,0,353.03,0,1,0,179.71,0,0,1,162.21,#28,1,0,0,353.03,0,1,0,179.71,0,0,1,162.21,#29,1,0,0,353.03,0,1,0,179.71,0,0,1,162.21,#30,1,0,0,353.03,0,1,0,179.71,0,0,1,162.21,#31,1,0,0,353.03,0,1,0,179.71,0,0,1,162.21
> view matrix models
> #26,1,0,0,354.78,0,1,0,130.47,0,0,1,162.64,#27,1,0,0,354.78,0,1,0,130.47,0,0,1,162.64,#28,1,0,0,354.78,0,1,0,130.47,0,0,1,162.64,#29,1,0,0,354.78,0,1,0,130.47,0,0,1,162.64,#30,1,0,0,354.78,0,1,0,130.47,0,0,1,162.64,#31,1,0,0,354.78,0,1,0,130.47,0,0,1,162.64
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.99976,0.0017322,-0.021724,354.62,-0.0074231,0.96429,-0.26473,128.05,0.02049,0.26482,0.96408,165.04,#27,0.99976,0.0017322,-0.021724,354.62,-0.0074231,0.96429,-0.26473,128.05,0.02049,0.26482,0.96408,165.04,#28,0.99976,0.0017322,-0.021724,354.62,-0.0074231,0.96429,-0.26473,128.05,0.02049,0.26482,0.96408,165.04,#29,0.99976,0.0017322,-0.021724,354.62,-0.0074231,0.96429,-0.26473,128.05,0.02049,0.26482,0.96408,165.04,#30,0.99976,0.0017322,-0.021724,354.62,-0.0074231,0.96429,-0.26473,128.05,0.02049,0.26482,0.96408,165.04,#31,0.99976,0.0017322,-0.021724,354.62,-0.0074231,0.96429,-0.26473,128.05,0.02049,0.26482,0.96408,165.04
> view matrix models
> #26,0.99641,-0.027713,-0.08003,353.87,-0.058377,0.45986,-0.88607,118.11,0.061359,0.88756,0.45659,167.36,#27,0.99641,-0.027713,-0.08003,353.87,-0.058377,0.45986,-0.88607,118.11,0.061359,0.88756,0.45659,167.36,#28,0.99641,-0.027713,-0.08003,353.87,-0.058377,0.45986,-0.88607,118.11,0.061359,0.88756,0.45659,167.36,#29,0.99641,-0.027713,-0.08003,353.87,-0.058377,0.45986,-0.88607,118.11,0.061359,0.88756,0.45659,167.36,#30,0.99641,-0.027713,-0.08003,353.87,-0.058377,0.45986,-0.88607,118.11,0.061359,0.88756,0.45659,167.36,#31,0.99641,-0.027713,-0.08003,353.87,-0.058377,0.45986,-0.88607,118.11,0.061359,0.88756,0.45659,167.36
> view matrix models
> #26,0.97839,-0.18605,-0.090176,352.12,0.005967,0.46138,-0.88718,119.03,0.20667,0.86747,0.45253,169.22,#27,0.97839,-0.18605,-0.090176,352.12,0.005967,0.46138,-0.88718,119.03,0.20667,0.86747,0.45253,169.22,#28,0.97839,-0.18605,-0.090176,352.12,0.005967,0.46138,-0.88718,119.03,0.20667,0.86747,0.45253,169.22,#29,0.97839,-0.18605,-0.090176,352.12,0.005967,0.46138,-0.88718,119.03,0.20667,0.86747,0.45253,169.22,#30,0.97839,-0.18605,-0.090176,352.12,0.005967,0.46138,-0.88718,119.03,0.20667,0.86747,0.45253,169.22,#31,0.97839,-0.18605,-0.090176,352.12,0.005967,0.46138,-0.88718,119.03,0.20667,0.86747,0.45253,169.22
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.97839,-0.18605,-0.090176,448.65,0.005967,0.46138,-0.88718,143.03,0.20667,0.86747,0.45253,185,#27,0.97839,-0.18605,-0.090176,448.65,0.005967,0.46138,-0.88718,143.03,0.20667,0.86747,0.45253,185,#28,0.97839,-0.18605,-0.090176,448.65,0.005967,0.46138,-0.88718,143.03,0.20667,0.86747,0.45253,185,#29,0.97839,-0.18605,-0.090176,448.65,0.005967,0.46138,-0.88718,143.03,0.20667,0.86747,0.45253,185,#30,0.97839,-0.18605,-0.090176,448.65,0.005967,0.46138,-0.88718,143.03,0.20667,0.86747,0.45253,185,#31,0.97839,-0.18605,-0.090176,448.65,0.005967,0.46138,-0.88718,143.03,0.20667,0.86747,0.45253,185
> view matrix models
> #26,0.97839,-0.18605,-0.090176,445.68,0.005967,0.46138,-0.88718,216.05,0.20667,0.86747,0.45253,176.25,#27,0.97839,-0.18605,-0.090176,445.68,0.005967,0.46138,-0.88718,216.05,0.20667,0.86747,0.45253,176.25,#28,0.97839,-0.18605,-0.090176,445.68,0.005967,0.46138,-0.88718,216.05,0.20667,0.86747,0.45253,176.25,#29,0.97839,-0.18605,-0.090176,445.68,0.005967,0.46138,-0.88718,216.05,0.20667,0.86747,0.45253,176.25,#30,0.97839,-0.18605,-0.090176,445.68,0.005967,0.46138,-0.88718,216.05,0.20667,0.86747,0.45253,176.25,#31,0.97839,-0.18605,-0.090176,445.68,0.005967,0.46138,-0.88718,216.05,0.20667,0.86747,0.45253,176.25
> select subtract #27
15000 atoms, 15255 bonds, 1820 residues, 5 models selected
> select subtract #28
12000 atoms, 12204 bonds, 1456 residues, 4 models selected
> select subtract #29
9000 atoms, 9153 bonds, 1092 residues, 3 models selected
> select subtract #30
6000 atoms, 6102 bonds, 728 residues, 2 models selected
> select subtract #31
3000 atoms, 3051 bonds, 364 residues, 1 model selected
> view matrix models
> #26,0.97839,-0.18605,-0.090176,364.84,0.005967,0.46138,-0.88718,116.08,0.20667,0.86747,0.45253,205.94
> view matrix models
> #26,0.97839,-0.18605,-0.090176,366.08,0.005967,0.46138,-0.88718,98.395,0.20667,0.86747,0.45253,165.67
> view matrix models
> #26,0.97839,-0.18605,-0.090176,349.59,0.005967,0.46138,-0.88718,99.774,0.20667,0.86747,0.45253,174.21
> view matrix models
> #26,0.97839,-0.18605,-0.090176,347.22,0.005967,0.46138,-0.88718,98.372,0.20667,0.86747,0.45253,151.02
> view matrix models
> #26,0.97839,-0.18605,-0.090176,349.81,0.005967,0.46138,-0.88718,120.02,0.20667,0.86747,0.45253,156.45
> fitmap #26 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#26) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.009604, steps = 80
shifted from previous position = 4.66
rotated from previous position = 4.4 degrees
atoms outside contour = 1638, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#26) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.99095832 -0.12732914 -0.04229540 348.72422743
0.02130832 0.46059175 -0.88735629 116.15241974
0.13246722 0.87843186 0.45914040 158.94538969
Axis 0.99166488 -0.09814652 0.08347465
Axis point 0.00000000 -31.74773307 188.65199171
Rotation angle (degrees) 62.91285056
Shift along axis 347.68552652
> fitmap #26 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#26) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.009604, steps = 48
shifted from previous position = 0.0173
rotated from previous position = 0.486 degrees
atoms outside contour = 1639, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#26) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.99081929 -0.13067073 -0.03467425 348.71015746
0.02931675 0.45804974 -0.88844300 116.13587719
0.13197602 0.87926992 0.45767536 158.96154931
Axis 0.99156840 -0.09347963 0.08974224
Axis point 0.00000000 -30.41823890 186.01327426
Rotation angle (degrees) 63.04618095
Shift along axis 349.17919971
> select subtract #26
Nothing selected
> select add #27
3000 atoms, 3051 bonds, 364 residues, 1 model selected
> view matrix models
> #27,0.97839,-0.18605,-0.090176,387.83,0.005967,0.46138,-0.88718,180.85,0.20667,0.86747,0.45253,210.83
> view matrix models
> #27,0.97839,-0.18605,-0.090176,367.4,0.005967,0.46138,-0.88718,158.27,0.20667,0.86747,0.45253,164.47
> view matrix models
> #27,0.97839,-0.18605,-0.090176,365.76,0.005967,0.46138,-0.88718,180.89,0.20667,0.86747,0.45253,153.66
> fitmap #27 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.01953, steps = 280
shifted from previous position = 8.48
rotated from previous position = 25.9 degrees
atoms outside contour = 1513, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.94621886 -0.21346030 0.24311432 366.79271649
0.32340230 0.64494702 -0.69242638 173.76134240
-0.00899032 0.73381063 0.67929458 158.67334416
Axis 0.92334252 0.16321195 0.34756360
Axis point 0.00000000 40.77645214 130.52364332
Rotation angle (degrees) 50.56293760
Shift along axis 422.18431665
> ui mousemode right "rotate selected models"
> view matrix models
> #27,0.94842,-0.22882,0.21943,366.51,0.31326,0.57,-0.75959,172.44,0.048731,0.78914,0.61228,159.48
> fitmap #27 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.01953, steps = 112
shifted from previous position = 1.67
rotated from previous position = 6.02 degrees
atoms outside contour = 1509, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.93694303 -0.22175852 0.27011277 366.74037708
0.34906509 0.63155990 -0.69230460 173.82299032
-0.01706795 0.74293691 0.66914380 158.66734319
Axis 0.91354959 0.18279420 0.36333653
Axis point 0.00000000 45.20597981 114.94745236
Rotation angle (degrees) 51.76973869
Shift along axis 424.45899636
> ui mousemode right "translate selected models"
> view matrix models
> #27,0.93694,-0.22176,0.27011,363.53,0.34907,0.63156,-0.6923,167.67,-0.017068,0.74294,0.66914,153.05
> ui mousemode right "rotate selected models"
> view matrix models
> #27,0.99739,-0.069445,-0.01991,363.57,0.036735,0.72484,-0.68794,164.1,0.062205,0.68541,0.72549,154.09
> ui mousemode right "translate selected models"
> view matrix models
> #27,0.99739,-0.069445,-0.01991,361.19,0.036735,0.72484,-0.68794,175.13,0.062205,0.68541,0.72549,151.33
> fitmap #27 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.01953, steps = 252
shifted from previous position = 9.28
rotated from previous position = 18.1 degrees
atoms outside contour = 1513, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.94451291 -0.21523489 0.24813161 366.78885526
0.32830983 0.64248911 -0.69240191 173.76722235
-0.01039280 0.73544659 0.67750299 158.66921128
Axis 0.92147509 0.16684109 0.35078156
Axis point 0.00000000 41.77122619 127.55656810
Rotation angle (degrees) 50.78349537
Shift along axis 422.63654135
> fitmap #27 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.01953, steps = 44
shifted from previous position = 0.0355
rotated from previous position = 0.553 degrees
atoms outside contour = 1511, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.94168851 -0.21779536 0.25649157 366.78468020
0.33623482 0.63850725 -0.69228220 173.79043891
-0.01299588 0.73815559 0.67450532 158.67110367
Axis 0.91843447 0.17302854 0.35572355
Axis point 0.00000000 43.17052236 122.67762247
Rotation angle (degrees) 51.14508035
Shift along axis 423.38144847
> fitmap #27 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.01953, steps = 44
shifted from previous position = 0.0272
rotated from previous position = 0.412 degrees
atoms outside contour = 1510, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.93953384 -0.21962719 0.26275476 366.78043220
0.34212723 0.63558863 -0.69208096 173.80679755
-0.01500414 0.74012904 0.67229746 158.66602576
Axis 0.91613847 0.17767339 0.35933615
Axis point 0.00000000 44.15249879 119.05884916
Rotation angle (degrees) 51.41243521
Shift along axis 423.91694639
> fitmap #27 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.01953, steps = 44
shifted from previous position = 0.0298
rotated from previous position = 0.267 degrees
atoms outside contour = 1509, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.93814735 -0.22049321 0.26694997 366.75288842
0.34583549 0.63383328 -0.69184766 173.81071375
-0.01665406 0.74137583 0.67088339 158.68003700
Axis 0.91466615 0.18099271 0.36142422
Axis point 0.00000000 44.57773271 116.64247738
Rotation angle (degrees) 51.57921689
Shift along axis 424.26573464
> fitmap #27 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.01953, steps = 44
shifted from previous position = 0.0305
rotated from previous position = 0.168 degrees
atoms outside contour = 1509, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.93732646 -0.22104332 0.26936771 366.73295202
0.34802072 0.63233285 -0.69212481 173.83040193
-0.01734049 0.74249244 0.66962996 158.67650720
Axis 0.91390575 0.18264403 0.36251544
Axis point 0.00000000 44.83490732 115.33507825
Rotation angle (degrees) 51.70981167
Shift along axis 424.43112130
> fitmap #27 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.01953, steps = 40
shifted from previous position = 0.0131
rotated from previous position = 0.0733 degrees
atoms outside contour = 1509, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.93692286 -0.22148591 0.27040626 366.74192142
0.34909609 0.63174923 -0.69211620 173.83481465
-0.01753496 0.74285725 0.66922016 158.67040115
Axis 0.91349144 0.18330084 0.36322746
Axis point 0.00000000 45.07288716 114.75396515
Rotation angle (degrees) 51.76078401
Shift along axis 424.51312093
> fitmap #27 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.01953, steps = 40
shifted from previous position = 0.0221
rotated from previous position = 0.0406 degrees
atoms outside contour = 1508, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.93668367 -0.22184159 0.27094283 366.76066305
0.34972966 0.63172718 -0.69181640 173.82264727
-0.01768830 0.74276987 0.66931312 158.67046326
Axis 0.91316788 0.18372452 0.36382650
Axis point 0.00000000 45.27925825 114.39758722
Rotation angle (degrees) 51.76692208
Shift along axis 424.57805917
> fitmap #27 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.01953, steps = 60
shifted from previous position = 0.0119
rotated from previous position = 0.0423 degrees
atoms outside contour = 1508, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.93645390 -0.22196751 0.27163307 366.74937626
0.35032711 0.63156659 -0.69166072 173.82173880
-0.01802817 0.74286881 0.66919423 158.67535648
Axis 0.91289870 0.18433316 0.36419397
Axis point 0.00000000 45.34117454 113.98980109
Rotation angle (degrees) 51.78549254
Shift along axis 424.63474809
> fitmap #27 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.01953, steps = 40
shifted from previous position = 0.022
rotated from previous position = 0.0249 degrees
atoms outside contour = 1509, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#27) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.93641420 -0.22200474 0.27173945 366.72842419
0.35043859 0.63123101 -0.69191055 173.81554024
-0.01792295 0.74314286 0.66889271 158.67860446
Axis 0.91292264 0.18427145 0.36416518
Axis point 0.00000000 45.32820172 113.96930463
Rotation angle (degrees) 51.81016499
Shift along axis 424.60914647
> select subtract #27
Nothing selected
> select add #28
3000 atoms, 3051 bonds, 364 residues, 1 model selected
> view matrix models
> #28,0.97839,-0.18605,-0.090176,407.63,0.005967,0.46138,-0.88718,240.95,0.20667,0.86747,0.45253,198.78
> view matrix models
> #28,0.97839,-0.18605,-0.090176,404.43,0.005967,0.46138,-0.88718,242.84,0.20667,0.86747,0.45253,144.69
> view matrix models
> #28,0.97839,-0.18605,-0.090176,373.29,0.005967,0.46138,-0.88718,255.57,0.20667,0.86747,0.45253,151.77
> fitmap #28 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#28) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.01097, steps = 228
shifted from previous position = 8.43
rotated from previous position = 15.6 degrees
atoms outside contour = 1624, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#28) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.96962065 -0.16470294 0.18085559 378.55526378
0.23468402 0.41784682 -0.87768300 251.51814896
0.06898703 0.89346347 0.44380605 157.22083100
Axis 0.97365954 0.06149795 0.21955661
Axis point 0.00000000 61.59450883 216.38731833
Rotation angle (degrees) 65.44057736
Shift along axis 418.57066763
> fitmap #28 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#28) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.01097, steps = 40
shifted from previous position = 0.0353
rotated from previous position = 0.453 degrees
atoms outside contour = 1623, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#28) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.96785016 -0.16733909 0.18778632 378.54759744
0.24190452 0.41473614 -0.87719789 251.54205267
0.06890772 0.89442248 0.44188252 157.21758383
Axis 0.97226621 0.06524064 0.22459312
Axis point 0.00000000 62.89813805 213.57096048
Rotation angle (degrees) 65.65472577
Shift along axis 419.76979097
> fitmap #28 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#28) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.01097, steps = 40
shifted from previous position = 0.0069
rotated from previous position = 0.367 degrees
atoms outside contour = 1621, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#28) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.96642648 -0.16912838 0.19343072 378.53988770
0.24760643 0.41192127 -0.87693325 251.52922671
0.06863607 0.89538620 0.43996890 157.22179321
Axis 0.97117290 0.06838338 0.22835700
Axis point 0.00000000 63.82158988 211.22031347
Rotation angle (degrees) 65.84802671
Shift along axis 420.73079339
> select subtract #28
Nothing selected
> select add #29
3000 atoms, 3051 bonds, 364 residues, 1 model selected
> view matrix models
> #29,0.97839,-0.18605,-0.090176,373.89,0.005967,0.46138,-0.88718,324.26,0.20667,0.86747,0.45253,184.36
> view matrix models
> #29,0.97839,-0.18605,-0.090176,371.23,0.005967,0.46138,-0.88718,319.21,0.20667,0.86747,0.45253,146.58
> fitmap #29 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#29) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.02245, steps = 504
shifted from previous position = 17.7
rotated from previous position = 33.6 degrees
atoms outside contour = 1392, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#29) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.84135778 -0.47082416 0.26540854 375.49868125
0.51855821 0.56476964 -0.64197557 312.43852446
0.15236293 0.67776092 0.71932307 162.31677833
Axis 0.79824961 0.06837624 0.59843317
Axis point 0.00000000 244.30686457 276.50745024
Rotation angle (degrees) 55.75552324
Shift along axis 418.24078842
> fitmap #29 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#29) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.02245, steps = 44
shifted from previous position = 0.0341
rotated from previous position = 0.305 degrees
atoms outside contour = 1395, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#29) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.83886247 -0.47297828 0.26944629 375.52410862
0.52301181 0.56310945 -0.63981746 312.40990588
0.15089201 0.67764245 0.71974461 162.31258260
Axis 0.79565230 0.07159837 0.60150734
Axis point 0.00000000 245.45134357 273.81259008
Rotation angle (degrees) 55.88482651
Shift along axis 418.78687207
> fitmap #29 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#29) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.02245, steps = 40
shifted from previous position = 0.0681
rotated from previous position = 0.151 degrees
atoms outside contour = 1395, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#29) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.83767841 -0.47428935 0.27082188 375.55000338
0.52509783 0.56299504 -0.63820753 312.34592944
0.15022366 0.67682065 0.72065710 162.32948341
Axis 0.79405835 0.07282128 0.60346367
Axis point 0.00000000 246.32151465 272.94625527
Rotation angle (degrees) 55.89818138
Shift along axis 418.91399034
> select subtract #29
Nothing selected
> select add #30
3000 atoms, 3051 bonds, 364 residues, 1 model selected
> view matrix models
> #30,0.97839,-0.18605,-0.090176,357.3,0.005967,0.46138,-0.88718,391.81,0.20667,0.86747,0.45253,164.46
> view matrix models
> #30,0.97839,-0.18605,-0.090176,357.25,0.005967,0.46138,-0.88718,391.27,0.20667,0.86747,0.45253,153.12
> fitmap #30 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#30) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.009582, steps = 332
shifted from previous position = 9.07
rotated from previous position = 32.1 degrees
atoms outside contour = 1626, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#30) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.83681149 -0.36147699 0.41119451 360.83544897
0.53272880 0.36436984 -0.76382894 387.06992970
0.12627971 0.85823598 0.49747807 160.65068025
Axis 0.86556304 0.15203567 0.47716431
Axis point 0.00000000 205.96509663 246.21483287
Rotation angle (degrees) 69.55367780
Shift along axis 447.83103400
> fitmap #30 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#30) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.009584, steps = 44
shifted from previous position = 0.0295
rotated from previous position = 0.641 degrees
atoms outside contour = 1626, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#30) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.83128043 -0.36359286 0.42044390 360.84323222
0.54145412 0.35861978 -0.76040732 387.07745863
0.12569918 0.85976281 0.49498246 160.66997286
Axis 0.86221528 0.15685600 0.48164407
Axis point 0.00000000 206.86543815 241.88919034
Rotation angle (degrees) 69.97431665
Shift along axis 449.22570860
> select subtract #30
Nothing selected
> select add #31
3000 atoms, 3051 bonds, 364 residues, 1 model selected
> view matrix models
> #31,0.97839,-0.18605,-0.090176,333.18,0.005967,0.46138,-0.88718,457.94,0.20667,0.86747,0.45253,182.62
> view matrix models
> #31,0.97839,-0.18605,-0.090176,313.86,0.005967,0.46138,-0.88718,445.94,0.20667,0.86747,0.45253,147.94
> fitmap #31 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#31) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.01593, steps = 480
shifted from previous position = 21.8
rotated from previous position = 24 degrees
atoms outside contour = 1531, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#31) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.95756860 -0.26229008 0.11944153 332.73523687
0.27236315 0.68805016 -0.67261081 443.20274564
0.09423738 0.67660246 0.73029338 158.21029701
Axis 0.92952734 0.01736415 0.36834414
Axis point 0.00000000 193.48951283 559.50287744
Rotation angle (degrees) 46.53146878
Shift along axis 375.25817671
> fitmap #31 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#31) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.01593, steps = 48
shifted from previous position = 0.034
rotated from previous position = 0.685 degrees
atoms outside contour = 1532, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#31) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.95461114 -0.26842846 0.12908810 332.73618752
0.28320888 0.68376816 -0.67249820 443.21906684
0.09225133 0.67853317 0.72875403 158.22434078
Axis 0.92550584 0.02523453 0.37789173
Axis point 0.00000000 198.34203428 551.57767550
Rotation angle (degrees) 46.87701264
Shift along axis 378.92538118
> fitmap #31 inMap #6
Fit molecule fold_2024_08_24_18_52_cj_pilno_model_0.cif (#31) to map Cage.mrc
gaussian (#6) using 3000 atoms
average map value = 0.01593, steps = 48
shifted from previous position = 0.0322
rotated from previous position = 0.679 degrees
atoms outside contour = 1532, contour level = 0.0029
Position of fold_2024_08_24_18_52_cj_pilno_model_0.cif (#31) relative to
Cage.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.95152123 -0.27459898 0.13857402 332.73547423
0.29399069 0.67949479 -0.67220258 443.23453555
0.09042582 0.68035449 0.72728325 158.23565836
Axis 0.92136060 0.03279851 0.38732274
Axis point 0.00000000 203.12466892 543.86883226
Rotation angle (degrees) 47.22277192
Shift along axis 382.39505641
> color #23 #72727259 models
> surface dust #23 size 12.6
> volume gaussian #23 sDev 3
Opened 4x-FlgY-PflA.mrc gaussian as #32, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
> close #32
> volume gaussian #23 sDev 2
Opened 4x-FlgY-PflA.mrc gaussian as #32, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
> close #24
> surface dust #32 size 50
> color #32 #72727259 models
> show #22 models
> show #20 models
> show #18 models
> show #!19 models
> show #16 models
> split #16
Split FlgY-PflA-PflB-comp (#16) into 35 models
Chain information for FlgY-PflA-PflB-comp A #16.1
---
Chain | Description
A | No description available
Chain information for FlgY-PflA-PflB-comp B #16.2
---
Chain | Description
B | No description available
Chain information for FlgY-PflA-PflB-comp C #16.3
---
Chain | Description
C | No description available
Chain information for FlgY-PflA-PflB-comp D #16.4
---
Chain | Description
D | No description available
Chain information for FlgY-PflA-PflB-comp E #16.5
---
Chain | Description
E | No description available
Chain information for FlgY-PflA-PflB-comp F #16.6
---
Chain | Description
F | No description available
Chain information for FlgY-PflA-PflB-comp G #16.7
---
Chain | Description
G | No description available
Chain information for FlgY-PflA-PflB-comp H #16.8
---
Chain | Description
H | No description available
Chain information for FlgY-PflA-PflB-comp I #16.9
---
Chain | Description
I | No description available
Chain information for FlgY-PflA-PflB-comp J #16.10
---
Chain | Description
J | No description available
Chain information for FlgY-PflA-PflB-comp K #16.11
---
Chain | Description
K | No description available
Chain information for FlgY-PflA-PflB-comp L #16.12
---
Chain | Description
L | No description available
Chain information for FlgY-PflA-PflB-comp M #16.13
---
Chain | Description
M | No description available
Chain information for FlgY-PflA-PflB-comp N #16.14
---
Chain | Description
N | No description available
Chain information for FlgY-PflA-PflB-comp O #16.15
---
Chain | Description
O | No description available
Chain information for FlgY-PflA-PflB-comp P #16.16
---
Chain | Description
P | No description available
Chain information for FlgY-PflA-PflB-comp Q #16.17
---
Chain | Description
Q | No description available
Chain information for FlgY-PflA-PflB-comp R #16.18
---
Chain | Description
R | No description available
Chain information for FlgY-PflA-PflB-comp S #16.19
---
Chain | Description
S | No description available
Chain information for FlgY-PflA-PflB-comp T #16.20
---
Chain | Description
T | No description available
Chain information for FlgY-PflA-PflB-comp U #16.21
---
Chain | Description
U | No description available
Chain information for FlgY-PflA-PflB-comp V #16.22
---
Chain | Description
V | No description available
Chain information for FlgY-PflA-PflB-comp W #16.23
---
Chain | Description
W | No description available
Chain information for FlgY-PflA-PflB-comp X #16.24
---
Chain | Description
X | No description available
Chain information for FlgY-PflA-PflB-comp Y #16.25
---
Chain | Description
Y | No description available
Chain information for FlgY-PflA-PflB-comp Z #16.26
---
Chain | Description
Z | No description available
Chain information for FlgY-PflA-PflB-comp a #16.27
---
Chain | Description
a | No description available
Chain information for FlgY-PflA-PflB-comp b #16.28
---
Chain | Description
b | No description available
Chain information for FlgY-PflA-PflB-comp c #16.29
---
Chain | Description
c | No description available
Chain information for FlgY-PflA-PflB-comp d #16.30
---
Chain | Description
d | No description available
Chain information for FlgY-PflA-PflB-comp e #16.31
---
Chain | Description
e | No description available
Chain information for FlgY-PflA-PflB-comp f #16.32
---
Chain | Description
f | No description available
Chain information for FlgY-PflA-PflB-comp g #16.33
---
Chain | Description
g | No description available
Chain information for FlgY-PflA-PflB-comp h #16.34
---
Chain | Description
h | No description available
Chain information for FlgY-PflA-PflB-comp i #16.35
---
Chain | Description
i | No description available
> hide #18 models
> hide #!19 models
> hide #20 models
> hide #22 models
> hide #16.1 models
> show #16.1 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!5 models
> hide #16.1 models
> show #16.1 models
> hide #16.2 models
> show #16.2 models
> hide #16.2 models
> hide #16.3 models
> show #16.3 models
> hide #16.4 models
> hide #16.5 models
> show #16.5 models
> hide #16.5 models
> hide #16.6 models
> show #16.6 models
> hide #16.6 models
> hide #16.7 models
> show #16.7 models
> hide #16.8 models
> hide #16.9 models
> show #16.9 models
> hide #16.10 models
> show #16.10 models
> hide #16.12 models
> show #16.12 models
> hide #16.13 models
> show #16.13 models
> hide #16.14 models
> show #16.14 models
> hide #16.15 models
> show #16.15 models
> hide #16.16 models
> show #16.16 models
> hide #16.16 models
> hide #16.17 models
> hide #16.18 models
> show #16.18 models
> hide #16.18 models
> hide #16.19 models
> show #16.19 models
> hide #16.20 models
> show #16.20 models
> hide #16.21 models
> show #16.21 models
> hide #16.22 models
> show #16.22 models
> hide #16.23 models
> show #16.23 models
> hide #16.24 models
> show #16.24 models
> hide #16.24 models
> hide #16.25 models
> hide #16.26 models
> hide #16.27 models
> hide #16.28 models
> hide #16.29 models
Drag select of 369 residues
> hide sel cartoons
> show sel cartoons
> select clear
Drag select of 314 residues
> hide sel cartoons
Drag select of 42 residues
> hide sel cartoons
Drag select of 3 residues
Drag select of 75 residues
> hide sel cartoons
Drag select of 5 PflB-cage.mrc gaussian , 12 residues
> hide sel cartoons
Drag select of 10 residues
> hide sel cartoons
> select add #16.1/A:318
3679 atoms, 6 bonds, 457 residues, 1 model selected
> select add #16.1/A:347
3687 atoms, 13 bonds, 458 residues, 1 model selected
> select add #16.1/A:346
3695 atoms, 20 bonds, 459 residues, 1 model selected
> select add #16.1/A:345
3703 atoms, 27 bonds, 460 residues, 1 model selected
> select add #16.1/A:309
3711 atoms, 34 bonds, 461 residues, 1 model selected
> hide sel cartoons
> select add #16.1/A:780
3722 atoms, 45 bonds, 462 residues, 1 model selected
> hide sel cartoons
> hide #!5 models
Drag select of 12 residues
> hide sel cartoons
> select add #16.1
5455 atoms, 5553 bonds, 678 residues, 1 model selected
> select subtract #16.1
Nothing selected
> select add #16.1
5455 atoms, 5553 bonds, 678 residues, 1 model selected
> show sel cartoons
> select clear
> show #!5 models
> show #!8 models
> color #8 #72727259 models
> show #!19 models
> color #19 #5da36dff models
> select add #16.35
1235 atoms, 1241 bonds, 155 residues, 1 model selected
> select add #16.33
2470 atoms, 2482 bonds, 310 residues, 2 models selected
> select add #16.31
3705 atoms, 3723 bonds, 465 residues, 3 models selected
> select add #16.3
4584 atoms, 4617 bonds, 574 residues, 4 models selected
> select subtract #16.3
3705 atoms, 3723 bonds, 465 residues, 3 models selected
> select add #16.7
9160 atoms, 9276 bonds, 1143 residues, 4 models selected
> select subtract #16.7
3705 atoms, 3723 bonds, 465 residues, 3 models selected
> select add #16.23
4940 atoms, 4964 bonds, 620 residues, 4 models selected
> color sel magenta
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> select add #16.22
1235 atoms, 1241 bonds, 155 residues, 1 model selected
> select add #16.30
2470 atoms, 2482 bonds, 310 residues, 2 models selected
> select add #16.32
3705 atoms, 3723 bonds, 465 residues, 3 models selected
> select add #16.34
4940 atoms, 4964 bonds, 620 residues, 4 models selected
> color sel #e9cdeaff
> select clear
> select add #16.31
1235 atoms, 1241 bonds, 155 residues, 1 model selected
> select add #16.33
2470 atoms, 2482 bonds, 310 residues, 2 models selected
> select add #16.35
3705 atoms, 3723 bonds, 465 residues, 3 models selected
> select add #16.23
4940 atoms, 4964 bonds, 620 residues, 4 models selected
> color sel orchid models.
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel orchid models.
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel orchid models.
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel orchid models
> select clear
> select add #16.19
5071 atoms, 5156 bonds, 621 residues, 1 model selected
> select add #16.20
10142 atoms, 10312 bonds, 1242 residues, 2 models selected
> select add #16.21
15213 atoms, 15468 bonds, 1863 residues, 3 models selected
> select add #16.15
20284 atoms, 20624 bonds, 2484 residues, 4 models selected
> color sel #ca4949ff
> select clear
> select add #16.9
5455 atoms, 5553 bonds, 678 residues, 1 model selected
> select subtract #16.9
Nothing selected
> select add #16.10
879 atoms, 894 bonds, 109 residues, 1 model selected
> select add #16.11
6334 atoms, 6447 bonds, 787 residues, 2 models selected
> select subtract #16.11
879 atoms, 894 bonds, 109 residues, 1 model selected
> select add #16.12
1758 atoms, 1788 bonds, 218 residues, 2 models selected
> select add #16.13
7213 atoms, 7341 bonds, 896 residues, 3 models selected
> select subtract #16.13
1758 atoms, 1788 bonds, 218 residues, 2 models selected
> select add #16.14
2637 atoms, 2682 bonds, 327 residues, 3 models selected
> select add #16.3
3516 atoms, 3576 bonds, 436 residues, 4 models selected
> color sel #ca4949ff
> select subtract #16.3
2637 atoms, 2682 bonds, 327 residues, 3 models selected
> select subtract #16.10
1758 atoms, 1788 bonds, 218 residues, 2 models selected
> select subtract #16.12
879 atoms, 894 bonds, 109 residues, 1 model selected
> select add #16.1
6334 atoms, 6447 bonds, 787 residues, 2 models selected
> select subtract #16.14
5455 atoms, 5553 bonds, 678 residues, 1 model selected
> select add #16.9
10910 atoms, 11106 bonds, 1356 residues, 2 models selected
> select subtract #16.9
5455 atoms, 5553 bonds, 678 residues, 1 model selected
> select add #16.10
6334 atoms, 6447 bonds, 787 residues, 2 models selected
> select subtract #16.10
5455 atoms, 5553 bonds, 678 residues, 1 model selected
> select add #16.11
10910 atoms, 11106 bonds, 1356 residues, 2 models selected
> select subtract #16.11
5455 atoms, 5553 bonds, 678 residues, 1 model selected
> select add #16.11
10910 atoms, 11106 bonds, 1356 residues, 2 models selected
> select add #16.7
16365 atoms, 16659 bonds, 2034 residues, 3 models selected
> color sel #8c3092ff
> select add #16.9
21820 atoms, 22212 bonds, 2712 residues, 4 models selected
> select clear
> select add #16.9
5455 atoms, 5553 bonds, 678 residues, 1 model selected
> select add #16.13
10910 atoms, 11106 bonds, 1356 residues, 2 models selected
> color sel magenta
> select clear
> select add #25
3000 atoms, 3051 bonds, 364 residues, 1 model selected
> select add #26
6000 atoms, 6102 bonds, 728 residues, 2 models selected
> select add #27
9000 atoms, 9153 bonds, 1092 residues, 3 models selected
> select add #28
12000 atoms, 12204 bonds, 1456 residues, 4 models selected
> select add #29
15000 atoms, 15255 bonds, 1820 residues, 5 models selected
> select add #30
18000 atoms, 18306 bonds, 2184 residues, 6 models selected
> select add #31
21000 atoms, 21357 bonds, 2548 residues, 7 models selected
> color sel #4a9ed2ff
> ui tool show "Side View"
> color sel #52cdd6ff
> color sel #4a9ed2ff
> select clear
> select add #25
3000 atoms, 3051 bonds, 364 residues, 1 model selected
> select add #26
6000 atoms, 6102 bonds, 728 residues, 2 models selected
> select add #27
9000 atoms, 9153 bonds, 1092 residues, 3 models selected
> select add #28
12000 atoms, 12204 bonds, 1456 residues, 4 models selected
> select add #29
15000 atoms, 15255 bonds, 1820 residues, 5 models selected
> select add #30
18000 atoms, 18306 bonds, 2184 residues, 6 models selected
> select add #31
21000 atoms, 21357 bonds, 2548 residues, 7 models selected
Alignment identifier is 1
Alignment identifier is 2
> select #25/A:175 #26/A:175 #27/A:175 #28/A:175 #29/A:175 #30/A:175 #31/A:175
84 atoms, 77 bonds, 7 residues, 7 models selected
> select #25/A:167-175 #26/A:167-175 #27/A:167-175 #28/A:167-175 #29/A:167-175
> #30/A:167-175 #31/A:167-175
483 atoms, 483 bonds, 63 residues, 7 models selected
. [ID: 1] region 7 chains [167-175] RMSD: 212.124
> select #25/B:1 #26/B:1 #27/B:1 #28/B:1 #29/B:1 #30/B:1 #31/B:1
56 atoms, 49 bonds, 7 residues, 7 models selected
> select #25/B:1-20 #26/B:1-20 #27/B:1-20 #28/B:1-20 #29/B:1-20 #30/B:1-20
> #31/B:1-20
1099 atoms, 1099 bonds, 140 residues, 7 models selected
. [ID: 2] region 7 chains [1-20] RMSD: 202.239
> select #25/B:27 #26/B:27 #27/B:27 #28/B:27 #29/B:27 #30/B:27 #31/B:27
56 atoms, 49 bonds, 7 residues, 7 models selected
> select #25/B:1-27 #26/B:1-27 #27/B:1-27 #28/B:1-27 #29/B:1-27 #30/B:1-27
> #31/B:1-27
1498 atoms, 1498 bonds, 189 residues, 7 models selected
. [ID: 2] region 7 chains [1-27] RMSD: 201.751
> hide sel surfaces
> hide sel cartoons
> select #25/B:28 #26/B:28 #27/B:28 #28/B:28 #29/B:28 #30/B:28 #31/B:28
56 atoms, 49 bonds, 7 residues, 7 models selected
> select #25/B:28-189 #26/B:28-189 #27/B:28-189 #28/B:28-189 #29/B:28-189
> #30/B:28-189 #31/B:28-189
9296 atoms, 9436 bonds, 1134 residues, 7 models selected
. [ID: 2] region 7 chains [28-189] RMSD: 205.519
> select #25/A:1 #26/A:1 #27/A:1 #28/A:1 #29/A:1 #30/A:1 #31/A:1
56 atoms, 49 bonds, 7 residues, 7 models selected
> select #25/A #26/A #27/A #28/A #29/A #30/A #31/A
10206 atoms, 10416 bonds, 1225 residues, 7 models selected
. [ID: 1] region 7 chains [1-175] RMSD: 207.285
> show sel surfaces
> select clear
> select add #19
112125 atoms, 113781 bonds, 39 pseudobonds, 14157 residues, 2 models selected
> show #!2 models
> select clear
> view orient
Drag select of 8 MS-ring.mrc gaussian , 6282 residues, 19 pseudobonds, 32
4x-FlgY-PflA.mrc gaussian
> hide sel cartoons
Drag select of 8 residues
> hide sel cartoons
> select clear
> volume gaussian #1.1 sDev 5
Opened IM.mrc gaussian as #24, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at step 1, values float32
> hide #!2 models
> volume #24 level 0.006253
> color #24 #797979ff models
> color #24 #5e5e5eff models
> color #24 #919191ff models
> color #24 #797979ff models
> color #24 darkgrey models
> color #24 #424242ff models
> color #24 #797979ff models
> color #24 #d6d6d6ff models
> color #24 #919191ff models
> select add #19
112125 atoms, 113781 bonds, 39 pseudobonds, 14157 residues, 2 models selected
> show sel surfaces
> select clear
> view orient
Drag select of Hp-FliF-comp_0 SES surface, 166552 of 308174 triangles, Hp-
FliF-comp_1 SES surface, Hp-FliF-comp_2 SES surface, Hp-FliF-comp_3 SES
surface, Hp-FliF-comp_4 SES surface, Hp-FliF-comp_5 SES surface, Hp-FliF-
comp_6 SES surface, Hp-FliF-comp_7 SES surface, 301470 of 307576 triangles,
Hp-FliF-comp_8 SES surface, 281198 of 307462 triangles, Hp-FliF-comp_9 SES
surface, 248114 of 307956 triangles, Hp-FliF-comp_AA SES surface, 72054 of
307878 triangles, Hp-FliF-comp_AP SES surface, 860 of 308526 triangles, Hp-
FliF-comp_AQ SES surface, 11313 of 307878 triangles, Hp-FliF-comp_AR SES
surface, 26305 of 308154 triangles, Hp-FliF-comp_AS SES surface, 45567 of
307454 triangles, Hp-FliF-comp_B SES surface, 22032 of 102586 triangles, Hp-
FliF-comp_C SES surface, Hp-FliF-comp_D SES surface, Hp-FliF-comp_E SES
surface, Hp-FliF-comp_F SES surface, Hp-FliF-comp_G SES surface, Hp-FliF-
comp_H SES surface, Hp-FliF-comp_I SES surface, Hp-FliF-comp_J SES surface,
Hp-FliF-comp_K SES surface, 49177 of 102380 triangles, Hp-FliF-comp_V SES
surface, 47719 of 126200 triangles, Hp-FliF-comp_W SES surface, Hp-FliF-comp_X
SES surface, Hp-FliF-comp_Y SES surface, Hp-FliF-comp_Z SES surface, Hp-FliF-
comp_a SES surface, Hp-FliF-comp_b SES surface, Hp-FliF-comp_c SES surface,
Hp-FliF-comp_d SES surface, 121510 of 126402 triangles, Hp-FliF-comp_e SES
surface, 62271 of 126996 triangles, Hp-FliF-comp_f SES surface, 3912 of 126310
triangles, Hp-FliF-comp_q SES surface, 66882 of 307794 triangles, Hp-FliF-
comp_r SES surface, 140106 of 308144 triangles, Hp-FliF-comp_s SES surface,
221141 of 307492 triangles, Hp-FliF-comp_t SES surface, 307651 of 308006
triangles, Hp-FliF-comp_u SES surface, Hp-FliF-comp_v SES surface, Hp-FliF-
comp_w SES surface, Hp-FliF-comp_x SES surface, Hp-FliF-comp_y SES surface,
Hp-FliF-comp_z SES surface, 8 MS-ring.mrc gaussian , 172 residues, 32 4x-FlgY-
PflA.mrc gaussian
> hide sel surfaces
[Repeated 1 time(s)]
> select clear
Drag select of Hp-FliF-comp_0 SES surface, 154076 of 308174 triangles, Hp-
FliF-comp_1 SES surface, Hp-FliF-comp_2 SES surface, Hp-FliF-comp_3 SES
surface, Hp-FliF-comp_4 SES surface, Hp-FliF-comp_5 SES surface, Hp-FliF-
comp_6 SES surface, 308144 of 308152 triangles, Hp-FliF-comp_7 SES surface,
295307 of 307576 triangles, Hp-FliF-comp_8 SES surface, 272973 of 307462
triangles, Hp-FliF-comp_9 SES surface, 235380 of 307956 triangles, Hp-FliF-
comp_AA SES surface, 53451 of 307878 triangles, Hp-FliF-comp_AP SES surface,
482 of 308526 triangles, Hp-FliF-comp_AQ SES surface, 8117 of 307878
triangles, Hp-FliF-comp_AR SES surface, 22368 of 308154 triangles, Hp-FliF-
comp_AS SES surface, 41356 of 307454 triangles, Hp-FliF-comp_B SES surface,
17461 of 102586 triangles, Hp-FliF-comp_C SES surface, Hp-FliF-comp_D SES
surface, Hp-FliF-comp_E SES surface, Hp-FliF-comp_F SES surface, Hp-FliF-
comp_G SES surface, Hp-FliF-comp_H SES surface, Hp-FliF-comp_I SES surface,
Hp-FliF-comp_J SES surface, 102531 of 102648 triangles, Hp-FliF-comp_K SES
surface, 39861 of 102380 triangles, Hp-FliF-comp_V SES surface, 34776 of
126200 triangles, Hp-FliF-comp_W SES surface, 126738 of 126760 triangles, Hp-
FliF-comp_X SES surface, Hp-FliF-comp_Y SES surface, Hp-FliF-comp_Z SES
surface, Hp-FliF-comp_a SES surface, Hp-FliF-comp_b SES surface, Hp-FliF-
comp_c SES surface, Hp-FliF-comp_d SES surface, 117758 of 126402 triangles,
Hp-FliF-comp_e SES surface, 55739 of 126996 triangles, Hp-FliF-comp_f SES
surface, 1108 of 126310 triangles, Hp-FliF-comp_q SES surface, 60184 of 307794
triangles, Hp-FliF-comp_r SES surface, 120961 of 308144 triangles, Hp-FliF-
comp_s SES surface, 209518 of 307492 triangles, Hp-FliF-comp_t SES surface,
306665 of 308006 triangles, Hp-FliF-comp_u SES surface, Hp-FliF-comp_v SES
surface, Hp-FliF-comp_w SES surface, Hp-FliF-comp_x SES surface, Hp-FliF-
comp_y SES surface, Hp-FliF-comp_z SES surface, 8 MS-ring.mrc gaussian , 103
residues, 32 4x-FlgY-PflA.mrc gaussian
> select clear
> view orient
> turn x 90
[Repeated 2 time(s)]
> undo
[Repeated 1 time(s)]
> turn x 90
[Repeated 1 time(s)]Drag select of Hp-FliF-comp_0 SES surface, 149331 of
308174 triangles, Hp-FliF-comp_1 SES surface, Hp-FliF-comp_2 SES surface, Hp-
FliF-comp_3 SES surface, Hp-FliF-comp_4 SES surface, Hp-FliF-comp_5 SES
surface, 302887 of 307026 triangles, Hp-FliF-comp_6 SES surface, 292299 of
308152 triangles, Hp-FliF-comp_7 SES surface, 274500 of 307576 triangles, Hp-
FliF-comp_8 SES surface, 254402 of 307462 triangles, Hp-FliF-comp_9 SES
surface, 213499 of 307956 triangles, Hp-FliF-comp_AA SES surface, 71335 of
307878 triangles, Hp-FliF-comp_AS SES surface, 2423 of 307454 triangles, Hp-
FliF-comp_C SES surface, 83086 of 102940 triangles, Hp-FliF-comp_D SES
surface, Hp-FliF-comp_E SES surface, Hp-FliF-comp_F SES surface, Hp-FliF-
comp_G SES surface, Hp-FliF-comp_H SES surface, Hp-FliF-comp_I SES surface,
Hp-FliF-comp_J SES surface, Hp-FliF-comp_K SES surface, 52860 of 102380
triangles, Hp-FliF-comp_W SES surface, 77317 of 126760 triangles, Hp-FliF-
comp_X SES surface, Hp-FliF-comp_Y SES surface, Hp-FliF-comp_Z SES surface,
Hp-FliF-comp_a SES surface, Hp-FliF-comp_b SES surface, Hp-FliF-comp_c SES
surface, 126547 of 126700 triangles, Hp-FliF-comp_d SES surface, 110830 of
126402 triangles, Hp-FliF-comp_e SES surface, 52984 of 126996 triangles, Hp-
FliF-comp_f SES surface, 494 of 126310 triangles, Hp-FliF-comp_q SES surface,
16449 of 307794 triangles, Hp-FliF-comp_r SES surface, 43873 of 308144
triangles, Hp-FliF-comp_s SES surface, 106026 of 307492 triangles, Hp-FliF-
comp_t SES surface, 221057 of 308006 triangles, Hp-FliF-comp_u SES surface,
Hp-FliF-comp_v SES surface, Hp-FliF-comp_w SES surface, Hp-FliF-comp_x SES
surface, Hp-FliF-comp_y SES surface, Hp-FliF-comp_z SES surface, 8 MS-ring.mrc
gaussian , 41 residues, 24 IM.mrc gaussian
Drag select of Hp-FliF-comp_1 SES surface, 55583 of 307826 triangles, Hp-FliF-
comp_2 SES surface, 66829 of 307256 triangles, Hp-FliF-comp_3 SES surface,
69397 of 307570 triangles, Hp-FliF-comp_4 SES surface, 66274 of 308450
triangles, Hp-FliF-comp_5 SES surface, 54668 of 307026 triangles, Hp-FliF-
comp_6 SES surface, 34167 of 308152 triangles, Hp-FliF-comp_7 SES surface,
10791 of 307576 triangles, Hp-FliF-comp_y SES surface, 732 of 306240
triangles, Hp-FliF-comp_z SES surface, 28688 of 307204 triangles
> select clear
Drag select of Hp-FliF-comp_0 SES surface, 83311 of 308174 triangles, Hp-FliF-
comp_1 SES surface, 306551 of 307826 triangles, Hp-FliF-comp_2 SES surface,
300559 of 307256 triangles, Hp-FliF-comp_3 SES surface, 291476 of 307570
triangles, Hp-FliF-comp_4 SES surface, 281658 of 308450 triangles, Hp-FliF-
comp_5 SES surface, 265641 of 307026 triangles, Hp-FliF-comp_6 SES surface,
253115 of 308152 triangles, Hp-FliF-comp_7 SES surface, 219184 of 307576
triangles, Hp-FliF-comp_8 SES surface, 182124 of 307462 triangles, Hp-FliF-
comp_9 SES surface, 139238 of 307956 triangles, Hp-FliF-comp_AA SES surface,
64 of 307878 triangles, Hp-FliF-comp_D SES surface, 79118 of 102534 triangles,
Hp-FliF-comp_E SES surface, Hp-FliF-comp_F SES surface, Hp-FliF-comp_G SES
surface, Hp-FliF-comp_H SES surface, Hp-FliF-comp_I SES surface, 99609 of
102666 triangles, Hp-FliF-comp_J SES surface, 63093 of 102648 triangles, Hp-
FliF-comp_X SES surface, 35929 of 127586 triangles, Hp-FliF-comp_Y SES
surface, 115109 of 125848 triangles, Hp-FliF-comp_Z SES surface, 125524 of
126584 triangles, Hp-FliF-comp_a SES surface, 124149 of 126398 triangles, Hp-
FliF-comp_b SES surface, 113214 of 126186 triangles, Hp-FliF-comp_c SES
surface, 84162 of 126700 triangles, Hp-FliF-comp_d SES surface, 46299 of
126402 triangles, Hp-FliF-comp_e SES surface, 2181 of 126996 triangles, Hp-
FliF-comp_s SES surface, 1749 of 307492 triangles, Hp-FliF-comp_t SES surface,
21680 of 308006 triangles, Hp-FliF-comp_u SES surface, 143651 of 308588
triangles, Hp-FliF-comp_v SES surface, 300723 of 308590 triangles, Hp-FliF-
comp_w SES surface, Hp-FliF-comp_x SES surface, Hp-FliF-comp_y SES surface,
Hp-FliF-comp_z SES surface, 307180 of 307204 triangles
> select add #19
112125 atoms, 113781 bonds, 39 pseudobonds, 14157 residues, 36 models selected
> volume #!5-6,8,24,32 showOutlineBox true
> view orient
> ui mousemode right "crop volume"
> volume #!5-6,8,24,32 showOutlineBox false
> select clear
> hide #!24 models
> hide #!25 models
> hide #!26 models
> hide #!27 models
> hide #!28 models
> hide #!29 models
> hide #!30 models
> hide #!31 models
> hide #!32 models
> hide #!16 models
> hide #!5 models
> hide #!6 models
> view orient
Drag select of Hp-FliF-comp_0 SES surface, 143157 of 308174 triangles, Hp-
FliF-comp_1 SES surface, Hp-FliF-comp_2 SES surface, Hp-FliF-comp_3 SES
surface, Hp-FliF-comp_4 SES surface, Hp-FliF-comp_5 SES surface, 306617 of
307026 triangles, Hp-FliF-comp_6 SES surface, 297776 of 308152 triangles, Hp-
FliF-comp_7 SES surface, 279954 of 307576 triangles, Hp-FliF-comp_8 SES
surface, 256577 of 307462 triangles, Hp-FliF-comp_9 SES surface, 214640 of
307956 triangles, Hp-FliF-comp_AA SES surface, 53365 of 307878 triangles, Hp-
FliF-comp_AQ SES surface, 74 of 307878 triangles, Hp-FliF-comp_AR SES surface,
7294 of 308154 triangles, Hp-FliF-comp_AS SES surface, 25284 of 307454
triangles, Hp-FliF-comp_B SES surface, 20152 of 102586 triangles, Hp-FliF-
comp_C SES surface, Hp-FliF-comp_D SES surface, Hp-FliF-comp_E SES surface,
Hp-FliF-comp_F SES surface, Hp-FliF-comp_G SES surface, Hp-FliF-comp_H SES
surface, Hp-FliF-comp_I SES surface, Hp-FliF-comp_J SES surface, Hp-FliF-
comp_K SES surface, 48901 of 102380 triangles, Hp-FliF-comp_V SES surface,
29501 of 126200 triangles, Hp-FliF-comp_W SES surface, 125127 of 126760
triangles, Hp-FliF-comp_X SES surface, Hp-FliF-comp_Y SES surface, Hp-FliF-
comp_Z SES surface, Hp-FliF-comp_a SES surface, Hp-FliF-comp_b SES surface,
Hp-FliF-comp_c SES surface, Hp-FliF-comp_d SES surface, 115537 of 126402
triangles, Hp-FliF-comp_e SES surface, 53093 of 126996 triangles, Hp-FliF-
comp_q SES surface, 49856 of 307794 triangles, Hp-FliF-comp_r SES surface,
100944 of 308144 triangles, Hp-FliF-comp_s SES surface, 199515 of 307492
triangles, Hp-FliF-comp_t SES surface, Hp-FliF-comp_u SES surface, Hp-FliF-
comp_v SES surface, Hp-FliF-comp_w SES surface, Hp-FliF-comp_x SES surface,
Hp-FliF-comp_y SES surface, Hp-FliF-comp_z SES surface, 23 residues
> select add #19
112125 atoms, 113781 bonds, 39 pseudobonds, 14157 residues, 5 models selected
> select subtract #19
81 models selected
> select add #19
112125 atoms, 113781 bonds, 39 pseudobonds, 14157 residues, 2 models selected
> select subtract #19
81 models selected
Drag select of Hp-FliF-comp_0 SES surface, 148981 of 308174 triangles, Hp-
FliF-comp_1 SES surface, Hp-FliF-comp_2 SES surface, Hp-FliF-comp_3 SES
surface, Hp-FliF-comp_4 SES surface, Hp-FliF-comp_5 SES surface, Hp-FliF-
comp_6 SES surface, 300852 of 308152 triangles, Hp-FliF-comp_7 SES surface,
284597 of 307576 triangles, Hp-FliF-comp_8 SES surface, 261021 of 307462
triangles, Hp-FliF-comp_9 SES surface, 226705 of 307956 triangles, Hp-FliF-
comp_AA SES surface, 63490 of 307878 triangles, Hp-FliF-comp_AQ SES surface,
600 of 307878 triangles, Hp-FliF-comp_AR SES surface, 10882 of 308154
triangles, Hp-FliF-comp_AS SES surface, 30600 of 307454 triangles, Hp-FliF-
comp_B SES surface, 25923 of 102586 triangles, Hp-FliF-comp_C SES surface, Hp-
FliF-comp_D SES surface, Hp-FliF-comp_E SES surface, Hp-FliF-comp_F SES
surface, Hp-FliF-comp_G SES surface, Hp-FliF-comp_H SES surface, Hp-FliF-
comp_I SES surface, Hp-FliF-comp_J SES surface, Hp-FliF-comp_K SES surface,
54434 of 102380 triangles, Hp-FliF-comp_V SES surface, 38106 of 126200
triangles, Hp-FliF-comp_W SES surface, 126732 of 126760 triangles, Hp-FliF-
comp_X SES surface, Hp-FliF-comp_Y SES surface, Hp-FliF-comp_Z SES surface,
Hp-FliF-comp_a SES surface, Hp-FliF-comp_b SES surface, Hp-FliF-comp_c SES
surface, Hp-FliF-comp_d SES surface, 118350 of 126402 triangles, Hp-FliF-
comp_e SES surface, 57474 of 126996 triangles, Hp-FliF-comp_f SES surface,
1323 of 126310 triangles, Hp-FliF-comp_q SES surface, 54683 of 307794
triangles, Hp-FliF-comp_r SES surface, 112699 of 308144 triangles, Hp-FliF-
comp_s SES surface, 208916 of 307492 triangles, Hp-FliF-comp_t SES surface,
308000 of 308006 triangles, Hp-FliF-comp_u SES surface, Hp-FliF-comp_v SES
surface, Hp-FliF-comp_w SES surface, Hp-FliF-comp_x SES surface, Hp-FliF-
comp_y SES surface, Hp-FliF-comp_z SES surface, 67 residues
> hide sel surfaces
[Repeated 1 time(s)]
> select clear
> select add #19
112125 atoms, 113781 bonds, 39 pseudobonds, 14157 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
> show sel cartoons
> select clear
Drag select of 8 MS-ring.mrc gaussian , 7753 residues, 20 pseudobonds
> hide #19.33 models
> hide #19.34 models
> hide #19.35 models
> hide #19.36 models
> hide #19.37 models
> hide #19.38 models
> hide #19.39 models
> hide #19.40 models
> hide #19.53 models
> hide #19.54 models
> hide #19.55 models
> hide #19.56 models
> hide #19.57 models
> hide #19.58 models
> hide #19.59 models
> hide #19.76 models
> hide #19.77 models
> hide #19.78 models
> hide #19.79 models
> hide #19.80 models
> hide #19.81 models
> hide #19.82 models
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> show sel surfaces
> select add #19
112125 atoms, 113781 bonds, 39 pseudobonds, 14157 residues, 58 models selected
> select subtract #19.1
112125 atoms, 113781 bonds, 14157 residues, 84 models selected
> select add #19
112125 atoms, 113781 bonds, 39 pseudobonds, 14157 residues, 85 models selected
> hide sel cartoons
> select clear
> show #!25 models
> show #!26 models
> show #!27 models
> show #!28 models
> show #!29 models
> show #!30 models
> show #!31 models
Cell requested for row 125 is out of bounds for table with 131 rows! Resizing
table model.
> select add #25
3000 atoms, 3051 bonds, 364 residues, 1 model selected
> select add #26
6000 atoms, 6102 bonds, 728 residues, 3 models selected
> select add #27
9000 atoms, 9153 bonds, 1092 residues, 5 models selected
> select add #28
12000 atoms, 12204 bonds, 1456 residues, 7 models selected
> select add #29
15000 atoms, 15255 bonds, 1820 residues, 9 models selected
> select add #30
18000 atoms, 18306 bonds, 2184 residues, 11 models selected
> select add #31
21000 atoms, 21357 bonds, 2548 residues, 13 models selected
Alignment identifier is 1
Alignment identifier is 2
> hide sel surfaces
> show sel surfaces
> hide sel cartoons
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> select #25/A:1 #26/A:1 #27/A:1 #28/A:1 #29/A:1 #30/A:1 #31/A:1
56 atoms, 49 bonds, 7 residues, 7 models selected
> select #25/A:1-5 #26/A:1-5 #27/A:1-5 #28/A:1-5 #29/A:1-5 #30/A:1-5 #31/A:1-5
308 atoms, 315 bonds, 35 residues, 7 models selected
. [ID: 1] region 7 chains [1-5] RMSD: 190.059
> select #25/B:1 #26/B:1 #27/B:1 #28/B:1 #29/B:1 #30/B:1 #31/B:1
56 atoms, 49 bonds, 7 residues, 7 models selected
> select #25/B:1-27 #26/B:1-27 #27/B:1-27 #28/B:1-27 #29/B:1-27 #30/B:1-27
> #31/B:1-27
1498 atoms, 1498 bonds, 189 residues, 7 models selected
. [ID: 2] region 7 chains [1-27] RMSD: 201.751
> hide sel surfaces
> select clear
> show #18 models
> show #20 models
> show #22 models
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 5
Alignment identifier is 6
Alignment identifier is 7
Alignment identifier is 8
Alignment identifier is 9
Alignment identifier is 10
Alignment identifier is 11
> select #20/A,L-T:52 #18/A,L-T:52 #22/A,L-T:52
180 atoms, 150 bonds, 30 residues, 3 models selected
> select #20/A,L-T #18/A,L-T #22/A,L-T
5580 atoms, 5640 bonds, 720 residues, 3 models selected
9 [ID: 9] region 30 chains [1-24] RMSD: 107.276
> select add #18
13570 atoms, 13710 bonds, 1700 residues, 3 models selected
> select add #20
21560 atoms, 21780 bonds, 2680 residues, 3 models selected
> select add #22
29550 atoms, 29850 bonds, 3660 residues, 3 models selected
> hide sel cartoons
> show sel surfaces
> select #20/A,L-T:52 #18/A,L-T:52 #22/A,L-T:52
180 atoms, 150 bonds, 30 residues, 3 models selected
> select #20/A,L-T #18/A,L-T #22/A,L-T
5580 atoms, 5640 bonds, 720 residues, 3 models selected
9 [ID: 9] region 30 chains [1-24] RMSD: 107.276
> hide sel surfaces
> color #18 #b7a359ff models
> color #20 #b7a359ff models
> color #22 #b7a359ff models
> select clear
> show #!14 models
> hide #!14 models
> show #!16 models
> hide #!16 models
> show #!16 models
> select add #16.1
5455 atoms, 5553 bonds, 678 residues, 1 model selected
> select add #16.3
6334 atoms, 6447 bonds, 787 residues, 2 models selected
> select add #16.7
11789 atoms, 12000 bonds, 1465 residues, 3 models selected
> select add #16.9
17244 atoms, 17553 bonds, 2143 residues, 4 models selected
> select add #16.10
18123 atoms, 18447 bonds, 2252 residues, 5 models selected
> select add #16.11
23578 atoms, 24000 bonds, 2930 residues, 6 models selected
> select add #16.12
24457 atoms, 24894 bonds, 3039 residues, 7 models selected
> select add #16.13
29912 atoms, 30447 bonds, 3717 residues, 8 models selected
> select add #16.14
30791 atoms, 31341 bonds, 3826 residues, 9 models selected
> select add #16.15
35862 atoms, 36497 bonds, 4447 residues, 10 models selected
> select add #16.18
40933 atoms, 41653 bonds, 5068 residues, 11 models selected
> select subtract #16.18
35862 atoms, 36497 bonds, 4447 residues, 10 models selected
> select add #16.19
40933 atoms, 41653 bonds, 5068 residues, 11 models selected
> select add #16.20
46004 atoms, 46809 bonds, 5689 residues, 12 models selected
> select add #16.21
51075 atoms, 51965 bonds, 6310 residues, 13 models selected
> select add #16.22
52310 atoms, 53206 bonds, 6465 residues, 14 models selected
> select add #16.23
53545 atoms, 54447 bonds, 6620 residues, 15 models selected
> select add #16.30
54780 atoms, 55688 bonds, 6775 residues, 16 models selected
> select add #16.31
56015 atoms, 56929 bonds, 6930 residues, 17 models selected
> select add #16.32
57250 atoms, 58170 bonds, 7085 residues, 18 models selected
> select add #16.33
58485 atoms, 59411 bonds, 7240 residues, 19 models selected
> select add #16.34
59720 atoms, 60652 bonds, 7395 residues, 20 models selected
> select add #16.35
60955 atoms, 61893 bonds, 7550 residues, 21 models selected
> hide sel cartoons
> show sel surfaces
> select clear
Cell requested for row 20 is out of bounds for table with 83 rows! Resizing
table model.
> show #!10 models
> open /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/PDB-
> files/BbMotB_dimer_extended.pdb
Chain information for BbMotB_dimer_extended.pdb #33
---
Chain | Description
K | No description available
L | No description available
> select add #33
4099 atoms, 4171 bonds, 2 pseudobonds, 518 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #33,1,0,0,21.679,0,1,0,19.023,0,0,1,69.811
> view matrix models #33,1,0,0,216.28,0,1,0,67.682,0,0,1,108.49
> view matrix models #33,1,0,0,180.91,0,1,0,66.862,0,0,1,108.02
> view matrix models #33,1,0,0,173.74,0,1,0,68.504,0,0,1,102.5
> ui mousemode right "rotate selected models"
> view matrix models
> #33,0.82212,0.19102,-0.53631,216.23,-0.030867,0.9556,0.29305,52.42,0.56847,-0.22437,0.79152,83.495
> view matrix models
> #33,0.74317,0.51518,-0.42695,185.49,-0.30248,0.82785,0.47241,76.836,0.59682,-0.22194,0.77107,82.089
> ui mousemode right "translate selected models"
> view matrix models
> #33,0.74317,0.51518,-0.42695,222.76,-0.30248,0.82785,0.47241,52.168,0.59682,-0.22194,0.77107,83.322
> ui mousemode right "rotate selected models"
> view matrix models
> #33,0.82295,0.51043,-0.24942,201.24,-0.34242,0.79599,0.49915,56.935,0.45332,-0.32537,0.82984,102.39
> ui mousemode right "translate selected models"
> view matrix models
> #33,0.82295,0.51043,-0.24942,188.94,-0.34242,0.79599,0.49915,52.835,0.45332,-0.32537,0.82984,98.389
> ui mousemode right "rotate selected models"
> view matrix models
> #33,0.79756,0.50803,-0.32527,197.69,-0.31282,0.80936,0.49707,48.84,0.51579,-0.29469,0.80444,91.397
> ui mousemode right "translate selected models"
> view matrix models
> #33,0.79756,0.50803,-0.32527,201.01,-0.31282,0.80936,0.49707,50.28,0.51579,-0.29469,0.80444,92.963
> view matrix models
> #33,0.79756,0.50803,-0.32527,203.08,-0.31282,0.80936,0.49707,52.155,0.51579,-0.29469,0.80444,89.909
> ui mousemode right "rotate selected models"
> view matrix models
> #33,0.74765,0.61942,-0.23944,190.95,-0.41678,0.71836,0.557,66.071,0.51703,-0.31665,0.79525,92.539
> ui mousemode right "translate selected models"
> view matrix models
> #33,0.74765,0.61942,-0.23944,194.55,-0.41678,0.71836,0.557,61.303,0.51703,-0.31665,0.79525,91.721
> select clear
> open /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/PDB-
> files/BbMotB_dimer_extended.pdb
Chain information for BbMotB_dimer_extended.pdb #34
---
Chain | Description
K | No description available
L | No description available
> select add #34
4099 atoms, 4171 bonds, 2 pseudobonds, 518 residues, 2 models selected
> view matrix models #34,1,0,0,161.65,0,1,0,136.58,0,0,1,-67.038
> view matrix models #34,1,0,0,237.53,0,1,0,161.8,0,0,1,76.649
> view matrix models #34,1,0,0,199.38,0,1,0,175.58,0,0,1,82.821
> close #34
> combine #33 modelId #34 name BbMotB_dimer_extended.pdb
> select add #34
4099 atoms, 4171 bonds, 2 pseudobonds, 518 residues, 2 models selected
> view matrix models
> #34,0.74765,0.61942,-0.23944,215.85,-0.41678,0.71836,0.557,171.61,0.51703,-0.31665,0.79525,89.654
> view matrix models
> #34,0.74765,0.61942,-0.23944,215.72,-0.41678,0.71836,0.557,169.76,0.51703,-0.31665,0.79525,89.668
> combine #34 modelId #35 name BbMotB_dimer_extended.pdb
> select subtract #34
Nothing selected
> select add #35
4099 atoms, 4171 bonds, 2 pseudobonds, 518 residues, 2 models selected
> view matrix models
> #35,0.74765,0.61942,-0.23944,198.58,-0.41678,0.71836,0.557,281.85,0.51703,-0.31665,0.79525,88.152
> ui mousemode right "rotate selected models"
> view matrix models
> #35,0.8127,0.47483,-0.33771,213.27,-0.26798,0.81924,0.50698,261.8,0.5174,-0.32152,0.79305,88.739
> ui mousemode right "translate selected models"
> view matrix models
> #35,0.8127,0.47483,-0.33771,215.47,-0.26798,0.81924,0.50698,267.82,0.5174,-0.32152,0.79305,88.742
> select clear
> select add #33
4099 atoms, 4171 bonds, 2 pseudobonds, 518 residues, 2 models selected
> select add #34
8198 atoms, 8342 bonds, 4 pseudobonds, 1036 residues, 4 models selected
> select add #35
12297 atoms, 12513 bonds, 6 pseudobonds, 1554 residues, 6 models selected
> color #33-35 #905d12ff models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Alignment identifier is 1
Alignment identifier is 2
> select #33/K:260 #34/K:260 #35/K:260
27 atoms, 24 bonds, 3 residues, 3 models selected
> select #33/K:159-260 #34/K:159-260 #35/K:159-260
2433 atoms, 2481 bonds, 3 pseudobonds, 303 residues, 6 models selected
1 [ID: 1] region 3 chains [158-258] RMSD: 158.691
> select #33/K:1 #34/K:1 #35/K:1
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #33/K:1-84 #34/K:1-84 #35/K:1-84
1977 atoms, 2019 bonds, 252 residues, 3 models selected
1 [ID: 1] region 3 chains [1-84] RMSD: 159.798
> select #33/K:1-2 #34/K:1-2 #35/K:1-2
39 atoms, 36 bonds, 6 residues, 3 models selected
> select #33/K:1-42 #34/K:1-42 #35/K:1-42
999 atoms, 1017 bonds, 126 residues, 3 models selected
1 [ID: 1] region 3 chains [1-42] RMSD: 161.188
> select #33/L:1-2 #34/L:1-2 #35/L:1-2
39 atoms, 36 bonds, 6 residues, 3 models selected
> select #33/L:1-6 #34/L:1-6 #35/L:1-6
147 atoms, 144 bonds, 18 residues, 3 models selected
2 [ID: 2] region 3 chains [1-6] RMSD: 162.586
> select #33/K:1 #34/K:1 #35/K:1
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #33/K:1-42 #34/K:1-42 #35/K:1-42
999 atoms, 1017 bonds, 126 residues, 3 models selected
1 [ID: 1] region 3 chains [1-42] RMSD: 161.188
> select #33/K:1-2 #34/K:1-2 #35/K:1-2
39 atoms, 36 bonds, 6 residues, 3 models selected
> select #33/K:1-16 #34/K:1-16 #35/K:1-16
360 atoms, 363 bonds, 48 residues, 3 models selected
1 [ID: 1] region 3 chains [1-16] RMSD: 161.945
> select #33/K:1-2 #34/K:1-2 #35/K:1-2
39 atoms, 36 bonds, 6 residues, 3 models selected
> select #33/K:1-36 #34/K:1-36 #35/K:1-36
852 atoms, 867 bonds, 108 residues, 3 models selected
1 [ID: 1] region 3 chains [1-36] RMSD: 161.445
> select #33/K:42 #34/K:42 #35/K:42
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #33/K:1-42 #34/K:1-42 #35/K:1-42
999 atoms, 1017 bonds, 126 residues, 3 models selected
1 [ID: 1] region 3 chains [1-42] RMSD: 161.188
> select add #33
4765 atoms, 4849 bonds, 2 pseudobonds, 602 residues, 4 models selected
> select add #34
8531 atoms, 8681 bonds, 4 pseudobonds, 1078 residues, 5 models selected
> select add #35
12297 atoms, 12513 bonds, 6 pseudobonds, 1554 residues, 6 models selected
> hide sel cartoons
> show sel surfaces
> select #33/K:1-2 #34/K:1-2 #35/K:1-2
39 atoms, 36 bonds, 6 residues, 3 models selected
> select #33/K:1-42 #34/K:1-42 #35/K:1-42
999 atoms, 1017 bonds, 126 residues, 3 models selected
1 [ID: 1] region 3 chains [1-42] RMSD: 161.188
> hide sel surfaces
> select #33/L:1-2 #34/L:1-2 #35/L:1-2
39 atoms, 36 bonds, 6 residues, 3 models selected
> select #33/L:1-40 #34/L:1-40 #35/L:1-40
951 atoms, 969 bonds, 120 residues, 3 models selected
2 [ID: 2] region 3 chains [1-40] RMSD: 161.008
> hide sel surfaces
> select clear
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/Develop-model-Figure.cxs
> includeMaps true
> select add #10
2 models selected
> ui tool show "Segment Map"
Segmenting MotBpg.mrc, density threshold 0.002900
Only showing 60 of 1058 regions.
Showing 60 of 1058 region surfaces
46770 watershed regions, grouped to 1058 regions
Showing MotBpg.seg - 1058 regions, 60 surfaces
> select subtract #10
Nothing selected
> hide #!10 models
> hide #!8 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> hide #!21 models
> show #!21 models
> hide #!22 models
> hide #!25 models
> hide #!26 models
> hide #!27 models
> hide #!28 models
> hide #!29 models
> hide #!30 models
> hide #!31 models
> hide #!33 models
> hide #!34 models
> hide #!35 models
> select #21.1
1 model selected
> select add #21.4
2 models selected
Opened MotBpg_imasked as #36, grid size 220,250,200, pixel 2.15,2.15,2.15,
shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/For-chimera/cyc3/Re-
> segment_Aug2420204/3xMotBpg.mrc models #36
> close #21
> volume gaussian #36 sDev 3
Opened 3xMotBpg.mrc gaussian as #21, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
> close #21
> volume gaussian #36 sDev 2
Opened 3xMotBpg.mrc gaussian as #21, grid size 220,250,200, pixel
2.15,2.15,2.15, shown at step 1, values float32
> surface dust #21 size 12.6
> surface dust #21 size 50
> surface dust #21 size 60
> ui tool show "Map Eraser"
> volume erase #21 center 309.37,266.92,146.96 radius 190.15 outside true
> color #21 #72727259 models
> close #36
> show #!33 models
> show #!34 models
> show #!35 models
> 30\. combine #33-35 modelId #36 name 3x-BbMotB_dimer_extended.pdb
Unknown command: 30. combine #33-35 modelId #36 name
3x-BbMotB_dimer_extended.pdb
> combine #33-35 modelId #36 name 3x-BbMotB_dimer_extended.pdb
Remapping chain ID 'K' in BbMotB_dimer_extended.pdb #34 to 'M'
Remapping chain ID 'L' in BbMotB_dimer_extended.pdb #34 to 'N'
Remapping chain ID 'K' in BbMotB_dimer_extended.pdb #35 to 'O'
Remapping chain ID 'L' in BbMotB_dimer_extended.pdb #35 to 'P'
> hide #!33 models
> hide #!34 models
> hide #!35 models
> select add #36.1
6 pseudobonds, 1 model selected
> select subtract #36.1
Nothing selected
> close #36
> show #!33 models
> show #!34 models
> show #!35 models
> show #!25 models
> show #!26 models
> show #!27 models
> show #!28 models
> show #!29 models
> show #!31 models
> show #!30 models
> show #!32 models
> show #!24 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!22 models
> hide #!22 models
> show #!22 models
> show #!20 models
> show #!18 models
> show #!19 models
> show #!17 models
> show #!15 models
> hide #!15 models
> show #!16 models
> show #!15 models
> open /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/PDB-files/7cbl.pdb
7cbl.pdb title:
Cryo-em structure of the flagellar LP ring from salmonella [more info...]
Chain information for 7cbl.pdb #36
---
Chain | Description | UniProt
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z | basal BODY L-RING protein | FLGH_SALTY 1-232
a b c d e f g h i j k l m n o p q r s t u v w x y z | basal BODY P-RING protein | FLGI_SALTY 1-365
Non-standard residues in 7cbl.pdb #36
---
OCA — octanoic acid (caprylic acid)
> select add #36
99242 atoms, 100516 bonds, 52 pseudobonds, 13390 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #36,0.99952,-0.023444,-0.020012,14.476,0.023458,0.99972,0.00046154,-7.9312,0.019995,-0.00093074,0.9998,-6.3355
> view matrix models
> #36,0.99016,0.091812,0.10556,-61.574,0.12368,-0.92715,-0.35369,717.2,0.065401,0.36327,-0.92939,481.42
> view matrix models
> #36,0.95439,0.16729,0.24728,-120.69,0.24621,-0.90949,-0.33497,664.1,0.16886,0.38057,-0.9092,434.38
> ui mousemode right "translate selected models"
> view matrix models
> #36,0.95439,0.16729,0.24728,-411.87,0.24621,-0.90949,-0.33497,634.98,0.16886,0.38057,-0.9092,400.89
> view matrix models
> #36,0.95439,0.16729,0.24728,-430.05,0.24621,-0.90949,-0.33497,585.73,0.16886,0.38057,-0.9092,470.59
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> view matrix models
> #36,0.95439,0.16729,0.24728,-430.2,0.24621,-0.90949,-0.33497,584.34,0.16886,0.38057,-0.9092,468.67
> ui mousemode right "rotate selected models"
> view matrix models
> #36,0.94876,0.1594,0.27286,-433.95,0.18496,-0.98021,-0.070503,542.9,0.25622,0.11736,-0.95947,543.61
> ui mousemode right "translate selected models"
> view matrix models
> #36,0.94876,0.1594,0.27286,-432.12,0.18496,-0.98021,-0.070503,562.18,0.25622,0.11736,-0.95947,530
> view matrix models
> #36,0.94876,0.1594,0.27286,-426.95,0.18496,-0.98021,-0.070503,549.55,0.25622,0.11736,-0.95947,532.65
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #36 inMap #15
Fit molecule 7cbl.pdb (#36) to map LP-ring.mrc gaussian (#15) using 99242
atoms
average map value = 0.01848, steps = 192
shifted from previous position = 26.5
rotated from previous position = 19.1 degrees
atoms outside contour = 51926, contour level = 0.0029
Position of 7cbl.pdb (#36) relative to LP-ring.mrc gaussian (#15) coordinates:
Matrix rotation and translation
0.98109265 0.18738329 -0.04842298 -364.80581143
0.18778874 -0.98220164 0.00392332 530.82087661
-0.04682597 -0.01294243 -0.99881924 690.06118649
Axis -0.99526186 -0.09424097 0.02392613
Axis point 0.00000000 284.13402910 339.44972981
Rotation angle (degrees) 179.51452584
Shift along axis 329.56273090
> fitmap #36 inMap #15
Fit molecule 7cbl.pdb (#36) to map LP-ring.mrc gaussian (#15) using 99242
atoms
average map value = 0.01848, steps = 76
shifted from previous position = 0.0186
rotated from previous position = 0.0136 degrees
atoms outside contour = 51931, contour level = 0.0029
Position of 7cbl.pdb (#36) relative to LP-ring.mrc gaussian (#15) coordinates:
Matrix rotation and translation
0.98107948 0.18742063 -0.04854515 -364.76747896
0.18781829 -0.98219677 0.00372290 530.87666956
-0.04698315 -0.01277014 -0.99881408 690.07249131
Axis -0.99525856 -0.09425801 0.02399637
Axis point 0.00000000 284.13118826 339.46925121
Rotation angle (degrees) 179.52525271
Shift along axis 329.55781165
> ui mousemode right "rotate selected models"
> view matrix models
> #36,0.97923,0.19635,0.050588,-399.23,0.19648,-0.9805,0.0024405,527.82,0.050081,0.0075498,-0.99872,650.67
> view orient
[Repeated 1 time(s)]
> turn x 90
[Repeated 2 time(s)]
> turn y 90
[Repeated 1 time(s)]
> view matrix models
> #36,0.98047,0.1965,0.0085164,-386.07,0.19648,-0.9805,0.0024405,527.82,0.0088299,-0.0007195,-0.99996,667.68
> turn y 90
[Repeated 1 time(s)]
> select clear
> select add #36
99242 atoms, 100516 bonds, 52 pseudobonds, 13390 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select clear
[Repeated 1 time(s)]
> view orient
Drag select of Hp-FliF-comp_0 SES surface, 6028 of 308174 triangles, Hp-FliF-
comp_8 SES surface, 257 of 307462 triangles, Hp-FliF-comp_9 SES surface, 1366
of 307956 triangles, Hp-FliF-comp_AA SES surface, 519 of 307878 triangles, Hp-
FliF-comp_B SES surface, 2758 of 102586 triangles, Hp-FliF-comp_K SES surface,
4194 of 102380 triangles, Hp-FliF-comp_V SES surface, 2762 of 126200
triangles, Hp-FliF-comp_d SES surface, 80 of 126402 triangles, Hp-FliF-comp_e
SES surface, 1736 of 126996 triangles, Hp-FliF-comp_f SES surface, 2142 of
126310 triangles, Hp-FliF-comp_q SES surface, 84 of 307794 triangles, Hp-FliF-
comp_r SES surface, 2877 of 308144 triangles, Hp-FliF-comp_s SES surface, 8253
of 307492 triangles, 6021 residues, 22 pseudobonds
> select add #36
99242 atoms, 100516 bonds, 52 pseudobonds, 13390 residues, 15 models selected
> hide sel cartoons
> show sel surfaces
> select clear
Drag select of Hp-FliF-comp_0 SES surface, 8612 of 308174 triangles, Hp-FliF-
comp_7 SES surface, 45 of 307576 triangles, Hp-FliF-comp_8 SES surface, 458 of
307462 triangles, Hp-FliF-comp_9 SES surface, 1993 of 307956 triangles, Hp-
FliF-comp_AA SES surface, 1094 of 307878 triangles, Hp-FliF-comp_AR SES
surface, 87 of 308154 triangles, Hp-FliF-comp_AS SES surface, 41 of 307454
triangles, Hp-FliF-comp_B SES surface, 4026 of 102586 triangles, Hp-FliF-
comp_K SES surface, 5110 of 102380 triangles, Hp-FliF-comp_V SES surface, 3952
of 126200 triangles, Hp-FliF-comp_d SES surface, 251 of 126402 triangles, Hp-
FliF-comp_e SES surface, 2486 of 126996 triangles, Hp-FliF-comp_f SES surface,
2965 of 126310 triangles, Hp-FliF-comp_q SES surface, 442 of 307794 triangles,
Hp-FliF-comp_r SES surface, 4432 of 308144 triangles, Hp-FliF-comp_s SES
surface, 11349 of 307492 triangles, 7cbl.pdb_A SES surface, 196414 of 260654
triangles, 7cbl.pdb_B SES surface, 148709 of 260418 triangles, 7cbl.pdb_C SES
surface, 62358 of 261904 triangles, 7cbl.pdb_D SES surface, 209 of 260742
triangles, 7cbl.pdb_L SES surface, 1561 of 260934 triangles, 7cbl.pdb_M SES
surface, 23481 of 260974 triangles, 7cbl.pdb_N SES surface, 39311 of 261482
triangles, 7cbl.pdb_O SES surface, 54398 of 261300 triangles, 7cbl.pdb_P SES
surface, 75031 of 260648 triangles, 7cbl.pdb_Q SES surface, 166049 of 261816
triangles, 7cbl.pdb_R SES surface, 248845 of 261108 triangles, 7cbl.pdb_S SES
surface, 7cbl.pdb_T SES surface, 7cbl.pdb_U SES surface, 7cbl.pdb_V SES
surface, 7cbl.pdb_W SES surface, 7cbl.pdb_X SES surface, 248707 of 260098
triangles, 7cbl.pdb_Y SES surface, 226883 of 260558 triangles, 7cbl.pdb_Z SES
surface, 211544 of 261230 triangles, 7cbl.pdb_a SES surface, 275677 of 294626
triangles, 7cbl.pdb_b SES surface, 209108 of 294054 triangles, 7cbl.pdb_c SES
surface, 103190 of 294726 triangles, 7cbl.pdb_d SES surface, 5641 of 293734
triangles, 7cbl.pdb_o SES surface, 1360 of 294010 triangles, 7cbl.pdb_p SES
surface, 59071 of 294246 triangles, 7cbl.pdb_q SES surface, 157050 of 294206
triangles, 7cbl.pdb_r SES surface, 249024 of 294146 triangles, 7cbl.pdb_s SES
surface, 7cbl.pdb_t SES surface, 7cbl.pdb_u SES surface, 7cbl.pdb_v SES
surface, 7cbl.pdb_w SES surface, 7cbl.pdb_x SES surface, 7cbl.pdb_y SES
surface, 7cbl.pdb_z SES surface
> select clear
> view orient
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> show #!15 models
> hide #!20 models
> hide #!21 models
> hide #!22 models
> hide #!24 models
> hide #!25 models
> hide #!26 models
> hide #!27 models
> show #!27 models
> hide #!28 models
> hide #!27 models
> hide #!29 models
> hide #!30 models
> hide #!31 models
> hide #!32 models
> hide #!33 models
> hide #!34 models
> hide #!35 models
> hide #!36 models
> show #!36 models
Drag select of 7cbl.pdb_A SES surface, 61024 of 260654 triangles, 7cbl.pdb_B
SES surface, 102410 of 260418 triangles, 7cbl.pdb_C SES surface, 193053 of
261904 triangles, 7cbl.pdb_D SES surface, 259705 of 260742 triangles,
7cbl.pdb_E SES surface, 7cbl.pdb_F SES surface, 7cbl.pdb_G SES surface,
7cbl.pdb_H SES surface, 7cbl.pdb_I SES surface, 7cbl.pdb_J SES surface,
7cbl.pdb_K SES surface, 7cbl.pdb_L SES surface, 253330 of 260934 triangles,
7cbl.pdb_M SES surface, 232905 of 260974 triangles, 7cbl.pdb_N SES surface,
217973 of 261482 triangles, 7cbl.pdb_O SES surface, 203923 of 261300
triangles, 7cbl.pdb_P SES surface, 177720 of 260648 triangles, 7cbl.pdb_Q SES
surface, 86697 of 261816 triangles, 7cbl.pdb_R SES surface, 9907 of 261108
triangles, 7cbl.pdb_X SES surface, 4385 of 260098 triangles, 7cbl.pdb_Y SES
surface, 28510 of 260558 triangles, 7cbl.pdb_Z SES surface, 45909 of 261230
triangles, 7cbl.pdb_a SES surface, 30285 of 294626 triangles, 7cbl.pdb_b SES
surface, 92255 of 294054 triangles, 7cbl.pdb_c SES surface, 203860 of 294726
triangles, 7cbl.pdb_d SES surface, 288442 of 293734 triangles, 7cbl.pdb_e SES
surface, 7cbl.pdb_f SES surface, 7cbl.pdb_g SES surface, 7cbl.pdb_h SES
surface, 7cbl.pdb_i SES surface, 7cbl.pdb_j SES surface, 7cbl.pdb_k SES
surface, 7cbl.pdb_l SES surface, 7cbl.pdb_m SES surface, 7cbl.pdb_n SES
surface, 7cbl.pdb_o SES surface, 7cbl.pdb_p SES surface, 248362 of 294246
triangles, 7cbl.pdb_q SES surface, 146650 of 294206 triangles, 7cbl.pdb_r SES
surface, 51098 of 294146 triangles, 15 LP-ring.mrc gaussian
> hide #!36 cartoons
> hide #!36 surfaces
> show #!36 surfaces
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
[Repeated 1 time(s)]Drag select of 7cbl.pdb_A SES surface, 197163 of 260654
triangles, 7cbl.pdb_B SES surface, 151113 of 260418 triangles, 7cbl.pdb_C SES
surface, 63838 of 261904 triangles, 7cbl.pdb_D SES surface, 373 of 260742
triangles, 7cbl.pdb_L SES surface, 2822 of 260934 triangles, 7cbl.pdb_M SES
surface, 24778 of 260974 triangles, 7cbl.pdb_N SES surface, 40288 of 261482
triangles, 7cbl.pdb_O SES surface, 55033 of 261300 triangles, 7cbl.pdb_P SES
surface, 76588 of 260648 triangles, 7cbl.pdb_Q SES surface, 169195 of 261816
triangles, 7cbl.pdb_R SES surface, 250270 of 261108 triangles, 7cbl.pdb_S SES
surface, 7cbl.pdb_T SES surface, 7cbl.pdb_U SES surface, 7cbl.pdb_V SES
surface, 7cbl.pdb_W SES surface, 7cbl.pdb_X SES surface, 249974 of 260098
triangles, 7cbl.pdb_Y SES surface, 227596 of 260558 triangles, 7cbl.pdb_Z SES
surface, 212233 of 261230 triangles, 7cbl.pdb_a SES surface, 274902 of 294626
triangles, 7cbl.pdb_b SES surface, 208716 of 294054 triangles, 7cbl.pdb_c SES
surface, 103666 of 294726 triangles, 7cbl.pdb_d SES surface, 5923 of 293734
triangles, 7cbl.pdb_o SES surface, 974 of 294010 triangles, 7cbl.pdb_p SES
surface, 58312 of 294246 triangles, 7cbl.pdb_q SES surface, 156995 of 294206
triangles, 7cbl.pdb_r SES surface, 249259 of 294146 triangles, 7cbl.pdb_s SES
surface, 7cbl.pdb_t SES surface, 7cbl.pdb_u SES surface, 7cbl.pdb_v SES
surface, 7cbl.pdb_w SES surface, 7cbl.pdb_x SES surface, 7cbl.pdb_y SES
surface, 7cbl.pdb_z SES surface
> hide #!36 cartoons
[Repeated 1 time(s)]
> hide #!36 surfaces
> show #!36 surfaces
> hide #!15 models
Drag select of 7cbl.pdb_A SES surface, 199076 of 260654 triangles, 7cbl.pdb_B
SES surface, 158273 of 260418 triangles, 7cbl.pdb_C SES surface, 68832 of
261904 triangles, 7cbl.pdb_D SES surface, 3423 of 260742 triangles, 7cbl.pdb_L
SES surface, 4187 of 260934 triangles, 7cbl.pdb_M SES surface, 25974 of 260974
triangles, 7cbl.pdb_N SES surface, 41975 of 261482 triangles, 7cbl.pdb_O SES
surface, 56368 of 261300 triangles, 7cbl.pdb_P SES surface, 81787 of 260648
triangles, 7cbl.pdb_Q SES surface, 179929 of 261816 triangles, 7cbl.pdb_R SES
surface, 256994 of 261108 triangles, 7cbl.pdb_S SES surface, 7cbl.pdb_T SES
surface, 7cbl.pdb_U SES surface, 7cbl.pdb_V SES surface, 7cbl.pdb_W SES
surface, 7cbl.pdb_X SES surface, 251898 of 260098 triangles, 7cbl.pdb_Y SES
surface, 229243 of 260558 triangles, 7cbl.pdb_Z SES surface, 213592 of 261230
triangles, 7cbl.pdb_a SES surface, 280602 of 294626 triangles, 7cbl.pdb_b SES
surface, 217020 of 294054 triangles, 7cbl.pdb_c SES surface, 118932 of 294726
triangles, 7cbl.pdb_d SES surface, 9141 of 293734 triangles, 7cbl.pdb_o SES
surface, 3185 of 294010 triangles, 7cbl.pdb_p SES surface, 65819 of 294246
triangles, 7cbl.pdb_q SES surface, 165577 of 294206 triangles, 7cbl.pdb_r SES
surface, 254701 of 294146 triangles, 7cbl.pdb_s SES surface, 7cbl.pdb_t SES
surface, 7cbl.pdb_u SES surface, 7cbl.pdb_v SES surface, 7cbl.pdb_w SES
surface, 7cbl.pdb_x SES surface, 7cbl.pdb_y SES surface, 7cbl.pdb_z SES
surface
> select clear
Drag select of 7cbl.pdb_A SES surface, 204662 of 260654 triangles, 7cbl.pdb_B
SES surface, 184165 of 260418 triangles, 7cbl.pdb_C SES surface, 98778 of
261904 triangles, 7cbl.pdb_D SES surface, 26869 of 260742 triangles,
7cbl.pdb_L SES surface, 11362 of 260934 triangles, 7cbl.pdb_M SES surface,
31859 of 260974 triangles, 7cbl.pdb_N SES surface, 47755 of 261482 triangles,
7cbl.pdb_O SES surface, 62792 of 261300 triangles, 7cbl.pdb_P SES surface,
113171 of 260648 triangles, 7cbl.pdb_Q SES surface, 202809 of 261816
triangles, 7cbl.pdb_R SES surface, 7cbl.pdb_S SES surface, 7cbl.pdb_T SES
surface, 7cbl.pdb_U SES surface, 7cbl.pdb_V SES surface, 7cbl.pdb_W SES
surface, 7cbl.pdb_X SES surface, 259223 of 260098 triangles, 7cbl.pdb_Y SES
surface, 236028 of 260558 triangles, 7cbl.pdb_Z SES surface, 219836 of 261230
triangles, 7cbl.pdb_a SES surface, 292754 of 294626 triangles, 7cbl.pdb_b SES
surface, 239690 of 294054 triangles, 7cbl.pdb_c SES surface, 164138 of 294726
triangles, 7cbl.pdb_d SES surface, 39856 of 293734 triangles, 7cbl.pdb_o SES
surface, 20901 of 294010 triangles, 7cbl.pdb_p SES surface, 99572 of 294246
triangles, 7cbl.pdb_q SES surface, 201882 of 294206 triangles, 7cbl.pdb_r SES
surface, 282357 of 294146 triangles, 7cbl.pdb_s SES surface, 7cbl.pdb_t SES
surface, 7cbl.pdb_u SES surface, 292711 of 293402 triangles, 7cbl.pdb_v SES
surface, 285896 of 295054 triangles, 7cbl.pdb_w SES surface, 279452 of 294020
triangles, 7cbl.pdb_x SES surface, 292892 of 293348 triangles, 7cbl.pdb_y SES
surface, 7cbl.pdb_z SES surface
> select clear
> select add #36
99242 atoms, 100516 bonds, 52 pseudobonds, 13390 residues, 2 models selected
> hide sel surfaces
[Repeated 1 time(s)]
> show sel cartoons
> select clear
Drag select of 6265 residues, 23 pseudobonds
> select clear
> show #!15 models
Drag select of 15 LP-ring.mrc gaussian , 7309 residues, 29 pseudobonds
> show sel surfaces
> select add #36
99242 atoms, 100516 bonds, 52 pseudobonds, 13390 residues, 42 models selected
> hide sel cartoons
> select clear
> color #36 #92aa93ff models
> hide #!15 models
> show #!35 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #!18-35 models
> hide #!23 models
> show #!17 models
> show #!16 models
> show #!13 models
> show #!12 models
> view orient
> turn x 90
[Repeated 2 time(s)]
> turn z -0.1
[Repeated 4 time(s)]
> ui tool show "Side View"
> View name Side1
Unknown command: View name Side1
> view name Side1
> turn x 45
> view name Tilt45
> hide #!12 models
> hide #!13 models
> save /Users/shoichitachiyama/Desktop/CJ-local-tilt45_08242024.png
> supersample 2 transparentBackground true
> view Side1
> turn x 90
> save /Users/shoichitachiyama/Desktop/CJ-local-Top_08242024.png supersample 2
> transparentBackground true
> save /Users/shoichitachiyama/Desktop/CJ-local-Top2_08242024.png supersample
> 2 transparentBackground true
> view Side1
> show #!12 models
> show #!13 models
> save /Users/shoichitachiyama/Desktop/CJ-local-Side_08242024.png supersample
> 2 transparentBackground true
> save /Volumes/Backup-95/Chimera-2023/C.jejuni_motor_April_2024/For-2nd-
> manuscript/Start_Aug_2024/Local-ref-PflAB/Develop-model-Figure.cxs
> includeMaps true
——— End of log from Sat Aug 24 21:36:37 2024 ———
opened ChimeraX session
> hide #!12 models
> show #!12 models
> hide #!13 models
> hide #!12 models
> hide #!16 models
> show #!16 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> hide #!21 models
> show #!21 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> hide #!24 models
> hide #!33 models
> hide #!34 models
> hide #!35 models
> hide #!21 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> close session
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-Chimera-PflAB/Rev-CJFlgYPlfAB-msk-2.1A.mrc"
Opened Rev-CJFlgYPlfAB-msk-2.1A.mrc as #1, grid size 200,200,200, pixel 2.14,
shown at level 0.047, step 1, values float32
> volume #1 level 0.002308
> volume #1 level 0.001238
> ui tool show "Segment Map"
Segmenting Rev-CJFlgYPlfAB-msk-2.1A.mrc, density threshold 0.001238
Showing 336 region surfaces
6595 watershed regions, grouped to 336 regions
Showing Rev-CJFlgYPlfAB-msk-2.1A.seg - 336 regions, 336 surfaces
> select #2.52
1 model selected
> select add #2.224
2 models selected
> select add #2.191
3 models selected
> select add #2.20
4 models selected
> select add #2.7
5 models selected
> hide #!1 models
Grouped 5 regions
> select add #2.11
2 models selected
Grouped 2 regions
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Opened Rev-CJFlgYPlfAB-msk-2.1A_imasked as #3, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 2 time(s)]
> save /Users/shoichitachiyama/Desktop/For-Chimera-PflAB/Resegment/LP-ring.mrc
> models #3
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Opened Rev-CJFlgYPlfAB-msk-2.1A_imasked as #4, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-msk-2.1A_imasked, density threshold 0.001238
Showing 330 region surfaces
6371 watershed regions, grouped to 330 regions
Showing Rev-CJFlgYPlfAB-msk-2.seg - 330 regions, 330 surfaces
> hide #!4 models
> hide #!3 models
> select #2.160
1 model selected
> select add #2.5
2 models selected
> select add #2.107
3 models selected
> select add #2.15
4 models selected
Grouped 4 regions
> select add #2.44
2 models selected
> select subtract #2.44
1 model selected
Opened Rev-CJFlgYPlfAB-msk-2_imasked as #5, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/For-Chimera-PflAB/Resegment/Other.mrc
> models #5
Opened Rev-CJFlgYPlfAB-msk-2_imasked as #6, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-msk-2_imasked, density threshold 0.001238
Showing 326 region surfaces
6227 watershed regions, grouped to 326 regions
Showing Rev-CJFlgYPlfAB-msk-2_imasked.seg - 326 regions, 326 surfaces
> hide #!5 models
> select #2.42
1 model selected
> select add #2.182
2 models selected
> select add #2.197
3 models selected
> select add #2.156
4 models selected
> select add #2.132
5 models selected
> select add #2.85
6 models selected
> select add #2.69
7 models selected
> select add #2.72
8 models selected
> select add #2.245
9 models selected
> select add #2.195
10 models selected
> select add #2.171
11 models selected
> select add #2.151
12 models selected
> select add #2.78
13 models selected
> select add #2.117
14 models selected
> select add #2.193
15 models selected
> select add #2.209
16 models selected
> select add #2.212
17 models selected
> select add #2.191
18 models selected
> select add #2.226
19 models selected
> select add #2.161
20 models selected
> select add #2.127
21 models selected
> select add #2.141
22 models selected
> select add #2.146
23 models selected
> select add #2.76
24 models selected
> hide #!6 models
> select add #2.252
25 models selected
> select add #2.260
26 models selected
> select add #2.292
27 models selected
> select add #2.110
28 models selected
> select add #2.261
29 models selected
> select add #2.241
30 models selected
> select add #2.190
31 models selected
> select add #2.131
32 models selected
> select add #2.214
33 models selected
> select add #2.159
34 models selected
> select add #2.123
35 models selected
> select add #2.97
36 models selected
> select add #2.263
37 models selected
> select add #2.256
38 models selected
> select add #2.8
39 models selected
> select add #2.106
40 models selected
> select add #2.66
41 models selected
> select add #2.273
42 models selected
> select add #2.270
43 models selected
> select add #2.246
44 models selected
> select add #2.183
45 models selected
> select add #2.138
46 models selected
> select add #2.208
47 models selected
Grouped 47 regions
Opened Rev-CJFlgYPlfAB-msk-2_imasked_imasked as #7, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/For-Chimera-PflAB/Resegment/Basal-
> disk.mrc models #7
Opened Rev-CJFlgYPlfAB-msk-2_imasked_imasked as #8, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-msk-2_imasked_imasked, density threshold 0.001238
Showing 279 region surfaces
5451 watershed regions, grouped to 279 regions
Showing Rev-CJFlgYPlfAB-msk-2_imasked_imasked.seg - 279 regions, 279 surfaces
> hide #!7 models
> hide #!8 models
Drag select of 7449, 12517 of 12600 triangles, 7491, 9665 of 9824 triangles,
7584, 7688, 7659, 7229, 6847, 3925 of 4688 triangles, 7197, 6853, 1512 of 4224
triangles, 6825, 1357 of 4016 triangles, 6739, 1277 of 3888 triangles, 7205,
3917 of 3976 triangles, 6098, 811 of 3972 triangles, 7562, 550 of 4888
triangles, 7448, 5755, 2371 of 3760 triangles, 6371, 58 of 3076 triangles,
7476, 7706, 57 of 3484 triangles, 7598, 557 of 3328 triangles, 7639, 7605,
7539, 1984 of 2320 triangles, 6010, 7350, 5448, 7351, 7602, 2872
> select add #2.267
30 models selected
> select add #2.252
31 models selected
Grouped 31 regions
> select clear
> select #2.152
1 model selected
Opened Rev-CJFlgYPlfAB-msk-2_imasked_imasked_imasked as #9, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-msk-2_imasked_imasked_imasked, density threshold
0.001238
Showing 248 region surfaces
5248 watershed regions, grouped to 248 regions
Showing Rev-CJFlgYPlfAB-msk-2_imasked_imasked_imasked.seg - 248 regions, 248
surfaces
> select #2.86
1 model selected
> select add #2.53
2 models selected
> select add #2.141
3 models selected
> select add #2.4
4 models selected
> select add #2.99
5 models selected
> select add #2.161
6 models selected
> select add #2.88
7 models selected
> select add #2.25
8 models selected
> select add #2.118
9 models selected
> select add #2.75
10 models selected
> select add #2.56
11 models selected
> select add #2.148
12 models selected
> select add #2.73
13 models selected
> select add #2.32
14 models selected
> select add #2.144
15 models selected
> select add #2.101
16 models selected
> select add #2.46
17 models selected
> select add #2.155
18 models selected
> select add #2.89
19 models selected
> select add #2.95
20 models selected
> select add #2.34
21 models selected
> select add #2.152
22 models selected
> select add #2.110
23 models selected
> select add #2.12
24 models selected
> select add #2.137
25 models selected
> select add #2.16
26 models selected
> select add #2.97
27 models selected
> select add #2.96
28 models selected
> select add #2.170
29 models selected
> select add #2.178
30 models selected
> select add #2.47
31 models selected
> select add #2.87
32 models selected
> select add #2.43
33 models selected
> select add #2.100
34 models selected
> select add #2.90
35 models selected
> select add #2.146
36 models selected
> hide #!9 models
Grouped 36 regions
> select clear
> select #2.4
1 model selected
> select clear
> select #2.4
1 model selected
Opened Rev-CJFlgYPlfAB-msk-2_imasked_imasked_imasked_imasked as #10, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/For-Chimera-PflAB/Resegment/PflC.mrc
> models #10
Opened Rev-CJFlgYPlfAB-msk-2_imasked_imasked_imasked_imasked as #11, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-msk-2_imasked_imasked_imasked_imasked, density
threshold 0.001238
Showing 213 region surfaces
4519 watershed regions, grouped to 213 regions
Showing Rev-CJFlgYPlfAB-msk-2_imasked_imasked_imasked_imasked.seg - 213
regions, 213 surfaces
> hide #!10 models
> hide #!11 models
> select #2.100
1 model selected
> select add #2.92
2 models selected
> select add #2.80
3 models selected
Grouped 3 regions
Opened Rev-CJFlgYPlfAB-msk-2_imasked_imasked_imasked_imasked_imasked as #12,
grid size 200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/For-Chimera-PflAB/Resegment/PflD.mrc
> models #12
Opened Rev-CJFlgYPlfAB-msk-2_imasked_imasked_imasked_imasked_imasked as #13,
grid size 200,200,200, pixel 2.14, shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-msk-2_imasked_imasked_imasked_imasked_imasked,
density threshold 0.001238
Showing 210 region surfaces
4459 watershed regions, grouped to 210 regions
Showing Rev-CJFlgYPlfAB-msk-2_imasked_imasked_imasked_imasked_imasked.seg -
210 regions, 210 surfaces
> hide #!12 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> select #2.70
1 model selected
> select add #2.54
2 models selected
> select add #2.56
3 models selected
> select add #2.39
4 models selected
Opened Rev-CJFlgYPlfAB-msk-2_imasked_imasked_imasked_imasked_imasked_imasked
as #14, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/For-Chimera-PflAB/Resegment/MotBpg.mrc
> models #14
Opened Rev-CJFlgYPlfAB-msk-2_imasked_imasked_imasked_imasked_imasked_imasked
as #15, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked, density threshold
0.001238
Showing 206 region surfaces
4420 watershed regions, grouped to 206 regions
Showing Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked.seg - 206 regions, 206
surfaces
> hide #!14 models
> select #2.44
1 model selected
Ungrouped to 3 regions
Ungrouped to 10 regions
> select #2.213
1 model selected
> select add #2.212
2 models selected
> select add #2.217
3 models selected
> select add #2.216
4 models selected
> select add #2.100
5 models selected
> hide #!15 models
> select add #2.44
6 models selected
> select subtract #2.212
5 models selected
> select add #2.212
6 models selected
> select add #2.211
7 models selected
Grouped 7 regions
> select add #2.68
2 models selected
Grouped 2 regions
> select add #2.218
2 models selected
Grouped 2 regions
> select clear
> select #2.137
1 model selected
> select #2.117
1 model selected
Ungrouped to 2 regions
Ungrouped to 5 regions
[Repeated 1 time(s)]
> select #2.212
1 model selected
> select add #2.117
2 models selected
> select add #2.137
3 models selected
> select add #2.99
4 models selected
> select add #2.59
5 models selected
Grouped 5 regions
> select #2.86
1 model selected
Ungrouped to 4 regions
Ungrouped to 10 regions
Ungrouped to 7 regions
Ungrouped to 0 regions
> select #2.207
1 model selected
> select add #2.220
2 models selected
> select add #2.99
3 models selected
> select add #2.224
4 models selected
> select add #2.225
5 models selected
> select add #2.227
6 models selected
> select add #2.72
7 models selected
> select add #2.58
8 models selected
Grouped 8 regions
> select add #2.59
2 models selected
> select #2.230
1 model selected
> select #2.228
1 model selected
> select #2.83
1 model selected
Ungrouped to 5 regions
Ungrouped to 8 regions
Ungrouped to 9 regions
Ungrouped to 0 regions
> select #2.224
1 model selected
> select add #2.221
2 models selected
> select add #2.234
3 models selected
> select add #2.236
4 models selected
> select add #2.99
5 models selected
> select add #2.71
6 models selected
> select #2.50
1 model selected
> select add #2.71
2 models selected
> select add #2.236
3 models selected
> select add #2.221
4 models selected
> select #2.50
1 model selected
> select add #2.71
2 models selected
> select add #2.221
3 models selected
> select add #2.236
4 models selected
> select add #2.224
5 models selected
> select add #2.234
6 models selected
> select add #2.99
7 models selected
> select add #2.237
8 models selected
Grouped 8 regions
> select add #2.58
2 models selected
Grouped 2 regions
> select add #2.59
2 models selected
> select add #2.44
3 models selected
Grouped 3 regions
> select #2.54
1 model selected
> select #2.54
1 model selected
Ungrouped to 5 regions
Ungrouped to 7 regions
Ungrouped to 12 regions
Ungrouped to 0 regions
> select #2.237
1 model selected
> select #2.71
1 model selected
> select add #2.237
2 models selected
> select add #2.244
3 models selected
> select add #2.243
4 models selected
> select add #2.226
5 models selected
> select add #2.242
6 models selected
> select add #2.69
7 models selected
> select add #2.70
8 models selected
> select add #2.193
9 models selected
> select add #2.44
10 models selected
Grouped 10 regions
> select #2.82
1 model selected
> select add #2.123
2 models selected
> select add #2.29
3 models selected
> select add #2.76
4 models selected
> select add #2.166
5 models selected
> select add #2.135
6 models selected
> select add #2.170
7 models selected
> select #2.76
1 model selected
> select add #2.29
2 models selected
> select subtract #2.77
232 models selected
> select subtract #2.30
231 models selected
> select subtract #2.166
230 models selected
> select subtract #2.168
229 models selected
Grouped 229 regions
> undo
Ungrouped to 233 regions
> select clear
> select #2.30
1 model selected
> select add #2.77
2 models selected
> select add #2.29
3 models selected
> select add #2.76
4 models selected
> select add #2.166
5 models selected
> select add #2.136
6 models selected
> select subtract #2.136
5 models selected
> select add #2.238
6 models selected
> select add #2.239
7 models selected
Grouped 7 regions
> select #2.136
1 model selected
Ungrouped to 5 regions
> select #2.77
1 model selected
> select add #2.1
2 models selected
Grouped 2 regions
> select #2.25
1 model selected
> select #2.11
1 model selected
Ungrouped to 2 regions
Ungrouped to 6 regions
Ungrouped to 21 regions
> select #2.250
1 model selected
> select add #2.246
2 models selected
> select add #2.248
3 models selected
> select add #2.254
4 models selected
> select add #2.245
5 models selected
Grouped 5 regions
> select add #2.244
2 models selected
Grouped 2 regions
> select add #2.253
2 models selected
Grouped 2 regions
> select clear
> select #2.11
1 model selected
> select add #2.1
2 models selected
> select add #2.25
3 models selected
> select add #2.124
4 models selected
> select subtract #2.1
3 models selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #2.1
4 models selected
Grouped 4 regions
> select #2.213
1 model selected
> select #2.31
1 model selected
Ungrouped to 15 regions
> select subtract #2.250
14 models selected
> select subtract #2.263
13 models selected
> select subtract #2.248
12 models selected
> select subtract #2.168
11 models selected
> select subtract #2.246
10 models selected
Grouped 10 regions
> select add #2.1
2 models selected
Grouped 2 regions
> select #2.231
1 model selected
> select add #2.50
2 models selected
> select add #2.1
3 models selected
Grouped 3 regions
> select #2.159
1 model selected
Ungrouped to 2 regions
Ungrouped to 4 regions
Ungrouped to 13 regions
> select #2.231
1 model selected
> select add #2.244
2 models selected
> select add #2.245
3 models selected
> select add #2.238
4 models selected
> select add #2.25
5 models selected
> select add #2.11
6 models selected
Grouped 6 regions
> select add #2.1
2 models selected
Grouped 2 regions
> select clear
> select #2.1
1 model selected
> select clear
> select #2.1
1 model selected
Ungrouped to 2 regions
> select #2.25
1 model selected
Ungrouped to 3 regions
> select #2.31
1 model selected
Ungrouped to 2 regions
> select #2.231
1 model selected
Ungrouped to 4 regions
> select #2.245
1 model selected
Ungrouped to 2 regions
> select #2.267
1 model selected
> select #2.267
1 model selected
Ungrouped to 7 regions
> select #2.268
1 model selected
Ungrouped to 9 regions
> select #2.272
1 model selected
> select #2.272
1 model selected
Ungrouped to 7 regions
> select #2.282
1 model selected
Ungrouped to 6 regions
> select #2.1
1 model selected
> select add #2.275
2 models selected
> select add #2.281
3 models selected
> select add #2.276
4 models selected
> select add #2.274
5 models selected
> select add #2.244
6 models selected
> select add #2.269
7 models selected
> select add #2.271
8 models selected
> select add #2.273
9 models selected
> select add #2.238
10 models selected
Grouped 10 regions
> select #2.231
1 model selected
Ungrouped to 4 regions
Ungrouped to 3 regions
> select #2.269
1 model selected
> select add #2.1
2 models selected
> select add #2.271
3 models selected
Grouped 3 regions
> select #2.267
1 model selected
> select add #2.244
2 models selected
> select add #2.274
3 models selected
> select add #2.231
4 models selected
> select add #2.273
5 models selected
> select #2.1
1 model selected
> select clear
> select #2.1
1 model selected
> select add #2.287
2 models selected
> select add #2.270
3 models selected
> select add #2.50
4 models selected
> select add #2.11
5 models selected
> select add #2.31
6 models selected
> select add #2.245
7 models selected
Grouped 7 regions
> select #2.291
1 model selected
> select add #2.289
2 models selected
> select add #2.290
3 models selected
> select #2.25
1 model selected
> select add #2.1
2 models selected
Grouped 2 regions
> select clear
> select #2.1
1 model selected
> select clear
Showing 278 region surfaces
> select #2.1
1 model selected
Opened Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked as #16, grid
size 200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/For-Chimera-PflAB/Resegment/Cage.mrc
> models #16
Opened Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked as #17, grid
size 200,200,200, pixel 2.14, shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked, density
threshold 0.001238
Showing 203 region surfaces
4214 watershed regions, grouped to 203 regions
Showing Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg - 203
regions, 203 surfaces
> hide #!16 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!16 models
> select #2.111
1 model selected
> select add #2.60
2 models selected
> select add #2.152
3 models selected
> select add #2.160
4 models selected
> select add #2.74
5 models selected
Grouped 5 regions
> select #2.39
1 model selected
Ungrouped to 2 regions
Ungrouped to 7 regions
Ungrouped to 13 regions
Ungrouped to 12 regions
Ungrouped to 0 regions
> select #2.160
1 model selected
> select add #2.60
2 models selected
Grouped 2 regions
> select #2.60
1 model selected
> select #2.43
1 model selected
Ungrouped to 5 regions
Ungrouped to 12 regions
Ungrouped to 7 regions
Ungrouped to 0 regions
> select #16
2 models selected
> select #2.240
1 model selected
> select add #2.218
2 models selected
> select subtract #2.240
1 model selected
Grouped 1 regions
> select add #2.240
2 models selected
Grouped 2 regions
> select add #2.60
2 models selected
Grouped 2 regions
> select #2.119
1 model selected
> select #2.34
1 model selected
Ungrouped to 2 regions
Ungrouped to 4 regions
Ungrouped to 19 regions
Ungrouped to 6 regions
Ungrouped to 0 regions
> select #2.240
1 model selected
> select add #2.258
2 models selected
> select add #2.119
3 models selected
> select add #2.48
4 models selected
> select #2.48
1 model selected
Ungrouped to 2 regions
Ungrouped to 8 regions
> select #2.266
1 model selected
> select add #2.119
2 models selected
> select add #2.240
3 models selected
> select add #2.258
4 models selected
Grouped 4 regions
> select add #2.60
2 models selected
Grouped 2 regions
> set bgColor black
> select #2.60
1 model selected
Ungrouped to 2 regions
Ungrouped to 6 regions
Ungrouped to 12 regions
Ungrouped to 13 regions
> select #2.284
1 model selected
> select add #2.283
2 models selected
Ungrouped to 5 regions
Ungrouped to 12 regions
Ungrouped to 24 regions
> select #2.316
1 model selected
> select add #2.313
2 models selected
> select add #2.314
3 models selected
> select add #2.298
4 models selected
> select add #2.309
5 models selected
> select add #2.315
6 models selected
> select add #2.307
7 models selected
> select add #2.310
8 models selected
> select add #2.303
9 models selected
> select add #2.302
10 models selected
> select add #2.312
11 models selected
> select add #2.311
12 models selected
> select clear
> select #2.278
1 model selected
> select add #2.60
2 models selected
> select add #2.287
3 models selected
> select add #2.277
4 models selected
> select add #2.317
5 models selected
> select add #2.276
6 models selected
> select add #2.308
7 models selected
> select add #2.273
8 models selected
> select add #2.285
9 models selected
> select add #2.286
10 models selected
> select add #2.306
11 models selected
> select add #2.304
12 models selected
> select add #2.301
13 models selected
> select add #2.288
14 models selected
> select add #2.299
15 models selected
> select add #2.258
16 models selected
> select add #2.246
17 models selected
> select add #2.268
18 models selected
> select add #2.279
19 models selected
> select add #2.281
20 models selected
> select add #2.270
21 models selected
> select add #2.271
22 models selected
> select add #2.269
23 models selected
> select add #2.272
24 models selected
> select add #2.119
25 models selected
Grouped 25 regions
> select #2.240
1 model selected
> select add #2.60
2 models selected
Grouped 2 regions
> select #2.280
1 model selected
> select add #2.300
2 models selected
> select add #2.274
3 models selected
> select add #2.292
4 models selected
> select subtract #2.292
3 models selected
> select add #2.275
4 models selected
Grouped 4 regions
> select add #2.247
2 models selected
Ungrouped to 4 regions
Ungrouped to 2 regions
> select #2.258
1 model selected
> select add #2.247
2 models selected
> select add #2.246
3 models selected
> select add #2.269
4 models selected
> select add #2.119
5 models selected
> select add #2.240
6 models selected
> select add #2.60
7 models selected
Grouped 7 regions
Showing 280 region surfaces
> select clear
> select #16
2 models selected
> select #2.49
1 model selected
Ungrouped to 2 regions
Ungrouped to 10 regions
Ungrouped to 11 regions
> select add #2.60
12 models selected
> select #2.119
1 model selected
> select add #2.274
2 models selected
> select add #2.276
3 models selected
> select subtract #2.276
2 models selected
> select clear
> select #2.60
1 model selected
> select add #2.276
2 models selected
> select add #2.277
3 models selected
> select add #2.281
4 models selected
> select add #2.278
5 models selected
> select add #2.280
6 models selected
Grouped 6 regions
> select add #2.275
2 models selected
Grouped 2 regions
> select add #2.279
2 models selected
Grouped 2 regions
> select add #2.283
2 models selected
Grouped 2 regions
Showing 289 region surfaces
> select clear
> select #2.60
1 model selected
> hide #!16 models
Opened Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked as #18,
grid size 200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/For-Chimera-PflAB/Resegment/Cage-
> connection.mrc models #18
Opened Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked as #19,
grid size 200,200,200, pixel 2.14, shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked, density
threshold 0.001238
Showing 205 region surfaces
4150 watershed regions, grouped to 205 regions
Showing Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg -
205 regions, 205 surfaces
> hide #!19 models
> hide #!18 models
> select #2.16
1 model selected
> select add #2.24
2 models selected
> select add #2.118
3 models selected
> select add #2.133
4 models selected
> select add #2.109
5 models selected
> select add #2.18
6 models selected
> select add #2.81
7 models selected
> select add #2.9
8 models selected
> select add #2.54
9 models selected
> select add #2.20
10 models selected
> select add #2.85
11 models selected
> select add #2.126
12 models selected
Grouped 12 regions
> select add #2.104
2 models selected
> select add #2.35
3 models selected
> select add #2.98
4 models selected
> select add #2.30
5 models selected
> select add #2.136
6 models selected
> select add #2.31
7 models selected
> select add #2.89
8 models selected
> select add #2.97
9 models selected
> select add #2.153
10 models selected
> select add #2.96
11 models selected
> select add #2.116
12 models selected
Grouped 12 regions
> select add #2.103
2 models selected
> select add #2.67
3 models selected
> select add #2.45
4 models selected
> select add #2.26
5 models selected
> select add #2.70
6 models selected
> select add #2.110
7 models selected
> select add #2.58
8 models selected
Grouped 8 regions
> select clear
> select #2.9
1 model selected
Opened Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #20, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/For-Chimera-PflAB/Resegment/Crings.mrc
> models #20
Opened Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #21, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.001238
Showing 175 region surfaces
3429 watershed regions, grouped to 175 regions
Showing Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 175 regions, 175 surfaces
> hide #!20 models
> select #2.14
1 model selected
> select add #2.65
2 models selected
> select add #2.44
3 models selected
Grouped 3 regions
> select clear
> select #2.14
1 model selected
Opened Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #22, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/For-Chimera-PflAB/Resegment/FlaA.mrc
> models #22
Opened Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #23, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.001238
Showing 172 region surfaces
3324 watershed regions, grouped to 172 regions
Showing Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 172 regions, 172 surfaces
> hide #!21 models
> hide #!22 models
> hide #!23 models
> select #2.31
1 model selected
> select #2.11
1 model selected
> select add #2.1
2 models selected
> select add #2.25
3 models selected
> select add #2.107
4 models selected
Grouped 4 regions
> select add #2.21
2 models selected
> select add #2.31
3 models selected
> select add #2.61
4 models selected
Grouped 4 regions
> select #2.1
1 model selected
Ungrouped to 4 regions
> select subtract #2.21
3 models selected
Grouped 3 regions
> select clear
> select #2.1
1 model selected
Showing 167 region surfaces
Opened Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #24, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/For-Chimera-PflAB/Resegment/MS-ring.mrc
> models #24
Opened Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #25, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.001238
Showing 166 region surfaces
3094 watershed regions, grouped to 166 regions
Showing Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 166 regions, 166 surfaces
> hide #!24 models
> hide #!25 models
> select #2.9
1 model selected
> select add #2.7
2 models selected
> select add #2.8
3 models selected
> select add #2.91
4 models selected
> select add #2.95
5 models selected
> select add #2.99
6 models selected
> select add #2.2
7 models selected
> select add #2.18
8 models selected
> select add #2.13
9 models selected
> select add #2.40
10 models selected
> select add #2.74
11 models selected
> select add #2.78
12 models selected
> select add #2.14
13 models selected
> select add #2.46
14 models selected
> select add #2.49
15 models selected
> select add #2.20
16 models selected
Showing 166 region surfaces
> select clear
> select #2.20
1 model selected
> select clear
Drag select of 4374, 4356, 4394, 4396, 4381, 4373, 4382, 4304, 4269, 4297,
4036, 4309, 3974, 3887, 3715
Grouped 15 regions
Showing 152 region surfaces
> select clear
> select #2.2
1 model selected
Opened Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #26, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/For-Chimera-PflAB/Resegment/Stator-
> region.mrc models #26
Opened Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #27, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.001238
Showing 149 region surfaces
2640 watershed regions, grouped to 149 regions
Showing Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 149 regions, 149 surfaces
> hide #!26 models
> show #!26 models
> hide #!26 models
> select #2.51
1 model selected
> select add #2.62
2 models selected
> select add #2.16
3 models selected
> select add #2.26
4 models selected
> select add #2.76
5 models selected
> select add #2.68
6 models selected
> select add #2.38
7 models selected
> select add #2.39
8 models selected
> select add #2.3
9 models selected
> select add #2.59
10 models selected
> select add #2.4
11 models selected
> select add #2.5
12 models selected
> select add #2.69
13 models selected
> select add #2.120
14 models selected
> select add #2.42
15 models selected
Grouped 15 regions
> select add #2.21
2 models selected
> select add #2.107
3 models selected
> select add #2.66
4 models selected
> select add #2.15
5 models selected
> select add #2.89
6 models selected
> select add #2.93
7 models selected
> select add #2.71
8 models selected
> select add #2.46
9 models selected
Grouped 9 regions
> select add #2.63
2 models selected
> select add #2.121
3 models selected
> select add #2.41
4 models selected
> select subtract #2.41
3 models selected
> select add #2.41
4 models selected
> select add #2.104
5 models selected
> select add #2.119
6 models selected
> select add #2.96
7 models selected
> select add #2.101
8 models selected
Grouped 8 regions
> select add #2.1
2 models selected
Grouped 2 regions
> select add #2.122
2 models selected
> select add #2.125
3 models selected
> select add #2.98
4 models selected
> select add #2.81
5 models selected
> select add #2.114
6 models selected
> select add #2.72
7 models selected
> select add #2.54
8 models selected
> select add #2.74
9 models selected
> select add #2.67
10 models selected
> select add #2.123
11 models selected
> select add #2.88
12 models selected
> select add #2.113
13 models selected
> select add #2.61
14 models selected
> select add #2.100
15 models selected
> select add #2.85
16 models selected
> select add #2.86
17 models selected
> select add #2.12
18 models selected
> select add #2.99
19 models selected
> select add #2.57
20 models selected
> select add #2.50
21 models selected
> select add #2.58
22 models selected
> select add #2.106
23 models selected
> select add #2.111
24 models selected
> select add #2.108
25 models selected
> select add #2.45
26 models selected
> select add #2.112
27 models selected
> select add #2.60
28 models selected
> select add #2.10
29 models selected
> select subtract #2.10
28 models selected
Grouped 28 regions
> select #2.1
1 model selected
> hide #!27 models
> select clear
> select #2.2
1 model selected
> select add #2.23
2 models selected
> select add #2.34
3 models selected
> select add #2.35
4 models selected
> select add #2.40
5 models selected
> select add #2.36
6 models selected
> select add #2.22
7 models selected
> select add #2.43
8 models selected
> select add #2.37
9 models selected
> select add #2.27
10 models selected
> select add #2.65
11 models selected
> select add #2.79
12 models selected
> select add #2.52
13 models selected
> select add #2.29
14 models selected
> select add #2.18
15 models selected
> select add #2.33
16 models selected
> select add #2.53
17 models selected
> select add #2.64
18 models selected
> select add #2.92
19 models selected
> select add #2.32
20 models selected
> select add #2.95
21 models selected
> select add #2.19
22 models selected
> select add #2.94
23 models selected
> select add #2.17
24 models selected
> select add #2.117
25 models selected
> select add #2.87
26 models selected
> select add #2.30
27 models selected
> select add #2.73
28 models selected
> select add #2.14
29 models selected
> select add #2.48
30 models selected
> select add #2.9
31 models selected
> select add #2.109
32 models selected
> select add #2.56
33 models selected
> select add #2.78
34 models selected
> select add #2.11
35 models selected
> select add #2.31
36 models selected
> select add #2.10
37 models selected
> select add #2.47
38 models selected
> select add #2.97
39 models selected
> select add #2.7
40 models selected
> select add #2.126
41 models selected
> select add #2.6
42 models selected
> select add #2.84
43 models selected
> select add #2.83
44 models selected
> select add #2.24
45 models selected
> select add #2.49
46 models selected
> select add #2.55
47 models selected
Grouped 47 regions
> select #2.1
1 model selected
> select add #2.8
2 models selected
> select add #2.70
3 models selected
> select add #2.77
4 models selected
> select add #2.91
5 models selected
> select add #2.103
6 models selected
> select add #2.80
7 models selected
> select add #2.105
8 models selected
> select add #2.102
9 models selected
> select add #2.28
10 models selected
Grouped 10 regions
> select add #2.116
2 models selected
> select add #2.129
3 models selected
> select add #2.75
4 models selected
> select add #2.90
5 models selected
Grouped 5 regions
> select add #2.118
2 models selected
> select add #2.141
3 models selected
Grouped 3 regions
> select add #2.135
2 models selected
Grouped 2 regions
Showing 30 region surfaces
> select add #2.115
2 models selected
Grouped 2 regions
> select clear
> select #2.110
1 model selected
> select add #2.132
2 models selected
> select add #2.131
3 models selected
> select add #2.1
4 models selected
Grouped 4 regions
Grouped 1 regions
> select #2.44
1 model selected
Ungrouped to 2 regions
Ungrouped to 11 regions
> select #2.7
1 model selected
> select add #2.16
2 models selected
Drag select of 3729, 267 of 22140 triangles, 3088, 105 of 3812 triangles, 435,
17 of 1940 triangles, 2986, 78 of 3528 triangles, 2979, 126 of 4372 triangles
> select subtract #2.13
4 models selected
Grouped 4 regions
> select add #2.12
2 models selected
Grouped 2 regions
> select add #2.10
2 models selected
> select add #2.5
3 models selected
Grouped 3 regions
> select add #2.1
2 models selected
Grouped 2 regions
> select clear
> select #2.1
1 model selected
Opened Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #28, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/For-Chimera-PflAB/Resegment/IM.mrc
> models #28
Opened Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #29, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.001238
Showing 71 region surfaces
1231 watershed regions, grouped to 71 regions
Showing Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 71 regions, 71 surfaces
> hide #!28 models
> hide #!29 models
> select #2.9
1 model selected
> select #2.30
1 model selected
> select add #2.35
2 models selected
Grouped 2 regions
> select #2.9
1 model selected
Ungrouped to 2 regions
Ungrouped to 6 regions
Ungrouped to 14 regions
> select #2.79
1 model selected
Ungrouped to 5 regions
Ungrouped to 0 regions
> select #2.80
1 model selected
> select add #2.30
2 models selected
> select add #2.77
3 models selected
> select add #2.78
4 models selected
> select add #2.8
5 models selected
Grouped 5 regions
> select #2.38
1 model selected
Ungrouped to 3 regions
Ungrouped to 4 regions
Ungrouped to 8 regions
Ungrouped to 0 regions
> select #2.8
1 model selected
> select add #2.30
2 models selected
> select add #2.97
3 models selected
> select #2.44
1 model selected
> select add #2.4
2 models selected
> select add #2.6
3 models selected
> select #2.6
1 model selected
> select #2.6
1 model selected
Ungrouped to 4 regions
Ungrouped to 9 regions
> select #2.102
1 model selected
Ungrouped to 6 regions
> select #2.107
1 model selected
Ungrouped to 4 regions
Ungrouped to 0 regions
Ungrouped to 43 regions
> select #2.3
1 model selected
Ungrouped to 6 regions
Ungrouped to 19 regions
[Repeated 1 time(s)]Ungrouped to 0 regions
> select #2.173
1 model selected
> select add #2.29
2 models selected
> select #2.8
1 model selected
> select add #2.30
2 models selected
> select add #2.97
3 models selected
> select subtract #2.92
162 models selected
> select subtract #2.78
161 models selected
> select #2.8
1 model selected
Ungrouped to 5 regions
Ungrouped to 14 regions
> select #2.178
1 model selected
Ungrouped to 6 regions
> select #2.18
1 model selected
> select add #2.49
2 models selected
Ungrouped to 8 regions
> select #2.187
1 model selected
> select add #2.192
2 models selected
> select add #2.50
3 models selected
> select #2.50
1 model selected
> select clear
> select #2.50
1 model selected
Ungrouped to 7 regions
> select subtract #2.49
6 models selected
> select subtract #2.195
5 models selected
> select clear
> select #2.49
1 model selected
> select add #2.195
2 models selected
> select add #2.175
3 models selected
> select #2.175
1 model selected
Ungrouped to 2 regions
> select clear
> select #2.199
1 model selected
> select #2.155
1 model selected
> select #2.156
1 model selected
Ungrouped to 9 regions
> select #2.205
1 model selected
> select add #2.206
2 models selected
> select add #2.200
3 models selected
> select add #2.207
4 models selected
> select add #2.198
5 models selected
> select add #2.18
6 models selected
> select add #2.190
7 models selected
> select add #2.203
8 models selected
> select add #2.175
9 models selected
> select add #2.191
10 models selected
> select clear
> select #2.191
1 model selected
> select #2.193
1 model selected
> select #2.194
1 model selected
Ungrouped to 0 regions
> select #2.194
1 model selected
Ungrouped to 0 regions
> select #2.186
1 model selected
> select #2.8
1 model selected
Ungrouped to 10 regions
> select #2.215
1 model selected
> select #2.185
1 model selected
Ungrouped to 3 regions
> select #2.8
1 model selected
> select #2.201
1 model selected
Ungrouped to 4 regions
> select #2.185
1 model selected
> select add #2.221
2 models selected
> select clear
> select #2.209
1 model selected
> select add #2.213
2 models selected
> select #2.220
1 model selected
Ungrouped to 0 regions
> select #2.97
1 model selected
Ungrouped to 0 regions
Drag select of 207, 276, 355, 226, 231, 1499, 227, 315, 91, 121, 120, 109,
209, 1481, 151, 150, 246, 100, 1277, 1420, 90, 425, 504, 282, 358, 230, 4550
of 4628 triangles, 193, 178, 277, 3758 of 3760 triangles, 1409, 131, 225, 390,
340
Grouped 34 regions
Showing 187 region surfaces
> select clear
> select #2.13
1 model selected
Opened Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #30, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/For-Chimera-PflAB/Resegment/1xFliL.mrc
> models #30
> hide #!30 models
> select #2.95
1 model selected
> select add #2.13
2 models selected
Grouped 2 regions
Opened Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #31, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/For-Chimera-PflAB/Resegment/1xFliL.mrc
> models #31
> select clear
> select #2.150
1 model selected
> select add #2.149
2 models selected
> select add #2.79
3 models selected
> select add #2.80
4 models selected
> select add #2.108
5 models selected
> select add #2.179
6 models selected
> select add #2.44
7 models selected
> select add #2.123
8 models selected
> select add #2.5
9 models selected
> select add #2.4
10 models selected
> select add #2.99
11 models selected
> select add #2.29
12 models selected
> select add #2.2
13 models selected
> select subtract #2.4
12 models selected
> select add #2.173
13 models selected
> select add #2.174
14 models selected
Drag select of 1595, 27 of 6488 triangles, 170, 24 of 2304 triangles, 255, 31
of 1496 triangles
> select #2.5
1 model selected
> select add #2.4
2 models selected
> select add #2.173
3 models selected
> select add #2.2
4 models selected
> select add #2.174
5 models selected
> select add #2.29
6 models selected
> select add #2.99
7 models selected
> select subtract #2.99
6 models selected
> select add #2.99
7 models selected
> select add #2.149
8 models selected
> select add #2.150
9 models selected
> select add #2.79
10 models selected
> select add #2.108
11 models selected
> select add #2.80
12 models selected
> select add #2.179
13 models selected
> select add #2.44
14 models selected
> select add #2.25
15 models selected
> select add #2.169
16 models selected
> select add #2.170
17 models selected
> select add #2.22
18 models selected
> select add #2.167
19 models selected
> select add #2.168
20 models selected
> select add #2.13
21 models selected
> hide #!31 models
> select clear
> select #2.44
1 model selected
Ungrouped to 6 regions
> select #2.30
1 model selected
> select add #2.50
2 models selected
> select add #2.53
3 models selected
> select clear
> select #2.78
1 model selected
Ungrouped to 0 regions
> select #2.19
1 model selected
Ungrouped to 2 regions
Ungrouped to 0 regions
> select #2.150
1 model selected
Ungrouped to 5 regions
Ungrouped to 24 regions
Ungrouped to 23 regions
> select #2.226
1 model selected
> select add #2.228
2 models selected
> select add #2.211
3 models selected
> select add #2.237
4 models selected
> select add #2.236
5 models selected
> select add #2.214
6 models selected
> select add #2.235
7 models selected
> select add #2.156
8 models selected
> select add #2.179
9 models selected
> select subtract #2.179
8 models selected
> select add #2.19
9 models selected
> select add #2.197
10 models selected
> select #2.179
1 model selected
Ungrouped to 6 regions
> select #2.182
1 model selected
> select add #2.183
2 models selected
> select add #2.97
3 models selected
> select add #2.216
4 models selected
> select add #2.212
5 models selected
> select #2.108
1 model selected
Ungrouped to 0 regions
> select #2.108
1 model selected
> select #2.201
1 model selected
> select #2.202
1 model selected
Ungrouped to 8 regions
> select #2.244
1 model selected
> select subtract #2.244
Nothing selected
> select add #2.244
1 model selected
> select add #2.149
2 models selected
> select subtract #2.149
1 model selected
> select add #2.149
2 models selected
> select #2.181
1 model selected
Ungrouped to 0 regions
> select add #2.218
1 model selected
> select add #2.78
2 models selected
> select #2.99
1 model selected
Ungrouped to 8 regions
> select #2.248
1 model selected
> select add #2.246
2 models selected
> select add #2.251
3 models selected
> select add #2.245
4 models selected
> select add #2.202
5 models selected
> select clear
> select #2.247
1 model selected
> select #2.202
1 model selected
Ungrouped to 3 regions
Ungrouped to 0 regions
> select #2.29
1 model selected
Ungrouped to 4 regions
Ungrouped to 23 regions
> select clear
> select #2.277
1 model selected
> select add #2.274
2 models selected
> select add #2.278
3 models selected
> select add #2.275
4 models selected
> select add #2.276
5 models selected
> select add #2.262
6 models selected
> select #2.169
1 model selected
> select add #2.170
2 models selected
> select add #2.5
3 models selected
> select #2.5
1 model selected
Ungrouped to 4 regions
> select #2.255
1 model selected
Ungrouped to 10 regions
> select #2.286
1 model selected
> select add #2.283
2 models selected
> select add #2.273
3 models selected
> select add #2.272
4 models selected
> select add #2.266
5 models selected
> select add #2.29
6 models selected
> select add #2.202
7 models selected
> select add #2.257
8 models selected
> select add #2.268
9 models selected
> select add #2.265
10 models selected
> select add #2.256
11 models selected
> select #2.271
1 model selected
Ungrouped to 2 regions
> select clear
> select #2.289
1 model selected
> select #2.181
1 model selected
> select clear
> select #2.217
1 model selected
> select add #2.168
2 models selected
> select add #2.167
3 models selected
> select #2.13
1 model selected
Drag select of 132, 303 of 4172 triangles, 288, 389 of 1296 triangles, 233, 5
of 3452 triangles, 329, 108 of 2248 triangles, 1599, 181 of 7828 triangles,
104, 2566 of 4364 triangles, 1246, 27 of 2812 triangles, 187, 1002 of 2892
triangles, 185, 1426, 4810 of 6384 triangles, 1433, 4864 of 11184 triangles,
308, 874 of 2308 triangles, 293, 278 of 2080 triangles
> select clear
Drag select of 113, 1257, 201, 256, 170, 127, 141, 240, 1710, 180, 300, 210,
462, 317, 124, 304, 112, 132, 288, 195, 233, 252, 329, 135, 213, 287, 264,
263, 363, 302, 343, 92, 182, 289, 267, 285, 316, 362, 328, 1581, 168, 122,
211, 212, 1419, 270, 1406, 290, 346, 347, 126, 138, 136, 157, 137, 1284, 184,
199, 183, 139, 1599, 104, 1246, 187, 185, 1426, 1433, 308, 293, 217
Grouped 70 regions
Showing 219 region surfaces
Opened Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #32, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/For-Chimera-PflAB/Resegment/3xFliL.mrc
> models #32
> select clear
> select #2.27
1 model selected
> select add #2.141
2 models selected
> select add #2.142
3 models selected
> select add #2.114
4 models selected
> select add #2.112
5 models selected
> select add #2.104
6 models selected
> select add #2.98
7 models selected
> select add #2.6
8 models selected
> select add #2.39
9 models selected
> select add #2.246
10 models selected
> select add #2.248
11 models selected
> select add #2.20
12 models selected
> select add #2.247
13 models selected
> select add #2.245
14 models selected
> select add #2.251
15 models selected
> select add #2.105
16 models selected
> select add #2.103
17 models selected
> select add #2.91
18 models selected
> select add #2.106
19 models selected
> select add #2.109
20 models selected
> select add #2.102
21 models selected
> select add #2.108
22 models selected
Grouped 22 regions
> select #2.2
1 model selected
> select #2.110
1 model selected
> select add #2.2
2 models selected
Grouped 2 regions
Showing 197 region surfaces
> select #2.4
1 model selected
> select #2.28
1 model selected
> select add #2.125
2 models selected
> select add #2.126
3 models selected
> select add #2.17
4 models selected
> select add #2.144
5 models selected
> select add #2.50
6 models selected
> select add #2.86
7 models selected
> select add #2.85
8 models selected
> select add #2.75
9 models selected
> select add #2.88
10 models selected
> select add #2.46
11 models selected
> select add #2.89
12 models selected
> select add #2.83
13 models selected
> select add #2.81
14 models selected
> select add #2.82
15 models selected
> select add #2.90
16 models selected
> select add #2.72
17 models selected
> select add #2.87
18 models selected
> select add #2.51
19 models selected
> select add #2.35
20 models selected
> select add #2.30
21 models selected
> select add #2.78
22 models selected
> select add #2.53
23 models selected
Grouped 23 regions
> select add #2.4
2 models selected
Grouped 2 regions
> select #2.123
1 model selected
> select add #2.120
2 models selected
> select clear
Showing 174 region surfaces
> select #2.120
1 model selected
> select add #2.4
2 models selected
> select add #2.122
3 models selected
> select add #2.37
4 models selected
> select add #2.40
5 models selected
> select add #2.128
6 models selected
> select add #2.127
7 models selected
> select add #2.133
8 models selected
> select add #2.96
9 models selected
> select add #2.47
10 models selected
> select add #2.130
11 models selected
> select add #2.36
12 models selected
Grouped 12 regions
> hide #!32 models
> select clear
> select #2.4
1 model selected
> select add #2.228
2 models selected
> select add #2.139
3 models selected
Grouped 3 regions
> select clear
> select #2.4
1 model selected
Opened Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #33, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/For-Chimera-PflAB/Resegment/3xPflAB.mrc
> models #33
> select clear
> select #2.4
1 model selected
> hide #!33 models
> select #2.93
1 model selected
> select add #2.77
2 models selected
> select add #2.2
3 models selected
> select add #2.76
4 models selected
> select add #2.74
5 models selected
> select add #2.84
6 models selected
> select add #2.221
7 models selected
> select add #2.123
8 models selected
> select add #2.201
9 models selected
Grouped 9 regions
> select clear
> select #2.163
1 model selected
> select add #2.169
2 models selected
> select add #2.165
3 models selected
> select add #2.166
4 models selected
> select add #2.160
5 models selected
> select add #2.26
6 models selected
> select add #2.170
7 models selected
> select add #2.32
8 models selected
> select add #2.159
9 models selected
> select add #2.33
10 models selected
> select clear
Showing 153 region surfaces
> select #2.2
1 model selected
Opened Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #34, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/For-Chimera-PflAB/Resegment/3xFliL.mrc
> models #34
> select clear
> select #2.2
1 model selected
> select add #2.4
2 models selected
> hide #!34 models
Opened Rev-CJFlgYPlfAB-
msk-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #35, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/For-Chimera-
> PflAB/Resegment/Segmentations.cxs includeMaps true
> close session
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-Chimera-PflAB/Resegment/3xPflAB.mrc"
Opened 3xPflAB.mrc as #1, grid size 200,200,200, pixel 2.14, shown at level
0.0208, step 1, values float32
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-Chimera-PflAB/Resegment/3xFliL.mrc"
Opened 3xFliL.mrc as #2, grid size 200,200,200, pixel 2.14, shown at level
0.00115, step 1, values float32
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/CJ_PflAB-cage_Sep2024/Model-
> from-Jack/PflAB-Cage.pdb"
Chain information for PflAB-Cage.pdb
---
Chain | Description
3.1/A 3.2/A 3.3/A 3.4/A | No description available
3.5/A 3.8/D 3.11/G 3.14/J 3.17/M 3.20/P 3.23/S 3.26/V | No description available
3.1/B 3.2/B 3.3/B 3.4/B | No description available
3.6/B 3.9/E 3.12/H 3.15/K 3.18/N 3.21/Q 3.24/T 3.27/W | No description available
3.7/C 3.10/F 3.13/I 3.16/L 3.19/O 3.22/R 3.25/U 3.28/X | No description available
3.29/Y 3.30/Z 3.31/a 3.32/b 3.33/c | No description available
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/CJ_PflAB-cage_Sep2024/Model-
> from-Jack/Multimer-CJ-unit.pdb"
Chain information for Multimer-CJ-unit.pdb
---
Chain | Description
4.27/? 4.50/? 4.73/? 4.96/? | No description available
4.38/? 4.39/? 4.40/? 4.41/? 4.42/? 4.43/? 4.44/? 4.45/? 4.46/? 4.47/? 4.61/? 4.62/? 4.63/? 4.64/? 4.65/? 4.66/? 4.67/? 4.68/? 4.69/? 4.70/? 4.84/? 4.85/? 4.86/? 4.87/? 4.88/? 4.89/? 4.90/? 4.91/? 4.92/? 4.93/? 4.107/? 4.108/? 4.109/? 4.110/? 4.111/? 4.112/? 4.113/? 4.114/? 4.115/? 4.116/? | No description available
4.1/A 4.2/A 4.3/A 4.4/A 4.5/A 4.6/A 4.7/A 4.8/A | No description available
4.9/A 4.10/A 4.11/A 4.12/A 4.13/A | No description available
4.14/A 4.15/A 4.16/A 4.17/A 4.18/A | No description available
4.25/A 4.26/A 4.48/A 4.49/A 4.71/A 4.72/A 4.94/A 4.95/A | No description available
4.117/A 4.118/A 4.119/A 4.120/A 4.121/A 4.122/A 4.117/B 4.118/B 4.119/B 4.120/B 4.121/B 4.122/B | No description available
4.1/B 4.2/B 4.3/B 4.4/B 4.5/B 4.6/B 4.7/B 4.8/B | No description available
4.14/B 4.15/B 4.16/B 4.17/B 4.18/B | No description available
4.28/B 4.29/B 4.30/B 4.31/B 4.32/B 4.33/B 4.34/B 4.35/B 4.36/B 4.37/B 4.51/B 4.52/B 4.53/B 4.54/B 4.55/B 4.56/B 4.57/B 4.58/B 4.59/B 4.60/B 4.74/B 4.75/B 4.76/B 4.77/B 4.78/B 4.79/B 4.80/B 4.81/B 4.82/B 4.83/B 4.97/B 4.98/B 4.99/B 4.100/B 4.101/B 4.102/B 4.103/B 4.104/B 4.105/B 4.106/B | No description available
4.1/C 4.2/C 4.3/C 4.4/C 4.5/C 4.6/C 4.7/C 4.8/C | No description available
4.19/C 4.20/C 4.21/C 4.22/C 4.23/C 4.24/C | No description available
> select add #4
224507 atoms, 227843 bonds, 42 pseudobonds, 26692 residues, 141 models
selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,-66.228,0,1,0,-349.31,0,0,1,23.812
> close #3
> view matrix models #4,1,0,0,-405.38,0,1,0,-311.45,0,0,1,58.256
> view matrix models #4,1,0,0,-254.62,0,1,0,-339.9,0,0,1,-50.92
> view matrix models #4,1,0,0,-426.07,0,1,0,-256.92,0,0,1,-34.021
> view matrix models #4,1,0,0,-530.23,0,1,0,-265.12,0,0,1,-194.49
> view matrix models #4,1,0,0,-513.93,0,1,0,-314.27,0,0,1,-191.45
> view matrix models #4,1,0,0,-513.75,0,1,0,-313.02,0,0,1,-191.47
> combine #4
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.2 to 'D'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.2 to 'E'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.2 to 'F'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.3 to 'G'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.3 to 'H'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.3 to 'I'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.4 to 'J'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.4 to 'K'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.4 to 'L'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.5 to 'M'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.5 to 'N'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.5 to 'O'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.6 to 'P'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.6 to 'Q'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.6 to 'R'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.7 to 'S'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.7 to 'T'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.7 to 'U'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.8 to 'V'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.8 to 'W'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.8 to 'X'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.9 to 'Y'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.10 to 'Z'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.11 to 'a'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.12 to 'b'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.13 to 'c'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.14 to 'd'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.14 to 'e'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.15 to 'f'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.15 to 'g'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.16 to 'h'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.16 to 'i'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.17 to 'j'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.17 to 'k'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.18 to 'l'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.18 to 'm'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.19 to 'n'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.20 to 'o'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.21 to 'p'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.22 to 'q'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.23 to 'r'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.24 to 's'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.25 to 't'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.26 to 'u'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.27 to 'v'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.28 to 'w'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.29 to 'x'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.30 to 'y'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.31 to 'z'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.32 to '1'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.33 to '2'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.34 to '3'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.35 to '4'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.36 to '5'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.37 to '6'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.38 to '7'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.39 to '8'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.40 to '9'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.41 to '0'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.42 to 'AA'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.43 to 'AB'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.44 to 'AC'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.45 to 'AD'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.46 to 'AE'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.47 to 'AF'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.48 to 'AG'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.49 to 'AH'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.50 to 'AI'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.51 to 'AJ'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.52 to 'AK'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.53 to 'AL'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.54 to 'AM'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.55 to 'AN'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.56 to 'AO'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.57 to 'AP'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.58 to 'AQ'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.59 to 'AR'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.60 to 'AS'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.61 to 'AT'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.62 to 'AU'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.63 to 'AV'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.64 to 'AW'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.65 to 'AX'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.66 to 'AY'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.67 to 'AZ'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.68 to 'Aa'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.69 to 'Ab'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.70 to 'Ac'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.71 to 'Ad'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.72 to 'Ae'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.73 to 'Af'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.74 to 'Ag'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.75 to 'Ah'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.76 to 'Ai'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.77 to 'Aj'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.78 to 'Ak'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.79 to 'Al'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.80 to 'Am'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.81 to 'An'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.82 to 'Ao'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.83 to 'Ap'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.84 to 'Aq'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.85 to 'Ar'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.86 to 'As'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.87 to 'At'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.88 to 'Au'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.89 to 'Av'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.90 to 'Aw'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.91 to 'Ax'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.92 to 'Ay'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.93 to 'Az'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.94 to 'A1'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.95 to 'A2'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.96 to 'A3'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.97 to 'A4'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.98 to 'A5'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.99 to 'A6'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.100 to 'A7'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.101 to 'A8'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.102 to 'A9'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.103 to 'A0'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.104 to 'BA'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.105 to 'BB'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.106 to 'BC'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.107 to 'BD'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.108 to 'BE'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.109 to 'BF'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.110 to 'BG'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.111 to 'BH'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.112 to 'BI'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.113 to 'BJ'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.114 to 'BK'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.115 to 'BL'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.116 to 'BM'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.117 to 'BN'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.117 to 'BO'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.118 to 'BP'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.118 to 'BQ'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.119 to 'BR'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.119 to 'BS'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.120 to 'BT'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.120 to 'BU'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.121 to 'BV'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.121 to 'BW'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.122 to 'BX'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.122 to 'BY'
> select subtract #4
Nothing selected
> select add #3
224507 atoms, 227843 bonds, 42 pseudobonds, 26692 residues, 2 models selected
> hide #!4 models
> view matrix models #3,1,0,0,-503.4,0,1,0,-322.53,0,0,1,-242.38
> view matrix models #3,1,0,0,-508.08,0,1,0,-316.17,0,0,1,-241.55
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.99384,-0.10889,-0.020595,-437.23,0.10906,0.99401,0.0069264,-397.45,0.019718,-0.0091298,0.99976,-251.37
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.99384,-0.10889,-0.020595,-497.59,0.10906,0.99401,0.0069264,-443.27,0.019718,-0.0091298,0.99976,-253.96
> color #2 #ffffb289 models
> color #2 #ffffb26c models
Cell requested for row 2 is out of bounds for table with 5 rows! Resizing
table model.
> color #3 #4e6ceeff
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #3 inMap #2
Fit molecule combination (#3) to map 3xFliL.mrc (#2) using 224507 atoms
average map value = 0.001642, steps = 204
shifted from previous position = 24.5
rotated from previous position = 15 degrees
atoms outside contour = 207179, contour level = 0.0011513
Position of combination (#3) relative to 3xFliL.mrc (#2) coordinates:
Matrix rotation and translation
0.98858703 0.14365941 0.04536134 -672.25005535
-0.14419119 0.98951195 0.00866005 -244.68410126
-0.04364149 -0.01510192 0.99893311 -219.69361290
Axis -0.07862165 0.29448528 -0.95241643
Axis point -2403.97482385 4384.48479255 0.00000000
Rotation angle (degrees) 8.69160231
Shift along axis 190.03734942
> fitmap #3 inMap #2
Fit molecule combination (#3) to map 3xFliL.mrc (#2) using 224507 atoms
average map value = 0.001642, steps = 28
shifted from previous position = 0.049
rotated from previous position = 0.00519 degrees
atoms outside contour = 207185, contour level = 0.0011513
Position of combination (#3) relative to 3xFliL.mrc (#2) coordinates:
Matrix rotation and translation
0.98858397 0.14368297 0.04535359 -672.22491614
-0.14421080 0.98950986 0.00857197 -244.58744867
-0.04364618 -0.01501458 0.99893422 -219.74771178
Axis -0.07803440 0.29444933 -0.95247584
Axis point -2402.40026643 4384.60173062 0.00000000
Rotation angle (degrees) 8.69236933
Shift along axis 189.74244580
> color #1 #b2b2b286 models
> color #1 #b2b2b280 models
> fitmap #3 inMap #2
Fit molecule combination (#3) to map 3xFliL.mrc (#2) using 224507 atoms
average map value = 0.001642, steps = 28
shifted from previous position = 0.049
rotated from previous position = 0.00961 degrees
atoms outside contour = 207177, contour level = 0.0011513
Position of combination (#3) relative to 3xFliL.mrc (#2) coordinates:
Matrix rotation and translation
0.98859095 0.14362700 0.04537860 -672.24238357
-0.14416208 0.98951558 0.00873027 -244.74546523
-0.04364893 -0.01517254 0.99893171 -219.64726321
Axis -0.07909821 0.29460620 -0.95233957
Axis point -2405.37688551 4384.62827327 0.00000000
Rotation angle (degrees) 8.69043685
Shift along axis 190.24841566
> fitmap #3 inMap #2
Fit molecule combination (#3) to map 3xFliL.mrc (#2) using 224507 atoms
average map value = 0.001642, steps = 40
shifted from previous position = 0.0317
rotated from previous position = 0.00727 degrees
atoms outside contour = 207178, contour level = 0.0011513
Position of combination (#3) relative to 3xFliL.mrc (#2) coordinates:
Matrix rotation and translation
0.98858534 0.14367343 0.04535395 -672.23245438
-0.14420305 0.98951063 0.00861303 -244.62683977
-0.04364075 -0.01505490 0.99893385 -219.72580475
Axis -0.07830664 0.29444384 -0.95245519
Axis point -2403.06464622 4384.47520465 0.00000000
Rotation angle (degrees) 8.69203333
Shift along axis 189.89038322
> fitmap #3 inMap #2
Fit molecule combination (#3) to map 3xFliL.mrc (#2) using 224507 atoms
average map value = 0.001642, steps = 28
shifted from previous position = 0.0314
rotated from previous position = 0.00482 degrees
atoms outside contour = 207177, contour level = 0.0011513
Position of combination (#3) relative to 3xFliL.mrc (#2) coordinates:
Matrix rotation and translation
0.98858892 0.14364411 0.04536878 -672.24593804
-0.14417737 0.98951369 0.00869172 -244.71227686
-0.04364452 -0.01513369 0.99893249 -219.67301583
Axis -0.07883669 0.29453907 -0.95238202
Axis point -2404.62006849 4384.56658655 0.00000000
Rotation angle (degrees) 8.69103238
Shift along axis 190.13294908
> fitmap #3 inMap #2
Fit molecule combination (#3) to map 3xFliL.mrc (#2) using 224507 atoms
average map value = 0.001642, steps = 40
shifted from previous position = 0.0229
rotated from previous position = 0.00351 degrees
atoms outside contour = 207180, contour level = 0.0011513
Position of combination (#3) relative to 3xFliL.mrc (#2) coordinates:
Matrix rotation and translation
0.98858671 0.14366431 0.04535290 -672.23289860
-0.14419488 0.98951163 0.00863530 -244.65177137
-0.04363663 -0.01507640 0.99893370 -219.71539500
Axis -0.07845525 0.29444093 -0.95244386
Axis point -2403.50683165 4384.50379888 0.00000000
Rotation angle (degrees) 8.69161151
Shift along axis 189.97128347
> view orient
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.99226,0.11567,0.045091,-660.47,-0.11622,0.99317,0.0099124,-267.91,-0.043637,-0.015076,0.99893,-219.72
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.99226,0.11567,0.045091,-660.22,-0.11622,0.99317,0.0099124,-267.44,-0.043637,-0.015076,0.99893,-219.72
> fitmap #3 inMap #2
Fit molecule combination (#3) to map 3xFliL.mrc (#2) using 224507 atoms
average map value = 0.001642, steps = 60
shifted from previous position = 2.26
rotated from previous position = 1.62 degrees
atoms outside contour = 207179, contour level = 0.0011513
Position of combination (#3) relative to 3xFliL.mrc (#2) coordinates:
Matrix rotation and translation
0.98858235 0.14369538 0.04534951 -672.24494734
-0.14422453 0.98950759 0.00860317 -244.60240474
-0.04363745 -0.01504545 0.99893414 -219.73488330
Axis -0.07823302 0.29438163 -0.95248047
Axis point -2402.48860800 4383.99198374 0.00000000
Rotation angle (degrees) 8.69312209
Shift along axis 189.87847858
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.99165,0.12076,0.045138,-662.66,-0.12131,0.99257,0.0096501,-263.68,-0.043637,-0.015045,0.99893,-219.73
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.99165,0.12076,0.045138,-663.1,-0.12131,0.99257,0.0096501,-262.22,-0.043637,-0.015045,0.99893,-219.73
> view matrix models
> #3,0.99165,0.12076,0.045138,-662.4,-0.12131,0.99257,0.0096501,-261.77,-0.043637,-0.015045,0.99893,-219.73
Cell requested for row 2 is out of bounds for table with 126 rows! Resizing
table model.
> save /Users/shoichitachiyama/Desktop/For-Chimera-
> PflAB/Resegment/Docking_Jack_model.cxs includeMaps true
> combine #4
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.2 to 'D'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.2 to 'E'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.2 to 'F'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.3 to 'G'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.3 to 'H'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.3 to 'I'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.4 to 'J'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.4 to 'K'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.4 to 'L'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.5 to 'M'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.5 to 'N'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.5 to 'O'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.6 to 'P'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.6 to 'Q'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.6 to 'R'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.7 to 'S'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.7 to 'T'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.7 to 'U'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.8 to 'V'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.8 to 'W'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.8 to 'X'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.9 to 'Y'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.10 to 'Z'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.11 to 'a'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.12 to 'b'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.13 to 'c'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.14 to 'd'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.14 to 'e'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.15 to 'f'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.15 to 'g'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.16 to 'h'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.16 to 'i'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.17 to 'j'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.17 to 'k'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.18 to 'l'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.18 to 'm'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.19 to 'n'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.20 to 'o'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.21 to 'p'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.22 to 'q'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.23 to 'r'
Remapping chain ID 'C' in Multimer-CJ-unit.pdb #4.24 to 's'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.25 to 't'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.26 to 'u'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.27 to 'v'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.28 to 'w'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.29 to 'x'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.30 to 'y'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.31 to 'z'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.32 to '1'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.33 to '2'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.34 to '3'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.35 to '4'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.36 to '5'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.37 to '6'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.38 to '7'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.39 to '8'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.40 to '9'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.41 to '0'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.42 to 'AA'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.43 to 'AB'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.44 to 'AC'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.45 to 'AD'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.46 to 'AE'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.47 to 'AF'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.48 to 'AG'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.49 to 'AH'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.50 to 'AI'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.51 to 'AJ'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.52 to 'AK'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.53 to 'AL'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.54 to 'AM'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.55 to 'AN'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.56 to 'AO'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.57 to 'AP'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.58 to 'AQ'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.59 to 'AR'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.60 to 'AS'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.61 to 'AT'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.62 to 'AU'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.63 to 'AV'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.64 to 'AW'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.65 to 'AX'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.66 to 'AY'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.67 to 'AZ'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.68 to 'Aa'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.69 to 'Ab'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.70 to 'Ac'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.71 to 'Ad'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.72 to 'Ae'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.73 to 'Af'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.74 to 'Ag'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.75 to 'Ah'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.76 to 'Ai'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.77 to 'Aj'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.78 to 'Ak'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.79 to 'Al'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.80 to 'Am'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.81 to 'An'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.82 to 'Ao'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.83 to 'Ap'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.84 to 'Aq'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.85 to 'Ar'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.86 to 'As'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.87 to 'At'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.88 to 'Au'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.89 to 'Av'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.90 to 'Aw'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.91 to 'Ax'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.92 to 'Ay'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.93 to 'Az'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.94 to 'A1'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.95 to 'A2'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.96 to 'A3'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.97 to 'A4'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.98 to 'A5'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.99 to 'A6'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.100 to 'A7'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.101 to 'A8'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.102 to 'A9'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.103 to 'A0'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.104 to 'BA'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.105 to 'BB'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.106 to 'BC'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.107 to 'BD'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.108 to 'BE'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.109 to 'BF'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.110 to 'BG'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.111 to 'BH'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.112 to 'BI'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.113 to 'BJ'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.114 to 'BK'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.115 to 'BL'
Remapping chain ID ' ' in Multimer-CJ-unit.pdb #4.116 to 'BM'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.117 to 'BN'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.117 to 'BO'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.118 to 'BP'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.118 to 'BQ'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.119 to 'BR'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.119 to 'BS'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.120 to 'BT'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.120 to 'BU'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.121 to 'BV'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.121 to 'BW'
Remapping chain ID 'A' in Multimer-CJ-unit.pdb #4.122 to 'BX'
Remapping chain ID 'B' in Multimer-CJ-unit.pdb #4.122 to 'BY'
> matchmaker #5 to #3
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 combination, chain v (#3) with combination, chain v (#5), sequence
alignment score = 6376.6
RMSD between 1250 pruned atom pairs is 0.000 angstroms; (across all 1250
pairs: 0.000)
> select subtract #3
Nothing selected
> hide #!3 models
> splits #5
Unknown command: splits #5
> split #5
Split combination (#5) into 149 models
Chain information for combination 0 #5.1
---
Chain | Description
0 | No description available
Chain information for combination 1 #5.2
---
Chain | Description
1 | No description available
Chain information for combination 2 #5.3
---
Chain | Description
2 | No description available
Chain information for combination 3 #5.4
---
Chain | Description
3 | No description available
Chain information for combination 4 #5.5
---
Chain | Description
4 | No description available
Chain information for combination 5 #5.6
---
Chain | Description
5 | No description available
Chain information for combination 6 #5.7
---
Chain | Description
6 | No description available
Chain information for combination 7 #5.8
---
Chain | Description
7 | No description available
Chain information for combination 8 #5.9
---
Chain | Description
8 | No description available
Chain information for combination 9 #5.10
---
Chain | Description
9 | No description available
Chain information for combination A #5.11
---
Chain | Description
A | No description available
Chain information for combination A0 #5.12
---
Chain | Description
A0 | No description available
Chain information for combination A1 #5.13
---
Chain | Description
A1 | No description available
Chain information for combination A2 #5.14
---
Chain | Description
A2 | No description available
Chain information for combination A3 #5.15
---
Chain | Description
A3 | No description available
Chain information for combination A4 #5.16
---
Chain | Description
A4 | No description available
Chain information for combination A5 #5.17
---
Chain | Description
A5 | No description available
Chain information for combination A6 #5.18
---
Chain | Description
A6 | No description available
Chain information for combination A7 #5.19
---
Chain | Description
A7 | No description available
Chain information for combination A8 #5.20
---
Chain | Description
A8 | No description available
Chain information for combination A9 #5.21
---
Chain | Description
A9 | No description available
Chain information for combination AA #5.22
---
Chain | Description
AA | No description available
Chain information for combination AB #5.23
---
Chain | Description
AB | No description available
Chain information for combination AC #5.24
---
Chain | Description
AC | No description available
Chain information for combination AD #5.25
---
Chain | Description
AD | No description available
Chain information for combination AE #5.26
---
Chain | Description
AE | No description available
Chain information for combination AF #5.27
---
Chain | Description
AF | No description available
Chain information for combination AG #5.28
---
Chain | Description
AG | No description available
Chain information for combination AH #5.29
---
Chain | Description
AH | No description available
Chain information for combination AI #5.30
---
Chain | Description
AI | No description available
Chain information for combination AJ #5.31
---
Chain | Description
AJ | No description available
Chain information for combination AK #5.32
---
Chain | Description
AK | No description available
Chain information for combination AL #5.33
---
Chain | Description
AL | No description available
Chain information for combination AM #5.34
---
Chain | Description
AM | No description available
Chain information for combination AN #5.35
---
Chain | Description
AN | No description available
Chain information for combination AO #5.36
---
Chain | Description
AO | No description available
Chain information for combination AP #5.37
---
Chain | Description
AP | No description available
Chain information for combination AQ #5.38
---
Chain | Description
AQ | No description available
Chain information for combination AR #5.39
---
Chain | Description
AR | No description available
Chain information for combination AS #5.40
---
Chain | Description
AS | No description available
Chain information for combination AT #5.41
---
Chain | Description
AT | No description available
Chain information for combination AU #5.42
---
Chain | Description
AU | No description available
Chain information for combination AV #5.43
---
Chain | Description
AV | No description available
Chain information for combination AW #5.44
---
Chain | Description
AW | No description available
Chain information for combination AX #5.45
---
Chain | Description
AX | No description available
Chain information for combination AY #5.46
---
Chain | Description
AY | No description available
Chain information for combination AZ #5.47
---
Chain | Description
AZ | No description available
Chain information for combination Aa #5.48
---
Chain | Description
Aa | No description available
Chain information for combination Ab #5.49
---
Chain | Description
Ab | No description available
Chain information for combination Ac #5.50
---
Chain | Description
Ac | No description available
Chain information for combination Ad #5.51
---
Chain | Description
Ad | No description available
Chain information for combination Ae #5.52
---
Chain | Description
Ae | No description available
Chain information for combination Af #5.53
---
Chain | Description
Af | No description available
Chain information for combination Ag #5.54
---
Chain | Description
Ag | No description available
Chain information for combination Ah #5.55
---
Chain | Description
Ah | No description available
Chain information for combination Ai #5.56
---
Chain | Description
Ai | No description available
Chain information for combination Aj #5.57
---
Chain | Description
Aj | No description available
Chain information for combination Ak #5.58
---
Chain | Description
Ak | No description available
Chain information for combination Al #5.59
---
Chain | Description
Al | No description available
Chain information for combination Am #5.60
---
Chain | Description
Am | No description available
Chain information for combination An #5.61
---
Chain | Description
An | No description available
Chain information for combination Ao #5.62
---
Chain | Description
Ao | No description available
Chain information for combination Ap #5.63
---
Chain | Description
Ap | No description available
Chain information for combination Aq #5.64
---
Chain | Description
Aq | No description available
Chain information for combination Ar #5.65
---
Chain | Description
Ar | No description available
Chain information for combination As #5.66
---
Chain | Description
As | No description available
Chain information for combination At #5.67
---
Chain | Description
At | No description available
Chain information for combination Au #5.68
---
Chain | Description
Au | No description available
Chain information for combination Av #5.69
---
Chain | Description
Av | No description available
Chain information for combination Aw #5.70
---
Chain | Description
Aw | No description available
Chain information for combination Ax #5.71
---
Chain | Description
Ax | No description available
Chain information for combination Ay #5.72
---
Chain | Description
Ay | No description available
Chain information for combination Az #5.73
---
Chain | Description
Az | No description available
Chain information for combination B #5.74
---
Chain | Description
B | No description available
Chain information for combination BA #5.75
---
Chain | Description
BA | No description available
Chain information for combination BB #5.76
---
Chain | Description
BB | No description available
Chain information for combination BC #5.77
---
Chain | Description
BC | No description available
Chain information for combination BD #5.78
---
Chain | Description
BD | No description available
Chain information for combination BE #5.79
---
Chain | Description
BE | No description available
Chain information for combination BF #5.80
---
Chain | Description
BF | No description available
Chain information for combination BG #5.81
---
Chain | Description
BG | No description available
Chain information for combination BH #5.82
---
Chain | Description
BH | No description available
Chain information for combination BI #5.83
---
Chain | Description
BI | No description available
Chain information for combination BJ #5.84
---
Chain | Description
BJ | No description available
Chain information for combination BK #5.85
---
Chain | Description
BK | No description available
Chain information for combination BL #5.86
---
Chain | Description
BL | No description available
Chain information for combination BM #5.87
---
Chain | Description
BM | No description available
Chain information for combination BN #5.88
---
Chain | Description
BN | No description available
Chain information for combination BO #5.89
---
Chain | Description
BO | No description available
Chain information for combination BP #5.90
---
Chain | Description
BP | No description available
Chain information for combination BQ #5.91
---
Chain | Description
BQ | No description available
Chain information for combination BR #5.92
---
Chain | Description
BR | No description available
Chain information for combination BS #5.93
---
Chain | Description
BS | No description available
Chain information for combination BT #5.94
---
Chain | Description
BT | No description available
Chain information for combination BU #5.95
---
Chain | Description
BU | No description available
Chain information for combination BV #5.96
---
Chain | Description
BV | No description available
Chain information for combination BW #5.97
---
Chain | Description
BW | No description available
Chain information for combination BX #5.98
---
Chain | Description
BX | No description available
Chain information for combination BY #5.99
---
Chain | Description
BY | No description available
Chain information for combination C #5.100
---
Chain | Description
C | No description available
Chain information for combination D #5.101
---
Chain | Description
D | No description available
Chain information for combination E #5.102
---
Chain | Description
E | No description available
Chain information for combination F #5.103
---
Chain | Description
F | No description available
Chain information for combination G #5.104
---
Chain | Description
G | No description available
Chain information for combination H #5.105
---
Chain | Description
H | No description available
Chain information for combination I #5.106
---
Chain | Description
I | No description available
Chain information for combination J #5.107
---
Chain | Description
J | No description available
Chain information for combination K #5.108
---
Chain | Description
K | No description available
Chain information for combination L #5.109
---
Chain | Description
L | No description available
Chain information for combination M #5.110
---
Chain | Description
M | No description available
Chain information for combination N #5.111
---
Chain | Description
N | No description available
Chain information for combination O #5.112
---
Chain | Description
O | No description available
Chain information for combination P #5.113
---
Chain | Description
P | No description available
Chain information for combination Q #5.114
---
Chain | Description
Q | No description available
Chain information for combination R #5.115
---
Chain | Description
R | No description available
Chain information for combination S #5.116
---
Chain | Description
S | No description available
Chain information for combination T #5.117
---
Chain | Description
T | No description available
Chain information for combination U #5.118
---
Chain | Description
U | No description available
Chain information for combination V #5.119
---
Chain | Description
V | No description available
Chain information for combination W #5.120
---
Chain | Description
W | No description available
Chain information for combination X #5.121
---
Chain | Description
X | No description available
Chain information for combination Y #5.122
---
Chain | Description
Y | No description available
Chain information for combination Z #5.123
---
Chain | Description
Z | No description available
Chain information for combination a #5.124
---
Chain | Description
a | No description available
Chain information for combination b #5.125
---
Chain | Description
b | No description available
Chain information for combination c #5.126
---
Chain | Description
c | No description available
Chain information for combination d #5.127
---
Chain | Description
d | No description available
Chain information for combination e #5.128
---
Chain | Description
e | No description available
Chain information for combination f #5.129
---
Chain | Description
f | No description available
Chain information for combination g #5.130
---
Chain | Description
g | No description available
Chain information for combination h #5.131
---
Chain | Description
h | No description available
Chain information for combination i #5.132
---
Chain | Description
i | No description available
Chain information for combination j #5.133
---
Chain | Description
j | No description available
Chain information for combination k #5.134
---
Chain | Description
k | No description available
Chain information for combination l #5.135
---
Chain | Description
l | No description available
Chain information for combination m #5.136
---
Chain | Description
m | No description available
Chain information for combination n #5.137
---
Chain | Description
n | No description available
Chain information for combination o #5.138
---
Chain | Description
o | No description available
Chain information for combination p #5.139
---
Chain | Description
p | No description available
Chain information for combination q #5.140
---
Chain | Description
q | No description available
Chain information for combination r #5.141
---
Chain | Description
r | No description available
Chain information for combination s #5.142
---
Chain | Description
s | No description available
Chain information for combination t #5.143
---
Chain | Description
t | No description available
Chain information for combination u #5.144
---
Chain | Description
u | No description available
Chain information for combination v #5.145
---
Chain | Description
v | No description available
Chain information for combination w #5.146
---
Chain | Description
w | No description available
Chain information for combination x #5.147
---
Chain | Description
x | No description available
Chain information for combination y #5.148
---
Chain | Description
y | No description available
Chain information for combination z #5.149
---
Chain | Description
z | No description available
> surface dust #1 size 21.4
> surface dust #2 size 21.4
> hide #5.1 models
> show #5.1 models
> hide #5.1 models
> show #5.1 models
> select add #5.1
186 atoms, 188 bonds, 24 residues, 1 model selected
> select subtract #5.1
Nothing selected
> hide #5.1 models
> hide #5.2 models
> show #5.2 models
> show #5.1 models
> hide #5.1 models
> show #5.1 models
> hide #5.4 models
> show #5.4 models
> hide #5.4 models
> show #5.4 models
Drag select of 2201 residues
> hide #!5.11 models
> hide #5.15 models
> hide #5.30 models
> hide #5.53 models
> hide #!5.100 models
> hide #!5.101 models
> hide #5.102 models
> hide #!5.103 models
> hide #!5.104 models
> hide #5.105 models
> hide #!5.106 models
> hide #!5.107 models
> hide #5.108 models
> hide #!5.109 models
> hide #!5.110 models
> hide #5.111 models
> hide #!5.112 models
> hide #!5.113 models
> hide #5.114 models
> hide #!5.115 models
> hide #!5.116 models
> hide #5.117 models
> hide #!5.118 models
> hide #!5.119 models
> hide #5.120 models
> hide #!5.121 models
> hide #5.145 models
> hide #5.74 models
Drag select of 334 residues
> hide #5.78 models
> hide #5.79 models
> hide #5.80 models
> hide #5.81 models
> hide #5.82 models
> hide #5.83 models
> hide #5.84 models
> hide #5.85 models
> hide #5.86 models
> hide #5.87 models
> hide #5.73 models
> hide #5.72 models
> hide #5.71 models
> hide #5.70 models
> hide #5.69 models
> hide #5.68 models
> hide #5.67 models
> hide #5.66 models
> hide #5.65 models
> hide #5.64 models
> hide #5.41 models
> hide #5.42 models
> hide #5.43 models
> hide #5.44 models
> hide #5.45 models
> hide #5.46 models
> hide #5.47 models
> hide #5.48 models
> hide #5.49 models
> hide #5.50 models
> hide #5.22 models
> hide #5.23 models
> hide #5.24 models
> hide #5.25 models
> hide #5.26 models
> hide #5.27 models
> hide #5.8 models
> hide #5.9 models
> hide #5.10 models
> hide #5.1 models
Drag select of 165 residues
> hide #!5.122 models
> hide #!5.123 models
> hide #!5.124 models
> hide #!5.125 models
> hide #!5.126 models
Drag select of 129 residues
> hide #5.90 models
> hide #5.91 models
Drag select of 38 residues
> hide #5.138 models
Drag select of 339 residues
> hide #5.139 models
> hide #5.140 models
> hide #5.92 models
> hide #5.93 models
> hide #5.17 models
Drag select of 32 residues
> hide #5.94 models
> hide #5.95 models
> select clear
Drag select of 928 residues, 1 pseudobonds
> hide #5.129 models
> hide #!5.130 models
> hide #5.131 models
> hide #!5.132 models
> show #!5.132 models
Drag select of 54 residues
> select clear
Drag select of 336 residues
> hide #!5.132 models
> show #!5.132 models
> hide #5.77 models
> hide #5.76 models
> hide #5.20 models
> hide #5.19 models
> hide #5.18 models
> hide #5.16 models
Drag select of 26 residues
> hide #5.21 models
> hide #5.12 models
> select clear
[Repeated 1 time(s)]Drag select of 3 residues
> hide #5.75 models
Drag select of 5 residues
> hide #5.29 models
Drag select of 110 residues
> hide #5.51 models
> hide #5.52 models
Drag select of 48 residues
> hide #5.143 models
> hide #5.144 models
Drag select of 100 residues
> hide #5.13 models
> hide #5.14 models
> select clear
Drag select of 70 residues
> hide #5.28 models
> volume #1 level 0.008564
> close #5.8-10,12-30#5.11
> close #5.41-53
> close #5.64-87
> close #5.90-95
> close
> #5.102,105,108,111,114,117,120#5.100-101,103-104,106-107,109-110,112-113,115-116,118-119,121-126
> close #5.129,131#5.130
> close #5.138-140
> close #5.143-145
> show #5.1 models
> hide #5.1 models
> show #5.1 models
> hide #5.1 models
> close #5.1
> hide #!5.134 models
> show #!5.134 models
> hide #!5.134 models
> show #!5.134 models
> hide #5.133 models
> show #5.133 models
> hide #5.133 models
> show #5.133 models
> hide #!5.134 models
> show #!5.134 models
> hide #!5.134 models
> show #!5.134 models
> hide #5.135 models
> show #5.135 models
> hide #!5.136 models
> show #!5.136 models
> hide #!5.136 models
> show #!5.136 models
> volume #1 level 0.002682
> volume #1 level 0.0208
> volume #1 level 0.01342
> save /Users/shoichitachiyama/Desktop/For-Chimera-
> PflAB/Resegment/Docking_Jack_model.cxs includeMaps true
——— End of log from Thu Jul 10 22:06:04 2025 ———
opened ChimeraX session
> open /Users/shoichi/Desktop/Resegment-Fixed/Part3/PflABY.mrc
Opened PflABY.mrc as #6, grid size 200,200,200, pixel 2.14, shown at level
0.0308, step 1, values float32
> hide #!2 models
> hide #!1 models
> volume #6 level 0.00115
> surface dust #6 size 21.4
> surface dust #6 size 50
> vop gaussian #6 sd 3
Opened PflABY.mrc gaussian as #7, grid size 200,200,200, pixel 2.14, shown at
step 1, values float32
> volume #7 level 0.00115
> close #7
> vop gaussian #6 sd 2
Opened PflABY.mrc gaussian as #7, grid size 200,200,200, pixel 2.14, shown at
step 1, values float32
> volume #7 level 0.00115
> hide #!7 models
> color #7 #5e5e5e80 models
> show #!7 models
> hide #5.2 models
> show #5.2 models
> hide #5.2 models
> hide #5.3 models
> hide #!5 models
> show #!5 models
> hide #!7 models
Drag select of 2343 residues
> select clear
> view orient
> turn x 90
[Repeated 2 time(s)]Drag select of 1274 residues
> select add #5.4
10820 atoms, 807 bonds, 1318 residues, 28 models selected
> select subtract #5.4
10021 atoms, 1220 residues, 27 models selected
> hide #5.4 models
> hide #5.5 models
> hide #5.6 models
> hide #5.7 models
> hide #5.31 models
> hide #5.32 models
> hide #5.33 models
> hide #5.34 models
> hide #5.35 models
> hide #5.36 models
> hide #5.37 models
> hide #5.38 models
> hide #5.39 models
> hide #5.40 models
> hide #5.54 models
> hide #5.55 models
> hide #5.56 models
> hide #5.57 models
> hide #5.58 models
> hide #5.59 models
> hide #5.60 models
> hide #5.61 models
> hide #5.62 models
> hide #5.63 models
> hide #5.146 models
> hide #5.147 models
> hide #5.148 models
> hide #5.149 models
> select clear
> select add #5.88
1235 atoms, 1241 bonds, 155 residues, 1 model selected
> select add #5.89
2470 atoms, 2482 bonds, 310 residues, 2 models selected
> select add #5.96
3705 atoms, 3723 bonds, 465 residues, 3 models selected
> select add #5.97
4940 atoms, 4964 bonds, 620 residues, 4 models selected
> select add #5.98
6175 atoms, 6205 bonds, 775 residues, 5 models selected
> select add #5.99
7410 atoms, 7446 bonds, 930 residues, 6 models selected
> select add #5.127
8602 atoms, 8664 bonds, 1079 residues, 7 models selected
> select add #5.128
13705 atoms, 13860 bonds, 1 pseudobond, 1712 residues, 9 models selected
> select add #5.132
18808 atoms, 19056 bonds, 2 pseudobonds, 2345 residues, 11 models selected
> select add #5.133
20000 atoms, 20274 bonds, 2 pseudobonds, 2494 residues, 12 models selected
> select add #5.134
25103 atoms, 25470 bonds, 3 pseudobonds, 3127 residues, 14 models selected
> select add #5.135
26295 atoms, 26688 bonds, 3 pseudobonds, 3276 residues, 15 models selected
> select add #5.136
31398 atoms, 31884 bonds, 4 pseudobonds, 3909 residues, 17 models selected
> select add #5.137
36469 atoms, 37040 bonds, 4 pseudobonds, 4530 residues, 18 models selected
> select add #5.141
41540 atoms, 42196 bonds, 4 pseudobonds, 5151 residues, 19 models selected
> select add #5.142
46611 atoms, 47352 bonds, 4 pseudobonds, 5772 residues, 20 models selected
> save /Users/shoichi/Desktop/Resegment-Fixed/Part3/FlgY_PflAB_JMB.pdb
> selectedOnly true
> open /Users/shoichi/Desktop/Resegment-Fixed/Part3/FlgY_PflAB_JMB.pdb
Summary of feedback from opening /Users/shoichi/Desktop/Resegment-
Fixed/Part3/FlgY_PflAB_JMB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 49 1 48
Start residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1
42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
491 messages similar to the above omitted
Chain information for FlgY_PflAB_JMB.pdb
---
Chain | Description
8.1/BN 8.2/BO 8.3/BV 8.4/BW 8.5/BX 8.6/BY | No description available
8.7/d 8.10/j 8.12/l | No description available
8.8/e 8.9/i 8.11/k 8.13/m | No description available
8.14/n 8.15/r 8.16/s | No description available
> select add #5
70581 atoms, 71562 bonds, 4 pseudobonds, 8712 residues, 51 models selected
> hide #!5 models
> select subtract #5
Nothing selected
> show #!7 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!7 models
> show #!7 models
> select add #8.1
1235 atoms, 1241 bonds, 155 residues, 1 model selected
> select subtract #8.1
Nothing selected
> select add #8.16
5071 atoms, 5156 bonds, 621 residues, 1 model selected
> select add #8.15
10142 atoms, 10312 bonds, 1242 residues, 2 models selected
> select add #8.14
15213 atoms, 15468 bonds, 1863 residues, 3 models selected
> select add #8.13
20316 atoms, 20664 bonds, 1 pseudobond, 2496 residues, 5 models selected
> select subtract #8.13
15213 atoms, 15468 bonds, 1863 residues, 3 models selected
> select add #8.12
16405 atoms, 16686 bonds, 2012 residues, 4 models selected
> select add #8.11
21508 atoms, 21882 bonds, 1 pseudobond, 2645 residues, 6 models selected
> select subtract #8.11
16405 atoms, 16686 bonds, 2012 residues, 4 models selected
> select add #8.10
17597 atoms, 17904 bonds, 2161 residues, 5 models selected
> select add #8.9
22700 atoms, 23100 bonds, 1 pseudobond, 2794 residues, 7 models selected
> select subtract #8.9
17597 atoms, 17904 bonds, 2161 residues, 5 models selected
> select add #8.8
22700 atoms, 23100 bonds, 1 pseudobond, 2794 residues, 7 models selected
> select subtract #8.8
17597 atoms, 17904 bonds, 2161 residues, 5 models selected
> select add #8.7
18789 atoms, 19122 bonds, 2310 residues, 6 models selected
> color sel #ffea0eff models
> color sel #ffea0eff
> color sel #a7c5d2ff models
> select clear
> color sel #ffea0eff models
> color sel #ca4949ff models
> select add #8.7
1192 atoms, 1218 bonds, 149 residues, 1 model selected
> select add #8.10
2384 atoms, 2436 bonds, 298 residues, 2 models selected
> select add #8.12
3576 atoms, 3654 bonds, 447 residues, 3 models selected
> select add #8.14
8647 atoms, 8810 bonds, 1068 residues, 4 models selected
> select add #8.15
13718 atoms, 13966 bonds, 1689 residues, 5 models selected
> select add #8.16
18789 atoms, 19122 bonds, 2310 residues, 6 models selected
> color sel #ca4949ff models
> select clear
> select add #8.1
1235 atoms, 1241 bonds, 155 residues, 1 model selected
> select subtract #8.1
Nothing selected
> select add #8.8
5103 atoms, 5196 bonds, 1 pseudobond, 633 residues, 2 models selected
> select add #8.11
10206 atoms, 10392 bonds, 2 pseudobonds, 1266 residues, 4 models selected
> select add #8.9
15309 atoms, 15588 bonds, 3 pseudobonds, 1899 residues, 6 models selected
> select add #8.13
20412 atoms, 20784 bonds, 4 pseudobonds, 2532 residues, 8 models selected
> color sel magenta models
> select clear
> select add #8.1
1235 atoms, 1241 bonds, 155 residues, 1 model selected
> select add #8.2
2470 atoms, 2482 bonds, 310 residues, 2 models selected
> select subtract #8.2
1235 atoms, 1241 bonds, 155 residues, 1 model selected
> select add #8.3
2470 atoms, 2482 bonds, 310 residues, 2 models selected
> select subtract #8.3
1235 atoms, 1241 bonds, 155 residues, 1 model selected
> select add #8.4
2470 atoms, 2482 bonds, 310 residues, 2 models selected
> select subtract #8.4
1235 atoms, 1241 bonds, 155 residues, 1 model selected
> select add #8.5
2470 atoms, 2482 bonds, 310 residues, 2 models selected
> select add #8.4
3705 atoms, 3723 bonds, 465 residues, 3 models selected
> select subtract #8.4
2470 atoms, 2482 bonds, 310 residues, 2 models selected
> select add #8.3
3705 atoms, 3723 bonds, 465 residues, 3 models selected
> color sel orchid models
> select add #8.2
4940 atoms, 4964 bonds, 620 residues, 4 models selected
> select clear
> select add #8.2
1235 atoms, 1241 bonds, 155 residues, 1 model selected
> select add #8.4
2470 atoms, 2482 bonds, 310 residues, 2 models selected
> select add #8.6
3705 atoms, 3723 bonds, 465 residues, 3 models selected
> color sel #bf370fff models
> color sel #bf6f27ff models
> select clear
> color sel #e9cdeaff models
> select add #8.2
1235 atoms, 1241 bonds, 155 residues, 1 model selected
> select add #8.4
2470 atoms, 2482 bonds, 310 residues, 2 models selected
> select add #8.6
3705 atoms, 3723 bonds, 465 residues, 3 models selected
> color sel #e9cdeaff models
> select clear
> ui tool show "Segment Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Segmenting PflABY.mrc gaussian, density threshold 0.001150
Showing 30 region surfaces
258 watershed regions, grouped to 30 regions
Showing PflABY gaussian.seg - 30 regions, 30 surfaces
> select #9.13
1 model selected
> select add #9.17
2 models selected
> select add #9.10
3 models selected
> select add #9.18
4 models selected
> select add #9.23
5 models selected
> select add #9.6
6 models selected
> close #9
Segmenting PflABY.mrc, density threshold 0.001150
Only showing 60 of 625 regions.
Showing 60 of 625 region surfaces
16069 watershed regions, grouped to 625 regions
Showing PflABY.seg - 625 regions, 60 surfaces
> select clear
> select #9.18
1 model selected
> select add #9.16
2 models selected
> select add #9.11
3 models selected
> select add #9.7
4 models selected
> select add #9.22
5 models selected
> select add #9.15
6 models selected
Grouped 6 regions
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Opened PflABY_imasked as #10, grid size 200,200,200, pixel 2.14, shown at step
1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/Resegment-Fixed/Part3/PflABY_out_side-spokes.mrc
> models #10
> close #9
> hide #!7 models
> color #10 #42424233 models
> color #10 #a9a9a94d models
Segmenting PflABY.mrc, density threshold 0.001150
Only showing 60 of 625 regions.
Showing 60 of 625 region surfaces
16069 watershed regions, grouped to 625 regions
Showing PflABY.seg - 625 regions, 60 surfaces
> select #9.18
1 model selected
> select add #9.16
2 models selected
> select add #9.11
3 models selected
> select add #9.15
4 models selected
> select add #9.22
5 models selected
> select add #9.7
6 models selected
> select add #9.31
7 models selected
Drag select of 22750, 4474 of 7172 triangles, 22803, 51 of 5408 triangles,
22795, 2202 of 4036 triangles, 22888, 205 of 4104 triangles, 10
PflABY_out_side-spokes.mrc
Grouped 11 regions
> select subtract #10
1 model selected
> select clear
> select #9.6
1 model selected
Ungrouped to 4 regions
Ungrouped to 20 regions, but did not show all surfaces, see Options
Ungrouped to 46 regions, but did not show all surfaces, see Options
Ungrouped to 23 regions, but did not show their surfaces, see Options
> hide #!10 models
Only showing 60 of 688 regions.
Showing 60 of 688 region surfaces
> select clear
> select #9.7
1 model selected
> select add #9.38
2 models selected
> select subtract #9.38
1 model selected
> select add #9.54
2 models selected
> select add #9.62
3 models selected
> select add #9.38
4 models selected
Grouped 4 regions
Opened PflABY_imasked as #11, grid size 200,200,200, pixel 2.14, shown at step
1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/Resegment-Fixed/Part3/PflABY_out_side-spokes.mrc
> models #11
> close #10
> hide #!8 models
> select add #9
58 models selected
> select subtract #9
Nothing selected
> hide #!9 models
> color #11 #a9a9a94d models
> show #!5 models
> hide #!5 models
> show #!8 models
> surface dust #11 size 21.4
Segmenting PflABY.mrc, density threshold 0.001150
Only showing 60 of 625 regions.
Showing 60 of 625 region surfaces
16069 watershed regions, grouped to 625 regions
Showing PflABY.seg - 625 regions, 60 surfaces
> hide #!11 models
> hide #!8 models
> show #!8 models
> select #9.11
1 model selected
> select add #9.16
2 models selected
> select add #9.18
3 models selected
> select add #9.31
4 models selected
Grouped 4 regions
> select clear
> select #9.6
1 model selected
Ungrouped to 4 regions
Ungrouped to 20 regions, but did not show all surfaces, see Options
Ungrouped to 36 regions, but did not show all surfaces, see Options
Ungrouped to 18 regions, but did not show their surfaces, see Options
Only showing 60 of 686 regions.
Showing 60 of 686 region surfaces
> select #9.11
1 model selected
> select add #9.65
2 models selected
> select add #9.62
3 models selected
> select add #9.61
4 models selected
> select add #9.71
5 models selected
> select add #9.10
6 models selected
> select #9.11
1 model selected
> select #9.65
1 model selected
> select add #9.62
2 models selected
> select add #9.61
3 models selected
> select add #9.11
4 models selected
Grouped 4 regions
> select #9.71
1 model selected
> select #9.6
1 model selected
> select #9.10
1 model selected
Ungrouped to 2 regions
Ungrouped to 9 regions, but did not show all surfaces, see Options
Ungrouped to 22 regions, but did not show all surfaces, see Options
Ungrouped to 0 regions, but did not show their surfaces, see Options
Only showing 60 of 710 regions.
Showing 60 of 710 region surfaces
> select #9.10
1 model selected
> select add #9.62
2 models selected
> select add #9.59
3 models selected
> select add #9.55
4 models selected
> select #9.11
1 model selected
> select #9.10
1 model selected
> select add #9.55
2 models selected
> select #9.11
1 model selected
> select #9.10
1 model selected
> select add #9.59
2 models selected
> select add #9.62
3 models selected
Grouped 3 regions
> select add #9.11
2 models selected
> select add #9.7
3 models selected
> select add #9.22
4 models selected
> select add #9.15
5 models selected
Grouped 5 regions
Opened PflABY_imasked as #10, grid size 200,200,200, pixel 2.14, shown at step
1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/Resegment-Fixed/Part3/PflABY_out_side-spokes.mrc
> models #11
> hide #!9 models
> select clear
> show #!11 models
> hide #!10 models
> hide #!11 models
> show #!10 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/Resegment-Fixed/Part3/PflABY_out_side-spokes.mrc
> models #10
> close #11
> color #10 #a9a9a94d models
> surface dust #10 size 21.4
> vop gaussian #10 sd 2
Opened PflABY_out_side-spokes.mrc gaussian as #11, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #11 level 0.00115
> color #11 #a9a9a94d models
> combine #8
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #12 inMap #11
Fit molecule combination (#12) to map PflABY_out_side-spokes.mrc gaussian
(#11) using 46611 atoms
average map value = 0.02939, steps = 60
shifted from previous position = 1.24
rotated from previous position = 1.72 degrees
atoms outside contour = 7665, contour level = 0.00115
Position of combination (#12) relative to PflABY_out_side-spokes.mrc gaussian
(#11) coordinates:
Matrix rotation and translation
0.99958992 0.01868787 -0.02169684 1.39946613
-0.01887900 0.99978446 -0.00863789 5.21627993
0.02153074 0.00904396 0.99972728 -6.69400298
Axis 0.29500325 -0.72120711 -0.62676422
Axis point 286.86842756 0.00000000 47.57096221
Rotation angle (degrees) 1.71734906
Shift along axis 0.84639044
> hide #!8 models
> view orient
Drag select of 114 residues
> hide sel cartoons
> select clear
> ui tool show "Map Eraser"
> volume erase #11 center 365.25,312.43,309.2 radius 54.908
> volume erase #11 center 379.53,297.75,271.6 radius 54.908
> view orient
> hide #13 models
> save /Users/shoichi/Desktop/Resegment-Fixed/Part3/Fitting_PflABY-
> JMB_07112025.cxs includeMaps true
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> save /Users/shoichi/Desktop/Fig2-G_07112025.png supersample 2
> transparentBackground true
> color #11 #a9a9a999 models
> save /Users/shoichi/Desktop/Fig2-G_07112025.png supersample 2
> transparentBackground true
> color #11 darkgrey models
> color #11 #929292ff models
> color #11 darkgrey models
> color #11 #919191ff models
> color #11 #91919100 models
> color #11 #91919199 models
> color #11 #91919180 models
> save /Users/shoichi/Desktop/Fig2-G_07112025.png supersample 2
> transparentBackground true
> color #11 silver models
> color #11 darkgrey models
> color #11 silver models
> color #11 darkgrey models
> hide #!11 models
> show #!11 models
> color #11 #929292ff models
> color #11 silver models
> color #11 #c0c0c080 models
> save /Users/shoichi/Desktop/Fig2-G_07112025.png supersample 2
> transparentBackground true
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> set bgColor white
> graphics silhouettes false
> graphics silhouettes true
> set bgColor black
> save /Users/shoichi/Desktop/Fig2-G_07112025.png supersample 2
> transparentBackground true
> ui tool show "Segment Map"
Segmenting PflABY.mrc, density threshold 0.001150
Showing 625 region surfaces
16069 watershed regions, grouped to 625 regions
Showing PflABY.seg - 625 regions, 625 surfaces
> hide #!12 models
> hide #!11 models
> show #!12 models
Drag select of 22931, 296 of 5252 triangles, 22828, 1098 of 4036 triangles,
22857, 3625 of 4104 triangles, 22887, 156 of 3972 triangles, 22885, 202 of
3876 triangles, 22897, 1330 of 3876 triangles, 22947, 882 of 3604 triangles,
22972, 2658 of 3596 triangles, 22790, 1600 of 3652 triangles, 22869, 112 of
3448 triangles, 22881, 927 of 3464 triangles, 22874, 2551 of 3560 triangles,
22763, 792 of 3428 triangles, 22909, 1334 of 3244 triangles, 22039, 2125 of
3168 triangles, 23021, 1998 of 3032 triangles, 22940, 1884 of 2876 triangles,
22823, 1470 of 2860 triangles, 22939, 1917 of 2884 triangles, 22755, 2707 of
2760 triangles, 22945, 2552 of 2568 triangles, 23032, 537 of 2484 triangles,
22787, 1681 of 2532 triangles, 22405, 1437 of 2432 triangles, 22918, 1571 of
2324 triangles, 22845, 980 of 2252 triangles, 22903, 2427 of 2460 triangles,
22760, 1215 of 2276 triangles, 22917, 703 of 2216 triangles, 22212, 88 of 1972
triangles, 22781, 1134 of 2180 triangles, 22772, 1526 of 2032 triangles,
22853, 600 of 2024 triangles, 22911, 776 of 1888 triangles, 22834, 1503 of
1988 triangles, 22839, 1216 of 2048 triangles, 22746, 1121 of 1948 triangles,
22770, 1220 of 1960 triangles, 23042, 1697 of 1840 triangles, 23004, 956 of
1760 triangles, 22352, 390 of 1696 triangles, 22950, 1568 of 1700 triangles,
22865, 1156 of 1612 triangles, 22371, 22809, 1276 of 1656 triangles, 22305,
308 of 1612 triangles, 22404, 1244 of 1596 triangles, 22475, 328 of 1584
triangles, 22377, 259 of 1496 triangles, 22819, 442 of 1540 triangles, 22989,
1113 of 1408 triangles, 22930, 344 of 1308 triangles, 20627, 971 of 1288
triangles, 22756, 661 of 1292 triangles, 22916, 1112 of 1308 triangles, 22143,
22270, 1076 of 1264 triangles, 22987, 1022 of 1148 triangles, 22336, 638 of
1132 triangles, 20155, 748 of 1100 triangles, 22205, 772 of 1120 triangles,
22256, 99 of 916 triangles, 22502, 1047 of 1076 triangles, 22974, 23017,
23013, 359 of 984 triangles, 22831, 703 of 1036 triangles, 22360, 289 of 1048
triangles, 22242, 747 of 1024 triangles, 22139, 916 of 1000 triangles, 22415,
906 of 940 triangles, 22376, 911 of 1008 triangles, 22975, 340 of 952
triangles, 22365, 580 of 1004 triangles, 20287, 458 of 876 triangles, 20407,
135 of 944 triangles, 22421, 892 of 896 triangles, 22012, 22076, 796 of 800
triangles, 22148, 582 of 784 triangles, 22497, 625 of 804 triangles, 23025,
671 of 752 triangles, 22299, 648 of 740 triangles, 22574, 646 of 716
triangles, 22264, 348 of 772 triangles, 22899, 688 of 788 triangles, 22866, 48
of 692 triangles, 22797, 76 of 720 triangles, 22358, 499 of 696 triangles,
22355, 544 of 604 triangles, 22604, 22921, 120 of 600 triangles, 22610, 344 of
572 triangles, 22821, 163 of 540 triangles, 20518, 92 of 516 triangles, 22380,
370 of 556 triangles, 22973, 103 of 508 triangles, 22952, 22936, 225 of 488
triangles, 22924, 20128, 424 of 576 triangles, 22554, 180 of 492 triangles,
22023, 452 of 500 triangles, 22926, 276 of 476 triangles, 22927, 285 of 468
triangles, 22583, 21088, 20775, 220 of 376 triangles, 22111, 242 of 412
triangles, 22598, 21569, 22370, 240 of 356 triangles, 22925, 272 of 412
triangles, 21820, 19 of 376 triangles, 22985, 188 of 304 triangles, 21382,
21319, 274 of 288 triangles, 22684, 212 of 268 triangles, 21463, 21143, 95 of
252 triangles, 22115, 22696, 246 of 296 triangles, 22695, 48 of 328 triangles,
22935, 22817, 66 of 332 triangles, 22996, 45 of 236 triangles, 21330, 214 of
244 triangles, 21060, 21576, 22764, 208 of 264 triangles, 22420, 48 of 196
triangles, 21426, 97 of 232 triangles, 21436, 22901, 21975, 17035, 21368,
22089, 145 of 184 triangles, 21412, 95 of 124 triangles, 17425, 22533, 21670,
48 of 76 triangles, 15290, 17 of 56 triangles, 15088, 15175, 15135
Drag select of 23038, 20 of 20192 triangles, 23006, 21 of 18912 triangles,
22934, 12 of 21656 triangles, 22812, 38 of 21436 triangles, 22961, 158 of 7316
triangles, 22806, 8877 of 9572 triangles, 22908, 8245 of 9216 triangles,
22784, 4842 of 7612 triangles, 22846, 7261 of 7484 triangles, 22943, 4668 of
7512 triangles, 22894, 22833, 22915, 366 of 6596 triangles, 22877, 6105 of
6376 triangles, 22829, 22872, 22959, 4517 of 5836 triangles, 22835, 4188 of
5540 triangles, 22814, 3687 of 5408 triangles, 22758, 4653 of 4688 triangles,
22822, 22991, 4103 of 4336 triangles, 22795, 3948 of 4336 triangles, 22788,
397 of 4320 triangles, 22937, 22780, 22847, 256 of 3688 triangles, 22762,
22993, 22967, 3476 of 3484 triangles, 22802, 22838, 2558 of 3252 triangles,
22963, 22929, 1730 of 2932 triangles, 22761, 22891, 1835 of 3080 triangles,
22855, 22941, 2580 of 2832 triangles, 22836, 2281 of 2808 triangles, 22849,
1924 of 2748 triangles, 22882, 22954, 440 of 2752 triangles, 22786, 23030,
22852, 2428 of 2544 triangles, 23033, 22902, 22907, 22867, 22914, 1800 of 2264
triangles, 22906, 2083 of 2324 triangles, 22369, 1988 of 2184 triangles,
22810, 180 of 2268 triangles, 22913, 22444, 1899 of 2180 triangles, 22752,
1968 of 2116 triangles, 23028, 22759, 1962 of 2196 triangles, 23029, 22785,
22463, 1476 of 2080 triangles, 22841, 1698 of 2060 triangles, 22944, 22745,
1832 of 2148 triangles, 22896, 23007, 22870, 22843, 23041, 21998, 22830,
22783, 22983, 1109 of 1956 triangles, 22850, 22791, 22765, 252 of 1808
triangles, 22803, 223 of 1776 triangles, 22933, 1329 of 1720 triangles, 22152,
23024, 1588 of 1820 triangles, 22864, 22988, 22103, 22769, 22227, 22507, 1462
of 1688 triangles, 22808, 23022, 22271, 22000, 1256 of 1696 triangles, 22171,
22949, 22966, 22425, 95 of 1696 triangles, 22964, 22757, 1360 of 1652
triangles, 22285, 496 of 1588 triangles, 22825, 22969, 1241 of 1432 triangles,
22960, 22311, 988 of 1480 triangles, 22922, 23011, 22811, 157 of 1348
triangles, 22863, 22488, 22096, 22072, 1136 of 1308 triangles, 22416, 952 of
1196 triangles, 22851, 1030 of 1240 triangles, 22873, 22799, 823 of 1248
triangles, 22515, 22505, 22958, 1197 of 1228 triangles, 22805, 22842, 22773,
1043 of 1232 triangles, 22801, 22768, 684 of 1228 triangles, 22951, 22920,
22409, 22858, 592 of 1176 triangles, 22861, 22314, 982 of 1104 triangles,
22986, 22198, 22304, 28 of 1064 triangles, 22910, 22704, 22820, 23003, 22879,
22876, 22138, 22383, 22538, 22968, 22957, 22982, 22815, 22826, 22439, 423 of
944 triangles, 22257, 764 of 948 triangles, 23026, 22300, 48 of 956 triangles,
22321, 354 of 972 triangles, 22743, 23009, 22144, 22250, 904 of 932 triangles,
22021, 22419, 273 of 836 triangles, 22888, 22994, 834 of 848 triangles, 22942,
22268, 22307, 712 of 828 triangles, 22793, 467 of 748 triangles, 22450, 22890,
781 of 872 triangles, 23018, 22002, 22932, 668 of 788 triangles, 22688, 22776,
22429, 796 of 804 triangles, 22003, 20263, 552 of 760 triangles, 22748, 22411,
23016, 22273, 22775, 22127, 20222, 22749, 68 of 740 triangles, 22424, 605 of
624 triangles, 22619, 180 of 720 triangles, 22434, 22729, 22946, 48 of 640
triangles, 22251, 22117, 22522, 20800, 22473, 22576, 22234, 22551, 22566, 120
of 628 triangles, 22750, 21914, 472 of 544 triangles, 22390, 22953, 22807, 216
of 548 triangles, 22816, 23002, 23037, 440 of 488 triangles, 22612, 22129,
21565, 22904, 306 of 532 triangles, 22970, 23034, 22159, 22151, 22905, 22327,
482 of 500 triangles, 22995, 23040, 22550, 372 of 408 triangles, 22248, 420 of
440 triangles, 22086, 362 of 388 triangles, 22731, 22656, 22854, 22580, 20974,
198 of 392 triangles, 22052, 20787, 112 of 472 triangles, 22716, 22343, 22840,
21273, 23000, 184 of 372 triangles, 22319, 22584, 22796, 22255, 22073, 22406,
23023, 22616, 21502, 21399, 21819, 23039, 20689, 22771, 22223, 22782, 21009,
22956, 17931, 16276, 20549, 21634, 22014, 185 of 264 triangles, 22504, 22309,
22132, 16560, 20836, 104 of 232 triangles, 22333, 22978, 18469, 21490, 16479,
22252, 156 of 204 triangles, 21408, 20722, 21700, 19727, 76 of 144 triangles,
19683, 21458, 16311, 21015, 16950, 16925, 20934, 20131, 21259, 19372, 22125,
19687, 99 of 100 triangles, 20208, 121, 4185, 1281, 3041, 3467, 3834
> select clear
Showing 625 region surfaces
Drag select of 22931, 609 of 5252 triangles, 22828, 1644 of 4036 triangles,
22857, 2664 of 4104 triangles, 22887, 110 of 3972 triangles, 22885, 389 of
3876 triangles, 22897, 266 of 3876 triangles, 22947, 1109 of 3604 triangles,
22895, 30 of 3696 triangles, 22972, 1881 of 3596 triangles, 22790, 2029 of
3652 triangles, 22881, 431 of 3464 triangles, 22874, 1745 of 3560 triangles,
22763, 642 of 3428 triangles, 22909, 1140 of 3244 triangles, 22039, 2024 of
3168 triangles, 23021, 1907 of 3032 triangles, 22940, 1821 of 2876 triangles,
22976, 351 of 2916 triangles, 22823, 298 of 2860 triangles, 22939, 222 of 2884
triangles, 22755, 624 of 2760 triangles, 22945, 1106 of 2568 triangles, 23032,
1032 of 2484 triangles, 22787, 1488 of 2532 triangles, 22405, 1722 of 2432
triangles, 22918, 1590 of 2324 triangles, 22845, 620 of 2252 triangles, 22903,
951 of 2460 triangles, 22760, 1097 of 2276 triangles, 22917, 667 of 2216
triangles, 22781, 435 of 2180 triangles, 22772, 188 of 2032 triangles, 22853,
744 of 2024 triangles, 22911, 297 of 1888 triangles, 22834, 1754 of 1988
triangles, 22839, 344 of 2048 triangles, 22746, 388 of 1948 triangles, 22770,
1110 of 1960 triangles, 23042, 1168 of 1840 triangles, 23004, 919 of 1760
triangles, 22352, 511 of 1696 triangles, 22950, 1229 of 1700 triangles, 22865,
772 of 1612 triangles, 22371, 1216 of 1652 triangles, 22809, 957 of 1656
triangles, 22305, 45 of 1612 triangles, 22404, 801 of 1596 triangles, 22475,
960 of 1584 triangles, 22377, 290 of 1496 triangles, 22819, 60 of 1540
triangles, 22989, 472 of 1408 triangles, 22060, 37 of 1388 triangles, 22930,
408 of 1308 triangles, 20627, 899 of 1288 triangles, 22981, 433 of 1364
triangles, 22756, 44 of 1292 triangles, 22916, 658 of 1308 triangles, 22143,
1120 of 1356 triangles, 22270, 772 of 1264 triangles, 22987, 148 of 1148
triangles, 22336, 1056 of 1132 triangles, 20155, 284 of 1100 triangles, 22205,
744 of 1120 triangles, 22256, 228 of 916 triangles, 22502, 248 of 1076
triangles, 23013, 92 of 984 triangles, 22360, 186 of 1048 triangles, 22139,
990 of 1000 triangles, 22415, 542 of 940 triangles, 22365, 104 of 1004
triangles, 20407, 281 of 944 triangles, 22421, 22012, 768 of 920 triangles,
22076, 449 of 800 triangles, 22148, 128 of 784 triangles, 22497, 268 of 804
triangles, 23025, 669 of 752 triangles, 22299, 566 of 740 triangles, 22574,
22264, 445 of 772 triangles, 22797, 45 of 720 triangles, 22358, 652 of 696
triangles, 22604, 398 of 612 triangles, 22921, 168 of 600 triangles, 22821, 88
of 540 triangles, 20518, 176 of 516 triangles, 22380, 357 of 556 triangles,
20128, 426 of 576 triangles, 22927, 348 of 468 triangles, 22583, 122 of 412
triangles, 21569, 43 of 360 triangles, 22925, 136 of 412 triangles, 23010, 9
of 324 triangles, 21382, 231 of 368 triangles, 21319, 240 of 288 triangles,
22115, 148 of 288 triangles, 22696, 248 of 296 triangles, 22935, 49 of 244
triangles, 21576, 100 of 280 triangles, 22764, 84 of 264 triangles, 21436,
21368, 22089, 17425, 73 of 136 triangles, 22533
> select clear
> select #9.20
1 model selected
> select add #9.17
2 models selected
> select add #9.12
3 models selected
> select add #9.5
4 models selected
> select add #9.14
5 models selected
> select add #9.27
6 models selected
> select add #9.30
7 models selected
> select add #9.4
8 models selected
> select add #9.24
9 models selected
Grouped 9 regions
> select #9.1
1 model selected
Grouped 1 regions
Showing 617 region surfaces
> select #9.1
1 model selected
> select add #9.4
2 models selected
Grouped 2 regions
Opened PflABY_imasked as #13, grid size 200,200,200, pixel 2.14, shown at step
1, values float32
Segmenting PflABY_imasked, density threshold 0.001150
Showing 11 region surfaces
506 watershed regions, grouped to 11 regions
Showing PflABY_imasked.seg - 11 regions, 11 surfaces
> hide #!12 models
> show #!8 models
> hide #8.1 models
> hide #8.2 models
> hide #8.3 models
> hide #8.4 models
> hide #8.5 models
> hide #8.6 models
> hide #8.7 models
> show #8.7 models
> hide #8.7 models
> hide #!8.8 models
> hide #!8.9 models
> hide #8.16 models
> show #8.16 models
> hide #8.15 models
> hide #8.14 models
> select #9.7
1 model selected
> select add #9.6
2 models selected
> select add #9.4
3 models selected
> hide #!13 models
> select add #9.3
4 models selected
Grouped 4 regions
> select clear
> select #9.3
1 model selected
> select #9.9
1 model selected
Ungrouped to 2 regions
Ungrouped to 4 regions
Ungrouped to 9 regions
Ungrouped to 15 regions
Ungrouped to 0 regions
> select #9.12
1 model selected
> select #9.12
1 model selected
> select add #9.32
2 models selected
> select clear
> select #9.12
1 model selected
> select add #9.32
2 models selected
> select add #9.27
3 models selected
> select add #9.24
4 models selected
> select add #9.17
5 models selected
> select add #9.4
6 models selected
> select add #9.26
7 models selected
> select add #9.10
8 models selected
Grouped 8 regions
Showing 24 region surfaces
> select add #9.3
2 models selected
Grouped 2 regions
> select #9.2
1 model selected
Ungrouped to 2 regions
Ungrouped to 21 regions
Ungrouped to 43 regions
Ungrouped to 16 regions
Ungrouped to 0 regions
> select #9.70
1 model selected
> select add #9.4
2 models selected
> select #9.70
1 model selected
> select #9.4
1 model selected
> select add #9.70
2 models selected
Grouped 2 regions
> select add #9.16
2 models selected
> select add #9.63
3 models selected
> select add #9.40
4 models selected
> select add #9.26
5 models selected
> select add #9.42
6 models selected
> select add #9.67
7 models selected
> select add #9.66
8 models selected
> select subtract #9.67
7 models selected
Grouped 7 regions
> select clear
> select #9.67
1 model selected
> show #!13 models
> hide #!13 models
> show #!12 models
> hide #!12 models
> select #9.67
1 model selected
> select add #9.4
2 models selected
> select add #9.60
3 models selected
> select add #9.62
4 models selected
> select subtract #9.62
3 models selected
> select add #9.62
4 models selected
> select add #9.41
5 models selected
Grouped 5 regions
Showing 73 region surfaces
> select add #9.3
2 models selected
Grouped 2 regions
> select clear
> select #9.3
1 model selected
> select clear
> select #9.27
1 model selected
> select add #9.14
2 models selected
> select #9.14
1 model selected
> select add #9.24
2 models selected
> select add #9.86
3 models selected
Grouped 3 regions
> select add #9.85
2 models selected
> select add #9.17
3 models selected
> select add #9.88
4 models selected
> select subtract #9.4
3 models selected
> select clear
> select #9.4
1 model selected
> select add #9.17
2 models selected
> select add #9.85
3 models selected
Grouped 3 regions
> select add #9.59
2 models selected
Grouped 2 regions
> select add #9.88
2 models selected
Grouped 2 regions
Showing 66 region surfaces
> select add #9.3
2 models selected
Grouped 2 regions
> select clear
> select #9.5
1 model selected
Grouped 1 regions
> select add #9.3
2 models selected
Grouped 2 regions
> select clear
> select #9.1
1 model selected
> select add #9.8
2 models selected
Ungrouped to 6 regions
Ungrouped to 16 regions
Ungrouped to 50 regions
Ungrouped to 77 regions
Ungrouped to 0 regions
> select add #9.46
1 model selected
> select add #9.193
2 models selected
> select add #9.195
3 models selected
> select #9.46
1 model selected
> select #9.193
1 model selected
> select add #9.46
2 models selected
> select add #9.195
3 models selected
> select add #9.14
4 models selected
Grouped 4 regions
Showing 171 region surfaces
> select add #9.3
2 models selected
Grouped 2 regions
> select #9.162
1 model selected
> select add #9.150
2 models selected
> select clear
> select #9.68
1 model selected
> select add #9.24
2 models selected
> select add #9.88
3 models selected
> select add #9.157
4 models selected
> select add #9.62
5 models selected
> select subtract #9.62
4 models selected
Grouped 4 regions
Showing 167 region surfaces
> select add #9.3
2 models selected
Grouped 2 regions
> select clear
> select #9.162
1 model selected
> select add #9.150
2 models selected
Grouped 2 regions
> select #9.149
1 model selected
> select add #9.143
2 models selected
> select add #9.166
3 models selected
> select add #9.66
4 models selected
> select add #9.60
5 models selected
> select add #9.5
6 models selected
Grouped 6 regions
> select add #9.160
2 models selected
> select #9.160
1 model selected
> select add #9.3
2 models selected
Grouped 2 regions
> select clear
> select #9.62
1 model selected
> select add #9.3
2 models selected
Grouped 2 regions
> select #9.144
1 model selected
> select add #9.3
2 models selected
Grouped 2 regions
> select add #9.40
2 models selected
Grouped 2 regions
> select #9.182
1 model selected
> select add #9.178
2 models selected
> select add #9.110
3 models selected
> select add #9.3
4 models selected
Grouped 4 regions
> select #9.104
1 model selected
> select add #9.103
2 models selected
> select add #9.106
3 models selected
> select add #9.5
4 models selected
Grouped 4 regions
> select add #9.146
2 models selected
> select add #9.147
3 models selected
> select add #9.145
4 models selected
> select add #9.105
5 models selected
> select add #9.67
6 models selected
> select add #9.127
7 models selected
> select add #9.125
8 models selected
> select add #9.102
9 models selected
> select subtract #9.102
8 models selected
> select add #9.142
9 models selected
> select add #9.102
10 models selected
> select add #9.3
11 models selected
> select subtract #9.3
10 models selected
> select add #9.100
11 models selected
> select subtract #9.100
10 models selected
> select subtract #9.102
9 models selected
Grouped 9 regions
> select #9.102
1 model selected
> select add #9.100
2 models selected
> select clear
> select #9.3
1 model selected
> select add #9.141
2 models selected
> select add #9.192
3 models selected
> select add #9.102
4 models selected
> select add #9.48
5 models selected
> select add #9.47
6 models selected
Grouped 6 regions
> select add #9.100
2 models selected
Grouped 2 regions
Showing 136 region surfaces
> select #9.27
1 model selected
> select add #9.77
2 models selected
> select add #9.5
3 models selected
Grouped 3 regions
> select clear
Showing 134 region surfaces
> select #9.3
1 model selected
Opened PflABY_imasked_imasked as #14, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/Resegment-Fixed/Part3/Single-Spoke-ring.mrc
> models #14
> select add #9
135 models selected
> select subtract #9
Nothing selected
> hide #!9 models
> show #!11 models
> hide #!11 models
> close #9-10
> close #13
> vop gaussian #14 sd 2
Opened Single-Spoke-ring.mrc gaussian as #9, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> surface dust #9 size 50
> show #!11 models
> hide #!11 models
> color #9 #c0c0c080 models
> select add #8.10
1192 atoms, 1218 bonds, 149 residues, 1 model selected
> select add #8.11
6295 atoms, 6414 bonds, 1 pseudobond, 782 residues, 3 models selected
> select add #8.12
7487 atoms, 7632 bonds, 1 pseudobond, 931 residues, 4 models selected
> select add #8.13
12590 atoms, 12828 bonds, 2 pseudobonds, 1564 residues, 6 models selected
> select add #8.16
17661 atoms, 17984 bonds, 2 pseudobonds, 2185 residues, 7 models selected
> select add #8.6
18896 atoms, 19225 bonds, 2 pseudobonds, 2340 residues, 8 models selected
> select subtract #8.6
17661 atoms, 17984 bonds, 2 pseudobonds, 2185 residues, 7 models selected
> show #8.6 models
> show #8.5 models
> select subtract #8.10
16469 atoms, 16766 bonds, 2 pseudobonds, 2036 residues, 6 models selected
> select subtract #8.11
11366 atoms, 11570 bonds, 1 pseudobond, 1403 residues, 4 models selected
> select subtract #8.12
10174 atoms, 10352 bonds, 1 pseudobond, 1254 residues, 3 models selected
> select subtract #8.13
5071 atoms, 5156 bonds, 621 residues, 1 model selected
> select subtract #8.16
Nothing selected
Drag select of 155 residues, 9 Single-Spoke-ring.mrc gaussian
> select subtract #9
1186 atoms, 155 residues, 2 models selected
> select add #8.6/BY:79
1194 atoms, 7 bonds, 156 residues, 2 models selected
> select add #8.6/BY:78
1203 atoms, 15 bonds, 157 residues, 2 models selected
> select add #8.6/BY:77
1212 atoms, 23 bonds, 158 residues, 2 models selected
> select add #8.6/BY:76
1221 atoms, 31 bonds, 159 residues, 2 models selected
> select add #8.5/BX:76
1230 atoms, 39 bonds, 160 residues, 2 models selected
> select add #8.5/BX:75
1239 atoms, 47 bonds, 161 residues, 2 models selected
> hide sel cartoons
> view orient
> hide #!9 models
> select add #8.6
1859 atoms, 1257 bonds, 236 residues, 2 models selected
> select subtract #8.6
624 atoms, 16 bonds, 81 residues, 1 model selected
> select add #8.5
1235 atoms, 1241 bonds, 155 residues, 1 model selected
> select subtract #8.5
Nothing selected
Drag select of 2334 residues, 2 pseudobonds
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/Resegment-Fixed/Part3/For-
> Support_figures/Single-unit_Spokes-ring.pdb selectedOnly true
> open /Users/shoichi/Desktop/Resegment-Fixed/Part3/For-
> Support_figures/Single-unit_Spokes-ring.pdb
Chain information for Single-unit_Spokes-ring.pdb
---
Chain | Description
10.1/BX | No description available
10.2/BY | No description available
10.3/j 10.5/l | No description available
10.4/k 10.6/m | No description available
10.7/s | No description available
> select clear
> hide #!8 models
> hide #10.1 models
> show #10.1 models
> show #8.1 models
> hide #8.1 models
> show #8.2 models
> show #8.1 models
> show #8.7 models
> select add #8.7
1192 atoms, 1218 bonds, 149 residues, 1 model selected
> select subtract #8.7
Nothing selected
> select add #8.6
1235 atoms, 1241 bonds, 155 residues, 1 model selected
> select add #8.5
2470 atoms, 2482 bonds, 310 residues, 2 models selected
> show sel cartoons
> select clear
> select add #10.1
611 atoms, 615 bonds, 74 residues, 1 model selected
> color sel orchid
> select subtract #10.1
Nothing selected
> select add #10.2
620 atoms, 624 bonds, 75 residues, 1 model selected
> color sel #e9cdeaff
> select clear
> hide #8.1 models
> hide #8.2 models
> show #8.1 models
> show #8.2 models
> show #8.3 models
> show #8.4 models
> show #!8.8 models
> show #!8.9 models
> show #8.14 models
> show #8.15 models
> hide #!8 models
> hide #10.3 models
> show #10.3 models
> hide #10.3 models
> show #10.3 models
> select add #10.3
1192 atoms, 1218 bonds, 149 residues, 1 model selected
> hide #!10.4 models
> show #!10.4 models
> hide #10.5 models
> show #10.5 models
> select add #10.5
2384 atoms, 2436 bonds, 298 residues, 2 models selected
> hide #!10.6 models
> show #!10.6 models
> hide #10.7 models
> show #10.7 models
> select add #10.7
7455 atoms, 7592 bonds, 919 residues, 3 models selected
> color sel #ca4949ff models
> select clear
> select add #10.4
5103 atoms, 5196 bonds, 1 pseudobond, 633 residues, 2 models selected
> select add #10.6
10206 atoms, 10392 bonds, 2 pseudobonds, 1266 residues, 4 models selected
> color sel magenta models
> select clear
> combine 10
Expected a keyword
> combine #10
> hide #!10 models
> hide #!13 models
> show #!13 models
> show #!9 models
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #13 inMap #9
Fit molecule combination (#13) to map Single-Spoke-ring.mrc gaussian (#9)
using 18892 atoms
average map value = 0.0339, steps = 60
shifted from previous position = 1.78
rotated from previous position = 1.69 degrees
atoms outside contour = 1156, contour level = 0.0003869
Position of combination (#13) relative to Single-Spoke-ring.mrc gaussian (#9)
coordinates:
Matrix rotation and translation
0.99956660 0.01511691 -0.02526044 3.09823887
-0.01511434 0.99988573 0.00029272 2.17927743
0.02526197 0.00008920 0.99968086 -5.77931779
Axis -0.00345672 -0.85810305 -0.51346588
Axis point 208.19316381 0.00000000 119.22852819
Rotation angle (degrees) 1.68694142
Shift along axis 1.08672813
> fitmap #13 inMap #9
Fit molecule combination (#13) to map Single-Spoke-ring.mrc gaussian (#9)
using 18892 atoms
average map value = 0.0339, steps = 44
shifted from previous position = 0.00686
rotated from previous position = 0.0119 degrees
atoms outside contour = 1154, contour level = 0.0003869
Position of combination (#13) relative to Single-Spoke-ring.mrc gaussian (#9)
coordinates:
Matrix rotation and translation
0.99956331 0.01532254 -0.02526676 3.05663171
-0.01531905 0.99988260 0.00033191 2.21688085
0.02526888 0.00005530 0.99968069 -5.77385238
Axis -0.00468041 -0.85508399 -0.51846839
Axis point 207.74836454 0.00000000 117.58460531
Rotation angle (degrees) 1.69334263
Shift along axis 1.08363436
Opened combination map 5 as #15, grid size 173,162,66, pixel 1.67, shown at
level 0.0975, step 1, values float32
> fitmap #13 inMap #9 resolution 5 metric correlation
Fit map combination map 5 in map Single-Spoke-ring.mrc gaussian using 71823
points
correlation = 0.7843, correlation about mean = 0.1189, overlap = 868.8
steps = 48, shift = 0.288, angle = 0.168 degrees
Position of combination map 5 (#15) relative to Single-Spoke-ring.mrc gaussian
(#9) coordinates:
Matrix rotation and translation
0.99961902 0.01382237 -0.02389061 2.89655351
-0.01376884 0.99990232 0.00240390 1.26702597
0.02392150 -0.00207404 0.99971169 -4.75618228
Axis -0.08085330 -0.86329261 -0.49818533
Axis point 178.60491525 0.00000000 121.91874732
Rotation angle (degrees) 1.58682134
Shift along axis 1.04145014
Average map value = 0.03389 for 18892 atoms, 1131 outside contour
> hide #!9 models
> show #!15 models
> hide #!15 models
> show #!9 models
> close #15
Opened combination map 10 as #15, grid size 96,90,42, pixel 3.33, shown at
level 0.0635, step 1, values float32
> fitmap #13 inMap #9 resolution 10 metric correlation
Fit map combination map 10 in map Single-Spoke-ring.mrc gaussian using 12829
points
correlation = 0.8633, correlation about mean = 0.5048, overlap = 106.4
steps = 60, shift = 0.0929, angle = 0.175 degrees
Position of combination map 10 (#15) relative to Single-Spoke-ring.mrc
gaussian (#9) coordinates:
Matrix rotation and translation
0.99967548 0.01451755 -0.02093243 2.06394488
-0.01446526 0.99989187 0.00264722 1.42614829
0.02096860 -0.00234357 0.99977739 -4.01679677
Axis -0.09749199 -0.81850955 -0.56616025
Axis point 168.17434649 0.00000000 100.21099695
Rotation angle (degrees) 1.46669925
Shift along axis 0.90561658
Average map value = 0.03388 for 18892 atoms, 1151 outside contour
> show #!15 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!15 models
> show #!9 models
> save /Users/shoichi/Desktop/SupFigXa_07112025.png supersample 2
> transparentBackground true
> save /Users/shoichi/Desktop/Resegment-Fixed/Part3/Fitting_PflABY-
> JMB_07112025.cxs includeMaps true
> turn x 90
> turn x -90
[Repeated 1 time(s)]
> turn x 90
> turn x -30
> turn x 30
> turn x 60
> turn x -60
[Repeated 1 time(s)]
> turn x 60
> turn x -45
> show #!1 models
> hide #!1 models
> save /Users/shoichi/Desktop/Resegment-Fixed/Part3/Fitting_PflABY-
> JMB_07112025.cxs includeMaps true
——— End of log from Fri Jul 11 12:46:52 2025 ———
opened ChimeraX session
> show #!14 models
> hide #!14 models
> show #!12 models
> hide #!13 models
> hide #!12 models
> show #!12 models
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-Chimera-PflAB/Resegment/Resegment-Fixed/MS-ring.mrc"
Opened MS-ring.mrc as #16, grid size 200,200,200, pixel 2.14, shown at level
0.00124, step 1, values float32
> hide #!16 models
> show #!16 models
> hide #!9 models
> show #!9 models
> show #!7 models
> hide #!7 models
> show #!11 models
> volume gaussian #16 sDev 2
Opened MS-ring.mrc gaussian as #17, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> close #17
> volume gaussian #16 sDev 4
Opened MS-ring.mrc gaussian as #17, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> close #17
> volume gaussian #16 sDev 3
Opened MS-ring.mrc gaussian as #17, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> color #17 #c0c0c080 models
> view orient
> save /Users/shoichi/Desktop/3XFlgY_PflAB_07112025.png supersample 2
> transparentBackground true
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> surface dust #11 size 21.4
> surface dust #17 size 21.4
> save /Users/shoichi/Desktop/3XFlgY_PflAB_07112025.png supersample 2
> transparentBackground true
> hide #!11 models
> hide #!12 models
> show #!12 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> combine #12
> hide #!12 models
> split #18
Split copy of combination (#18) into 16 models
Chain information for copy of combination BN #18.1
---
Chain | Description
BN | No description available
Chain information for copy of combination BO #18.2
---
Chain | Description
BO | No description available
Chain information for copy of combination BV #18.3
---
Chain | Description
BV | No description available
Chain information for copy of combination BW #18.4
---
Chain | Description
BW | No description available
Chain information for copy of combination BX #18.5
---
Chain | Description
BX | No description available
Chain information for copy of combination BY #18.6
---
Chain | Description
BY | No description available
Chain information for copy of combination d #18.7
---
Chain | Description
d | No description available
Chain information for copy of combination e #18.8
---
Chain | Description
e | No description available
Chain information for copy of combination i #18.9
---
Chain | Description
i | No description available
Chain information for copy of combination j #18.10
---
Chain | Description
j | No description available
Chain information for copy of combination k #18.11
---
Chain | Description
k | No description available
Chain information for copy of combination l #18.12
---
Chain | Description
l | No description available
Chain information for copy of combination m #18.13
---
Chain | Description
m | No description available
Chain information for copy of combination n #18.14
---
Chain | Description
n | No description available
Chain information for copy of combination r #18.15
---
Chain | Description
r | No description available
Chain information for copy of combination s #18.16
---
Chain | Description
s | No description available
> hide #!17 models
> show #!9 models
> hide #18.1 models
> hide #18.2 models
> hide #18.3 models
> hide #18.4 models
> hide #18.7 models
> hide #!18.8 models
> hide #!18.9 models
> show #!18.9 models
> hide #!18.9 models
> hide #18.10 models
> show #18.10 models
> hide #18.12 models
> show #18.12 models
> hide #18.14 models
> hide #18.15 models
Drag select of 153 residues
> hide sel cartoons
> select #18.6/BY:73
7 atoms, 6 bonds, 1 residue, 1 model selected
> select subtract #18.6/BY:73
Nothing selected
> select add #18.6/BY:74
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #18.6/BY:76
18 atoms, 16 bonds, 2 residues, 1 model selected
> select add #18.6/BY:77
27 atoms, 24 bonds, 3 residues, 1 model selected
> select add #18.6/BY:78
36 atoms, 32 bonds, 4 residues, 1 model selected
> select add #18.6/BY:80
44 atoms, 39 bonds, 5 residues, 1 model selected
> select add #18.6/BY:79
52 atoms, 46 bonds, 6 residues, 1 model selected
> select add #18.6/BY:81
60 atoms, 53 bonds, 7 residues, 1 model selected
> select add #18.5/BX:75
69 atoms, 61 bonds, 8 residues, 2 models selected
> select add #18.6/BY:75
78 atoms, 69 bonds, 9 residues, 2 models selected
> select add #18.5/BX:76
87 atoms, 77 bonds, 10 residues, 2 models selected
> select add #18.5/BX:74
96 atoms, 85 bonds, 11 residues, 2 models selected
> select add #18.5/BX:73
103 atoms, 91 bonds, 12 residues, 2 models selected
> select add #18.5/BX:72
111 atoms, 98 bonds, 13 residues, 2 models selected
> hide sel cartoons
> view orient
> select up
1592 atoms, 1602 bonds, 192 residues, 2 models selected
> select up
2470 atoms, 2482 bonds, 310 residues, 2 models selected
> select down
1592 atoms, 1602 bonds, 192 residues, 2 models selected
> select down
111 atoms, 98 bonds, 13 residues, 2 models selected
> undo
[Repeated 3 time(s)]
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> save /Users/shoichi/Desktop/1XFlgY_PflAB_07112025.png supersample 2
> transparentBackground true
> hide #!18 models
> select add #18
46611 atoms, 47352 bonds, 4 pseudobonds, 5772 residues, 21 models selected
> hide #!9 models
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-Chimera-PflAB/Resegment/Part1/PflC.mrc"
Opened PflC.mrc as #19, grid size 200,200,200, pixel 2.14, shown at level
0.0306, step 1, values float32
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-Chimera-PflAB/Resegment/Part1/PflD.mrc"
Opened PflD.mrc as #20, grid size 200,200,200, pixel 2.14, shown at level
0.00101, step 1, values float32
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-Chimera-PflAB/Resegment/Part3/Cages2.mrc"
Opened Cages2.mrc as #21, grid size 200,200,200, pixel 2.14, shown at level
0.00248, step 1, values float32
> volume #21 level 0.001871
> volume #19 level 0.007524
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-Chimera-PflAB/Rev-CJFlgYPlfAB-msk-2.1A.mrc"
Opened Rev-CJFlgYPlfAB-msk-2.1A.mrc as #22, grid size 200,200,200, pixel 2.14,
shown at level 0.047, step 1, values float32
> volume #22 level 0.00187
> hide #!22 models
> select subtract #18
Nothing selected
> show #!11 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #5.63 models
> hide #5.63 models
> show #5.63 models
> hide #5.63 models
> show #5.146 models
> hide #5.146 models
> hide #!19 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> hide #!21 models
> show #5.149 models
> hide #5.149 models
> show #5.146 models
> hide #5.146 models
> show #5.39 models
> hide #5.39 models
> show #5.2 models
> hide #5.2 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> combine #3
> hide #!5 models
> split #23
Split copy of combination (#23) into 149 models
Chain information for copy of combination 0 #23.1
---
Chain | Description
0 | No description available
Chain information for copy of combination 1 #23.2
---
Chain | Description
1 | No description available
Chain information for copy of combination 2 #23.3
---
Chain | Description
2 | No description available
Chain information for copy of combination 3 #23.4
---
Chain | Description
3 | No description available
Chain information for copy of combination 4 #23.5
---
Chain | Description
4 | No description available
Chain information for copy of combination 5 #23.6
---
Chain | Description
5 | No description available
Chain information for copy of combination 6 #23.7
---
Chain | Description
6 | No description available
Chain information for copy of combination 7 #23.8
---
Chain | Description
7 | No description available
Chain information for copy of combination 8 #23.9
---
Chain | Description
8 | No description available
Chain information for copy of combination 9 #23.10
---
Chain | Description
9 | No description available
Chain information for copy of combination A #23.11
---
Chain | Description
A | No description available
Chain information for copy of combination A0 #23.12
---
Chain | Description
A0 | No description available
Chain information for copy of combination A1 #23.13
---
Chain | Description
A1 | No description available
Chain information for copy of combination A2 #23.14
---
Chain | Description
A2 | No description available
Chain information for copy of combination A3 #23.15
---
Chain | Description
A3 | No description available
Chain information for copy of combination A4 #23.16
---
Chain | Description
A4 | No description available
Chain information for copy of combination A5 #23.17
---
Chain | Description
A5 | No description available
Chain information for copy of combination A6 #23.18
---
Chain | Description
A6 | No description available
Chain information for copy of combination A7 #23.19
---
Chain | Description
A7 | No description available
Chain information for copy of combination A8 #23.20
---
Chain | Description
A8 | No description available
Chain information for copy of combination A9 #23.21
---
Chain | Description
A9 | No description available
Chain information for copy of combination AA #23.22
---
Chain | Description
AA | No description available
Chain information for copy of combination AB #23.23
---
Chain | Description
AB | No description available
Chain information for copy of combination AC #23.24
---
Chain | Description
AC | No description available
Chain information for copy of combination AD #23.25
---
Chain | Description
AD | No description available
Chain information for copy of combination AE #23.26
---
Chain | Description
AE | No description available
Chain information for copy of combination AF #23.27
---
Chain | Description
AF | No description available
Chain information for copy of combination AG #23.28
---
Chain | Description
AG | No description available
Chain information for copy of combination AH #23.29
---
Chain | Description
AH | No description available
Chain information for copy of combination AI #23.30
---
Chain | Description
AI | No description available
Chain information for copy of combination AJ #23.31
---
Chain | Description
AJ | No description available
Chain information for copy of combination AK #23.32
---
Chain | Description
AK | No description available
Chain information for copy of combination AL #23.33
---
Chain | Description
AL | No description available
Chain information for copy of combination AM #23.34
---
Chain | Description
AM | No description available
Chain information for copy of combination AN #23.35
---
Chain | Description
AN | No description available
Chain information for copy of combination AO #23.36
---
Chain | Description
AO | No description available
Chain information for copy of combination AP #23.37
---
Chain | Description
AP | No description available
Chain information for copy of combination AQ #23.38
---
Chain | Description
AQ | No description available
Chain information for copy of combination AR #23.39
---
Chain | Description
AR | No description available
Chain information for copy of combination AS #23.40
---
Chain | Description
AS | No description available
Chain information for copy of combination AT #23.41
---
Chain | Description
AT | No description available
Chain information for copy of combination AU #23.42
---
Chain | Description
AU | No description available
Chain information for copy of combination AV #23.43
---
Chain | Description
AV | No description available
Chain information for copy of combination AW #23.44
---
Chain | Description
AW | No description available
Chain information for copy of combination AX #23.45
---
Chain | Description
AX | No description available
Chain information for copy of combination AY #23.46
---
Chain | Description
AY | No description available
Chain information for copy of combination AZ #23.47
---
Chain | Description
AZ | No description available
Chain information for copy of combination Aa #23.48
---
Chain | Description
Aa | No description available
Chain information for copy of combination Ab #23.49
---
Chain | Description
Ab | No description available
Chain information for copy of combination Ac #23.50
---
Chain | Description
Ac | No description available
Chain information for copy of combination Ad #23.51
---
Chain | Description
Ad | No description available
Chain information for copy of combination Ae #23.52
---
Chain | Description
Ae | No description available
Chain information for copy of combination Af #23.53
---
Chain | Description
Af | No description available
Chain information for copy of combination Ag #23.54
---
Chain | Description
Ag | No description available
Chain information for copy of combination Ah #23.55
---
Chain | Description
Ah | No description available
Chain information for copy of combination Ai #23.56
---
Chain | Description
Ai | No description available
Chain information for copy of combination Aj #23.57
---
Chain | Description
Aj | No description available
Chain information for copy of combination Ak #23.58
---
Chain | Description
Ak | No description available
Chain information for copy of combination Al #23.59
---
Chain | Description
Al | No description available
Chain information for copy of combination Am #23.60
---
Chain | Description
Am | No description available
Chain information for copy of combination An #23.61
---
Chain | Description
An | No description available
Chain information for copy of combination Ao #23.62
---
Chain | Description
Ao | No description available
Chain information for copy of combination Ap #23.63
---
Chain | Description
Ap | No description available
Chain information for copy of combination Aq #23.64
---
Chain | Description
Aq | No description available
Chain information for copy of combination Ar #23.65
---
Chain | Description
Ar | No description available
Chain information for copy of combination As #23.66
---
Chain | Description
As | No description available
Chain information for copy of combination At #23.67
---
Chain | Description
At | No description available
Chain information for copy of combination Au #23.68
---
Chain | Description
Au | No description available
Chain information for copy of combination Av #23.69
---
Chain | Description
Av | No description available
Chain information for copy of combination Aw #23.70
---
Chain | Description
Aw | No description available
Chain information for copy of combination Ax #23.71
---
Chain | Description
Ax | No description available
Chain information for copy of combination Ay #23.72
---
Chain | Description
Ay | No description available
Chain information for copy of combination Az #23.73
---
Chain | Description
Az | No description available
Chain information for copy of combination B #23.74
---
Chain | Description
B | No description available
Chain information for copy of combination BA #23.75
---
Chain | Description
BA | No description available
Chain information for copy of combination BB #23.76
---
Chain | Description
BB | No description available
Chain information for copy of combination BC #23.77
---
Chain | Description
BC | No description available
Chain information for copy of combination BD #23.78
---
Chain | Description
BD | No description available
Chain information for copy of combination BE #23.79
---
Chain | Description
BE | No description available
Chain information for copy of combination BF #23.80
---
Chain | Description
BF | No description available
Chain information for copy of combination BG #23.81
---
Chain | Description
BG | No description available
Chain information for copy of combination BH #23.82
---
Chain | Description
BH | No description available
Chain information for copy of combination BI #23.83
---
Chain | Description
BI | No description available
Chain information for copy of combination BJ #23.84
---
Chain | Description
BJ | No description available
Chain information for copy of combination BK #23.85
---
Chain | Description
BK | No description available
Chain information for copy of combination BL #23.86
---
Chain | Description
BL | No description available
Chain information for copy of combination BM #23.87
---
Chain | Description
BM | No description available
Chain information for copy of combination BN #23.88
---
Chain | Description
BN | No description available
Chain information for copy of combination BO #23.89
---
Chain | Description
BO | No description available
Chain information for copy of combination BP #23.90
---
Chain | Description
BP | No description available
Chain information for copy of combination BQ #23.91
---
Chain | Description
BQ | No description available
Chain information for copy of combination BR #23.92
---
Chain | Description
BR | No description available
Chain information for copy of combination BS #23.93
---
Chain | Description
BS | No description available
Chain information for copy of combination BT #23.94
---
Chain | Description
BT | No description available
Chain information for copy of combination BU #23.95
---
Chain | Description
BU | No description available
Chain information for copy of combination BV #23.96
---
Chain | Description
BV | No description available
Chain information for copy of combination BW #23.97
---
Chain | Description
BW | No description available
Chain information for copy of combination BX #23.98
---
Chain | Description
BX | No description available
Chain information for copy of combination BY #23.99
---
Chain | Description
BY | No description available
Chain information for copy of combination C #23.100
---
Chain | Description
C | No description available
Chain information for copy of combination D #23.101
---
Chain | Description
D | No description available
Chain information for copy of combination E #23.102
---
Chain | Description
E | No description available
Chain information for copy of combination F #23.103
---
Chain | Description
F | No description available
Chain information for copy of combination G #23.104
---
Chain | Description
G | No description available
Chain information for copy of combination H #23.105
---
Chain | Description
H | No description available
Chain information for copy of combination I #23.106
---
Chain | Description
I | No description available
Chain information for copy of combination J #23.107
---
Chain | Description
J | No description available
Chain information for copy of combination K #23.108
---
Chain | Description
K | No description available
Chain information for copy of combination L #23.109
---
Chain | Description
L | No description available
Chain information for copy of combination M #23.110
---
Chain | Description
M | No description available
Chain information for copy of combination N #23.111
---
Chain | Description
N | No description available
Chain information for copy of combination O #23.112
---
Chain | Description
O | No description available
Chain information for copy of combination P #23.113
---
Chain | Description
P | No description available
Chain information for copy of combination Q #23.114
---
Chain | Description
Q | No description available
Chain information for copy of combination R #23.115
---
Chain | Description
R | No description available
Chain information for copy of combination S #23.116
---
Chain | Description
S | No description available
Chain information for copy of combination T #23.117
---
Chain | Description
T | No description available
Chain information for copy of combination U #23.118
---
Chain | Description
U | No description available
Chain information for copy of combination V #23.119
---
Chain | Description
V | No description available
Chain information for copy of combination W #23.120
---
Chain | Description
W | No description available
Chain information for copy of combination X #23.121
---
Chain | Description
X | No description available
Chain information for copy of combination Y #23.122
---
Chain | Description
Y | No description available
Chain information for copy of combination Z #23.123
---
Chain | Description
Z | No description available
Chain information for copy of combination a #23.124
---
Chain | Description
a | No description available
Chain information for copy of combination b #23.125
---
Chain | Description
b | No description available
Chain information for copy of combination c #23.126
---
Chain | Description
c | No description available
Chain information for copy of combination d #23.127
---
Chain | Description
d | No description available
Chain information for copy of combination e #23.128
---
Chain | Description
e | No description available
Chain information for copy of combination f #23.129
---
Chain | Description
f | No description available
Chain information for copy of combination g #23.130
---
Chain | Description
g | No description available
Chain information for copy of combination h #23.131
---
Chain | Description
h | No description available
Chain information for copy of combination i #23.132
---
Chain | Description
i | No description available
Chain information for copy of combination j #23.133
---
Chain | Description
j | No description available
Chain information for copy of combination k #23.134
---
Chain | Description
k | No description available
Chain information for copy of combination l #23.135
---
Chain | Description
l | No description available
Chain information for copy of combination m #23.136
---
Chain | Description
m | No description available
Chain information for copy of combination n #23.137
---
Chain | Description
n | No description available
Chain information for copy of combination o #23.138
---
Chain | Description
o | No description available
Chain information for copy of combination p #23.139
---
Chain | Description
p | No description available
Chain information for copy of combination q #23.140
---
Chain | Description
q | No description available
Chain information for copy of combination r #23.141
---
Chain | Description
r | No description available
Chain information for copy of combination s #23.142
---
Chain | Description
s | No description available
Chain information for copy of combination t #23.143
---
Chain | Description
t | No description available
Chain information for copy of combination u #23.144
---
Chain | Description
u | No description available
Chain information for copy of combination v #23.145
---
Chain | Description
v | No description available
Chain information for copy of combination w #23.146
---
Chain | Description
w | No description available
Chain information for copy of combination x #23.147
---
Chain | Description
x | No description available
Chain information for copy of combination y #23.148
---
Chain | Description
y | No description available
Chain information for copy of combination z #23.149
---
Chain | Description
z | No description available
> hide #!11 models
Drag select of 5684 residues
> hide #!23.11 models
> show #!23.11 models
> hide #!23.11 models
> select add #23.11
46803 atoms, 1562 bonds, 2 pseudobonds, 5841 residues, 28 models selected
> select subtract #23.11
45261 atoms, 5652 residues, 26 models selected
> select add #23.11
46803 atoms, 1562 bonds, 2 pseudobonds, 5841 residues, 28 models selected
> select subtract #23.11
45261 atoms, 5652 residues, 26 models selected
> hide #23.15 models
> hide #23.30 models
> hide #23.53 models
> hide #23.85 models
> hide #!23.100 models
> hide #!23.101 models
> hide #23.102 models
> hide #!23.103 models
> hide #!23.104 models
> hide #23.105 models
> hide #!23.106 models
> hide #!23.107 models
> hide #23.108 models
> hide #!23.109 models
> hide #!23.110 models
> hide #23.111 models
> hide #!23.112 models
> hide #!23.116 models
> hide #23.117 models
> hide #!23.118 models
> hide #!23.119 models
> hide #23.120 models
> hide #!23.121 models
> hide #23.145 models
> select clear
> hide #!23 models
> show #!23 models
> hide #!23 models
> hide #!3 models
> show #!23 models
> show #!23.11 models
> show #23.15 models
> hide #23.15 models
Drag select of 426 residues
> hide #23.2 models
> hide #23.3 models
> hide #23.4 models
> hide #23.5 models
> hide #23.6 models
> hide #23.7 models
> hide #23.8 models
> hide #23.9 models
> hide #23.23 models
> hide #23.24 models
> hide #23.25 models
> hide #23.26 models
> hide #23.27 models
> hide #23.78 models
> hide #23.79 models
> hide #23.80 models
> hide #23.81 models
> hide #23.82 models
> hide #23.83 models
> hide #23.84 models
> hide #23.86 models
> hide #23.87 models
> hide #23.146 models
> hide #23.147 models
> hide #23.148 models
> hide #23.149 models
Drag select of 48 residues
> hide #23.64 models
> hide #23.65 models
> hide #23.66 models
> hide #23.67 models
> hide #23.68 models
> hide #23.69 models
> hide #23.70 models
> hide #23.71 models
> hide #23.72 models
> hide #23.73 models
> hide #23.42 models
> hide #23.43 models
> hide #23.44 models
> hide #23.45 models
> hide #23.46 models
Drag select of 49 residues
> hide #23.41 models
> show #23.46 models
> hide #23.46 models
> hide #23.47 models
> hide #23.48 models
> hide #23.49 models
> hide #23.50 models
> hide #23.1 models
> select clear
Drag select of 16 residues
> hide #23.22 models
> hide #23.10 models
Drag select of 259 residues
> hide #23.12 models
> hide #23.13 models
> hide #23.14 models
> hide #23.16 models
> hide #23.17 models
> hide #23.18 models
> hide #23.19 models
> hide #23.20 models
> hide #23.21 models
> hide #23.75 models
> hide #23.76 models
> hide #23.77 models
Drag select of 156 residues
> hide #23.54 models
> hide #23.55 models
> hide #23.56 models
> hide #23.57 models
> hide #23.58 models
> hide #23.59 models
> hide #23.60 models
> hide #23.61 models
> hide #23.62 models
> hide #23.63 models
Drag select of 267 residues
> hide #23.31 models
> hide #23.32 models
> hide #23.33 models
> hide #23.34 models
> hide #23.35 models
> hide #23.36 models
> hide #23.37 models
> hide #23.39 models
> hide #23.38 models
> hide #23.40 models
Drag select of 7 residues
> select clear
Drag select of 7 residues
Drag select of 10 residues
> show #!23.116 models
> show #23.117 models
> show #!23.118 models
> hide #!23.118 models
> show #!23.118 models
> show #!23.119 models
> show #23.120 models
> show #!23.121 models
> show #23.145 models
> hide #23.145 models
> show #23.146 models
> hide #23.146 models
> show #23.149 models
> hide #23.149 models
> select clear
Drag select of 284 residues
> show #23.75 models
> hide #23.75 models
> show #23.73 models
> hide #23.73 models
> show #23.73 models
> hide #23.73 models
> show #23.73 models
> hide #23.73 models
> show #23.72 models
> hide #23.72 models
> show #23.53 models
> hide #23.53 models
> show #23.54 models
> hide #23.54 models
> show #23.55 models
> hide #23.55 models
> show #23.57 models
> show #23.3 models
> hide #23.3 models
> show #23.3 models
> hide #23.3 models
> select add #23
224507 atoms, 227843 bonds, 42 pseudobonds, 26692 residues, 176 models
selected
> show sel &
> #23.28-29,51-52,57,74,88-99,114,117,120,127,129,131,133,135,137-144#!23.11,113,115-116,118-119,121-126,128,130,132,134,136
> cartoons
[Repeated 1 time(s)]
> show #23.1 models
> show #23.2 models
> show #23.3 models
> show #23.4 models
> show #23.5 models
> select clear
> show #23.6 models
> show #23.7 models
> show #23.8 models
> show #23.9 models
> show #23.10 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!23.11 models
> show #!23.11 models
> close #23.1-10
> show #23.12 models
> show #23.13 models
> show #23.14 models
> show #23.15 models
> hide #23.15 models
> hide #23.14 models
> show #23.14 models
> close #23
> combine #3
> split #23
Split copy of combination (#23) into 149 models
Chain information for copy of combination 0 #23.1
---
Chain | Description
0 | No description available
Chain information for copy of combination 1 #23.2
---
Chain | Description
1 | No description available
Chain information for copy of combination 2 #23.3
---
Chain | Description
2 | No description available
Chain information for copy of combination 3 #23.4
---
Chain | Description
3 | No description available
Chain information for copy of combination 4 #23.5
---
Chain | Description
4 | No description available
Chain information for copy of combination 5 #23.6
---
Chain | Description
5 | No description available
Chain information for copy of combination 6 #23.7
---
Chain | Description
6 | No description available
Chain information for copy of combination 7 #23.8
---
Chain | Description
7 | No description available
Chain information for copy of combination 8 #23.9
---
Chain | Description
8 | No description available
Chain information for copy of combination 9 #23.10
---
Chain | Description
9 | No description available
Chain information for copy of combination A #23.11
---
Chain | Description
A | No description available
Chain information for copy of combination A0 #23.12
---
Chain | Description
A0 | No description available
Chain information for copy of combination A1 #23.13
---
Chain | Description
A1 | No description available
Chain information for copy of combination A2 #23.14
---
Chain | Description
A2 | No description available
Chain information for copy of combination A3 #23.15
---
Chain | Description
A3 | No description available
Chain information for copy of combination A4 #23.16
---
Chain | Description
A4 | No description available
Chain information for copy of combination A5 #23.17
---
Chain | Description
A5 | No description available
Chain information for copy of combination A6 #23.18
---
Chain | Description
A6 | No description available
Chain information for copy of combination A7 #23.19
---
Chain | Description
A7 | No description available
Chain information for copy of combination A8 #23.20
---
Chain | Description
A8 | No description available
Chain information for copy of combination A9 #23.21
---
Chain | Description
A9 | No description available
Chain information for copy of combination AA #23.22
---
Chain | Description
AA | No description available
Chain information for copy of combination AB #23.23
---
Chain | Description
AB | No description available
Chain information for copy of combination AC #23.24
---
Chain | Description
AC | No description available
Chain information for copy of combination AD #23.25
---
Chain | Description
AD | No description available
Chain information for copy of combination AE #23.26
---
Chain | Description
AE | No description available
Chain information for copy of combination AF #23.27
---
Chain | Description
AF | No description available
Chain information for copy of combination AG #23.28
---
Chain | Description
AG | No description available
Chain information for copy of combination AH #23.29
---
Chain | Description
AH | No description available
Chain information for copy of combination AI #23.30
---
Chain | Description
AI | No description available
Chain information for copy of combination AJ #23.31
---
Chain | Description
AJ | No description available
Chain information for copy of combination AK #23.32
---
Chain | Description
AK | No description available
Chain information for copy of combination AL #23.33
---
Chain | Description
AL | No description available
Chain information for copy of combination AM #23.34
---
Chain | Description
AM | No description available
Chain information for copy of combination AN #23.35
---
Chain | Description
AN | No description available
Chain information for copy of combination AO #23.36
---
Chain | Description
AO | No description available
Chain information for copy of combination AP #23.37
---
Chain | Description
AP | No description available
Chain information for copy of combination AQ #23.38
---
Chain | Description
AQ | No description available
Chain information for copy of combination AR #23.39
---
Chain | Description
AR | No description available
Chain information for copy of combination AS #23.40
---
Chain | Description
AS | No description available
Chain information for copy of combination AT #23.41
---
Chain | Description
AT | No description available
Chain information for copy of combination AU #23.42
---
Chain | Description
AU | No description available
Chain information for copy of combination AV #23.43
---
Chain | Description
AV | No description available
Chain information for copy of combination AW #23.44
---
Chain | Description
AW | No description available
Chain information for copy of combination AX #23.45
---
Chain | Description
AX | No description available
Chain information for copy of combination AY #23.46
---
Chain | Description
AY | No description available
Chain information for copy of combination AZ #23.47
---
Chain | Description
AZ | No description available
Chain information for copy of combination Aa #23.48
---
Chain | Description
Aa | No description available
Chain information for copy of combination Ab #23.49
---
Chain | Description
Ab | No description available
Chain information for copy of combination Ac #23.50
---
Chain | Description
Ac | No description available
Chain information for copy of combination Ad #23.51
---
Chain | Description
Ad | No description available
Chain information for copy of combination Ae #23.52
---
Chain | Description
Ae | No description available
Chain information for copy of combination Af #23.53
---
Chain | Description
Af | No description available
Chain information for copy of combination Ag #23.54
---
Chain | Description
Ag | No description available
Chain information for copy of combination Ah #23.55
---
Chain | Description
Ah | No description available
Chain information for copy of combination Ai #23.56
---
Chain | Description
Ai | No description available
Chain information for copy of combination Aj #23.57
---
Chain | Description
Aj | No description available
Chain information for copy of combination Ak #23.58
---
Chain | Description
Ak | No description available
Chain information for copy of combination Al #23.59
---
Chain | Description
Al | No description available
Chain information for copy of combination Am #23.60
---
Chain | Description
Am | No description available
Chain information for copy of combination An #23.61
---
Chain | Description
An | No description available
Chain information for copy of combination Ao #23.62
---
Chain | Description
Ao | No description available
Chain information for copy of combination Ap #23.63
---
Chain | Description
Ap | No description available
Chain information for copy of combination Aq #23.64
---
Chain | Description
Aq | No description available
Chain information for copy of combination Ar #23.65
---
Chain | Description
Ar | No description available
Chain information for copy of combination As #23.66
---
Chain | Description
As | No description available
Chain information for copy of combination At #23.67
---
Chain | Description
At | No description available
Chain information for copy of combination Au #23.68
---
Chain | Description
Au | No description available
Chain information for copy of combination Av #23.69
---
Chain | Description
Av | No description available
Chain information for copy of combination Aw #23.70
---
Chain | Description
Aw | No description available
Chain information for copy of combination Ax #23.71
---
Chain | Description
Ax | No description available
Chain information for copy of combination Ay #23.72
---
Chain | Description
Ay | No description available
Chain information for copy of combination Az #23.73
---
Chain | Description
Az | No description available
Chain information for copy of combination B #23.74
---
Chain | Description
B | No description available
Chain information for copy of combination BA #23.75
---
Chain | Description
BA | No description available
Chain information for copy of combination BB #23.76
---
Chain | Description
BB | No description available
Chain information for copy of combination BC #23.77
---
Chain | Description
BC | No description available
Chain information for copy of combination BD #23.78
---
Chain | Description
BD | No description available
Chain information for copy of combination BE #23.79
---
Chain | Description
BE | No description available
Chain information for copy of combination BF #23.80
---
Chain | Description
BF | No description available
Chain information for copy of combination BG #23.81
---
Chain | Description
BG | No description available
Chain information for copy of combination BH #23.82
---
Chain | Description
BH | No description available
Chain information for copy of combination BI #23.83
---
Chain | Description
BI | No description available
Chain information for copy of combination BJ #23.84
---
Chain | Description
BJ | No description available
Chain information for copy of combination BK #23.85
---
Chain | Description
BK | No description available
Chain information for copy of combination BL #23.86
---
Chain | Description
BL | No description available
Chain information for copy of combination BM #23.87
---
Chain | Description
BM | No description available
Chain information for copy of combination BN #23.88
---
Chain | Description
BN | No description available
Chain information for copy of combination BO #23.89
---
Chain | Description
BO | No description available
Chain information for copy of combination BP #23.90
---
Chain | Description
BP | No description available
Chain information for copy of combination BQ #23.91
---
Chain | Description
BQ | No description available
Chain information for copy of combination BR #23.92
---
Chain | Description
BR | No description available
Chain information for copy of combination BS #23.93
---
Chain | Description
BS | No description available
Chain information for copy of combination BT #23.94
---
Chain | Description
BT | No description available
Chain information for copy of combination BU #23.95
---
Chain | Description
BU | No description available
Chain information for copy of combination BV #23.96
---
Chain | Description
BV | No description available
Chain information for copy of combination BW #23.97
---
Chain | Description
BW | No description available
Chain information for copy of combination BX #23.98
---
Chain | Description
BX | No description available
Chain information for copy of combination BY #23.99
---
Chain | Description
BY | No description available
Chain information for copy of combination C #23.100
---
Chain | Description
C | No description available
Chain information for copy of combination D #23.101
---
Chain | Description
D | No description available
Chain information for copy of combination E #23.102
---
Chain | Description
E | No description available
Chain information for copy of combination F #23.103
---
Chain | Description
F | No description available
Chain information for copy of combination G #23.104
---
Chain | Description
G | No description available
Chain information for copy of combination H #23.105
---
Chain | Description
H | No description available
Chain information for copy of combination I #23.106
---
Chain | Description
I | No description available
Chain information for copy of combination J #23.107
---
Chain | Description
J | No description available
Chain information for copy of combination K #23.108
---
Chain | Description
K | No description available
Chain information for copy of combination L #23.109
---
Chain | Description
L | No description available
Chain information for copy of combination M #23.110
---
Chain | Description
M | No description available
Chain information for copy of combination N #23.111
---
Chain | Description
N | No description available
Chain information for copy of combination O #23.112
---
Chain | Description
O | No description available
Chain information for copy of combination P #23.113
---
Chain | Description
P | No description available
Chain information for copy of combination Q #23.114
---
Chain | Description
Q | No description available
Chain information for copy of combination R #23.115
---
Chain | Description
R | No description available
Chain information for copy of combination S #23.116
---
Chain | Description
S | No description available
Chain information for copy of combination T #23.117
---
Chain | Description
T | No description available
Chain information for copy of combination U #23.118
---
Chain | Description
U | No description available
Chain information for copy of combination V #23.119
---
Chain | Description
V | No description available
Chain information for copy of combination W #23.120
---
Chain | Description
W | No description available
Chain information for copy of combination X #23.121
---
Chain | Description
X | No description available
Chain information for copy of combination Y #23.122
---
Chain | Description
Y | No description available
Chain information for copy of combination Z #23.123
---
Chain | Description
Z | No description available
Chain information for copy of combination a #23.124
---
Chain | Description
a | No description available
Chain information for copy of combination b #23.125
---
Chain | Description
b | No description available
Chain information for copy of combination c #23.126
---
Chain | Description
c | No description available
Chain information for copy of combination d #23.127
---
Chain | Description
d | No description available
Chain information for copy of combination e #23.128
---
Chain | Description
e | No description available
Chain information for copy of combination f #23.129
---
Chain | Description
f | No description available
Chain information for copy of combination g #23.130
---
Chain | Description
g | No description available
Chain information for copy of combination h #23.131
---
Chain | Description
h | No description available
Chain information for copy of combination i #23.132
---
Chain | Description
i | No description available
Chain information for copy of combination j #23.133
---
Chain | Description
j | No description available
Chain information for copy of combination k #23.134
---
Chain | Description
k | No description available
Chain information for copy of combination l #23.135
---
Chain | Description
l | No description available
Chain information for copy of combination m #23.136
---
Chain | Description
m | No description available
Chain information for copy of combination n #23.137
---
Chain | Description
n | No description available
Chain information for copy of combination o #23.138
---
Chain | Description
o | No description available
Chain information for copy of combination p #23.139
---
Chain | Description
p | No description available
Chain information for copy of combination q #23.140
---
Chain | Description
q | No description available
Chain information for copy of combination r #23.141
---
Chain | Description
r | No description available
Chain information for copy of combination s #23.142
---
Chain | Description
s | No description available
Chain information for copy of combination t #23.143
---
Chain | Description
t | No description available
Chain information for copy of combination u #23.144
---
Chain | Description
u | No description available
Chain information for copy of combination v #23.145
---
Chain | Description
v | No description available
Chain information for copy of combination w #23.146
---
Chain | Description
w | No description available
Chain information for copy of combination x #23.147
---
Chain | Description
x | No description available
Chain information for copy of combination y #23.148
---
Chain | Description
y | No description available
Chain information for copy of combination z #23.149
---
Chain | Description
z | No description available
Drag select of 3074 residues
> hide #23.1 models
> show #23.1 models
> hide #23.1 models
> hide #23.9 models
> show #23.9 models
> hide #23.9 models
> hide #23.10 models
> hide #!23.11 models
> show #23.10 models
> hide #23.10 models
> show #!23.11 models
> hide #23.15 models
> show #23.15 models
> hide #23.15 models
> hide #23.22 models
> show #23.22 models
> hide #23.22 models
> hide #23.23 models
> hide #23.26 models
> hide #23.30 models
> show #23.30 models
> hide #23.30 models
> hide #23.41 models
> show #23.41 models
> hide #23.41 models
> hide #23.42 models
> hide #23.43 models
> hide #23.44 models
> hide #23.45 models
> hide #23.46 models
> hide #23.47 models
> hide #23.48 models
> hide #23.49 models
> hide #23.50 models
> hide #23.53 models
> show #23.53 models
> hide #23.53 models
> hide #23.64 models
> hide #23.65 models
> hide #23.66 models
> hide #23.67 models
> hide #23.68 models
> hide #23.69 models
> hide #23.70 models
> hide #23.71 models
> hide #23.72 models
> hide #23.73 models
> hide #23.74 models
> show #23.74 models
> hide #!23.100 models
> show #!23.100 models
> hide #!23.101 models
> show #!23.101 models
> hide #23.102 models
> show #23.102 models
> hide #!23.104 models
> show #!23.104 models
> hide #!23.121 models
> show #!23.121 models
> hide #23.145 models
> select clear
Drag select of 10 residues
> hide #23.83 models
> hide #23.82 models
> hide #23.78 models
> select clear
Drag select of 17 residues
> hide #23.27 models
> hide #23.25 models
> hide #23.24 models
> select clear
Drag select of 5 residues
> hide #23.8 models
> select clear
Drag select of 17 residues
> hide #23.79 models
> hide #23.80 models
> hide #23.81 models
Drag select of 19 residues
> hide #23.84 models
> hide #23.85 models
> hide #23.86 models
> hide #23.87 models
Drag select of 2262 residues
Drag select of 417 residues
> hide #23.88 models
> hide #23.89 models
> hide #23.90 models
> hide #23.91 models
> hide #23.92 models
> hide #23.93 models
> hide #23.94 models
> hide #23.95 models
> hide #23.96 models
> hide #23.97 models
> hide #23.98 models
> hide #23.99 models
> hide #23.142 models
> hide #23.141 models
> hide #23.140 models
> hide #23.139 models
> hide #23.138 models
> hide #23.137 models
> save /Users/shoichi/Desktop/For-PflD_PflC.cxs includeMaps true
[Repeated 1 time(s)]
——— End of log from Fri Jul 11 17:08:26 2025 ———
opened ChimeraX session
Drag select of 281 residues
> hide #23.2 models
> hide #23.20 models
> hide #23.21 models
> hide #23.33 models
> hide #23.34 models
> hide #23.35 models
> select clear
Drag select of 34 residues
> hide #23.147 models
> hide #23.148 models
> hide #23.149 models
Drag select of 65 residues
> hide #23.3 models
> hide #23.4 models
> hide #23.5 models
Drag select of 137 residues
> hide #23.31 models
> hide #23.32 models
> hide #23.40 models
Drag select of 77 residues
> hide #23.146 models
> hide #23.6 models
> hide #23.7 models
Drag select of 21 residues
> hide #23.12 models
> hide #23.75 models
Drag select of 42 residues
> hide #23.39 models
> hide #23.38 models
> hide #23.37 models
Drag select of 20 residues
> hide #23.36 models
Drag select of 179 residues
> hide #23.56 models
> hide #23.57 models
> hide #23.58 models
> hide #23.59 models
> hide #23.60 models
> hide #23.61 models
Drag select of 51 residues
> hide #23.62 models
> hide #23.63 models
> select clear
Drag select of 93 residues
> hide #23.54 models
> hide #23.55 models
Drag select of 15 residues
> hide #23.76 models
> hide #23.77 models
Drag select of 171 residues
> hide #23.17 models
> hide #23.18 models
> hide #23.19 models
Drag select of 8 residues
> hide #23.16 models
Drag select of 859 residues
> hide #!23.123 models
> hide #23.129 models
> hide #!23.130 models
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> close #23.75-99
> close #23.53-73
> close #23.30-50
> close #23.15-27
> close #23.1-10
> close #23.12
> close #23.123
> close #23.129#23.130
> close #23.137-142
> close #23.145-149
> select add #23.11
1542 atoms, 1562 bonds, 2 pseudobonds, 189 residues, 2 models selected
> select add #23
92292 atoms, 93828 bonds, 40 pseudobonds, 10088 residues, 69 models selected
> save /Users/shoichitachiyama/Desktop/Cage-PflCD.pdb selectedOnly true
> open /Users/shoichitachiyama/Desktop/Cage-PflCD.pdb
Summary of feedback from opening /Users/shoichitachiyama/Desktop/Cage-
PflCD.pdb
---
warnings | Start residue of secondary structure not found: HELIX 9 9 LEU B 16 ILE B 102 1 87
Start residue of secondary structure not found: HELIX 10 10 VAL B 103 THR B
105 1 3
Start residue of secondary structure not found: HELIX 11 11 ARG B 129 LEU B
136 1 8
Start residue of secondary structure not found: HELIX 12 12 GLU B 137 PRO B
139 1 3
Start residue of secondary structure not found: HELIX 13 13 LEU B 140 SER B
142 1 3
1328 messages similar to the above omitted
Chain information for Cage-PflCD.pdb
---
Chain | Description
24.1/A 24.10/D 24.13/G 24.16/J 24.19/M 24.22/P 24.25/S 24.28/V | No description available
24.2/A1 24.3/A2 24.4/AG 24.5/AH 24.6/Ad 24.7/Ae 24.43/t 24.44/u | No description available
24.8/B 24.11/E 24.14/H 24.17/K 24.20/N 24.23/Q 24.26/T 24.29/W | No description available
24.9/C 24.12/F 24.15/I 24.18/L 24.21/O 24.24/R 24.27/U 24.30/X | No description available
24.31/Y 24.32/a 24.33/b 24.34/c | No description available
24.35/d 24.37/h 24.39/j 24.41/l | No description available
24.36/e 24.38/i 24.40/k 24.42/m | No description available
> select subtract #23
Nothing selected
> hide #!23 models
> show #!20 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> surface dust #19 size 21.4
> surface dust #20 size 21.4
> surface dust #20 size 50
> hide #!19 models
> show #!21 models
> color #21 #b2b2ff6c models
> color #21 #b2b2ff61 models
> close #24
> show #!23 models
Drag select of 36 residues
> select clear
Drag select of 29 residues
> hide #23.143 models
> hide #23.144 models
Drag select of 47 residues
> hide #23.13 models
> hide #23.14 models
Drag select of 69 residues
> hide #23.28 models
> hide #23.29 models
Drag select of 66 residues
> hide #23.51 models
> hide #23.52 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> close #23.13-14,28-29,51-52
Drag select of 8 residues
> select clear
Drag select of 26 residues
> hide #!23.136 models
Drag select of 12 residues
> hide #!23.134 models
Drag select of 20 residues
> hide #!23.128 models
Drag select of 5 residues
> hide #!23.132 models
Drag select of 9 residues
> hide #23.131 models
Drag select of 3 residues
> hide #23.133 models
Drag select of 1 residues
> hide #23.135 models
Drag select of 1 residues
> hide #23.127 models
> close #23.127,131,133,135,143-144#23.128,132,134,136
> show #!19 models
> hide #!19 models
> select add #23
46256 atoms, 47148 bonds, 36 pseudobonds, 5632 residues, 49 models selected
> save /Users/shoichitachiyama/Desktop/Cage-PflCD.pdb selectedOnly true
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-PflCD/Cage-PflCD.pdb"
Chain information for Cage-PflCD.pdb
---
Chain | Description
24.1/A 24.4/D 24.7/G 24.10/J 24.13/M 24.16/P 24.19/S 24.22/V | No description available
24.2/B 24.5/E 24.8/H 24.11/K 24.14/N 24.17/Q 24.20/T 24.23/W | No description available
24.3/C 24.6/F 24.9/I 24.12/L 24.15/O 24.18/R 24.21/U 24.24/X | No description available
24.25/Y 24.26/a 24.27/b 24.28/c | No description available
> hide #!23 models
> select subtract #23
Nothing selected
> show #!19 models
> color #19 #ffffb266 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!11 models
> show #!13 models
> hide #!13 models
> show #!13 models
Cell requested for row 12 is out of bounds for table with 25 rows! Resizing
table model.
> select add #13
18892 atoms, 19223 bonds, 2 pseudobonds, 2334 residues, 2 models selected
> show sel surfaces
> select clear
> color #19 #c0c0c080 models
> color #20 #c0c0c080 models
> color #21 #c0c0c080 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!19 models
> show #!19 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Segmenting PflC.mrc, density threshold 0.007524
Showing 36 region surfaces
512 watershed regions, grouped to 36 regions
Showing PflC.seg - 36 regions, 36 surfaces
> select #25.4
1 model selected
> select add #25.22
2 models selected
> select add #25.19
3 models selected
> select add #25.15
4 models selected
> select add #25.13
5 models selected
> select add #25.18
6 models selected
> select add #25.17
7 models selected
> select add #25.20
8 models selected
> select add #25.35
9 models selected
> select add #25.3
10 models selected
> select add #25.34
11 models selected
> select add #25.12
12 models selected
> select add #25.26
13 models selected
> select add #25.8
14 models selected
> select add #25.9
15 models selected
> select add #25.5
16 models selected
> select add #25.2
17 models selected
> select add #25.1
18 models selected
> select subtract #25.1
17 models selected
Grouped 17 regions
> select add #25.21
2 models selected
> select add #25.29
3 models selected
> select add #25.28
4 models selected
> select add #25.30
5 models selected
> select add #25.24
6 models selected
> select add #25.27
7 models selected
Grouped 7 regions
> select #25.2
1 model selected
> select #25.16
1 model selected
> hide #!20 models
> select #25.16
1 model selected
> select add #25.25
2 models selected
> select add #25.23
3 models selected
> select add #25.14
4 models selected
> select #25.23
1 model selected
> select add #25.25
2 models selected
> select add #25.1
3 models selected
> select subtract #25.1
2 models selected
> select add #25.31
3 models selected
> select add #25.33
4 models selected
> select add #25.32
5 models selected
Grouped 5 regions
Showing 10 region surfaces
> select add #25.2
2 models selected
Grouped 2 regions
> select #25.14
1 model selected
> select add #25.11
2 models selected
> select add #25.16
3 models selected
Ungrouped to 9 regions
> select #25.9
1 model selected
> select add #25.5
2 models selected
> select add #25.3
3 models selected
> select add #25.4
4 models selected
> select add #25.15
5 models selected
> select add #25.13
6 models selected
Grouped 6 regions
Showing 10 region surfaces
> select add #25.2
2 models selected
Grouped 2 regions
> select #25.12
1 model selected
Ungrouped to 4 regions
> select #25.4
1 model selected
> select add #25.9
2 models selected
> select add #25.3
3 models selected
> select add #25.2
4 models selected
Grouped 4 regions
> hide #!19 models
> select #25.8
1 model selected
> select add #25.5
2 models selected
> select add #25.17
3 models selected
Ungrouped to 9 regions
> select #25.9
1 model selected
> select add #25.4
2 models selected
> select #25.14
1 model selected
> select #25.10
1 model selected
> save /Users/shoichitachiyama/Desktop/PflCD.cxs includeMaps true
——— End of log from Fri Jul 11 20:48:14 2025 ———
opened ChimeraX session
Showing PflC.seg - 15 regions, 15 surfaces
> hide #!25 models
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-PflCD/Additional_Segment/PflCD.mrc"
Opened PflCD.mrc as #26, grid size 200,200,200, pixel 2.14, shown at level
0.0169, step 1, values float32
> volume #26 level 0.00187
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Segmenting PflCD.mrc, density threshold 0.001870
Showing 20 region surfaces
327 watershed regions, grouped to 20 regions
Showing PflCD.seg - 20 regions, 20 surfaces
> select #25.9
1 model selected
> select add #25.17
2 models selected
> select add #25.2
3 models selected
> hide #!26 models
> select add #25.19
4 models selected
> select add #25.18
5 models selected
> select add #25.16
6 models selected
> select add #25.1
7 models selected
> select add #25.12
8 models selected
> select add #25.11
9 models selected
> select add #25.15
10 models selected
> select add #25.20
11 models selected
Grouped 11 regions
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Opened PflCD_imasked as #27, grid size 200,200,200, pixel 2.14, shown at step
1, values float32
Segmenting PflCD_imasked, density threshold 0.001870
Showing 9 region surfaces
168 watershed regions, grouped to 9 regions
Showing PflCD_imasked.seg - 9 regions, 9 surfaces
> select #25.4
1 model selected
> select add #25.5
2 models selected
> select add #25.6
3 models selected
Ungrouped to 10 regions
> select #25.12
1 model selected
> hide #!27 models
> select add #25.17
2 models selected
> select add #25.19
3 models selected
> select subtract #25.19
2 models selected
Grouped 2 regions
> select #25.19
1 model selected
> select clear
> select #25.19
1 model selected
Ungrouped to 4 regions
> select #25.17
1 model selected
> select add #25.5
2 models selected
> select add #25.4
3 models selected
Grouped 3 regions
> select add #25.12
2 models selected
Grouped 2 regions
> select add #25.16
2 models selected
Grouped 2 regions
> select #25.18
1 model selected
Ungrouped to 2 regions
> select #25.5
1 model selected
Showing 15 region surfaces
> select add #25.4
2 models selected
Grouped 2 regions
> select #25.10
1 model selected
Ungrouped to 3 regions
> select #25.17
1 model selected
> select add #25.4
2 models selected
Grouped 2 regions
> select add #25.12
2 models selected
> select add #25.14
3 models selected
Grouped 3 regions
> select #25.11
1 model selected
> select add #25.4
2 models selected
Grouped 2 regions
> select add #25.15
4 models selected
> select clear
Showing 12 region surfaces
> select #25.4
1 model selected
> select add #25.15
2 models selected
> select add #25.2
3 models selected
> select subtract #25.2
2 models selected
Grouped 2 regions
> select clear
> select #25.4
1 model selected
Opened PflCD_imasked_imasked as #28, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
Segmenting PflCD_imasked_imasked, density threshold 0.001870
Showing 8 region surfaces
142 watershed regions, grouped to 8 regions
Showing PflCD_imasked_imasked.seg - 8 regions, 8 surfaces
> select #25.2
1 model selected
> select add #25.3
2 models selected
> select add #25.1
3 models selected
Ungrouped to 7 regions
Ungrouped to 33 regions
> select #25.2
1 model selected
> select add #25.3
2 models selected
> select add #25.1
3 models selected
> select add #25.18
4 models selected
> select add #25.17
5 models selected
> select add #25.20
6 models selected
> hide #!28 models
Segmenting PflCD_imasked_imasked, density threshold 0.001870
Showing 8 region surfaces
142 watershed regions, grouped to 8 regions
Showing PflCD_imasked_imasked.seg - 8 regions, 8 surfaces
> select #25.8
1 model selected
> select add #25.7
2 models selected
> select add #25.4
3 models selected
Ungrouped to 8 regions
Ungrouped to 15 regions
Ungrouped to 8 regions
Ungrouped to 0 regions
> select #25.23
1 model selected
> select add #25.16
2 models selected
> select add #25.24
3 models selected
> select add #25.22
4 models selected
> select add #25.27
5 models selected
> select subtract #25.27
4 models selected
Grouped 4 regions
> select #25.27
1 model selected
Ungrouped to 0 regions
Showing 25 region surfaces
> select #25.8
1 model selected
Opened PflCD_imasked_imasked_imasked as #29, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> hide #!25 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/Polished-PflCD.mrc models #29
Cell requested for row 25 is out of bounds for table with 54 rows! Resizing
table model.
> close #26-28
> select add #25
26 models selected
> select subtract #25
Nothing selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume gaussian #29 sDev 2
Opened Polished-PflCD.mrc gaussian as #26, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> surface dust #26 size 40
> color #26 #c0c0c080 models
Drag select of 357 residues
> hide #24.16 models
> hide #24.17 models
> hide #24.18 models
Drag select of 203 residues
> hide #24.26 models
> select clear
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!14 models
> hide #!14 models
> show #!9 models
Drag select of 423 residues
Drag select of 3 residues
> hide sel cartoons
Drag select of 10 residues
> hide sel cartoons
Drag select of 15 residues
> hide sel cartoons
Drag select of 2 residues
> hide sel cartoons
> hide #24.15 models
> show #24.15 models
> hide #24.15 models
> show #24.15 models
> hide #!26 models
> select clear
Drag select of 168 residues
> color #24.25 #b2c89dff
> color #24.25 #b9d0a3ff
> color #24.25 #95d0a7ff
> color #24.25 #95d0a4ff
> color #24.25 #9ed0afff
> color #24.25 #75d09dff
> color #24.25 #73d0a5ff
> color #24.25 #47d07eff
> color #24.25 #92d0aeff
> color #24.25 #82d08fff
> color #24.25 #9ed0a6ff
> color #24.25 #c2ffcbff
> color #24.25 #9db8ffff
> color #24.25 #7889ffff
> color #24.25 #7494ffff
> color #24.25 #7593ffff
> color #24.25 #7881ffff
> color #24.25 #7a83ffff
> color #24.25 #7b80ffff
> select clear
> show #24.26 models
> hide #24.26 models
> hide #24.25 models
> show #24.25 models
> hide #24.27 models
> show #24.27 models
> color #24.27 #7b80ffff
> color #24.28 #7b80ffff
> hide #24.21 models
> show #24.21 models
> hide #24.19 models
> show #24.19 models
> hide #24.19 models
> show #24.19 models
> hide #24.20 models
> show #24.20 models
> hide #24.21 models
> show #24.21 models
> color #24.21 #ff7b61ff
> color #24.21 #c7ffc7ff
> color #24.21 #caffddff
> color #24.21 #adffc1ff
> hide #24.23 models
> show #24.23 models
> hide #24.24 models
> show #24.24 models
> color #24.24 #adffc1ff
> hide #24.20 models
> show #24.20 models
> hide #24.15 models
> show #24.15 models
> color #24.15 #adffc1ff
> hide #24.3 models
> show #24.3 models
> color #24.3 #adffc1ff
> hide #24.10 models
> show #24.10 models
> hide #24.11 models
> show #24.11 models
> hide #24.12 models
> show #24.12 models
> color #24.12 #adffc1ff
> color #24.9 #adffc1ff
> color #24.6 #adffc1ff
> hide #24.2 models
> show #24.2 models
> color #24.2 #4a9ed2ff
> color #24.2 #3ab3ffff
> color #24.2 #23a0d0ff
> color #24.2 #1580d9ff
> color #24.2 #2c94d9ff
> color #24.2 #33aeffff
> color #24.2 #2275ffff
> color #24.2 #1c8bffff
> color #24.2 #1886ffff
> color #24.2 #1b7bffff
> color #24.2 #0b6dffff
> hide #24.5 models
> show #24.5 models
> hide #24.5 models
> show #24.5 models
> select add #24.5
1458 atoms, 1488 bonds, 175 residues, 1 model selected
> hide #24.14 models
> show #24.14 models
> select add #24.14
2916 atoms, 2976 bonds, 350 residues, 2 models selected
> hide #24.22 models
> show #24.22 models
> hide #24.22 models
> show #24.22 models
> hide #24.23 models
> show #24.23 models
> select add #24.23
4374 atoms, 4464 bonds, 525 residues, 3 models selected
> hide #24.10 models
> show #24.10 models
> hide #24.11 models
> show #24.11 models
> select add #24.11
5832 atoms, 5952 bonds, 700 residues, 4 models selected
> hide #24.1 models
> show #24.1 models
> select add #24.20
7290 atoms, 7440 bonds, 875 residues, 5 models selected
> color sel #0b6dffff
> select clear
> hide #24.10 models
> show #24.10 models
> color #24.10 #ffc32eff
> color #24.10 #1eddffff
> color #24.10 #20deffff
> color #24.10 #20e0ffff
> select add #24.13
1542 atoms, 1564 bonds, 189 residues, 1 model selected
> select add #24.19
3084 atoms, 3128 bonds, 378 residues, 2 models selected
> select subtract #24.19
1542 atoms, 1564 bonds, 189 residues, 1 model selected
> select add #24.19
3084 atoms, 3128 bonds, 378 residues, 2 models selected
> select add #24.22
4626 atoms, 4692 bonds, 567 residues, 3 models selected
> select add #24.4
6168 atoms, 6256 bonds, 756 residues, 4 models selected
> select add #24.1
7710 atoms, 7820 bonds, 945 residues, 5 models selected
> color sel #20e0ffff
> select clear
> hide #!13 models
> select add #13
18892 atoms, 19223 bonds, 2 pseudobonds, 2334 residues, 2 models selected
> show #!13 models
> select subtract #13
7 models selected
> show #!26 models
> surface dust #9 size 21.4
> surface dust #21 size 21.4
> surface dust #26 size 21.4
> hide #!26 models
> show #!26 models
> volume #26 level 0.001017
> combine #24
> hide #!24 models
> select #9
2 models selected
> select #9
2 models selected
> select clear
> select #9
2 models selected
> select #9
2 models selected
> select clear
> surface dust #9 size 50
> hide #!26 models
> hide #!21 models
> show #!21 models
Segmenting Cages2.mrc, density threshold 0.001871
Showing 18 region surfaces
194 watershed regions, grouped to 18 regions
Showing Cages2.seg - 18 regions, 18 surfaces
> select #25.7
1 model selected
> select add #25.17
2 models selected
> select add #25.12
3 models selected
Opened Cages2_imasked as #28, grid size 200,200,200, pixel 2.14, shown at step
1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/Polished_Cage2.mrc models #28
> select clear
> hide #!25 models
> hide #!21 models
> volume gaussian #28 sDev 2
Opened Polished_Cage2.mrc gaussian as #30, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> color #30 #c0c0c080 models
> hide #27 models
> show #!24 models
> select add #24.1
1542 atoms, 1564 bonds, 189 residues, 1 model selected
> select subtract #24.1
Nothing selected
> hide #24.1 models
> show #24.1 models
> hide #24.14 models
> show #24.14 models
> hide #24.4 models
> hide #24.5 models
> hide #24.6 models
> hide #24.9 models
> show #!29 models
> select add #29
2 models selected
> select subtract #29
Nothing selected
> hide #!29 models
> show #!26 models
> save /Users/shoichitachiyama/Desktop/For_PflCD.cxs includeMaps true
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-Chimera-PflAB/Resegment/Part3/IM2.mrc"
Opened IM2.mrc as #31, grid size 200,200,200, pixel 2.14, shown at level
0.0151, step 1, values float32
> volume #31 level 0.001791
Segmenting IM2.mrc, density threshold 0.001791
Showing 76 region surfaces
1167 watershed regions, grouped to 76 regions
Showing IM2.seg - 76 regions, 76 surfaces
> select #25.71
1 model selected
> select add #25.36
2 models selected
> select add #25.19
3 models selected
> select add #25.4
4 models selected
> select add #25.26
5 models selected
> select add #25.2
6 models selected
> select add #25.14
7 models selected
> select add #25.3
8 models selected
> select add #25.13
9 models selected
> select add #25.32
10 models selected
> select add #25.39
11 models selected
> select add #25.10
12 models selected
> select add #25.8
13 models selected
> select add #25.18
14 models selected
> select add #25.34
15 models selected
> select add #25.47
16 models selected
> select add #25.16
17 models selected
> select add #25.20
18 models selected
> select add #25.28
19 models selected
> select add #25.69
20 models selected
> select add #25.30
21 models selected
> select add #25.49
22 models selected
> select add #25.27
23 models selected
> select add #25.53
24 models selected
> select add #25.68
25 models selected
> select add #25.7
26 models selected
> select add #25.1
27 models selected
> hide #!31 models
> select add #25.42
28 models selected
> select add #25.76
29 models selected
> select add #25.52
30 models selected
> select add #25.29
31 models selected
> select add #25.57
32 models selected
> select add #25.9
33 models selected
> select add #25.60
34 models selected
> select add #25.43
35 models selected
> select add #25.72
36 models selected
> select add #25.73
37 models selected
> select add #25.21
38 models selected
> select add #25.50
39 models selected
> select add #25.40
40 models selected
> select add #25.37
41 models selected
> select add #25.38
42 models selected
> select add #25.33
43 models selected
> select add #25.70
44 models selected
> select add #25.61
45 models selected
> select add #25.46
46 models selected
> select add #25.62
47 models selected
> select add #25.75
48 models selected
> select add #25.74
49 models selected
> select add #25.17
50 models selected
> select add #25.41
51 models selected
> select add #25.65
52 models selected
> select add #25.12
53 models selected
> select add #25.22
54 models selected
> select add #25.15
55 models selected
> select add #25.35
56 models selected
> select add #25.45
57 models selected
> select add #25.5
58 models selected
> select add #25.66
59 models selected
> select add #25.6
60 models selected
> select add #25.51
61 models selected
> select add #25.23
62 models selected
Grouped 62 regions
Opened IM2_imasked as #32, grid size 200,200,200, pixel 2.14, shown at step 1,
values float32
Segmenting IM2_imasked, density threshold 0.001791
Showing 14 region surfaces
133 watershed regions, grouped to 14 regions
Showing IM2_imasked.seg - 14 regions, 14 surfaces
> hide #!25 models
> volume #32 level 0.001462
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/Polished-IM2.mrc models #32
> close #31
> volume gaussian #32 sDev 8
Opened Polished-IM2.mrc gaussian as #31, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> close #31
> volume gaussian #32 sDev 6
Opened Polished-IM2.mrc gaussian as #31, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> close #30
> show #!28 models
> volume gaussian #28 sDev 2
Opened Polished_Cage2.mrc gaussian as #30, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> color #30 #c0c0c080 models
> close #31
> volume gaussian #32 sDev 4
Opened Polished-IM2.mrc gaussian as #31, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> surface dust #31 size 50
> color #31 #c0c0c080 models
> save /Users/shoichitachiyama/Desktop/For_PflCD.cxs includeMaps true
> hide #24.1 models
> show #24.1 models
> hide #24.1 models
> show #24.1 models
> hide #!24 models
> show #27 models
> hide #27 models
> show #27 models
> hide #27 models
> show #!24 models
> hide #24.1 models
> show #24.1 models
> hide #24.1 models
> hide #24.2 models
> hide #24.3 models
> show #24.3 models
> show #24.2 models
> show #24.1 models
> hide #!24 models
> select add #24
46256 atoms, 47176 bonds, 5632 residues, 29 models selected
> select subtract #24
Nothing selected
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> hide #!31 models
> show #!31 models
> show #!30 models
> hide #!26 models
> show #!26 models
Segmenting Polished-PflCD.mrc gaussian, density threshold 0.001017
Showing 6 region surfaces
70 watershed regions, grouped to 6 regions
Showing Polished-PflCD gaussian.seg - 6 regions, 6 surfaces
> select #25.5
1 model selected
> select add #25.2
2 models selected
> select add #25.4
3 models selected
> select add #25.3
4 models selected
Opened Polished-PflCD_imasked as #33, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/Polished-PflCD_single.mrc models #33
> hide #!25 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #!30 models
Segmenting Polished_Cage2.mrc gaussian, density threshold 0.001839
Showing 14 region surfaces
88 watershed regions, grouped to 14 regions
Showing Polished_Cage2 gaussian.seg - 14 regions, 14 surfaces
> select #25.1
1 model selected
Opened Polished_Cage2_imasked as #34, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/Single-Cage.mrc models #34
> select clear
> select #25.1
1 model selected
> select add #25.10
2 models selected
> select add #25.12
3 models selected
> select add #25.6
4 models selected
Opened Polished_Cage2_imasked as #35, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/Single-Cage-arch.mrc models #35
> save /Users/shoichitachiyama/Desktop/For_PflCD.cxs includeMaps true
——— End of log from Fri Jul 11 22:22:46 2025 ———
opened ChimeraX session
Showing Polished_Cage2 gaussian.seg - 14 regions, 14 surfaces
> hide #!25 models
> hide #!35 models
> hide #!34 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> hide #!31 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> hide #!26 models
> hide #!24 models
> show #!24 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!34 models
> hide #!34 models
> select add #24.19
1542 atoms, 1564 bonds, 189 residues, 1 model selected
> select subtract #24.19
Nothing selected
> select add #24.20
1458 atoms, 1488 bonds, 175 residues, 1 model selected
> select subtract #24.20
Nothing selected
> select add #24.11
1458 atoms, 1488 bonds, 175 residues, 1 model selected
> select subtract #24.11
Nothing selected
> select add #24.1
1542 atoms, 1564 bonds, 189 residues, 1 model selected
> select subtract #24.1
Nothing selected
> select add #24.13
1542 atoms, 1564 bonds, 189 residues, 1 model selected
> select subtract #24.13
Nothing selected
> select add #24.10
1542 atoms, 1564 bonds, 189 residues, 1 model selected
> select add #24.11
3000 atoms, 3052 bonds, 364 residues, 2 models selected
> select subtract #24.11
1542 atoms, 1564 bonds, 189 residues, 1 model selected
> select subtract #24.10
Nothing selected
> select add #24.22
1542 atoms, 1564 bonds, 189 residues, 1 model selected
> select add #24.23
3000 atoms, 3052 bonds, 364 residues, 2 models selected
> select add #24.24
4355 atoms, 4440 bonds, 526 residues, 3 models selected
> mlp sel
Map values for surface "Cage-PflCD.pdb_V SES surface": minimum -25.84, mean
-2.565, maximum 23.8
Map values for surface "Cage-PflCD.pdb_X SES surface": minimum -25.94, mean
-2.294, maximum 23.72
Map values for surface "Cage-PflCD.pdb_W SES surface": minimum -28.76, mean
-1.748, maximum 22.7
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
[Repeated 1 time(s)]
> show sel surfaces
> hide sel surfaces
> select clear
[Repeated 2 time(s)]Drag select of 127 residues
> hide sel cartoons
> hide #!13 models
> hide #!9 models
Drag select of 432 residues
> select clear
Drag select of 910 residues
> select add #24.1
8516 atoms, 1564 bonds, 1043 residues, 10 models selected
> select subtract #24.1
6974 atoms, 854 residues, 9 models selected
> select add #24.2
7866 atoms, 1488 bonds, 959 residues, 9 models selected
> select subtract #24.2
6408 atoms, 784 residues, 8 models selected
> select add #24.3
7528 atoms, 1388 bonds, 917 residues, 8 models selected
> select subtract #24.3
6173 atoms, 755 residues, 7 models selected
> save /Users/shoichitachiyama/Desktop/Single_unit_cage-PflCD.pdb selectedOnly
> true
> show #!35 models
> select clear
> select add #24.22
1542 atoms, 1564 bonds, 189 residues, 1 model selected
> select add #24.23
3000 atoms, 3052 bonds, 364 residues, 3 models selected
> select add #24.24
4355 atoms, 4440 bonds, 526 residues, 5 models selected
> select add #24.28
7209 atoms, 7354 bonds, 882 residues, 7 models selected
> show sel cartoons
> select clear
Drag select of 152 residues
> hide sel cartoons
Drag select of 139 residues, 35 Single-Cage-arch.mrc
> hide sel cartoons
> hide #!35 models
Drag select of 1112 residues
> select add #24.1
11927 atoms, 1564 bonds, 1457 residues, 13 models selected
> select subtract #24.1
10385 atoms, 1268 residues, 12 models selected
> select add #24.2
10747 atoms, 1488 bonds, 1310 residues, 12 models selected
> select subtract #24.2
9289 atoms, 1135 residues, 11 models selected
> select add #24.3
9800 atoms, 1388 bonds, 1196 residues, 11 models selected
> select subtract #24.3
8445 atoms, 1034 residues, 10 models selected
> select clear
Drag select of 934 residues
> select add #24.1
8558 atoms, 1564 bonds, 1046 residues, 10 models selected
> select subtract #24.1
7016 atoms, 857 residues, 9 models selected
> select add #24.2
7789 atoms, 1488 bonds, 949 residues, 9 models selected
> select subtract #24.2
6331 atoms, 774 residues, 8 models selected
> select add #24.3
7433 atoms, 1388 bonds, 905 residues, 8 models selected
> select subtract #24.3
6078 atoms, 743 residues, 7 models selected
Drag select of 374 residues
> save /Users/shoichitachiyama/Desktop/Single_unit_cage-PflCD.pdb selectedOnly
> true
> select clear
> hide #!24 models
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-PflCD/For_correlation/Single_unit_cage-PflCD.pdb"
Chain information for Single_unit_cage-PflCD.pdb
---
Chain | Description
36.1/J | No description available
36.2/K | No description available
36.3/L | No description available
36.4/V | No description available
36.5/W | No description available
36.6/X | No description available
36.7/c | No description available
Cell requested for row 23 is out of bounds for table with 63 rows! Resizing
table model.
> show #!33 models
> select add #36.6
1094 atoms, 1122 bonds, 130 residues, 1 model selected
> select subtract #36.6
Nothing selected
> hide #36.1 models
> hide #36.2 models
> hide #36.3 models
> hide #36.4 models
> hide #36.5 models
> select add #36.6
1094 atoms, 1122 bonds, 130 residues, 1 model selected
Alignment identifier is 36.6/X
> select clear
> select #36.6/X:33
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #36.6/X:33-90
482 atoms, 496 bonds, 58 residues, 1 model selected
> hide sel cartoons
> hide #!33 models
> select clear
[Repeated 1 time(s)]Drag select of 428 residues
> save /Users/shoichitachiyama/Desktop/PflC-PflD_correlation.pdb selectedOnly
> true
> select clear
[Repeated 1 time(s)]
> show #!33 models
> hide #!36 models
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-PflCD/For_correlation/PflC-PflD_correlation.pdb"
Chain information for PflC-PflD_correlation.pdb
---
Chain | Description
37.1/X | No description available
37.2/c | No description available
> combine #37
> ui tool show "Fit in Map"
> hide #!37 models
> show #!37 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]Opened combination map 10 as #39, grid size 42,39,48,
pixel 3.33, shown at level 0.0506, step 1, values float32
> fitmap #38 inMap #33 resolution 10 metric correlation
Fit map combination map 10 in map Polished-PflCD_single.mrc using 2607 points
correlation = 0.8562, correlation about mean = 0.4646, overlap = 17.28
steps = 80, shift = 4.98, angle = 8.4 degrees
Position of combination map 10 (#39) relative to Polished-PflCD_single.mrc
(#33) coordinates:
Matrix rotation and translation
0.99274857 -0.11124388 0.04555301 8.94210763
0.11465872 0.99010784 -0.08086926 -6.41782952
-0.03610619 0.08550589 0.99568323 -5.68708707
Axis 0.56938774 0.27946328 0.77310923
Axis point 60.37593490 82.07118066 0.00000000
Rotation angle (degrees) 8.40098598
Shift along axis -1.09876073
Average map value = 0.02984 for 3466 atoms, 138 outside contour
> hide #!37 models
> split #38
Split combination (#38) into 2 models
Chain information for combination X #38.1
---
Chain | Description
X | No description available
Chain information for combination c #38.2
---
Chain | Description
c | No description available
> select add #38.2
2854 atoms, 2914 bonds, 356 residues, 1 model selected
> color sel #7b80ffff
> select subtract #38.2
Nothing selected
> select add #38.1
612 atoms, 625 bonds, 72 residues, 1 model selected
> color sel #adffc1ff
> select clear
> volume #33 level 0.008475
> volume #33 level 0.00102
> save /Users/shoichitachiyama/Desktop/PflC-PflD.png supersample 2
> transparentBackground true
> hide #!38 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!34 models
> show #!35 models
> hide #!34 models
> show #!38 models
> hide #!38 models
> show #!38 models
> hide #!38 models
> show #!38 models
> show #!37 models
> hide #!37 models
> show #!36 models
> hide #36.6 models
> hide #36.7 models
> hide #!38 models
> show #36.1 models
> show #36.2 models
> show #36.3 models
> show #36.4 models
> show #36.5 models
> select add #36.1
1021 atoms, 1038 bonds, 123 residues, 1 model selected
> select add #36.2
2052 atoms, 2085 bonds, 247 residues, 2 models selected
> select add #36.3
3119 atoms, 3179 bonds, 374 residues, 3 models selected
> select add #36.4
4182 atoms, 4259 bonds, 502 residues, 4 models selected
> select add #36.5
5249 atoms, 5342 bonds, 631 residues, 5 models selected
> save /Users/shoichitachiyama/Desktop/Cage_arch_single.pdb selectedOnly true
> select clear
[Repeated 1 time(s)]
> hide #!36 models
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-PflCD/For_correlation/Cage_arch_single.pdb"
Summary of feedback from opening /Volumes/Lab Backup/Jun Liu Lab 2025/Project
files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-refinment/For-
PflCD/For_correlation/Cage_arch_single.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 49 1 48
Start residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1
42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
150 messages similar to the above omitted
Chain information for Cage_arch_single.pdb
---
Chain | Description
40.1/J | No description available
40.2/K | No description available
40.3/L | No description available
40.4/V | No description available
40.5/W | No description available
Cell requested for row 35 is out of bounds for table with 46 rows! Resizing
table model.
> show #!24 models
> hide #40.1 models
> show #40.1 models
> hide #40.1 models
> show #40.1 models
> color #40.1 #20e0ffff
> hide #40.4 models
> show #40.4 models
> color #40.4 #20e0ffff
> hide #40.2 models
> show #40.2 models
> color #40.2 #0b6dffff
> color #40.5 #0b6dffff
> color #40.3 #adffc1ff
> hide #!24 models
> combine #40
> hide #!40 models
Opened combination map 10 as #42, grid size 38,53,56, pixel 3.33, shown at
level 0.0458, step 1, values float32
> fitmap #41 inMap #35 resolution 10 metric correlation
Fit map combination map 10 in map Single-Cage-arch.mrc using 4180 points
correlation = 0.7956, correlation about mean = 0.4574, overlap = 26.74
steps = 72, shift = 5.32, angle = 3.33 degrees
Position of combination map 10 (#42) relative to Single-Cage-arch.mrc (#35)
coordinates:
Matrix rotation and translation
0.99870695 -0.04614412 -0.02133420 10.32762731
0.04672537 0.99852640 0.02760031 -26.24679973
0.02002917 -0.02856147 0.99939135 -1.58990356
Axis -0.48354610 -0.35613357 0.79959493
Axis point 545.82748063 240.81579688 0.00000000
Rotation angle (degrees) 3.32920138
Shift along axis 3.08220380
Average map value = 0.03088 for 5249 atoms, 746 outside contour
> fitmap #41 inMap #35 resolution 10 metric correlation
Fit map combination map 10 in map Single-Cage-arch.mrc using 4180 points
correlation = 0.7956, correlation about mean = 0.4572, overlap = 26.75
steps = 48, shift = 0.05, angle = 0.0501 degrees
Position of combination map 10 (#42) relative to Single-Cage-arch.mrc (#35)
coordinates:
Matrix rotation and translation
0.99873977 -0.04552554 -0.02112587 10.16347165
0.04608967 0.99857148 0.02703206 -25.86218474
0.01986504 -0.02797168 0.99941131 -1.65252969
Axis -0.48058800 -0.35815276 0.80047596
Axis point 544.83671207 240.41933412 0.00000000
Rotation angle (degrees) 3.28056932
Shift along axis 3.05535998
Average map value = 0.03088 for 5249 atoms, 743 outside contour
> fitmap #41 inMap #35 resolution 10 metric correlation
Fit map combination map 10 in map Single-Cage-arch.mrc using 4180 points
correlation = 0.7956, correlation about mean = 0.4574, overlap = 26.74
steps = 28, shift = 0.0466, angle = 0.0465 degrees
Position of combination map 10 (#42) relative to Single-Cage-arch.mrc (#35)
coordinates:
Matrix rotation and translation
0.99871133 -0.04607228 -0.02128416 10.30393269
0.04665207 0.99852989 0.02759786 -26.21997239
0.01998138 -0.02855525 0.99939249 -1.57782840
Axis -0.48411769 -0.35576619 0.79941259
Axis point 546.14127084 240.71974845 0.00000000
Rotation angle (degrees) 3.32475180
Shift along axis 3.07852771
Average map value = 0.03088 for 5249 atoms, 746 outside contour
> fitmap #41 inMap #35 resolution 10 metric correlation
Fit map combination map 10 in map Single-Cage-arch.mrc using 4180 points
correlation = 0.7956, correlation about mean = 0.4572, overlap = 26.74
steps = 28, shift = 0.0332, angle = 0.0229 degrees
Position of combination map 10 (#42) relative to Single-Cage-arch.mrc (#35)
coordinates:
Matrix rotation and translation
0.99871967 -0.04586270 -0.02134548 10.28568035
0.04643765 0.99854895 0.02726791 -26.04076667
0.02006392 -0.02822424 0.99940024 -1.66680369
Axis -0.48093447 -0.35888334 0.79994049
Axis point 544.61451298 241.21362930 0.00000000
Rotation angle (degrees) 3.30734490
Shift along axis 3.06551528
Average map value = 0.03088 for 5249 atoms, 745 outside contour
> fitmap #41 inMap #35 resolution 10 metric correlation
Fit map combination map 10 in map Single-Cage-arch.mrc using 4180 points
correlation = 0.7956, correlation about mean = 0.4572, overlap = 26.75
steps = 44, shift = 0.0078, angle = 0.0237 degrees
Position of combination map 10 (#42) relative to Single-Cage-arch.mrc (#35)
coordinates:
Matrix rotation and translation
0.99873362 -0.04569750 -0.02104485 10.17702551
0.04625949 0.99856342 0.02704007 -25.92640893
0.01977895 -0.02797935 0.99941280 -1.62205828
Axis -0.47979568 -0.35600312 0.80190890
Axis point 544.45356004 239.59996732 0.00000000
Rotation angle (degrees) 3.28693076
Shift along axis 3.04624646
Average map value = 0.03088 for 5249 atoms, 743 outside contour
> fitmap #41 inMap #35 resolution 10 metric correlation
Fit map combination map 10 in map Single-Cage-arch.mrc using 4180 points
correlation = 0.7956, correlation about mean = 0.4572, overlap = 26.74
steps = 40, shift = 0.00396, angle = 0.0133 degrees
Position of combination map 10 (#42) relative to Single-Cage-arch.mrc (#35)
coordinates:
Matrix rotation and translation
0.99873019 -0.04569884 -0.02120454 10.21608250
0.04626865 0.99855842 0.02720834 -25.97226518
0.01993058 -0.02815489 0.99940486 -1.63858169
Axis -0.48159776 -0.35782929 0.80001362
Axis point 545.14877699 240.68089744 0.00000000
Rotation angle (degrees) 3.29510322
Shift along axis 3.06270699
Average map value = 0.03088 for 5249 atoms, 745 outside contour
> fitmap #41 inMap #35 resolution 10 metric correlation
Fit map combination map 10 in map Single-Cage-arch.mrc using 4180 points
correlation = 0.7956, correlation about mean = 0.4574, overlap = 26.74
steps = 40, shift = 0.0295, angle = 0.00651 degrees
Position of combination map 10 (#42) relative to Single-Cage-arch.mrc (#35)
coordinates:
Matrix rotation and translation
0.99872620 -0.04579540 -0.02118378 10.21798131
0.04636569 0.99855244 0.02726245 -26.04302015
0.01990463 -0.02820992 0.99940383 -1.61465143
Axis -0.48174761 -0.35683070 0.80036935
Axis point 545.50113893 240.33009133 0.00000000
Rotation angle (degrees) 3.30057793
Shift along axis 3.07814345
Average map value = 0.03088 for 5249 atoms, 746 outside contour
> fitmap #41 inMap #35 resolution 10 metric correlation
Fit map combination map 10 in map Single-Cage-arch.mrc using 4180 points
correlation = 0.7956, correlation about mean = 0.4572, overlap = 26.75
steps = 44, shift = 0.0312, angle = 0.0124 degrees
Position of combination map 10 (#42) relative to Single-Cage-arch.mrc (#35)
coordinates:
Matrix rotation and translation
0.99873308 -0.04567366 -0.02112243 10.19099109
0.04623894 0.99856284 0.02709625 -25.93458566
0.01985449 -0.02803860 0.99940964 -1.63536141
Axis -0.48049038 -0.35710648 0.80100184
Axis point 544.75360054 240.15232394 0.00000000
Rotation angle (degrees) 3.28906721
Shift along axis 3.05480800
Average map value = 0.03088 for 5249 atoms, 744 outside contour
> fitmap #41 inMap #35 resolution 10 metric correlation
Fit map combination map 10 in map Single-Cage-arch.mrc using 4180 points
correlation = 0.7956, correlation about mean = 0.4574, overlap = 26.74
steps = 72, shift = 5.32, angle = 3.33 degrees
Position of combination map 10 (#42) relative to Single-Cage-arch.mrc (#35)
coordinates:
Matrix rotation and translation
0.99870695 -0.04614412 -0.02133420 10.32762731
0.04672537 0.99852640 0.02760031 -26.24679973
0.02002917 -0.02856147 0.99939135 -1.58990356
Axis -0.48354610 -0.35613357 0.79959493
Axis point 545.82748063 240.81579688 0.00000000
Rotation angle (degrees) 3.32920138
Shift along axis 3.08220380
Average map value = 0.03088 for 5249 atoms, 746 outside contour
> fitmap #41 inMap #35 resolution 10 metric correlation
Fit map combination map 10 in map Single-Cage-arch.mrc using 4180 points
correlation = 0.7956, correlation about mean = 0.4574, overlap = 26.74
steps = 72, shift = 5.32, angle = 3.33 degrees
Position of combination map 10 (#42) relative to Single-Cage-arch.mrc (#35)
coordinates:
Matrix rotation and translation
0.99870695 -0.04614412 -0.02133420 10.32762731
0.04672537 0.99852640 0.02760031 -26.24679973
0.02002917 -0.02856147 0.99939135 -1.58990356
Axis -0.48354610 -0.35613357 0.79959493
Axis point 545.82748063 240.81579688 0.00000000
Rotation angle (degrees) 3.32920138
Shift along axis 3.08220380
Average map value = 0.03088 for 5249 atoms, 746 outside contour
> fitmap #41 inMap #35 resolution 10 metric correlation
Fit map combination map 10 in map Single-Cage-arch.mrc using 4180 points
correlation = 0.7956, correlation about mean = 0.4574, overlap = 26.74
steps = 72, shift = 5.32, angle = 3.33 degrees
Position of combination map 10 (#42) relative to Single-Cage-arch.mrc (#35)
coordinates:
Matrix rotation and translation
0.99870695 -0.04614412 -0.02133420 10.32762731
0.04672537 0.99852640 0.02760031 -26.24679973
0.02002917 -0.02856147 0.99939135 -1.58990356
Axis -0.48354610 -0.35613357 0.79959493
Axis point 545.82748063 240.81579688 0.00000000
Rotation angle (degrees) 3.32920138
Shift along axis 3.08220380
Average map value = 0.03088 for 5249 atoms, 746 outside contour
> hide #!35 models
> show #!35 models
> show #!36 models
> hide #!36 models
> show #!33 models
> hide #!35 models
> hide #41 models
> show #!38 models
> show #!37 models
> close #38
> combine #37
> hide #!37 models
> show #!37 models
> fitmap #38 inMap #33 resolution 10 metric correlation
Fit map combination map 10 in map Polished-PflCD_single.mrc using 2607 points
correlation = 0.8562, correlation about mean = 0.4646, overlap = 17.28
steps = 80, shift = 4.98, angle = 8.4 degrees
Position of combination map 10 (#39) relative to Polished-PflCD_single.mrc
(#33) coordinates:
Matrix rotation and translation
0.99274857 -0.11124388 0.04555301 8.94210763
0.11465872 0.99010784 -0.08086926 -6.41782952
-0.03610619 0.08550589 0.99568323 -5.68708707
Axis 0.56938774 0.27946328 0.77310923
Axis point 60.37593490 82.07118066 0.00000000
Rotation angle (degrees) 8.40098598
Shift along axis -1.09876073
Average map value = 0.02984 for 3466 atoms, 138 outside contour
> split #38
Split combination (#38) into 2 models
Chain information for combination X #38.1
---
Chain | Description
X | No description available
Chain information for combination c #38.2
---
Chain | Description
c | No description available
> color #38.1 #adffc1ff
> color #38.2 #7b80ffff
> save /Users/shoichitachiyama/Desktop/PflC-PflD.png supersample 2
> transparentBackground true
[Repeated 1 time(s)]
> hide #!33 models
> hide #!37 models
> show #!35 models
> show #!37 models
> hide #!37 models
> show #!37 models
> hide #!38 models
> hide #!37 models
> show #41 models
> show #!40 models
> hide #41 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #41 models
> show #!40 models
> hide #41 models
> show #41 models
> hide #!40 models
> show #!40 models
> fitmap #41 inMap #35 resolution 10 metric correlation
Fit map combination map 10 in map Single-Cage-arch.mrc using 4180 points
correlation = 0.7956, correlation about mean = 0.4574, overlap = 26.74
steps = 72, shift = 5.32, angle = 3.33 degrees
Position of combination map 10 (#42) relative to Single-Cage-arch.mrc (#35)
coordinates:
Matrix rotation and translation
0.99870695 -0.04614412 -0.02133420 10.32762731
0.04672537 0.99852640 0.02760031 -26.24679973
0.02002917 -0.02856147 0.99939135 -1.58990356
Axis -0.48354610 -0.35613357 0.79959493
Axis point 545.82748063 240.81579688 0.00000000
Rotation angle (degrees) 3.32920138
Shift along axis 3.08220380
Average map value = 0.03088 for 5249 atoms, 746 outside contour
> fitmap #41 inMap #35 resolution 10 metric correlation
Fit map combination map 10 in map Single-Cage-arch.mrc using 4180 points
correlation = 0.7956, correlation about mean = 0.4574, overlap = 26.74
steps = 72, shift = 5.32, angle = 3.33 degrees
Position of combination map 10 (#42) relative to Single-Cage-arch.mrc (#35)
coordinates:
Matrix rotation and translation
0.99870695 -0.04614412 -0.02133420 10.32762731
0.04672537 0.99852640 0.02760031 -26.24679973
0.02002917 -0.02856147 0.99939135 -1.58990356
Axis -0.48354610 -0.35613357 0.79959493
Axis point 545.82748063 240.81579688 0.00000000
Rotation angle (degrees) 3.32920138
Shift along axis 3.08220380
Average map value = 0.03088 for 5249 atoms, 746 outside contour
> save /Users/shoichitachiyama/Desktop/For_Cage_PflCD.cxs includeMaps true
——— End of log from Sat Jul 12 20:19:26 2025 ———
opened ChimeraX session
Showing Polished_Cage2 gaussian.seg - 14 regions, 14 surfaces
> hide #!25 models
> show #!1 models
> hide #!1 models
> close session
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-Chimera-PflAB/Rev-CJFlgYPlfAB-2.1A.mrc"
Opened Rev-CJFlgYPlfAB-2.1A.mrc as #1, grid size 200,200,200, pixel 2.14,
shown at level 0.0478, step 1, values float32
> volume #1 level 0.007113
> ui tool show "Segment Map"
Segmenting Rev-CJFlgYPlfAB-2.1A.mrc, density threshold 0.007113
Showing 628 region surfaces
38016 watershed regions, grouped to 628 regions
Showing Rev-CJFlgYPlfAB-2.1A.seg - 628 regions, 628 surfaces
> select #2.121
1 model selected
> select add #2.11
2 models selected
> select add #2.105
3 models selected
> select add #2.425
4 models selected
> select add #2.396
5 models selected
> select add #2.228
6 models selected
> select add #2.22
7 models selected
> select add #2.111
8 models selected
> select add #2.39
9 models selected
> select add #2.137
10 models selected
> select add #2.290
11 models selected
> select add #2.83
12 models selected
> select add #2.60
13 models selected
> select add #2.1
14 models selected
> select add #2.210
15 models selected
> select add #2.158
16 models selected
> select add #2.17
17 models selected
> select add #2.85
18 models selected
> select add #2.120
19 models selected
> select add #2.353
20 models selected
> select add #2.243
21 models selected
> select add #2.343
22 models selected
> select add #2.173
23 models selected
> select subtract #2.173
22 models selected
> select add #2.147
23 models selected
> select add #2.303
24 models selected
> select add #2.173
25 models selected
> select add #2.87
26 models selected
> select add #2.172
27 models selected
> select add #2.463
28 models selected
> select add #2.25
29 models selected
> select add #2.86
30 models selected
> select add #2.4
31 models selected
> select add #2.19
32 models selected
> select add #2.170
33 models selected
> select add #2.441
34 models selected
> select add #2.23
35 models selected
> select add #2.95
36 models selected
> select add #2.144
37 models selected
> select add #2.315
38 models selected
> select add #2.313
39 models selected
> hide #!1 models
> select add #2.129
40 models selected
> select add #2.54
41 models selected
> select add #2.40
42 models selected
> select add #2.55
43 models selected
> select add #2.88
44 models selected
> select add #2.27
45 models selected
> select add #2.116
46 models selected
> select add #2.457
47 models selected
> select add #2.10
48 models selected
> select add #2.208
49 models selected
> select add #2.104
50 models selected
> select add #2.250
51 models selected
> select add #2.234
52 models selected
> select add #2.84
53 models selected
> select add #2.282
54 models selected
> select add #2.5
55 models selected
> select add #2.14
56 models selected
> select add #2.275
57 models selected
> select add #2.185
58 models selected
> select add #2.75
59 models selected
> select add #2.108
60 models selected
> select add #2.52
61 models selected
> select add #2.126
62 models selected
> select add #2.68
63 models selected
> select add #2.59
64 models selected
> select add #2.112
65 models selected
> select add #2.221
66 models selected
> select add #2.26
67 models selected
> select add #2.139
68 models selected
> select add #2.179
69 models selected
> select add #2.207
70 models selected
> select add #2.347
71 models selected
> select add #2.56
72 models selected
> select add #2.29
73 models selected
> select add #2.361
74 models selected
> select add #2.163
75 models selected
> select add #2.321
76 models selected
> select add #2.15
77 models selected
> select add #2.141
78 models selected
> select add #2.154
79 models selected
> select add #2.198
80 models selected
> select add #2.248
81 models selected
> select add #2.251
82 models selected
> select add #2.7
83 models selected
> select add #2.306
84 models selected
> select add #2.316
85 models selected
> select subtract #2.316
84 models selected
> select add #2.301
85 models selected
> select add #2.316
86 models selected
> select add #2.12
87 models selected
> select add #2.162
88 models selected
> select add #2.49
89 models selected
> select add #2.182
90 models selected
> select add #2.258
91 models selected
> select add #2.267
92 models selected
> select add #2.36
93 models selected
> select subtract #2.36
92 models selected
> select add #2.136
93 models selected
> select add #2.94
94 models selected
> select add #2.216
95 models selected
> select add #2.36
96 models selected
> select add #2.82
97 models selected
> select add #2.194
98 models selected
> select add #2.69
99 models selected
> select add #2.195
100 models selected
> select add #2.53
101 models selected
> select add #2.100
102 models selected
> select add #2.98
103 models selected
> select add #2.80
104 models selected
> select add #2.35
105 models selected
> select add #2.410
106 models selected
> select add #2.218
107 models selected
> select add #2.357
108 models selected
> select add #2.271
109 models selected
> select add #2.435
110 models selected
> select add #2.349
111 models selected
> select add #2.493
112 models selected
> select add #2.276
113 models selected
> select add #2.272
114 models selected
> select add #2.264
115 models selected
> select add #2.18
116 models selected
> select add #2.38
117 models selected
> select add #2.399
118 models selected
> select add #2.67
119 models selected
> select add #2.134
120 models selected
> select add #2.72
121 models selected
> select add #2.43
122 models selected
> select add #2.449
123 models selected
> select add #2.184
124 models selected
> select add #2.127
125 models selected
> select add #2.192
126 models selected
> select add #2.77
127 models selected
> select add #2.151
128 models selected
> select add #2.155
129 models selected
> select add #2.78
130 models selected
> select add #2.58
131 models selected
> select add #2.246
132 models selected
> select add #2.193
133 models selected
> select add #2.235
134 models selected
> select add #2.160
135 models selected
> select add #2.142
136 models selected
> select add #2.48
137 models selected
> select add #2.226
138 models selected
> select add #2.102
139 models selected
> select add #2.62
140 models selected
> select add #2.150
141 models selected
> select add #2.103
142 models selected
> select add #2.90
143 models selected
Drag select of 47328, 47 of 17728 triangles, 50570, 10 of 23168 triangles,
47408, 36 of 14584 triangles, 50525, 30 of 24132 triangles, 50457, 34 of 20492
triangles, 50382, 33 of 21380 triangles
> select add #2.93
148 models selected
> select add #2.8
149 models selected
> select add #2.96
150 models selected
> select add #2.101
151 models selected
> select add #2.51
152 models selected
> select add #2.21
153 models selected
> select add #2.24
154 models selected
> select add #2.287
155 models selected
> select add #2.61
156 models selected
> select add #2.124
157 models selected
> select add #2.119
158 models selected
> select add #2.32
159 models selected
> select add #2.125
160 models selected
> select add #2.204
161 models selected
> select subtract #2.204
160 models selected
> select add #2.255
161 models selected
> select add #2.204
162 models selected
> select add #2.117
163 models selected
> select subtract #2.117
162 models selected
> select add #2.117
163 models selected
> select add #2.175
164 models selected
> select add #2.113
165 models selected
> select add #2.262
166 models selected
> select add #2.344
167 models selected
> select add #2.376
168 models selected
> select add #2.90
169 models selected
> select add #2.169
170 models selected
> select add #2.205
171 models selected
> select add #2.308
172 models selected
> select add #2.252
173 models selected
> select add #2.281
174 models selected
> select add #2.167
175 models selected
Drag select of 50372, 10 of 17540 triangles, 50387, 24 of 15784 triangles,
50187, 5 of 11000 triangles, 49741, 12 of 10360 triangles, 50750, 54 of 22704
triangles, 47396, 16 of 7912 triangles
> select subtract #2.167
180 models selected
> select add #2.115
181 models selected
> select add #2.164
182 models selected
> select add #2.206
183 models selected
> select add #2.232
184 models selected
> select add #2.143
185 models selected
> select add #2.214
186 models selected
> select add #2.178
187 models selected
> select add #2.259
188 models selected
> select add #2.66
189 models selected
> select add #2.202
190 models selected
> select add #2.146
191 models selected
> select add #2.199
192 models selected
> select add #2.135
193 models selected
> select add #2.63
194 models selected
> select add #2.254
195 models selected
> select add #2.16
196 models selected
> select add #2.317
197 models selected
> select add #2.168
198 models selected
> select add #2.196
199 models selected
> select add #2.132
200 models selected
> select add #2.334
201 models selected
> select add #2.392
202 models selected
> select add #2.294
203 models selected
> select add #2.318
204 models selected
> select add #2.167
205 models selected
> select add #2.291
206 models selected
> select add #2.2
207 models selected
> select add #2.176
208 models selected
> select add #2.437
209 models selected
> select add #2.46
210 models selected
> select add #2.378
211 models selected
> select add #2.398
212 models selected
> select add #2.212
213 models selected
> select add #2.231
214 models selected
> select add #2.34
215 models selected
> select add #2.419
216 models selected
> select add #2.213
217 models selected
> select add #2.340
218 models selected
> select add #2.31
219 models selected
> select add #2.13
220 models selected
> select add #2.292
221 models selected
> select add #2.330
222 models selected
> select add #2.240
223 models selected
> select add #2.106
224 models selected
> select add #2.237
225 models selected
> select add #2.30
226 models selected
> select add #2.89
227 models selected
> select add #2.33
228 models selected
> select add #2.107
229 models selected
> select add #2.42
230 models selected
> select add #2.114
231 models selected
> select add #2.439
232 models selected
> select subtract #2.439
231 models selected
> select add #2.300
232 models selected
> select add #2.401
233 models selected
> select add #2.265
234 models selected
> select add #2.322
235 models selected
> select add #2.293
236 models selected
> select add #2.338
237 models selected
> select add #2.358
238 models selected
> select add #2.257
239 models selected
> select add #2.331
240 models selected
> select add #2.389
241 models selected
> select add #2.201
242 models selected
> select add #2.286
243 models selected
> select add #2.450
244 models selected
> select add #2.426
245 models selected
> select add #2.203
246 models selected
> select add #2.390
247 models selected
> select add #2.138
248 models selected
> select add #2.97
249 models selected
> select add #2.152
250 models selected
> select add #2.3
251 models selected
> select add #2.45
252 models selected
> select add #2.305
253 models selected
Drag select of 49779, 128 of 23888 triangles, 50669, 118 of 45648 triangles,
50340, 22 of 13236 triangles, 50619, 47 of 23528 triangles, 50176, 35 of 3020
triangles
> select subtract #2.244
257 models selected
> select add #2.385
258 models selected
> select add #2.244
259 models selected
> select add #2.323
260 models selected
> select add #2.372
261 models selected
> select add #2.229
262 models selected
> select add #2.110
263 models selected
> select add #2.571
264 models selected
> select add #2.79
265 models selected
> select add #2.65
266 models selected
> select add #2.363
267 models selected
> select add #2.159
268 models selected
> select add #2.238
269 models selected
> select add #2.365
270 models selected
> select add #2.118
271 models selected
Drag select of 50643, 144 of 97072 triangles, 50569, 33 of 22748 triangles
> select add #2.241
274 models selected
> select add #2.391
275 models selected
> select subtract #2.391
274 models selected
Drag select of 50680, 67 of 32524 triangles, 49971, 76 of 15912 triangles,
49036, 21 of 4700 triangles
> select subtract #2.47
276 models selected
> select add #2.81
277 models selected
> select add #2.47
278 models selected
> select add #2.165
279 models selected
> select add #2.197
280 models selected
> select add #2.76
281 models selected
> select add #2.71
282 models selected
> select add #2.74
283 models selected
> select add #2.145
284 models selected
> select add #2.233
285 models selected
> select add #2.370
286 models selected
> select add #2.386
287 models selected
> select add #2.487
288 models selected
Grouped 288 regions
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> select #2.1
1 model selected
> select add #2.266
2 models selected
> select add #2.411
3 models selected
> select add #2.400
4 models selected
> select add #2.222
5 models selected
> select add #2.603
6 models selected
> select add #2.384
7 models selected
> select add #2.345
8 models selected
> select add #2.403
9 models selected
> select add #2.373
10 models selected
> select add #2.310
11 models selected
> select add #2.288
12 models selected
> select add #2.274
13 models selected
> select add #2.354
14 models selected
> select add #2.408
15 models selected
Grouped 15 regions
> select clear
> select #2.1
1 model selected
> select #2.1
1 model selected
> select add #2.355
2 models selected
> select #2.1
1 model selected
> select clear
> select #2.1
1 model selected
> select add #2.355
2 models selected
> select add #2.609
3 models selected
> select add #2.387
4 models selected
Grouped 4 regions
> select clear
> select #2.1
1 model selected
Opened Rev-CJFlgYPlfAB-2.1A_imasked as #3, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> hide #!2 models
> show #!2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Segmenting Rev-CJFlgYPlfAB-2.1A_imasked, density threshold 0.007113
Showing 307 region surfaces
20735 watershed regions, grouped to 307 regions
Showing Rev-CJFlgYPlfAB-2.seg - 307 regions, 307 surfaces
> select #2.35
1 model selected
> select add #2.120
2 models selected
> select add #2.97
3 models selected
> select add #2.72
4 models selected
> select add #2.226
5 models selected
> select add #2.92
6 models selected
> hide #!3 models
> select add #2.290
7 models selected
> select add #2.280
8 models selected
> select add #2.107
9 models selected
> select add #2.10
10 models selected
> select add #2.8
11 models selected
> select add #2.20
12 models selected
> select add #2.187
13 models selected
> select add #2.210
14 models selected
> select add #2.254
15 models selected
> select add #2.270
16 models selected
> select add #2.19
17 models selected
> select add #2.99
18 models selected
> select add #2.152
19 models selected
> select add #2.103
20 models selected
> select add #2.206
21 models selected
> select add #2.170
22 models selected
> select add #2.55
23 models selected
> select add #2.205
24 models selected
> select add #2.118
25 models selected
> select add #2.128
26 models selected
> select add #2.166
27 models selected
> select add #2.57
28 models selected
> select add #2.168
29 models selected
> select add #2.209
30 models selected
> select add #2.178
31 models selected
> select add #2.125
32 models selected
> select add #2.230
33 models selected
> select add #2.173
34 models selected
> select add #2.101
35 models selected
> select add #2.242
36 models selected
> select add #2.227
37 models selected
> select add #2.145
38 models selected
> select add #2.180
39 models selected
> select add #2.184
40 models selected
> select add #2.204
41 models selected
> select add #2.172
42 models selected
> select add #2.236
43 models selected
> select add #2.221
44 models selected
> select add #2.185
45 models selected
> select add #2.259
46 models selected
> select add #2.143
47 models selected
> select add #2.190
48 models selected
> select add #2.154
49 models selected
Grouped 49 regions
> select add #2.15
2 models selected
> select add #2.80
3 models selected
> select add #2.146
4 models selected
> select add #2.163
5 models selected
> select add #2.83
6 models selected
> select add #2.115
7 models selected
> select add #2.114
8 models selected
> select add #2.79
9 models selected
> select add #2.108
10 models selected
> select add #2.147
11 models selected
> select add #2.88
12 models selected
> select add #2.44
13 models selected
> select subtract #2.44
12 models selected
> select add #2.44
13 models selected
> select add #2.271
14 models selected
> select add #2.249
15 models selected
> select add #2.279
16 models selected
> select add #2.281
17 models selected
> select add #2.294
18 models selected
> select add #2.16
19 models selected
> select add #2.222
20 models selected
> select add #2.1
21 models selected
> select add #2.176
22 models selected
> select add #2.138
23 models selected
Grouped 23 regions
> select add #2.110
2 models selected
> select add #2.52
3 models selected
Grouped 3 regions
> select add #2.109
2 models selected
> select add #2.67
3 models selected
> select add #2.66
4 models selected
> select add #2.87
5 models selected
> select add #2.95
6 models selected
> select add #2.91
7 models selected
> select add #2.192
8 models selected
> select add #2.40
9 models selected
> select add #2.153
10 models selected
> select add #2.54
11 models selected
> select add #2.46
12 models selected
> select add #2.45
13 models selected
> select add #2.9
14 models selected
> select add #2.111
15 models selected
> select subtract #2.111
14 models selected
> select add #2.81
15 models selected
> select add #2.111
16 models selected
> select add #2.161
17 models selected
> select add #2.157
18 models selected
> select add #2.94
19 models selected
> select add #2.78
20 models selected
> select subtract #2.78
19 models selected
> select subtract #2.94
18 models selected
Grouped 18 regions
> select clear
> select #2.1
1 model selected
> select add #2.29
2 models selected
> select add #2.241
3 models selected
> select add #2.18
4 models selected
> select add #2.202
5 models selected
> select add #2.4
6 models selected
Grouped 6 regions
> select clear
> select #2.1
1 model selected
Opened Rev-CJFlgYPlfAB-2_imasked as #4, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-2_imasked, density threshold 0.007113
Showing 215 region surfaces
14302 watershed regions, grouped to 215 regions
Showing Rev-CJFlgYPlfAB-2_imasked.seg - 215 regions, 215 surfaces
> select #2.1
1 model selected
> select add #2.63
2 models selected
> select #2.1
1 model selected
> select #2.111
1 model selected
> select #2.25
1 model selected
> select add #2.60
2 models selected
> select add #2.19
3 models selected
> select add #2.53
4 models selected
> select add #2.17
5 models selected
> select add #2.63
6 models selected
Grouped 6 regions
> select clear
> select #2.1
1 model selected
Ungrouped to 4 regions
> select #2.25
1 model selected
Ungrouped to 5 regions
> select #2.217
1 model selected
> select add #2.53
2 models selected
> select add #2.17
3 models selected
> select add #2.218
4 models selected
Grouped 4 regions
> select #2.54
1 model selected
> select add #2.17
2 models selected
> select clear
> select #2.111
1 model selected
> select add #2.17
2 models selected
Grouped 2 regions
> select clear
> select #2.17
1 model selected
> select clear
> select #2.17
1 model selected
> hide #!4 models
Opened Rev-CJFlgYPlfAB-2_imasked_imasked as #5, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/CJSef_no-mask/PflC2.mrc models #5
Opened Rev-CJFlgYPlfAB-2_imasked_imasked as #6, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-2_imasked_imasked, density threshold 0.007113
Showing 210 region surfaces
13006 watershed regions, grouped to 210 regions
Showing Rev-CJFlgYPlfAB-2_imasked_imasked.seg - 210 regions, 210 surfaces
> hide #!5 models
> hide #!6 models
> show #!5 models
> select #2.38
1 model selected
> select add #2.98
2 models selected
> select add #2.63
3 models selected
> select add #2.96
4 models selected
> select add #2.90
5 models selected
> select add #2.54
6 models selected
> select add #2.27
7 models selected
> hide #!5 models
Grouped 7 regions
> select add #2.89
2 models selected
Grouped 2 regions
> select clear
> select #2.27
1 model selected
Opened Rev-CJFlgYPlfAB-2_imasked_imasked_imasked as #7, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/CJSef_no-mask/PflC1.mrc models #7
Opened Rev-CJFlgYPlfAB-2_imasked_imasked_imasked as #8, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-2_imasked_imasked_imasked, density threshold
0.007113
Showing 202 region surfaces
12777 watershed regions, grouped to 202 regions
Showing Rev-CJFlgYPlfAB-2_imasked_imasked_imasked.seg - 202 regions, 202
surfaces
> hide #!7 models
> hide #!8 models
> select #2.74
1 model selected
> select add #2.65
2 models selected
> select add #2.61
3 models selected
> select clear
> select #2.61
1 model selected
> select add #2.65
2 models selected
> select add #2.74
3 models selected
Grouped 3 regions
> select clear
> select #2.61
1 model selected
Opened Rev-CJFlgYPlfAB-2_imasked_imasked_imasked_imasked as #9, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/CJSef_no-mask/PflD.mrc models #9
Opened Rev-CJFlgYPlfAB-2_imasked_imasked_imasked_imasked as #10, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-2_imasked_imasked_imasked_imasked, density
threshold 0.007113
Showing 199 region surfaces
12705 watershed regions, grouped to 199 regions
Showing Rev-CJFlgYPlfAB-2_imasked_imasked_imasked_imasked.seg - 199 regions,
199 surfaces
> hide #!9 models
> select #2.32
1 model selected
> select add #2.37
2 models selected
> select add #2.31
3 models selected
> select add #2.28
4 models selected
> hide #!10 models
> select clear
> select #2.28
1 model selected
> select add #2.31
2 models selected
> select add #2.37
3 models selected
> select add #2.32
4 models selected
Ungrouped to 16 regions
> select #2.203
1 model selected
Ungrouped to 6 regions
> select #2.217
1 model selected
> select add #2.32
2 models selected
> select add #2.28
3 models selected
Grouped 3 regions
> select add #2.216
2 models selected
> select add #2.37
3 models selected
Grouped 3 regions
> select #2.213
1 model selected
> select add #2.212
2 models selected
> select add #2.215
3 models selected
Grouped 3 regions
> select add #2.205
2 models selected
Grouped 2 regions
> select add #2.28
2 models selected
Grouped 2 regions
> select #2.201
1 model selected
> select clear
> select #2.201
1 model selected
Ungrouped to 7 regions
Ungrouped to 20 regions
> select #2.226
1 model selected
> select add #2.224
2 models selected
> select add #2.221
3 models selected
> select add #2.37
4 models selected
Grouped 4 regions
> select add #2.218
2 models selected
> select add #2.231
3 models selected
> select add #2.230
4 models selected
> select add #2.228
5 models selected
> select add #2.225
6 models selected
> select add #2.223
7 models selected
> select add #2.220
8 models selected
Grouped 8 regions
> select add #2.219
2 models selected
> select add #2.232
3 models selected
> select add #2.229
4 models selected
> select add #2.222
5 models selected
> select add #2.233
6 models selected
Grouped 6 regions
> select clear
> select #2.28
1 model selected
> select add #2.37
2 models selected
Grouped 2 regions
Showing 216 region surfaces
> select clear
> select #2.28
1 model selected
Opened Rev-CJFlgYPlfAB-2_imasked_imasked_imasked_imasked_imasked as #11, grid
size 200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/CJSef_no-mask/MotBpg.mrc models #11
Opened Rev-CJFlgYPlfAB-2_imasked_imasked_imasked_imasked_imasked as #12, grid
size 200,200,200, pixel 2.14, shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-2_imasked_imasked_imasked_imasked_imasked, density
threshold 0.007113
Showing 200 region surfaces
12639 watershed regions, grouped to 200 regions
Showing Rev-CJFlgYPlfAB-2_imasked_imasked_imasked_imasked_imasked.seg - 200
regions, 200 surfaces
> hide #!11 models
> select #2.39
1 model selected
> select add #2.53
2 models selected
> select add #2.57
3 models selected
Drag select of 16691, 40 of 44176 triangles, 16475, 11 of 17632 triangles,
16441, 10 of 16132 triangles, 12 Rev-
CJFlgYPlfAB-2_imasked_imasked_imasked_imasked_imasked
> select add #2.66
9 models selected
> select #2.48
1 model selected
> select add #2.66
2 models selected
> select add #2.105
3 models selected
> select add #2.89
4 models selected
> select add #2.39
5 models selected
> select add #2.53
6 models selected
> select add #2.57
7 models selected
> select add #2.51
8 models selected
> select add #2.69
9 models selected
> select add #2.29
10 models selected
> select add #2.32
11 models selected
> select add #2.156
12 models selected
> select subtract #2.156
11 models selected
> select add #2.56
12 models selected
> select add #2.80
13 models selected
> select add #2.156
14 models selected
> select add #2.45
15 models selected
> select add #2.52
16 models selected
> select add #2.41
17 models selected
> hide #!12 models
Grouped 17 regions
Opened Rev-CJFlgYPlfAB-2_imasked_imasked_imasked_imasked_imasked_imasked as
#13, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/CJSef_no-mask/PflA-FlgY.mrc models #13
Opened Rev-CJFlgYPlfAB-2_imasked_imasked_imasked_imasked_imasked_imasked as
#14, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-2_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.007113
Showing 182 region surfaces
11992 watershed regions, grouped to 182 regions
Showing Rev-CJFlgYPlfAB-2_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 182 regions, 182 surfaces
> hide #!14 models
> hide #!13 models
> select #2.142
1 model selected
> select add #2.73
2 models selected
> select add #2.113
3 models selected
> select add #2.79
4 models selected
> select add #2.22
5 models selected
> select add #2.13
6 models selected
> select clear
> select #2.14
1 model selected
> select add #2.65
2 models selected
Grouped 2 regions
> select clear
> select #2.10
1 model selected
> select add #2.37
2 models selected
> select #2.10
1 model selected
Ungrouped to 2 regions
> select #2.65
1 model selected
Ungrouped to 18 regions
> select #2.37
1 model selected
> select add #2.183
2 models selected
> select add #2.191
3 models selected
> select add #2.193
4 models selected
> select add #2.184
5 models selected
> select subtract #2.184
4 models selected
Grouped 4 regions
> select #2.184
1 model selected
Ungrouped to 10 regions
> select #2.14
1 model selected
> select add #2.199
2 models selected
> select add #2.201
3 models selected
> select add #2.188
4 models selected
> select add #2.186
5 models selected
> select add #2.185
6 models selected
> select add #2.200
7 models selected
> select add #2.195
8 models selected
> select add #2.194
9 models selected
Grouped 9 regions
> select add #2.197
2 models selected
Grouped 2 regions
> select clear
> select #2.166
1 model selected
> select add #2.189
2 models selected
> select add #2.187
3 models selected
> select add #2.205
4 models selected
> select add #2.202
5 models selected
> select add #2.206
6 models selected
> select add #2.183
7 models selected
> select add #2.203
8 models selected
> select add #2.196
9 models selected
> select #2.14
1 model selected
Ungrouped to 2 regions
Ungrouped to 11 regions
> select subtract #2.200
10 models selected
> select clear
> select #2.200
1 model selected
> select #2.197
1 model selected
> select #2.197
1 model selected
Ungrouped to 6 regions
Ungrouped to 0 regions
> select #2.14
1 model selected
> select add #2.186
2 models selected
> select add #2.191
3 models selected
> select subtract #2.191
2 models selected
> select add #2.193
3 models selected
> select add #2.191
4 models selected
> select add #2.65
5 models selected
> select add #2.185
6 models selected
> select add #2.198
7 models selected
> select add #2.212
8 models selected
> select add #2.184
9 models selected
> select add #2.201
10 models selected
> select add #2.211
11 models selected
> select add #2.194
12 models selected
> select add #2.195
13 models selected
> select add #2.209
14 models selected
> select add #2.15
15 models selected
Showing 211 region surfaces
> select clear
> save /Users/shoichi/Desktop/CJSef_no-mask/Segment-nomask.cxs
> save /Users/shoichi/Desktop/CJSef_no-mask/Segment-nomask.cxs includeMaps
> true
——— End of log from Tue Jul 22 14:40:48 2025 ———
opened ChimeraX session
Showing Rev-CJFlgYPlfAB-2_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 211 regions, 211 surfaces
> select #2.142
1 model selected
> select add #2.127
2 models selected
> select add #2.44
3 models selected
> select add #2.113
4 models selected
> select add #2.52
5 models selected
> select add #2.148
6 models selected
> select add #2.37
7 models selected
> select add #2.137
8 models selected
> select add #2.70
9 models selected
> select add #2.60
10 models selected
> select add #2.188
11 models selected
> select add #2.63
12 models selected
> select add #2.66
13 models selected
> select add #2.115
14 models selected
> select add #2.39
15 models selected
> select add #2.125
16 models selected
> select add #2.105
17 models selected
> select subtract #2.105
16 models selected
> select add #2.105
17 models selected
> select add #2.92
18 models selected
Grouped 18 regions
> select add #2.149
2 models selected
> select add #2.46
3 models selected
> select add #2.76
4 models selected
> select add #2.123
5 models selected
> select add #2.167
6 models selected
> select add #2.210
7 models selected
> select add #2.126
8 models selected
Grouped 8 regions
> select add #2.42
2 models selected
> select add #2.120
3 models selected
> select add #2.83
4 models selected
> select add #2.80
5 models selected
Grouped 5 regions
> select add #2.51
2 models selected
> select add #2.211
3 models selected
Grouped 3 regions
> select add #2.151
2 models selected
> select add #2.33
3 models selected
> select add #2.31
4 models selected
> select subtract #2.31
3 models selected
> select add #2.31
4 models selected
> select add #2.25
5 models selected
> select add #2.23
6 models selected
> select add #2.27
7 models selected
> select add #2.26
8 models selected
> select subtract #2.23
7 models selected
> select add #2.23
8 models selected
> select add #2.21
9 models selected
> select add #2.17
10 models selected
> select add #2.19
11 models selected
> select add #2.13
12 models selected
> select add #2.8
13 models selected
> select add #2.12
14 models selected
> select add #2.6
15 models selected
> select add #2.11
16 models selected
> select add #2.124
17 models selected
> select subtract #2.124
16 models selected
> select subtract #2.11
15 models selected
> select add #2.11
16 models selected
> select add #2.7
17 models selected
> select add #2.5
18 models selected
> select add #2.32
19 models selected
Grouped 19 regions
> select add #2.22
2 models selected
> select add #2.20
3 models selected
> select add #2.15
4 models selected
> select add #2.9
5 models selected
> select add #2.14
6 models selected
> select add #2.34
7 models selected
> select add #2.4
8 models selected
> select add #2.1
9 models selected
> select add #2.2
10 models selected
> select add #2.165
11 models selected
Grouped 11 regions
> select add #2.10
2 models selected
> select add #2.35
3 models selected
> select add #2.100
4 models selected
Grouped 4 regions
> select add #2.134
2 models selected
> select add #2.53
3 models selected
> select add #2.40
4 models selected
> select add #2.119
5 models selected
Grouped 5 regions
> select add #2.195
2 models selected
> select add #2.175
3 models selected
> select add #2.85
4 models selected
> select add #2.192
5 models selected
> select add #2.170
6 models selected
Grouped 6 regions
> select clear
> select #2.97
1 model selected
> select clear
> select #2.1
1 model selected
> select add #2.204
2 models selected
Grouped 2 regions
> select add #2.196
2 models selected
> select add #2.58
3 models selected
> select add #2.75
4 models selected
> select add #2.96
5 models selected
> select add #2.103
6 models selected
> select add #2.172
7 models selected
Grouped 7 regions
> select add #2.128
2 models selected
Grouped 2 regions
> select add #2.205
2 models selected
> select add #2.150
3 models selected
Grouped 3 regions
> select clear
> select #2.1
1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Showing 131 region surfaces
Opened Rev-
CJFlgYPlfAB-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked as #15,
grid size 200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Segmenting Rev-
CJFlgYPlfAB-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked, density
threshold 0.007113
Showing 55 region surfaces
2769 watershed regions, grouped to 55 regions
Showing Rev-
CJFlgYPlfAB-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg - 55
regions, 55 surfaces
> select #2.15
1 model selected
Ungrouped to 3 regions
> select #2.56
1 model selected
> select #2.1
1 model selected
Ungrouped to 5 regions
> select #2.56
1 model selected
> select add #2.59
2 models selected
> select add #2.60
3 models selected
> select add #2.61
4 models selected
> select add #2.62
5 models selected
Grouped 5 regions
> select clear
> select #2.15
1 model selected
Ungrouped to 5 regions
> select #2.62
1 model selected
> select add #2.61
2 models selected
> select add #2.60
3 models selected
> select add #2.1
4 models selected
Grouped 4 regions
> select add #2.56
2 models selected
Grouped 2 regions
> select clear
> select #2.1
1 model selected
> hide #!15 models
> select clear
> select #2.59
1 model selected
Ungrouped to 15 regions
> select #2.5
1 model selected
> select add #2.61
2 models selected
> select add #2.71
3 models selected
> select add #2.56
4 models selected
Grouped 4 regions
> select #2.70
1 model selected
> select add #2.66
2 models selected
> select add #2.65
3 models selected
> select add #2.62
4 models selected
> select add #2.64
5 models selected
> select add #2.67
6 models selected
> select add #2.69
7 models selected
> select add #2.60
8 models selected
Grouped 8 regions
Showing 61 region surfaces
> select add #2.1
2 models selected
Grouped 2 regions
> select #2.72
1 model selected
> select add #2.63
2 models selected
> select add #2.5
3 models selected
Grouped 3 regions
> select #2.28
1 model selected
Ungrouped to 3 regions
> select clear
> select #2.60
1 model selected
Showing 60 region surfaces
> select add #2.1
2 models selected
Grouped 2 regions
> select clear
> select #2.38
1 model selected
Ungrouped to 3 regions
> select #2.61
1 model selected
> select add #2.1
2 models selected
Grouped 2 regions
> select clear
> select #2.51
1 model selected
Ungrouped to 2 regions
> select #2.61
1 model selected
> select add #2.1
2 models selected
> select subtract #2.1
1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #2.1
2 models selected
Grouped 2 regions
> select #2.22
1 model selected
Ungrouped to 4 regions
> select #2.61
1 model selected
> select add #2.1
2 models selected
Grouped 2 regions
> select clear
> select #2.63
1 model selected
Ungrouped to 15 regions
Ungrouped to 7 regions
> select #2.1
1 model selected
> select add #2.64
2 models selected
> select add #2.74
3 models selected
> select add #2.24
4 models selected
Grouped 4 regions
> select clear
> select #2.1
1 model selected
> select clear
> select #2.21
1 model selected
Ungrouped to 5 regions
> select #2.77
1 model selected
Showing 82 region surfaces
> select add #2.1
2 models selected
Grouped 2 regions
> select add #2.76
2 models selected
> select add #2.73
3 models selected
Grouped 3 regions
> select clear
> select #2.1
1 model selected
Opened Rev-
CJFlgYPlfAB-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #16, grid size 200,200,200, pixel 2.14, shown at step 1, values float32
Segmenting Rev-
CJFlgYPlfAB-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.007113
Showing 52 region surfaces
2394 watershed regions, grouped to 52 regions
Showing Rev-
CJFlgYPlfAB-2_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 52 regions, 52 surfaces
> hide #!2 models
> surface dust #16 size 21.4
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/proximal-disk.mrc models #16
Segmenting proximal-disk.mrc, density threshold 0.007113
Showing 52 region surfaces
2394 watershed regions, grouped to 52 regions
Showing proximal-disk.seg - 52 regions, 52 surfaces
> select #2.25
1 model selected
Ungrouped to 3 regions
Ungrouped to 19 regions
Ungrouped to 7 regions
> select #2.65
1 model selected
> select add #2.17
2 models selected
> select add #2.29
3 models selected
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!14 models
> hide #!14 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!1 models
Segmenting Rev-CJFlgYPlfAB-2.1A.mrc, density threshold 0.007113
Showing 628 region surfaces
38016 watershed regions, grouped to 628 regions
Showing Rev-CJFlgYPlfAB-2.1A.seg - 628 regions, 628 surfaces
Segmenting Rev-CJFlgYPlfAB-2.1A.mrc, density threshold 0.007113
Showing 628 region surfaces
38016 watershed regions, grouped to 628 regions
Showing Rev-CJFlgYPlfAB-2.1A.seg - 628 regions, 628 surfaces
> select #2.105
1 model selected
> select add #2.425
2 models selected
> select add #2.396
3 models selected
> select add #2.121
4 models selected
> select add #2.11
5 models selected
> select add #2.22
6 models selected
> select add #2.228
7 models selected
Grouped 7 regions
> hide #!1 models
> hide #!16 models
> select add #2.8
2 models selected
> select add #2.376
3 models selected
> select add #2.262
4 models selected
> select add #2.344
5 models selected
Grouped 5 regions
> select add #2.111
2 models selected
> select add #2.204
3 models selected
> select add #2.255
4 models selected
> select add #2.117
5 models selected
> select add #2.175
6 models selected
> select add #2.113
7 models selected
> select add #2.21
8 models selected
Grouped 8 regions
> select add #2.16
2 models selected
> select subtract #2.16
1 model selected
> select add #2.16
2 models selected
> select add #2.93
3 models selected
> select add #2.96
4 models selected
> select add #2.130
5 models selected
> select add #2.90
6 models selected
> select add #2.101
7 models selected
> select add #2.51
8 models selected
> select add #2.205
9 models selected
> select add #2.169
10 models selected
> select add #2.281
11 models selected
> select add #2.308
12 models selected
> select add #2.225
13 models selected
> select add #2.123
14 models selected
> select add #2.356
15 models selected
> select add #2.164
16 models selected
> select add #2.132
17 models selected
> select add #2.232
18 models selected
> select add #2.178
19 models selected
> select add #2.196
20 models selected
> select add #2.259
21 models selected
> select add #2.202
22 models selected
> select add #2.168
23 models selected
Grouped 23 regions
> select add #2.146
2 models selected
> select add #2.64
3 models selected
> select add #2.317
4 models selected
> select add #2.234
5 models selected
> select add #2.104
6 models selected
> select add #2.108
7 models selected
> select add #2.100
8 models selected
> select add #2.77
9 models selected
> select add #2.78
10 models selected
> select add #2.124
11 models selected
> select add #2.46
12 models selected
> select add #2.62
13 models selected
> select add #2.35
14 models selected
> select add #2.53
15 models selected
> select add #2.392
16 models selected
> select add #2.334
17 models selected
> select add #2.115
18 models selected
> select add #2.206
19 models selected
> select add #2.143
20 models selected
> select add #2.214
21 models selected
> select add #2.66
22 models selected
> select subtract #2.66
21 models selected
> select add #2.199
22 models selected
> select add #2.66
23 models selected
> select add #2.135
24 models selected
> select add #2.254
25 models selected
> select subtract #2.64
24 models selected
> select subtract #2.254
23 models selected
> select subtract #2.146
22 models selected
Grouped 22 regions
> select add #2.252
2 models selected
> select add #2.217
3 models selected
> select add #2.224
4 models selected
> select add #2.291
5 models selected
> select add #2.167
6 models selected
> select add #2.319
7 models selected
> select add #2.294
8 models selected
> select add #2.64
9 models selected
> select add #2.146
10 models selected
> select add #2.254
11 models selected
> select add #2.10
12 models selected
> select subtract #2.10
11 models selected
> select add #2.10
12 models selected
> select add #2.126
13 models selected
> select add #2.94
14 models selected
> select add #2.194
15 models selected
> select add #2.52
16 models selected
> select add #2.184
17 models selected
> select add #2.69
18 models selected
> select add #2.195
19 models selected
> select add #2.127
20 models selected
> select add #2.398
21 models selected
> select add #2.379
22 models selected
> select add #2.437
23 models selected
> select subtract #2.252
22 models selected
> select subtract #2.217
21 models selected
> select subtract #2.224
20 models selected
> select subtract #2.167
19 models selected
> select subtract #2.291
18 models selected
> select add #2.291
19 models selected
Grouped 19 regions
> select add #2.252
2 models selected
> select add #2.217
3 models selected
> select add #2.224
4 models selected
> select add #2.167
5 models selected
> select add #2.192
6 models selected
> select add #2.439
7 models selected
Showing 550 region surfaces
Grouped 7 regions
> select add #2.125
2 models selected
> select add #2.32
3 models selected
> select add #2.58
4 models selected
> select add #2.155
5 models selected
> select add #2.176
6 models selected
> select add #2.2
7 models selected
> select add #2.171
8 models selected
> select add #2.103
9 models selected
> select add #2.102
10 models selected
> select add #2.151
11 models selected
> select add #2.80
12 models selected
> select add #2.83
13 models selected
> select add #2.39
14 models selected
> select add #2.98
15 models selected
> select add #2.75
16 models selected
> select add #2.84
17 models selected
> select add #2.4
18 models selected
Grouped 18 regions
> select add #2.17
2 models selected
> select add #2.282
3 models selected
> select add #2.1
4 models selected
> select add #2.137
5 models selected
> select add #2.290
6 models selected
> select add #2.210
7 models selected
> select add #2.158
8 models selected
> select add #2.85
9 models selected
> select add #2.7
10 models selected
> select add #2.251
11 models selected
> select add #2.410
12 models selected
> select add #2.248
13 models selected
> select add #2.198
14 models selected
> select add #2.15
15 models selected
> select add #2.141
16 models selected
> select add #2.275
17 models selected
> select add #2.14
18 models selected
> select add #2.5
19 models selected
> select add #2.25
20 models selected
> select add #2.60
21 models selected
> select add #2.250
22 models selected
> select add #2.19
23 models selected
> select add #2.116
24 models selected
> select add #2.185
25 models selected
> select add #2.154
26 models selected
> select add #2.119
27 models selected
> select add #2.24
28 models selected
> select add #2.426
29 models selected
> select add #2.257
30 models selected
> select add #2.450
31 models selected
> select add #2.389
32 models selected
> select add #2.286
33 models selected
> select add #2.338
34 models selected
Grouped 34 regions
> select add #2.331
2 models selected
> select add #2.272
3 models selected
> select add #2.276
4 models selected
> select add #2.264
5 models selected
> select add #2.218
6 models selected
> select add #2.357
7 models selected
> select add #2.435
8 models selected
> select add #2.349
9 models selected
> select add #2.271
10 models selected
> select add #2.110
11 models selected
> select add #2.147
12 models selected
> select add #2.303
13 models selected
> select subtract #2.147
12 models selected
> select add #2.173
13 models selected
> select add #2.243
14 models selected
> select add #2.343
15 models selected
> select add #2.147
16 models selected
> select subtract #2.303
15 models selected
> select subtract #2.147
14 models selected
> select add #2.87
15 models selected
> select add #2.172
16 models selected
> select add #2.447
17 models selected
> select add #2.120
18 models selected
> select add #2.353
19 models selected
> select add #2.370
20 models selected
> select add #2.463
21 models selected
> select add #2.147
22 models selected
> select add #2.303
23 models selected
> select add #2.365
24 models selected
> select add #2.79
25 models selected
> select add #2.65
26 models selected
> select add #2.306
27 models selected
> select add #2.363
28 models selected
> select add #2.159
29 models selected
> select add #2.358
30 models selected
> select add #2.233
31 models selected
> select add #2.386
32 models selected
> select add #2.487
33 models selected
> select subtract #2.487
32 models selected
Grouped 32 regions
> select add #2.238
2 models selected
> select add #2.391
3 models selected
Grouped 3 regions
> select add #2.118
2 models selected
> select add #2.157
3 models selected
> select subtract #2.157
2 models selected
> select add #2.157
3 models selected
> select add #2.241
4 models selected
> select add #2.47
5 models selected
> select add #2.81
6 models selected
> select add #2.165
7 models selected
> select add #2.197
8 models selected
> select add #2.149
9 models selected
> select add #2.161
10 models selected
> select add #2.307
11 models selected
> select add #2.190
12 models selected
> select add #2.131
13 models selected
> select add #2.44
14 models selected
> select add #2.236
15 models selected
> select add #2.37
16 models selected
> select add #2.6
17 models selected
> select add #2.180
18 models selected
Grouped 18 regions
> select add #2.43
2 models selected
> select add #2.82
3 models selected
> select add #2.29
4 models selected
> select add #2.68
5 models selected
> select add #2.27
6 models selected
> select add #2.88
7 models selected
> select add #2.86
8 models selected
> select add #2.61
9 models selected
> select add #2.287
10 models selected
> select add #2.48
11 models selected
> select add #2.226
12 models selected
> select add #2.72
13 models selected
> select add #2.67
14 models selected
> select add #2.399
15 models selected
> select add #2.55
16 models selected
> select add #2.267
17 models selected
> select add #2.361
18 models selected
> select add #2.59
19 models selected
> select add #2.26
20 models selected
> select add #2.54
21 models selected
> select add #2.129
22 models selected
> select add #2.56
23 models selected
> select add #2.170
24 models selected
> select add #2.208
25 models selected
> select add #2.42
26 models selected
> select add #2.107
27 models selected
> select add #2.33
28 models selected
> select add #2.136
29 models selected
> select add #2.89
30 models selected
> select add #2.30
31 models selected
> select add #2.150
32 models selected
> select add #2.114
33 models selected
> select add #2.133
34 models selected
> select add #2.237
35 models selected
> select add #2.510
36 models selected
> select add #2.112
37 models selected
> select add #2.222
38 models selected
> select add #2.40
39 models selected
> select add #2.139
40 models selected
> select add #2.163
41 models selected
> select add #2.36
42 models selected
> select add #2.216
43 models selected
> select add #2.134
44 models selected
> select add #2.142
45 models selected
> select add #2.160
46 models selected
> select add #2.106
47 models selected
> select add #2.99
48 models selected
> select add #2.300
49 models selected
> select add #2.401
50 models selected
> select add #2.322
51 models selected
> select add #2.203
52 models selected
> select add #2.235
53 models selected
> select subtract #2.235
52 models selected
> select add #2.449
53 models selected
> select add #2.258
54 models selected
> select add #2.193
55 models selected
> select add #2.235
56 models selected
> select add #2.321
57 models selected
> select add #2.182
58 models selected
> select add #2.207
59 models selected
> select add #2.179
60 models selected
> select add #2.23
61 models selected
> select add #2.95
62 models selected
> select add #2.144
63 models selected
> select add #2.18
64 models selected
> select add #2.419
65 models selected
> select add #2.38
66 models selected
> select add #2.31
67 models selected
> select add #2.246
68 models selected
> select add #2.13
69 models selected
> select add #2.244
70 models selected
> select add #2.292
71 models selected
> select add #2.330
72 models selected
> select add #2.240
73 models selected
> select add #2.201
74 models selected
> select add #2.3
75 models selected
> select add #2.148
76 models selected
> select add #2.45
77 models selected
> select add #2.265
78 models selected
> select add #2.390
79 models selected
Grouped 79 regions
> select add #2.138
2 models selected
> select add #2.385
3 models selected
> select add #2.49
4 models selected
> select add #2.301
5 models selected
> select add #2.12
6 models selected
> select add #2.315
7 models selected
> select add #2.313
8 models selected
> select add #2.34
9 models selected
> select subtract #2.385
8 models selected
> select add #2.122
9 models selected
> select add #2.305
10 models selected
> select add #2.156
11 models selected
> select subtract #2.156
10 models selected
> select add #2.323
11 models selected
> select add #2.156
12 models selected
> select add #2.152
13 models selected
> select add #2.293
14 models selected
Grouped 14 regions
> select clear
> select #2.1
1 model selected
> select add #2.487
2 models selected
Grouped 2 regions
> select add #2.283
2 models selected
> select add #2.441
3 models selected
> select add #2.457
4 models selected
> select add #2.316
5 models selected
Grouped 5 regions
> select clear
Drag select of 50595, 1440 of 86216 triangles, 50625, 2312 of 64668 triangles,
50703, 9854 of 48856 triangles, 50718, 6774 of 56308 triangles, 50642, 26564
of 45568 triangles, 50694, 13036 of 51768 triangles, 50639, 1050 of 53396
triangles, 50613, 11192 of 51080 triangles, 50608, 32799 of 51844 triangles,
50592, 39492 of 52252 triangles, 50601, 1174 of 53600 triangles, 50630, 4541
of 43048 triangles, 50518, 2727 of 35744 triangles, 50582, 23960 of 33860
triangles, 50649, 32025 of 44352 triangles, 50710, 1784 of 31260 triangles,
50622, 13627 of 48372 triangles, 50637, 2441 of 28260 triangles, 50756, 156 of
37176 triangles, 50742, 4464 of 25104 triangles, 49784, 328 of 21576
triangles, 50765, 2332 of 31760 triangles, 50597, 19795 of 24652 triangles,
50607, 20490 of 25184 triangles, 50536, 18475 of 28036 triangles, 50650, 322
of 25876 triangles, 50653, 346 of 26040 triangles, 50523, 10341 of 13084
triangles, 50725, 796 of 23616 triangles, 50617, 238 of 17452 triangles,
50749, 3547 of 22184 triangles, 50614, 1719 of 21132 triangles, 49644, 4980 of
13992 triangles, 49838, 1110 of 9144 triangles, 50779, 1004 of 16216
triangles, 49831, 12392 of 15304 triangles, 50712, 8531 of 14916 triangles,
50538, 2786 of 11440 triangles, 50588, 2373 of 11052 triangles, 50629, 1905 of
11804 triangles, 50556, 1156 of 9924 triangles, 50730, 6174 of 9832 triangles,
50527, 8606 of 9340 triangles, 50720, 7364 of 11340 triangles, 50750, 2319 of
9040 triangles, 49681, 50716, 265 of 7632 triangles, 50598, 8501 of 8712
triangles, 50455, 117 of 6572 triangles, 50600, 375 of 8704 triangles, 50604,
4479 of 7340 triangles, 50734, 5593 of 7192 triangles, 50398, 814 of 6028
triangles, 50238, 6252 of 6652 triangles, 49810, 2031 of 6908 triangles,
50774, 4201 of 6520 triangles, 50764, 50732, 533 of 6840 triangles, 47684,
5212 of 5532 triangles, 50655, 6490 of 6660 triangles, 50522, 2426 of 6408
triangles, 49705, 3118 of 5296 triangles, 50302, 4324 of 4892 triangles,
46163, 3083 of 3152 triangles, 50731, 4500 of 4820 triangles, 50221, 1131 of
3844 triangles, 50704, 328 of 3836 triangles, 50773, 49964, 3131 of 4336
triangles, 46533, 906 of 2912 triangles, 50575, 50129, 452 of 2640 triangles,
50501, 83 of 3140 triangles, 50176, 263 of 2816 triangles, 50672, 791 of 2280
triangles, 50326, 50463, 50482, 1227 of 1604 triangles, 50577, 69 of 1568
triangles, 50315, 49603
> select clear
> select #2.231
1 model selected
> select add #2.1
2 models selected
> select add #2.212
3 models selected
> select add #2.496
4 models selected
> select add #2.213
5 models selected
> select add #2.191
6 models selected
> select add #2.340
7 models selected
> select add #2.274
8 models selected
> select add #2.229
9 models selected
> select add #2.288
10 models selected
> select add #2.189
11 models selected
Grouped 11 regions
> select #2.1
1 model selected
> select add #2.373
2 models selected
> select add #2.162
3 models selected
> select add #2.285
4 models selected
> select add #2.326
5 models selected
> select add #2.310
6 models selected
Grouped 6 regions
> select add #2.608
2 models selected
> select add #2.603
3 models selected
Grouped 3 regions
> select clear
> select #2.1
1 model selected
Showing 331 region surfaces
Opened Rev-CJFlgYPlfAB-2.1A_imasked as #17, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-2.1A_imasked, density threshold 0.007113
Showing 296 region surfaces
20795 watershed regions, grouped to 296 regions
Showing Rev-CJFlgYPlfAB-2.seg - 296 regions, 296 surfaces
> select #2.90
1 model selected
> select add #2.20
2 models selected
> select add #2.281
3 models selected
> select add #2.276
4 models selected
> select add #2.192
5 models selected
> select add #2.269
6 models selected
> select add #2.258
7 models selected
> select add #2.215
8 models selected
> select add #2.105
9 models selected
Grouped 9 regions
> hide #!17 models
> select add #2.10
2 models selected
> select add #2.8
3 models selected
> select add #2.177
4 models selected
> select add #2.211
5 models selected
> select add #2.101
6 models selected
> select add #2.154
7 models selected
> select add #2.97
8 models selected
> select add #2.19
9 models selected
> select add #2.46
10 models selected
> select add #2.86
11 models selected
> select add #2.78
12 models selected
> select add #2.113
13 models selected
> select add #2.82
14 models selected
> select add #2.79
15 models selected
> select add #2.15
16 models selected
> select add #2.247
17 models selected
> select add #2.148
18 models selected
> select add #2.169
19 models selected
> select add #2.115
20 models selected
> select add #2.107
21 models selected
> select add #2.149
22 models selected
> select add #2.178
23 models selected
> select add #2.241
24 models selected
> select add #2.226
25 models selected
> select add #2.190
26 models selected
> select add #2.261
27 models selected
> select add #2.145
28 models selected
> select add #2.196
29 models selected
> select add #2.156
30 models selected
> select subtract #2.156
29 models selected
> select add #2.156
30 models selected
> select add #2.214
31 models selected
> select add #2.175
32 models selected
> select add #2.127
33 models selected
> select add #2.210
34 models selected
> select add #2.118
35 models selected
> select add #2.172
36 models selected
> select add #2.59
37 models selected
> select add #2.184
38 models selected
> select add #2.125
39 models selected
> select add #2.235
40 models selected
> select add #2.179
41 models selected
> select add #2.99
42 models selected
> select add #2.248
43 models selected
> select add #2.147
44 models selected
> select add #2.232
45 models selected
> select add #2.189
46 models selected
> select add #2.186
47 models selected
> select add #2.209
48 models selected
> select subtract #2.178
47 models selected
> select add #2.178
48 models selected
> select add #2.275
49 models selected
> select add #2.252
50 models selected
> select add #2.277
51 models selected
> select add #2.270
52 models selected
> select add #2.284
53 models selected
> select add #2.285
54 models selected
Grouped 54 regions
> select add #2.57
2 models selected
> select add #2.95
3 models selected
> select add #2.36
4 models selected
> select add #2.120
5 models selected
> select add #2.1
6 models selected
> select add #2.182
7 models selected
> select add #2.140
8 models selected
> select add #2.16
9 models selected
> select add #2.231
10 models selected
> select add #2.71
11 models selected
> select add #2.54
12 models selected
> select add #2.109
13 models selected
> select add #2.30
14 models selected
> select add #2.108
15 models selected
> select add #2.41
16 models selected
> select add #2.155
17 models selected
> select add #2.2
18 models selected
> select add #2.198
19 models selected
> select add #2.18
20 models selected
> select add #2.89
21 models selected
> select add #2.150
22 models selected
> select add #2.4
23 models selected
> select add #2.207
24 models selected
> select add #2.227
25 models selected
Grouped 25 regions
> select clear
> select #2.1
1 model selected
> select add #2.257
2 models selected
> select add #2.266
3 models selected
> select add #2.128
4 models selected
> select add #2.238
5 models selected
> select add #2.153
6 models selected
> select add #2.203
7 models selected
> select add #2.201
8 models selected
> select add #2.274
9 models selected
> select add #2.75
10 models selected
> select add #2.152
11 models selected
> select add #2.94
12 models selected
> select add #2.58
13 models selected
> select add #2.170
14 models selected
> select add #2.146
15 models selected
> select add #2.69
16 models selected
> select add #2.43
17 models selected
> select add #2.202
18 models selected
> select add #2.102
19 models selected
> select add #2.139
20 models selected
> select add #2.158
21 models selected
> select add #2.6
22 models selected
> select add #2.35
23 models selected
> select add #2.195
24 models selected
> select add #2.42
25 models selected
> select add #2.114
26 models selected
> select add #2.164
27 models selected
> select add #2.138
28 models selected
> select add #2.243
29 models selected
> select add #2.130
30 models selected
> select add #2.67
31 models selected
> select add #2.265
32 models selected
> select add #2.141
33 models selected
> select add #2.104
34 models selected
> select add #2.23
35 models selected
> select add #2.73
36 models selected
> select add #2.240
37 models selected
> select add #2.291
38 models selected
> select add #2.260
39 models selected
Grouped 39 regions
> select add #2.7
2 models selected
> select add #2.206
3 models selected
> select add #2.123
4 models selected
> select add #2.171
5 models selected
> select add #2.5
6 models selected
> select add #2.221
7 models selected
Showing 173 region surfaces
> select clear
> select #2.1
1 model selected
> select #2.3
1 model selected
> select add #2.12
2 models selected
> select add #2.17
3 models selected
> select add #2.11
4 models selected
Grouped 4 regions
> select #2.26
1 model selected
> select add #2.121
2 models selected
> select add #2.129
3 models selected
> select add #2.106
4 models selected
> select add #2.133
5 models selected
> select add #2.45
6 models selected
> select add #2.2
7 models selected
Grouped 7 regions
> select add #2.187
2 models selected
> select add #2.216
3 models selected
> select add #2.205
4 models selected
> select add #2.251
5 models selected
> select add #2.289
6 models selected
> select add #2.212
7 models selected
> select add #2.229
8 models selected
> select add #2.282
9 models selected
> select add #2.220
10 models selected
> select add #2.222
11 models selected
> select add #2.283
12 models selected
> select add #2.262
13 models selected
> select add #2.219
14 models selected
> select add #2.237
15 models selected
> select add #2.246
16 models selected
> select add #2.74
17 models selected
> select add #2.1
18 models selected
> select add #2.204
19 models selected
> select add #2.174
20 models selected
Grouped 20 regions
> select clear
> select #2.1
1 model selected
> select add #2.272
2 models selected
> select add #2.253
3 models selected
> select add #2.197
4 models selected
> select add #2.263
5 models selected
> select add #2.234
6 models selected
> select add #2.267
7 models selected
> select add #2.208
8 models selected
> select add #2.206
9 models selected
> select add #2.171
10 models selected
> select add #2.123
11 models selected
> select add #2.221
12 models selected
> select add #2.5
13 models selected
> select add #2.259
14 models selected
> select add #2.13
15 models selected
> select add #2.14
16 models selected
> select subtract #2.272
15 models selected
> select add #2.33
16 models selected
> select add #2.272
17 models selected
> select subtract #2.253
16 models selected
> select subtract #2.263
15 models selected
> select subtract #2.197
14 models selected
> select add #2.263
15 models selected
> select add #2.253
16 models selected
> select subtract #2.234
15 models selected
> select add #2.234
16 models selected
> select add #2.197
17 models selected
> select add #2.7
18 models selected
> select add #2.271
19 models selected
> select add #2.280
20 models selected
> select add #2.250
21 models selected
> select add #2.292
22 models selected
> select add #2.287
23 models selected
Grouped 23 regions
> select clear
> select #2.1
1 model selected
Opened Rev-CJFlgYPlfAB-2_imasked as #18, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/REDO/Others.mrc models #18
Opened Rev-CJFlgYPlfAB-2_imasked as #19, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-2_imasked, density threshold 0.007113
Showing 122 region surfaces
7061 watershed regions, grouped to 122 regions
Showing Rev-CJFlgYPlfAB-2_imasked.seg - 122 regions, 122 surfaces
> hide #!18 models
> select #2.13
1 model selected
> select add #2.38
2 models selected
> select add #2.79
3 models selected
> select add #2.17
4 models selected
> select add #2.42
5 models selected
> select add #2.46
6 models selected
> select add #2.73
7 models selected
> select add #2.9
8 models selected
> select add #2.28
9 models selected
> select add #2.80
10 models selected
> select add #2.18
11 models selected
> select add #2.53
12 models selected
> select add #2.37
13 models selected
> select add #2.7
14 models selected
> select add #2.44
15 models selected
> select add #2.29
16 models selected
> select add #2.77
17 models selected
> select add #2.70
18 models selected
> select add #2.49
19 models selected
> select add #2.25
20 models selected
> select add #2.32
21 models selected
> select add #2.31
22 models selected
Grouped 22 regions
> select #2.52
1 model selected
> select add #2.7
2 models selected
Grouped 2 regions
> select clear
> select #2.7
1 model selected
> hide #!19 models
> select add #2.61
2 models selected
> select add #2.57
3 models selected
> select add #2.23
4 models selected
> select add #2.54
5 models selected
> select add #2.21
6 models selected
> select add #2.39
7 models selected
> select add #2.60
8 models selected
> select add #2.19
9 models selected
> select add #2.87
10 models selected
> select add #2.48
11 models selected
> select add #2.27
12 models selected
Grouped 12 regions
> select add #2.30
2 models selected
> select add #2.74
3 models selected
> select add #2.40
4 models selected
> select add #2.65
5 models selected
> select add #2.34
6 models selected
> select add #2.5
7 models selected
> select add #2.4
8 models selected
> select add #2.6
9 models selected
> select add #2.33
10 models selected
> select add #2.62
11 models selected
> select add #2.43
12 models selected
Grouped 12 regions
> select add #2.58
2 models selected
Grouped 2 regions
> select #2.12
1 model selected
> select add #2.4
2 models selected
Grouped 2 regions
> select clear
> select #2.104
1 model selected
> select add #2.96
2 models selected
> select add #2.110
3 models selected
> select clear
> select #2.4
1 model selected
> select add #2.20
2 models selected
> select add #2.11
3 models selected
> select add #2.86
4 models selected
> select add #2.56
5 models selected
> select add #2.59
6 models selected
> select add #2.16
7 models selected
> select add #2.45
8 models selected
> select add #2.92
9 models selected
Grouped 9 regions
> select #2.26
1 model selected
> select add #2.67
2 models selected
> select add #2.69
3 models selected
> select add #2.71
4 models selected
Grouped 4 regions
> select add #2.4
2 models selected
Grouped 2 regions
> select #2.101
1 model selected
> select add #2.64
2 models selected
> select add #2.113
3 models selected
> select add #2.102
4 models selected
> select add #2.108
5 models selected
> select add #2.8
6 models selected
> select add #2.63
7 models selected
Grouped 7 regions
> select #2.85
1 model selected
> select add #2.81
2 models selected
> select add #2.90
3 models selected
> select add #2.89
4 models selected
> select add #2.97
5 models selected
> select add #2.10
6 models selected
Grouped 6 regions
> select add #2.4
2 models selected
Grouped 2 regions
> select #2.109
1 model selected
> select add #2.75
2 models selected
> select add #2.5
3 models selected
> select add #2.4
4 models selected
> select add #2.15
5 models selected
Grouped 5 regions
> select #2.76
1 model selected
> select add #2.98
2 models selected
> select add #2.112
3 models selected
Grouped 3 regions
> select add #2.4
2 models selected
Grouped 2 regions
> select #2.114
1 model selected
> select add #2.95
2 models selected
> select add #2.14
3 models selected
> select add #2.100
4 models selected
> select add #2.4
5 models selected
> select add #2.88
6 models selected
> select add #2.3
7 models selected
> select add #2.111
8 models selected
> select add #2.2
9 models selected
> select subtract #2.2
8 models selected
Grouped 8 regions
> select #2.115
1 model selected
> select add #2.94
2 models selected
> select add #2.3
3 models selected
Grouped 3 regions
> select clear
> select #2.91
1 model selected
> select add #2.78
2 models selected
> select add #2.82
3 models selected
> select add #2.93
4 models selected
> select add #2.72
5 models selected
> select add #2.107
6 models selected
> select add #2.83
7 models selected
> select add #2.105
8 models selected
> select add #2.106
9 models selected
> select clear
> select #2.41
1 model selected
> select add #2.3
2 models selected
> select add #2.117
3 models selected
Grouped 3 regions
> select #2.2
1 model selected
Ungrouped to 2 regions
> select #2.4
1 model selected
Ungrouped to 18 regions
> select #2.19
1 model selected
> select add #2.18
2 models selected
> select #2.18
1 model selected
Ungrouped to 6 regions
Ungrouped to 0 regions
> select #2.19
1 model selected
> select add #2.8
2 models selected
> select add #2.17
3 models selected
> select add #2.10
4 models selected
> select add #2.2
5 models selected
> select add #2.26
6 models selected
Grouped 6 regions
> select add #2.3
2 models selected
Grouped 2 regions
> select #2.7
1 model selected
> select add #2.2
2 models selected
> select add #2.14
3 models selected
Grouped 3 regions
> select #2.2
1 model selected
Opened Rev-CJFlgYPlfAB-2_imasked_imasked as #20, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
Segmenting Rev-CJFlgYPlfAB-2_imasked_imasked, density threshold 0.007113
Showing 89 region surfaces
5462 watershed regions, grouped to 89 regions
Showing Rev-CJFlgYPlfAB-2_imasked_imasked.seg - 89 regions, 89 surfaces
> hide #!2 models
> volume gaussian #20 sDev 4
Opened Rev-CJFlgYPlfAB-2_imasked_imasked gaussian as #21, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #21 level 0.002865
> close #21
> volume gaussian #20 sDev 2
Opened Rev-CJFlgYPlfAB-2_imasked_imasked gaussian as #21, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #21 level 0.005583
> volume #21 level 0.00407
> close #21
> volume gaussian #20 sDev 3
Opened Rev-CJFlgYPlfAB-2_imasked_imasked gaussian as #21, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #21 level 0.002332
> hide #!21 models
> show #!2 models
> select #2.41
1 model selected
> select add #2.5
2 models selected
> select add #2.31
3 models selected
> select add #2.7
4 models selected
> select add #2.39
5 models selected
> select add #2.11
6 models selected
Grouped 6 regions
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/REDO/PflABCD_Cage.mrc models #20
Opened PflABCD_Cage_imasked as #22, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/REDO/PflC.mrc models #22
Opened PflABCD_Cage_imasked as #23, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
Segmenting PflABCD_Cage_imasked, density threshold 0.007113
Showing 83 region surfaces
4415 watershed regions, grouped to 83 regions
Showing PflABCD_Cage_imasked.seg - 83 regions, 83 surfaces
> hide #!22 models
> select #2.36
1 model selected
> select add #2.28
2 models selected
> select add #2.59
3 models selected
> select add #2.54
4 models selected
> select add #2.12
5 models selected
> select add #2.22
6 models selected
> select add #2.60
7 models selected
> select add #2.37
8 models selected
> select add #2.13
9 models selected
> select add #2.33
10 models selected
> select add #2.58
11 models selected
> select add #2.53
12 models selected
> select add #2.18
13 models selected
> hide #!23 models
> show #!22 models
> select clear
> hide #!22 models
Segmenting PflABCD_Cage.mrc, density threshold 0.007113
Showing 89 region surfaces
5462 watershed regions, grouped to 89 regions
Showing PflABCD_Cage.seg - 89 regions, 89 surfaces
> select #2.11
1 model selected
> select add #2.39
2 models selected
> select add #2.7
3 models selected
> select add #2.31
4 models selected
> select add #2.5
5 models selected
> select add #2.41
6 models selected
> select add #2.59
7 models selected
> select add #2.37
8 models selected
> select add #2.64
9 models selected
> select subtract #2.37
8 models selected
> select add #2.37
9 models selected
> select add #2.43
10 models selected
> select add #2.66
11 models selected
> select add #2.16
12 models selected
> select add #2.21
13 models selected
> select add #2.15
14 models selected
> select add #2.60
15 models selected
> select add #2.25
16 models selected
> select add #2.65
17 models selected
> select add #2.32
18 models selected
> select add #2.42
19 models selected
Grouped 19 regions
> select #2.52
1 model selected
> select #2.45
1 model selected
> select add #2.48
2 models selected
> select add #2.52
3 models selected
Ungrouped to 19 regions
Ungrouped to 45 regions
Ungrouped to 26 regions
Ungrouped to 0 regions
> select #2.129
1 model selected
> select add #2.5
2 models selected
> select add #2.138
3 models selected
> select add #2.11
4 models selected
> select subtract #2.11
3 models selected
> select add #2.139
4 models selected
> select add #2.128
5 models selected
> select add #2.130
6 models selected
> select add #2.93
7 models selected
Grouped 7 regions
> select #2.11
1 model selected
Ungrouped to 0 regions
> select clear
> select #2.5
1 model selected
> select clear
> select #2.5
1 model selected
Opened PflABCD_Cage_imasked as #24, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/REDO/PflC.mrc models #24
Opened PflABCD_Cage_imasked as #25, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
Segmenting PflABCD_Cage_imasked, density threshold 0.007113
Showing 70 region surfaces
4050 watershed regions, grouped to 70 regions
Showing PflABCD_Cage_imasked.seg - 70 regions, 70 surfaces
> hide #!24 models
> hide #!25 models
> select #2.33
1 model selected
Ungrouped to 8 regions
Ungrouped to 24 regions
Ungrouped to 0 regions
> close #24-25
> close #22
Segmenting PflABCD_Cage_imasked, density threshold 0.007113
Showing 83 region surfaces
4415 watershed regions, grouped to 83 regions
Showing PflABCD_Cage_imasked.seg - 83 regions, 83 surfaces
> show #!23 models
> hide #!23 models
> show #!20 models
> hide #!2 models
> show #!2 models
> close #21,23
Segmenting PflABCD_Cage.mrc, density threshold 0.007113
Showing 89 region surfaces
5462 watershed regions, grouped to 89 regions
Showing PflABCD_Cage.seg - 89 regions, 89 surfaces
> select #2.28
1 model selected
> select clear
> select #2.41
1 model selected
> select add #2.5
2 models selected
> select add #2.31
3 models selected
> select add #2.7
4 models selected
> select add #2.39
5 models selected
> select add #2.11
6 models selected
Grouped 6 regions
> hide #!20 models
> select #2.48
1 model selected
> select clear
> select #2.45
1 model selected
> select add #2.48
2 models selected
> select add #2.52
3 models selected
Ungrouped to 19 regions
Ungrouped to 45 regions
Ungrouped to 26 regions
Ungrouped to 0 regions
> select #2.32
1 model selected
> select add #2.52
2 models selected
> select add #2.107
3 models selected
> select add #2.108
4 models selected
> select add #2.104
5 models selected
> select add #2.137
6 models selected
> select add #2.139
7 models selected
> select add #2.138
8 models selected
Showing 153 region surfaces
> select #2.5
1 model selected
> select #2.52
1 model selected
> select add #2.139
2 models selected
> select add #2.138
3 models selected
> select add #2.137
4 models selected
> select add #2.95
5 models selected
> select subtract #2.95
4 models selected
> select add #2.149
5 models selected
> select add #2.148
6 models selected
> select add #2.104
7 models selected
> select add #2.106
8 models selected
> select add #2.107
9 models selected
> select add #2.105
10 models selected
> select add #2.140
11 models selected
> select add #2.118
12 models selected
> select add #2.119
13 models selected
Showing 153 region surfaces
Segmenting PflABCD_Cage.mrc, density threshold 0.007113
Showing 89 region surfaces
5462 watershed regions, grouped to 89 regions
Showing PflABCD_Cage.seg - 89 regions, 89 surfaces
> select #2.7
1 model selected
> select add #2.39
2 models selected
> select add #2.11
3 models selected
> select add #2.31
4 models selected
> select add #2.5
5 models selected
> select add #2.41
6 models selected
> select add #2.32
7 models selected
> select add #2.60
8 models selected
> select add #2.25
9 models selected
> select add #2.43
10 models selected
> select add #2.37
11 models selected
> select add #2.59
12 models selected
> select add #2.64
13 models selected
> select add #2.66
14 models selected
> select add #2.65
15 models selected
> select add #2.42
16 models selected
Grouped 16 regions
> select #2.45
1 model selected
Ungrouped to 8 regions
Ungrouped to 25 regions
Ungrouped to 0 regions
Showing 100 region surfaces
> select #2.5
1 model selected
> select add #2.43
2 models selected
Grouped 2 regions
> select #2.48
1 model selected
> select add #2.52
2 models selected
Ungrouped to 11 regions
Ungrouped to 20 regions
Ungrouped to 26 regions
Ungrouped to 0 regions
> select #2.111
1 model selected
> select #2.48
1 model selected
> select add #2.52
2 models selected
> select add #2.5
3 models selected
> select add #2.111
4 models selected
> select subtract #2.111
3 models selected
Grouped 3 regions
> select #2.144
1 model selected
> select add #2.5
2 models selected
Grouped 2 regions
> select subtract #2.146
137 models selected
> select clear
> select #2.68
1 model selected
> select add #2.73
2 models selected
> select clear
> select #2.77
1 model selected
> select #2.72
1 model selected
> select clear
> select #2.72
1 model selected
> select add #2.73
2 models selected
> select add #2.68
3 models selected
Ungrouped to 10 regions
Ungrouped to 56 regions
> select #2.185
1 model selected
> select add #2.188
2 models selected
> select add #2.73
3 models selected
> select add #2.181
4 models selected
> select add #2.184
5 models selected
> select add #2.67
6 models selected
> select subtract #2.67
5 models selected
> select add #2.150
6 models selected
> select subtract #2.150
5 models selected
> select add #2.179
6 models selected
> select add #2.182
7 models selected
> select add #2.174
8 models selected
> select add #2.201
9 models selected
> select add #2.202
10 models selected
> select add #2.198
11 models selected
> select add #2.200
12 models selected
> select add #2.169
13 models selected
> select add #2.173
14 models selected
> select add #2.171
15 models selected
> select add #2.176
16 models selected
> select subtract #2.176
15 models selected
> select add #2.199
16 models selected
> select add #2.168
17 models selected
Grouped 17 regions
> select #2.176
1 model selected
Ungrouped to 15 regions
Ungrouped to 6 regions
Ungrouped to 0 regions
> select #2.48
1 model selected
> select add #2.181
2 models selected
> select add #2.112
3 models selected
> select add #2.119
4 models selected
> select add #2.174
5 models selected
Grouped 5 regions
> select #2.180
1 model selected
Ungrouped to 4 regions
Ungrouped to 2 regions
> select #2.48
1 model selected
> select add #2.112
2 models selected
Grouped 2 regions
> select add #2.187
2 models selected
> select add #2.72
3 models selected
Grouped 3 regions
> select #2.67
1 model selected
> select add #2.68
2 models selected
> select add #2.150
3 models selected
Ungrouped to 10 regions
Ungrouped to 37 regions
Ungrouped to 79 regions
Ungrouped to 49 regions
Showing 320 region surfaces
> select clear
> select #2.48
1 model selected
> select add #2.208
2 models selected
> select add #2.216
3 models selected
> select add #2.213
4 models selected
> select add #2.68
5 models selected
> select add #2.227
6 models selected
> select add #2.228
7 models selected
Grouped 7 regions
> select add #2.288
2 models selected
> select add #2.289
3 models selected
> select add #2.244
4 models selected
> select add #2.298
5 models selected
> select add #2.243
6 models selected
Grouped 6 regions
Showing 309 region surfaces
> select clear
> select #2.48
1 model selected
> select add #2.177
2 models selected
> select add #2.170
3 models selected
Grouped 3 regions
> select clear
> select #2.48
1 model selected
Opened PflABCD_Cage_imasked as #21, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
Segmenting PflABCD_Cage_imasked, density threshold 0.007113
Showing 89 region surfaces
5341 watershed regions, grouped to 89 regions
Showing PflABCD_Cage_imasked.seg - 89 regions, 89 surfaces
> hide #!2 models
> show #!2 models
> hide #!2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/REDO/PflABCD_Cage.mrc models #21
Segmenting PflABCD_Cage.mrc, density threshold 0.007113
Showing 89 region surfaces
5341 watershed regions, grouped to 89 regions
Showing PflABCD_Cage.seg - 89 regions, 89 surfaces
> volume gaussian #21 sDev 2.5
Opened PflABCD_Cage.mrc gaussian as #22, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> hide #!2 models
> volume #22 level 0.005564
> volume #22 level 0.003558
> close #22
> show #!2 models
> select #2.42
1 model selected
> select #2.11
1 model selected
> select add #2.39
2 models selected
> select add #2.7
3 models selected
> select add #2.31
4 models selected
> select add #2.5
5 models selected
> select add #2.41
6 models selected
> select add #2.52
7 models selected
> select add #2.48
8 models selected
> select add #2.45
9 models selected
Grouped 9 regions
Opened PflABCD_Cage_imasked as #22, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/REDO/PflCD.mrc models #22
Opened PflABCD_Cage_imasked as #23, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
Segmenting PflABCD_Cage_imasked, density threshold 0.007113
Showing 80 region surfaces
4222 watershed regions, grouped to 80 regions
Showing PflABCD_Cage_imasked.seg - 80 regions, 80 surfaces
> hide #!22 models
> hide #!23 models
> select #2.36
1 model selected
> select add #2.28
2 models selected
> select add #2.56
3 models selected
> select add #2.51
4 models selected
> select add #2.22
5 models selected
> select add #2.57
6 models selected
> select add #2.37
7 models selected
> select add #2.33
8 models selected
> select add #2.50
9 models selected
> select add #2.55
10 models selected
> select add #2.18
11 models selected
> select add #2.13
12 models selected
> select add #2.12
13 models selected
> select add #2.31
14 models selected
> select add #2.24
15 models selected
> select add #2.25
16 models selected
Grouped 16 regions
Opened PflABCD_Cage_imasked_imasked as #24, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/REDO/PflC.mrc models #24
Opened PflABCD_Cage_imasked_imasked as #25, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
Segmenting PflABCD_Cage_imasked_imasked, density threshold 0.007113
Showing 65 region surfaces
3706 watershed regions, grouped to 65 regions
Showing PflABCD_Cage_imasked_imasked.seg - 65 regions, 65 surfaces
> hide #!24 models
> select #2.14
1 model selected
> select add #2.15
2 models selected
> select add #2.19
3 models selected
Ungrouped to 14 regions
> select subtract #2.67
13 models selected
> select subtract #2.69
12 models selected
> select subtract #2.74
11 models selected
> select subtract #2.68
10 models selected
> select subtract #2.78
9 models selected
> select subtract #2.79
8 models selected
> select subtract #2.77
7 models selected
> select add #2.77
8 models selected
> select subtract #2.75
7 models selected
> select subtract #2.77
6 models selected
Grouped 6 regions
> select #2.77
1 model selected
Ungrouped to 6 regions
> select subtract #2.72
5 models selected
> select subtract #2.71
4 models selected
Grouped 4 regions
> select #2.14
1 model selected
> select add #2.15
2 models selected
> select #2.14
1 model selected
Ungrouped to 6 regions
> select subtract #2.66
5 models selected
> select subtract #2.70
4 models selected
> select subtract #2.76
3 models selected
Ungrouped to 11 regions
> select subtract #2.82
10 models selected
Grouped 10 regions
> select add #2.82
2 models selected
> select add #2.66
3 models selected
> select add #2.70
4 models selected
> select #2.66
1 model selected
> select add #2.70
2 models selected
> select clear
> select #2.70
1 model selected
Ungrouped to 8 regions
Ungrouped to 0 regions
> select #2.66
1 model selected
> select add #2.84
2 models selected
> select add #2.81
3 models selected
> select add #2.76
4 models selected
Grouped 4 regions
> hide #!25 models
> select add #2.86
2 models selected
> select add #2.85
3 models selected
> select add #2.77
4 models selected
> select add #2.83
5 models selected
> select add #2.15
6 models selected
> select add #2.14
7 models selected
Grouped 7 regions
Ungrouped to 7 regions
> select subtract #2.77
6 models selected
Grouped 6 regions
> select clear
> select #2.77
1 model selected
> select #2.14
1 model selected
> select #2.77
1 model selected
Ungrouped to 10 regions
> select subtract #2.15
9 models selected
Grouped 9 regions
> select add #2.14
2 models selected
Grouped 2 regions
> select clear
> select #2.14
1 model selected
Opened PflABCD_Cage_imasked_imasked_imasked as #26, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/REDO/MotBpg.mrc models #26
Opened PflABCD_Cage_imasked_imasked_imasked as #27, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
Segmenting PflABCD_Cage_imasked_imasked_imasked, density threshold 0.007113
Showing 62 region surfaces
3661 watershed regions, grouped to 62 regions
Showing PflABCD_Cage_imasked_imasked_imasked.seg - 62 regions, 62 surfaces
> hide #!26 models
> select #2.16
1 model selected
> select add #2.35
2 models selected
> select add #2.57
3 models selected
> select add #2.19
4 models selected
> select add #2.23
5 models selected
> select add #2.25
6 models selected
> select add #2.24
7 models selected
Grouped 7 regions
> select add #2.21
2 models selected
> select add #2.30
3 models selected
> select subtract #2.30
2 models selected
> select add #2.30
3 models selected
> select add #2.44
4 models selected
> select add #2.39
5 models selected
Grouped 5 regions
> hide #!27 models
Opened PflABCD_Cage_imasked_imasked_imasked_imasked as #28, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/REDO/PflAFlgY.mrc models #28
Opened PflABCD_Cage_imasked_imasked_imasked_imasked as #29, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
Segmenting PflABCD_Cage_imasked_imasked_imasked_imasked, density threshold
0.007113
Showing 50 region surfaces
3293 watershed regions, grouped to 50 regions
Showing PflABCD_Cage_imasked_imasked_imasked_imasked.seg - 50 regions, 50
surfaces
> hide #!28 models
> select #2.1
1 model selected
> select add #2.36
2 models selected
Grouped 2 regions
> select #2.18
1 model selected
Ungrouped to 3 regions
> select #2.36
1 model selected
Ungrouped to 10 regions
> select #2.1
1 model selected
> select add #2.54
2 models selected
> select add #2.18
3 models selected
> hide #!29 models
Grouped 3 regions
> select #2.10
1 model selected
> select add #2.13
2 models selected
> select add #2.26
3 models selected
> select subtract #2.13
2 models selected
Grouped 2 regions
> select #2.33
1 model selected
Ungrouped to 3 regions
Ungrouped to 7 regions
> select #2.10
1 model selected
> select add #2.63
2 models selected
> select add #2.64
3 models selected
Grouped 3 regions
> select #2.10
1 model selected
> select #2.65
1 model selected
Ungrouped to 0 regions
> select #2.13
1 model selected
Ungrouped to 3 regions
Ungrouped to 15 regions
Ungrouped to 28 regions
> select #2.10
1 model selected
> select add #2.85
2 models selected
> select add #2.88
3 models selected
> select add #2.86
4 models selected
> select add #2.89
5 models selected
> select add #2.95
6 models selected
> select add #2.69
7 models selected
> select add #2.94
8 models selected
> select add #2.76
9 models selected
> select add #2.74
10 models selected
Grouped 10 regions
> select #2.66
1 model selected
> select add #2.10
2 models selected
Grouped 2 regions
> select #2.54
1 model selected
Ungrouped to 2 regions
Ungrouped to 0 regions
> select #2.13
1 model selected
> select add #2.10
2 models selected
Grouped 2 regions
> select add #2.1
2 models selected
> select clear
> select #2.4
1 model selected
> select #2.37
1 model selected
Ungrouped to 7 regions
Ungrouped to 2 regions
Ungrouped to 0 regions
> select #2.72
1 model selected
> select add #2.4
2 models selected
> select add #2.27
3 models selected
Grouped 3 regions
> select #2.47
1 model selected
> select #2.47
1 model selected
Ungrouped to 2 regions
Ungrouped to 5 regions
Ungrouped to 2 regions
Ungrouped to 0 regions
> select #2.73
1 model selected
> select add #2.74
2 models selected
> select add #2.4
3 models selected
Grouped 3 regions
> select #2.2
1 model selected
Ungrouped to 3 regions
Ungrouped to 19 regions
Ungrouped to 27 regions
Ungrouped to 11 regions
Ungrouped to 0 regions
Ungrouped to 43 regions
> select #2.133
1 model selected
> select add #2.114
2 models selected
> select add #2.116
3 models selected
> select add #2.129
4 models selected
> select add #2.4
5 models selected
Grouped 5 regions
> select add #2.109
2 models selected
Grouped 2 regions
> select #2.160
1 model selected
> select add #2.125
2 models selected
> select add #2.3
3 models selected
> select add #2.126
4 models selected
Grouped 4 regions
> select add #2.132
2 models selected
> select add #2.159
3 models selected
Grouped 3 regions
> select clear
> select #2.3
1 model selected
> select add #2.4
2 models selected
> select add #2.10
3 models selected
> select add #2.1
4 models selected
> select clear
> select #2.4
1 model selected
Ungrouped to 2 regions
Ungrouped to 5 regions
> select subtract #2.15
4 models selected
> select #2.9
1 model selected
> select add #2.14
2 models selected
> select subtract #2.14
1 model selected
> select add #2.14
2 models selected
Grouped 2 regions
> select clear
> select #2.15
1 model selected
> select #2.15
1 model selected
Ungrouped to 0 regions
> select #2.4
1 model selected
> select add #2.17
2 models selected
> select add #2.11
3 models selected
> select add #2.5
4 models selected
Grouped 4 regions
Showing 152 region surfaces
> select clear
> select #2.4
1 model selected
Ungrouped to 4 regions
Ungrouped to 2 regions
Ungrouped to 3 regions
[Repeated 1 time(s)]Ungrouped to 8 regions
Ungrouped to 56 regions
Ungrouped to 47 regions
Ungrouped to 0 regions
> select #2.21
1 model selected
> select add #2.170
2 models selected
> select add #2.171
3 models selected
> select add #2.32
4 models selected
> select add #2.8
5 models selected
> select add #2.141
6 models selected
Grouped 6 regions
> select add #2.192
2 models selected
> select add #2.35
3 models selected
> select add #2.194
4 models selected
> select add #2.185
5 models selected
Grouped 5 regions
> select add #2.196
2 models selected
Grouped 2 regions
> select add #2.161
2 models selected
> select add #2.163
3 models selected
> select add #2.174
4 models selected
> select add #2.6
5 models selected
Grouped 5 regions
> select add #2.46
2 models selected
> select add #2.28
3 models selected
Grouped 3 regions
> select add #2.168
2 models selected
> select add #2.156
3 models selected
> select add #2.149
4 models selected
Grouped 4 regions
> select add #2.167
2 models selected
> select add #2.7
3 models selected
Grouped 3 regions
> select #2.176
1 model selected
> select add #2.119
2 models selected
> select add #2.118
3 models selected
> select add #2.143
4 models selected
> select add #2.144
5 models selected
> select add #2.22
6 models selected
Grouped 6 regions
> select add #2.175
2 models selected
Grouped 2 regions
> select #2.10
1 model selected
Ungrouped to 2 regions
[Repeated 1 time(s)]Ungrouped to 10 regions
Ungrouped to 3 regions
Ungrouped to 6 regions
Ungrouped to 13 regions
Ungrouped to 43 regions
Ungrouped to 63 regions
Ungrouped to 0 regions
> select #2.7
1 model selected
> select add #2.43
2 models selected
Grouped 2 regions
> select add #2.141
2 models selected
Grouped 2 regions
> select add #2.45
2 models selected
> select add #2.157
3 models selected
Grouped 3 regions
> select add #2.6
2 models selected
Grouped 2 regions
> select #2.12
1 model selected
> select add #2.19
2 models selected
> select add #2.120
3 models selected
> select add #2.123
4 models selected
> select add #2.151
5 models selected
> select add #2.153
6 models selected
> select add #2.154
7 models selected
> select subtract #2.154
6 models selected
Grouped 6 regions
> select add #2.152
2 models selected
Grouped 2 regions
> select add #2.49
2 models selected
Grouped 2 regions
> select add #2.6
2 models selected
Grouped 2 regions
> select add #2.102
2 models selected
> select add #2.100
3 models selected
> select add #2.101
4 models selected
> select add #2.103
5 models selected
> select add #2.63
6 models selected
> select add #2.98
7 models selected
> select subtract #2.98
6 models selected
> select add #2.81
7 models selected
> select add #2.80
8 models selected
> select add #2.54
9 models selected
> select add #2.71
10 models selected
> select add #2.68
11 models selected
> select add #2.93
12 models selected
> select add #2.92
13 models selected
> select add #2.82
14 models selected
> select add #2.26
15 models selected
> select add #2.18
16 models selected
> select add #2.83
17 models selected
> select add #2.99
18 models selected
> select add #2.98
19 models selected
> select add #2.97
20 models selected
> select add #2.13
21 models selected
> select add #2.36
22 models selected
> select add #2.62
23 models selected
> select add #2.66
24 models selected
> select add #2.42
25 models selected
> select add #2.33
26 models selected
Grouped 26 regions
> select add #2.169
2 models selected
> select add #2.72
3 models selected
> select add #2.2
4 models selected
> select add #2.73
5 models selected
> select add #2.104
6 models selected
> select add #2.95
7 models selected
> select add #2.88
8 models selected
> select add #2.89
9 models selected
> select add #2.85
10 models selected
> select add #2.139
11 models selected
> select add #2.122
12 models selected
> select add #2.121
13 models selected
> select add #2.137
14 models selected
> select add #2.113
15 models selected
> select add #2.111
16 models selected
> select add #2.140
17 models selected
> select add #2.138
18 models selected
> select add #2.108
19 models selected
> select add #2.112
20 models selected
> select add #2.135
21 models selected
> select subtract #2.135
20 models selected
> select add #2.134
21 models selected
> select add #2.135
22 models selected
> select add #2.77
23 models selected
> select add #2.15
24 models selected
> select add #2.136
25 models selected
> select add #2.105
26 models selected
> select add #2.107
27 models selected
> select add #2.86
28 models selected
> select add #2.78
29 models selected
> select add #2.94
30 models selected
> select add #2.130
31 models selected
Grouped 31 regions
> select #2.142
1 model selected
> select add #2.2
2 models selected
Grouped 2 regions
> select #2.2
1 model selected
> select add #2.51
2 models selected
> select add #2.58
3 models selected
> select add #2.57
4 models selected
> select add #2.59
5 models selected
> select add #2.55
6 models selected
Grouped 6 regions
> select add #2.56
2 models selected
Grouped 2 regions
> select add #2.173
2 models selected
> select add #2.40
3 models selected
> select #2.2
1 model selected
> select clear
> select #2.2
1 model selected
> select add #2.173
2 models selected
> select add #2.165
3 models selected
Grouped 3 regions
> select clear
> select #2.2
1 model selected
Opened PflABCD_Cage_imasked_imasked_imasked_imasked_imasked as #30, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/REDO/Cage-PflAB.mrc models #30
> hide #!2 models
> hide #!30 models
> show #!30 models
> show #!26 models
> show #!22 models
> save /Users/shoichitachiyama/Desktop/tmp/REDO/Resegmentation_no-mask.cxs
> includeMaps true
> close session
> open /Users/shoichitachiyama/Desktop/tmp/REDO/PflCD.mrc
Opened PflCD.mrc as #1, grid size 200,200,200, pixel 2.14, shown at level
0.00703, step 1, values float32
> open /Users/shoichitachiyama/Desktop/tmp/REDO/Cage-PflAB.mrc
Opened Cage-PflAB.mrc as #2, grid size 200,200,200, pixel 2.14, shown at level
0.0202, step 1, values float32
> volume #2 level 0.00703
> volume gaussian #1 sDev 2.5
Opened PflCD.mrc gaussian as #3, grid size 200,200,200, pixel 2.14, shown at
step 1, values float32
> close #3
> volume gaussian #1 sDev 3
Opened PflCD.mrc gaussian as #3, grid size 200,200,200, pixel 2.14, shown at
step 1, values float32
> volume gaussian #2 sDev 3
Opened Cage-PflAB.mrc gaussian as #4, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> volume #3 level 0.00703
> volume #3 level 0.0025
> volume #3 level 0.00136
> volume #4 level 0.00136
> surface dust #3 size 21.4
> surface dust #4 size 21.4
> surface dust #3 size 21.4
> surface dust #4 size 21.4
> hide #!4 models
> ui tool show "Map Eraser"
> volume erase #3 center 20.174,224.54,492.02 radius 236.77
> volume erase #3 center 65.467,171.46,92.433 radius 236.77
> volume erase #3 center 77.209,339.85,3.3018 radius 236.77
> volume erase #3 center 401.68,295.76,-1.6159 radius 236.77
> volume erase #3 center 407.21,44.159,53.128 radius 236.77
> volume erase #3 center 469.71,44.506,126.55 radius 236.77
> volume erase #3 center 515.86,325.83,152.59 radius 236.77
> volume erase #3 center 304.43,421.76,5.3757 radius 236.77
> volume erase #3 center 23.092,-59.062,487.37 radius 236.77
> volume erase #3 center 22.49,472.98,554.6 radius 236.77
> volume erase #3 center 360.47,-87.815,101.02 radius 236.77
> hide #!3 models
> show #!4 models
> volume erase #4 center 82.975,209.79,483.49 radius 214
> volume erase #4 center 36.493,188.42,56.438 radius 214
> volume erase #4 center 64.371,426.19,72.091 radius 214
> volume erase #4 center 544.73,447.17,222.02 radius 214
> volume erase #4 center 587.15,237.1,237.72 radius 214
> volume erase #4 center 538.34,-6.7222,246.41 radius 214
> volume erase #4 center 595.68,4.2899,35.265 radius 214
> volume erase #4 center -32.899,40.612,279.33 radius 214
[Repeated 1 time(s)]
> volume erase #4 center 11.837,480.63,487.85 radius 214
> volume erase #4 center 287.58,47.244,-158.46 radius 214
> surface dust #1 size 50
> surface dust #4 size 50
> volume erase #4 center 517.5,482.91,67.451 radius 214
> close #4
> volume gaussian #2 sDev 3
Opened Cage-PflAB.mrc gaussian as #4, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> volume #4 level 0.001306
> surface dust #4 size 50
> surface dust #4 size 100
> volume erase #4 center 558.64,398.88,78.048 radius 214
> volume erase #4 center -21.244,220.82,150.15 radius 214
> close #5
> show #!3 models
> surface dust #3 size 100
> color #4 #a9a9a967 models
> color #4 #7b80ffff models
> save /Users/shoichitachiyama/Desktop/tmp/REDO/Docking_models.cxs includeMaps
> true
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/For-PflCD/Cage-PflCD.pdb"
Chain information for Cage-PflCD.pdb
---
Chain | Description
5.1/A 5.4/D 5.7/G 5.10/J 5.13/M 5.16/P 5.19/S 5.22/V | No description available
5.2/B 5.5/E 5.8/H 5.11/K 5.14/N 5.17/Q 5.20/T 5.23/W | No description available
5.3/C 5.6/F 5.9/I 5.12/L 5.15/O 5.18/R 5.21/U 5.24/X | No description available
5.25/Y 5.26/a 5.27/b 5.28/c | No description available
> color #4 #a9a9a967 models
> color #3 #a9a9a967 models
> combine #5
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #6 inMap #4
Fit molecule combination (#6) to map Cage-PflAB.mrc gaussian (#4) using 46256
atoms
average map value = 0.01011, steps = 84
shifted from previous position = 5.88
rotated from previous position = 2.53 degrees
atoms outside contour = 30040, contour level = 0.0013059
Position of combination (#6) relative to Cage-PflAB.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.99921948 0.02312516 -0.03202601 0.55153051
-0.02374963 0.99953244 -0.01925771 7.88332673
0.03156570 0.02000328 0.99930149 -14.43575364
Axis 0.44504051 -0.72083986 -0.53134625
Axis point 419.20046007 0.00000000 -24.02856866
Rotation angle (degrees) 2.52810607
Shift along axis 2.23322092
> hide #!5 models
> fitmap #6 inMap #4
Fit molecule combination (#6) to map Cage-PflAB.mrc gaussian (#4) using 46256
atoms
average map value = 0.01012, steps = 40
shifted from previous position = 0.0416
rotated from previous position = 0.00353 degrees
atoms outside contour = 30045, contour level = 0.0013059
Position of combination (#6) relative to Cage-PflAB.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.99922138 0.02306617 -0.03200918 0.53302975
-0.02369055 0.99953368 -0.01926582 7.83564101
0.03154986 0.02000913 0.99930188 -14.42339574
Axis 0.44560291 -0.72112366 -0.53048912
Axis point 418.97638152 0.00000000 -24.70165846
Rotation angle (degrees) 2.52581118
Shift along axis 2.23850797
> fitmap #6 inMap #4
Fit molecule combination (#6) to map Cage-PflAB.mrc gaussian (#4) using 46256
atoms
average map value = 0.01011, steps = 40
shifted from previous position = 0.0322
rotated from previous position = 0.00166 degrees
atoms outside contour = 30040, contour level = 0.0013059
Position of combination (#6) relative to Cage-PflAB.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.99922152 0.02306628 -0.03200470 0.56113759
-0.02368967 0.99953425 -0.01923730 7.84052675
0.03154606 0.01998050 0.99930257 -14.42259568
Axis 0.44511533 -0.72129020 -0.53067202
Axis point 418.84422299 0.00000000 -23.92172561
Rotation angle (degrees) 2.52489847
Shift along axis 2.24814390
> fitmap #6 inMap #4
Fit molecule combination (#6) to map Cage-PflAB.mrc gaussian (#4) using 46256
atoms
average map value = 0.01012, steps = 44
shifted from previous position = 0.0365
rotated from previous position = 0.00837 degrees
atoms outside contour = 30042, contour level = 0.0013059
Position of combination (#6) relative to Cage-PflAB.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.99921675 0.02316253 -0.03208400 0.53098251
-0.02378984 0.99953047 -0.01931011 7.87882954
0.03162166 0.02005826 0.99929862 -14.45380155
Axis 0.44539356 -0.72073324 -0.53119504
Axis point 418.98009767 0.00000000 -24.71549644
Rotation angle (degrees) 2.53301404
Shift along axis 2.23574951
> hide #6 models
> show #6 models
> hide #6 models
> show #!5 models
> hide #5.3 models
> show #5.3 models
> hide #5.28 models
> show #5.28 models
> hide #!5 models
> show #6 models
> open
> /Users/shoichitachiyama/Desktop/tmp/REDO/fold_2025_07_22_09_45cj_pilmno/fold_2025_07_22_09_45cj_pilmno_model_0.cif
Chain information for fold_2025_07_22_09_45cj_pilmno_model_0.cif #7
---
Chain | Description
A | .
B | .
C | .
> select add #7
5637 atoms, 5737 bonds, 683 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,8.8892,0,1,0,-12.538,0,0,1,224.08
> view matrix models #7,1,0,0,345.54,0,1,0,65.693,0,0,1,212.5
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.84784,0.14233,0.51079,340.7,-0.46043,-0.6754,-0.57606,46.043,0.263,-0.72358,0.63817,205.61
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.84784,0.14233,0.51079,351.79,-0.46043,-0.6754,-0.57606,161.29,0.263,-0.72358,0.63817,160.26
> view matrix models
> #7,-0.84784,0.14233,0.51079,347.8,-0.46043,-0.6754,-0.57606,163.57,0.263,-0.72358,0.63817,160.49
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.77936,-0.051184,0.62449,346.55,-0.49138,-0.56848,-0.65983,164.23,0.38878,-0.8211,0.4179,159.45
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.77936,-0.051184,0.62449,327.63,-0.49138,-0.56848,-0.65983,175.12,0.38878,-0.8211,0.4179,155.63
> view matrix models
> #7,-0.77936,-0.051184,0.62449,327.88,-0.49138,-0.56848,-0.65983,173.06,0.38878,-0.8211,0.4179,150.22
> view matrix models
> #7,-0.77936,-0.051184,0.62449,334.14,-0.49138,-0.56848,-0.65983,174.64,0.38878,-0.8211,0.4179,151.85
> view matrix models
> #7,-0.77936,-0.051184,0.62449,333.76,-0.49138,-0.56848,-0.65983,196.03,0.38878,-0.8211,0.4179,132.67
> view matrix models
> #7,-0.77936,-0.051184,0.62449,326.38,-0.49138,-0.56848,-0.65983,101.33,0.38878,-0.8211,0.4179,154.88
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.77421,-0.05604,0.63044,326.37,-0.45181,-0.64862,-0.6125,100.86,0.44324,-0.75904,0.47685,155.87
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.77421,-0.05604,0.63044,325.89,-0.45181,-0.64862,-0.6125,94.416,0.44324,-0.75904,0.47685,158.06
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.84318,-0.13151,0.5213,324.57,-0.32745,-0.64341,-0.69195,94.756,0.4264,-0.75414,0.49945,158.1
> hide #7 models
> select subtract #7
Nothing selected
> show #7 models
> select add #7
5637 atoms, 5737 bonds, 683 residues, 1 model selected
> view matrix models
> #7,-0.85479,-0.11718,0.50557,324.61,-0.41822,-0.42128,-0.80475,96.198,0.30729,-0.89933,0.3111,155.68
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.85479,-0.11718,0.50557,326.23,-0.41822,-0.42128,-0.80475,116.83,0.30729,-0.89933,0.3111,151.17
> save /Users/shoichitachiyama/Desktop/tmp/REDO/Docking_models.cxs includeMaps
> true
——— End of log from Tue Jul 22 22:37:33 2025 ———
opened ChimeraX session
> hide #!3 models
> hide #!4 models
> hide #5.2 models
> show #5.2 models
> hide #6 models
> hide #5.1 models
> show #5.1 models
> hide #5.3 models
> show #5.3 models
> hide #5.4 models
> show #5.4 models
> hide #5.5 models
> show #5.5 models
> hide #5.28 models
> show #5.28 models
> hide #5.27 models
> show #5.27 models
> hide #5.25 models
> show #5.25 models
> hide #5.24 models
> show #5.24 models
> hide #5.23 models
> show #5.23 models
> hide #5.23 models
> show #5.23 models
> hide #5.24 models
> show #5.24 models
> hide #5.24 models
> hide #5.25 models
> hide #5.23 models
> show #5.23 models
> hide #5.23 models
> show #5.23 models
> select add #5.23
7095 atoms, 7225 bonds, 858 residues, 2 models selected
Alignment identifier is 1
Alignment identifier is 7/A
Alignment identifier is 7/C
> select subtract #7
1458 atoms, 1488 bonds, 175 residues, 1 model selected
> select add #7
7095 atoms, 7225 bonds, 858 residues, 2 models selected
Alignment identifier is 2
Alignment identifier is 7/A
Alignment identifier is 7/C
> select #7/A:1-2
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #7/A
2637 atoms, 2686 bonds, 319 residues, 1 model selected
> select #7/C:1-2
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #7/C
1542 atoms, 1563 bonds, 189 residues, 1 model selected
> split #7
Split fold_2025_07_22_09_45cj_pilmno_model_0.cif (#7) into 3 models
Chain information for fold_2025_07_22_09_45cj_pilmno_model_0.cif A #7.1
---
Chain | Description
A | No description available
Chain information for fold_2025_07_22_09_45cj_pilmno_model_0.cif B #7.2
---
Chain | Description
B | No description available
Chain information for fold_2025_07_22_09_45cj_pilmno_model_0.cif C #7.3
---
Chain | Description
C | No description available
> hide #7.1 models
> combine #7.2,7.3
No structures specified
> select add #7.2
1458 atoms, 1488 bonds, 175 residues, 1 model selected
> select add #7.3
3000 atoms, 3051 bonds, 364 residues, 2 models selected
> save /Users/shoichi/Desktop/PilNO_noPilM_predicted.pdb selectedOnly true
> select clear
> open /Users/shoichi/Desktop/PilNO_noPilM_predicted.pdb
Summary of feedback from opening
/Users/shoichi/Desktop/PilNO_noPilM_predicted.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 49 1 48
Start residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1
42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
21 messages similar to the above omitted
Chain information for PilNO_noPilM_predicted.pdb
---
Chain | Description
8.1/B | No description available
8.2/C | No description available
> combine #8
> hide #!8 models
> show #6 models
> hide #6 models
> show #6 models
> show #!4 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #!5 models
> split #6
Split combination (#6) into 28 models
Chain information for combination A #6.1
---
Chain | Description
A | No description available
Chain information for combination B #6.2
---
Chain | Description
B | No description available
Chain information for combination C #6.3
---
Chain | Description
C | No description available
Chain information for combination D #6.4
---
Chain | Description
D | No description available
Chain information for combination E #6.5
---
Chain | Description
E | No description available
Chain information for combination F #6.6
---
Chain | Description
F | No description available
Chain information for combination G #6.7
---
Chain | Description
G | No description available
Chain information for combination H #6.8
---
Chain | Description
H | No description available
Chain information for combination I #6.9
---
Chain | Description
I | No description available
Chain information for combination J #6.10
---
Chain | Description
J | No description available
Chain information for combination K #6.11
---
Chain | Description
K | No description available
Chain information for combination L #6.12
---
Chain | Description
L | No description available
Chain information for combination M #6.13
---
Chain | Description
M | No description available
Chain information for combination N #6.14
---
Chain | Description
N | No description available
Chain information for combination O #6.15
---
Chain | Description
O | No description available
Chain information for combination P #6.16
---
Chain | Description
P | No description available
Chain information for combination Q #6.17
---
Chain | Description
Q | No description available
Chain information for combination R #6.18
---
Chain | Description
R | No description available
Chain information for combination S #6.19
---
Chain | Description
S | No description available
Chain information for combination T #6.20
---
Chain | Description
T | No description available
Chain information for combination U #6.21
---
Chain | Description
U | No description available
Chain information for combination V #6.22
---
Chain | Description
V | No description available
Chain information for combination W #6.23
---
Chain | Description
W | No description available
Chain information for combination X #6.24
---
Chain | Description
X | No description available
Chain information for combination Y #6.25
---
Chain | Description
Y | No description available
Chain information for combination a #6.26
---
Chain | Description
a | No description available
Chain information for combination b #6.27
---
Chain | Description
b | No description available
Chain information for combination c #6.28
---
Chain | Description
c | No description available
> hide #!4 models
> show #!4 models
> hide #!6 models
> hide #!7 models
> show #!6 models
> select add #6.8
1458 atoms, 1488 bonds, 175 residues, 1 model selected
> select subtract #6.8
Nothing selected
> hide #!4 models
Drag select of 33 residues
> select add #6.10
1713 atoms, 1564 bonds, 211 residues, 3 models selected
> select add #6.11
3083 atoms, 3052 bonds, 375 residues, 3 models selected
> select add #6.12
4355 atoms, 4440 bonds, 526 residues, 3 models selected
> save /Users/shoichi/Desktop/One_unit_JBM_PilNO_PflD.pdb selectedOnly true
> hide #!6 models
> select clear
> open /Users/shoichi/Desktop/One_unit_JBM_PilNO_PflD.pdb
Summary of feedback from opening
/Users/shoichi/Desktop/One_unit_JBM_PilNO_PflD.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 49 1 48
Start residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1
42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
34 messages similar to the above omitted
Chain information for One_unit_JBM_PilNO_PflD.pdb
---
Chain | Description
10.1/J | No description available
10.2/K | No description available
10.3/L | No description available
> combine #10
> matchmaker #9 to #11
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 combination, chain J (#11) with combination, chain C (#9), sequence
alignment score = 960
RMSD between 153 pruned atom pairs is 0.777 angstroms; (across all 189 pairs:
12.653)
> show #!7 models
> hide #!7 models
> show #!7 models
> show #7.1 models
> combine #7
> matchmaker #12 to #9
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 combination, chain C (#9) with combination, chain C (#12), sequence
alignment score = 978
RMSD between 189 pruned atom pairs is 0.000 angstroms; (across all 189 pairs:
0.000)
> hide #11 models
> show #11 models
> hide #11 models
> hide #!10 models
> hide #9 models
> hide #!7 models
> show #!5 models
> hide #!5 models
> show #!4 models
> combine #12
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #13 inMap #4
Fit molecule copy of combination (#13) to map Cage-PflAB.mrc gaussian (#4)
using 5637 atoms
average map value = 0.01109, steps = 636
shifted from previous position = 24.6
rotated from previous position = 33.3 degrees
atoms outside contour = 1405, contour level = 0.0013059
Position of copy of combination (#13) relative to Cage-PflAB.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
-0.88826804 -0.00944555 0.45922835 323.13195928
-0.40374456 -0.46067511 -0.79042316 119.91203454
0.21902105 -0.88751857 0.40538939 156.26725860
Axis -0.20579620 0.50912545 -0.83572675
Axis point 155.86657636 86.42998297 0.00000000
Rotation angle (degrees) 166.35520893
Shift along axis -136.04578879
> hide #12 models
> show #12 models
> hide #12 models
> select add #13
5637 atoms, 5737 bonds, 683 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.50943,0.1189,0.85226,316.16,-0.78994,-0.45743,-0.40836,97.933,0.3413,-0.88126,0.32695,158.84
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.50943,0.1189,0.85226,317.58,-0.78994,-0.45743,-0.40836,114.97,0.3413,-0.88126,0.32695,156.12
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.50657,0.12206,0.85352,317.62,-0.80047,-0.43441,-0.41296,115.14,0.32037,-0.89241,0.31776,155.9
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.50657,0.12206,0.85352,317.73,-0.80047,-0.43441,-0.41296,116.34,0.32037,-0.89241,0.31776,155.65
> hide #!4 models
> select clear
> show #!10 models
> close #11-13
> hide #!10 models
> show #!10 models
> show #9 models
> hide #9 models
> show #9 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/PflCD_Docking_model_Fig3/REDO/Models/fold_2025_07_22_09_45cj_pilm_pilnnterm/fold_2025_07_22_09_45cj_pilm_pilnnterm_model_0.cif"
Chain information for fold_2025_07_22_09_45cj_pilm_pilnnterm_model_0.cif #11
---
Chain | Description
A | .
B | .
> select add #11
2872 atoms, 2930 bonds, 346 residues, 1 model selected
> view matrix models #11,1,0,0,76.462,0,1,0,-68.169,0,0,1,159.41
> view matrix models #11,1,0,0,307.15,0,1,0,91.026,0,0,1,102.81
> hide #!10 models
> show #!10 models
> hide #10.1 models
> show #10.1 models
> hide #10.1 models
> hide #10.3 models
> matchmaker #11 to #10.2
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 One_unit_JBM_PilNO_PflD.pdb, chain K (#10.2) with
fold_2025_07_22_09_45cj_pilm_pilnnterm_model_0.cif, chain B (#11), sequence
alignment score = 124
RMSD between 7 pruned atom pairs is 1.601 angstroms; (across all 27 pairs:
7.178)
> hide #9 models
> split #11
Split fold_2025_07_22_09_45cj_pilm_pilnnterm_model_0.cif (#11) into 2 models
Chain information for fold_2025_07_22_09_45cj_pilm_pilnnterm_model_0.cif A
#11.1
---
Chain | Description
A | No description available
Chain information for fold_2025_07_22_09_45cj_pilm_pilnnterm_model_0.cif B
#11.2
---
Chain | Description
B | No description available
> hide #11.1 models
> show #11.1 models
> hide #11.1 models
> matchmaker #11.2 to #10.2
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 One_unit_JBM_PilNO_PflD.pdb, chain K (#10.2) with
fold_2025_07_22_09_45cj_pilm_pilnnterm_model_0.cif B, chain B (#11.2),
sequence alignment score = 124
RMSD between 7 pruned atom pairs is 1.601 angstroms; (across all 27 pairs:
7.178)
> matchmaker #11.2 to #10.2
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 One_unit_JBM_PilNO_PflD.pdb, chain K (#10.2) with
fold_2025_07_22_09_45cj_pilm_pilnnterm_model_0.cif B, chain B (#11.2),
sequence alignment score = 124
RMSD between 7 pruned atom pairs is 1.601 angstroms; (across all 27 pairs:
7.178)
> show #11.1 models
> hide #11.1 models
> show #11.1 models
> hide #11.1 models
> show #11.1 models
> hide #11.1 models
> show #11.1 models
> hide #11.2 models
> show #10.3 models
> show #10.1 models
> select add #11.1
2637 atoms, 2686 bonds, 319 residues, 1 model selected
> select add #10.3
3992 atoms, 4074 bonds, 481 residues, 2 models selected
> select add #10.2
5450 atoms, 5562 bonds, 656 residues, 3 models selected
> select add #10.1
6992 atoms, 7126 bonds, 845 residues, 4 models selected
> save /Users/shoichi/Desktop/One_unit_JBM_PilNO_PflDwithPilM.pdb selectedOnly
> true
> select clear
> open /Users/shoichi/Desktop/One_unit_JBM_PilNO_PflDwithPilM.pdb
Summary of feedback from opening
/Users/shoichi/Desktop/One_unit_JBM_PilNO_PflDwithPilM.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 49 1 48
Start residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1
42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
35 messages similar to the above omitted
End residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1 42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
Start residue of secondary structure not found: HELIX 6 6 PRO A 146 ARG A 148
1 3
Start residue of secondary structure not found: HELIX 7 7 LEU A 149 ASP A 154
1 6
6 messages similar to the above omitted
Chain information for One_unit_JBM_PilNO_PflDwithPilM.pdb
---
Chain | Description
12.4/A | No description available
12.1/J | No description available
12.2/K | No description available
12.3/L | No description available
> hide #!10 models
> hide #!11 models
> combine #12
> hide #!12 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!6 models
> show #!4 models
> select add #13
6992 atoms, 7126 bonds, 845 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.99951,-0.00089194,-0.031358,5.7809,-0.0035041,0.99017,-0.13986,26.842,0.031174,0.1399,0.98968,-23.458
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.99951,-0.00089194,-0.031358,8.4964,-0.0035041,0.99017,-0.13986,39.04,0.031174,0.1399,0.98968,-24.631
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.99899,-0.0026302,-0.044765,11.214,-0.0063545,0.9799,-0.19939,51.565,0.044389,0.19947,0.9789,-33.477
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.99899,-0.0026302,-0.044765,12.596,-0.0063545,0.9799,-0.19939,57.776,0.044389,0.19947,0.9789,-34.052
> select clear
> hide #!4 models
> show #!10 models
> hide #!10 models
Drag select of 19 residues
Drag select of 181 residues
Drag select of 22 residues
> select add #6.22
3293 atoms, 1564 bonds, 404 residues, 4 models selected
> select add #6.23
4701 atoms, 3052 bonds, 573 residues, 4 models selected
> select add #6.24
5387 atoms, 4440 bonds, 656 residues, 4 models selected
> select add #6.28
7209 atoms, 7354 bonds, 882 residues, 4 models selected
> save /Users/shoichi/Desktop/2nd_unit_PilNO_PflDC_JMB.pdb selectedOnly true
> select clear
> open /Users/shoichi/Desktop/2nd_unit_PilNO_PflDC_JMB.pdb
Summary of feedback from opening
/Users/shoichi/Desktop/2nd_unit_PilNO_PflDC_JMB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 49 1 48
Start residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1
42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
47 messages similar to the above omitted
Chain information for 2nd_unit_PilNO_PflDC_JMB.pdb
---
Chain | Description
14.1/V | No description available
14.2/W | No description available
14.3/X | No description available
14.4/c | No description available
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/PflCD_Docking_model_Fig3/REDO/Models/fold_2025_07_22_09_45cj_pilm_pilnnterm/fold_2025_07_22_09_45cj_pilm_pilnnterm_model_0.cif"
Chain information for fold_2025_07_22_09_45cj_pilm_pilnnterm_model_0.cif #15
---
Chain | Description
A | .
B | .
> select add #15
2872 atoms, 2930 bonds, 346 residues, 1 model selected
> view matrix models #15,1,0,0,29.872,0,1,0,201.61,0,0,1,38.462
> view matrix models #15,1,0,0,167.09,0,1,0,209.12,0,0,1,202.88
> view matrix models #15,1,0,0,343.71,0,1,0,275.21,0,0,1,157.7
> view matrix models #15,1,0,0,364.43,0,1,0,188.41,0,0,1,97.033
> hide #!6 models
> hide #14.3 models
> hide #14.4 models
> hide #14.2 models
> show #14.2 models
> matchmaker #15 to #14.2
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 2nd_unit_PilNO_PflDC_JMB.pdb, chain W (#14.2) with
fold_2025_07_22_09_45cj_pilm_pilnnterm_model_0.cif, chain B (#15), sequence
alignment score = 124
RMSD between 7 pruned atom pairs is 1.601 angstroms; (across all 27 pairs:
7.178)
> show #!4 models
> show #14.3 models
> show #14.4 models
> show #!3 models
> select subtract #15
Nothing selected
> hide #!4 models
> hide #!3 models
> split #15
Split fold_2025_07_22_09_45cj_pilm_pilnnterm_model_0.cif (#15) into 2 models
Chain information for fold_2025_07_22_09_45cj_pilm_pilnnterm_model_0.cif A
#15.1
---
Chain | Description
A | No description available
Chain information for fold_2025_07_22_09_45cj_pilm_pilnnterm_model_0.cif B
#15.2
---
Chain | Description
B | No description available
> hide #15.1 models
> show #15.1 models
> hide #15.2 models
> select add #15.1
2637 atoms, 2686 bonds, 319 residues, 1 model selected
> select add #14.4
5491 atoms, 5600 bonds, 675 residues, 2 models selected
> select add #14.3
6846 atoms, 6988 bonds, 837 residues, 3 models selected
> select add #14.2
8304 atoms, 8476 bonds, 1012 residues, 4 models selected
> select add #14.1
9846 atoms, 10040 bonds, 1201 residues, 5 models selected
> show #!5 models
> hide #!5 models
> show #!4 models
> select clear
> select add #13
6992 atoms, 7126 bonds, 845 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.99917,0.0010713,-0.040602,11.396,-0.0082341,0.98424,-0.17667,53.883,0.039772,0.17685,0.98343,-30.897
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.99917,0.0010713,-0.040602,10.523,-0.0082341,0.98424,-0.17667,49.692,0.039772,0.17685,0.98343,-30.883
> view orient
> split #15turn x 90
Expected a structures specifier or a keyword
> turn x 90
[Repeated 1 time(s)]
> hide #!4 models
> select clear
> show #!3 models
> show #!4 models
> select add #13
6992 atoms, 7126 bonds, 845 residues, 1 model selected
> select add #14
14201 atoms, 14480 bonds, 1727 residues, 6 models selected
> select add #15.1
16838 atoms, 17166 bonds, 2046 residues, 7 models selected
> save /Users/shoichi/Desktop/Cage_PflDC_JMB_Modified.pdb selectedOnly true
> open /Users/shoichi/Desktop/Cage_PflDC_JMB_Modified.pdb
Summary of feedback from opening
/Users/shoichi/Desktop/Cage_PflDC_JMB_Modified.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 49 1 48
End residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1 42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
Start residue of secondary structure not found: HELIX 6 6 PRO A 146 ARG A 148
1 3
Start residue of secondary structure not found: HELIX 7 7 LEU A 149 ASP A 154
1 6
59 messages similar to the above omitted
End residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1 42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
Start residue of secondary structure not found: HELIX 6 6 PRO A 146 ARG A 148
1 3
Start residue of secondary structure not found: HELIX 7 7 LEU A 149 ASP A 154
1 6
6 messages similar to the above omitted
Chain information for Cage_PflDC_JMB_Modified.pdb
---
Chain | Description
16.1/A 16.6/A | No description available
16.1/J 16.2/V | No description available
16.1/K 16.3/W | No description available
16.1/L 16.4/X | No description available
16.5/c | No description available
> select clear
> select add #16
16838 atoms, 17166 bonds, 2046 residues, 7 models selected
> combine #16
Remapping chain ID 'A' in Cage_PflDC_JMB_Modified.pdb #16.6 to 'B'
> select subtract #16
Nothing selected
> hide #!16 models
> show #!6 models
> hide #!4 models
Drag select of 83 residues
> select add #6.1
2066 atoms, 1564 bonds, 254 residues, 6 models selected
> select add #6.2
3402 atoms, 3052 bonds, 414 residues, 6 models selected
> select add #6.3
4689 atoms, 4440 bonds, 568 residues, 6 models selected
> select add #6.13
6092 atoms, 6004 bonds, 739 residues, 6 models selected
> select add #6.14
7424 atoms, 7492 bonds, 898 residues, 6 models selected
> select add #6.15
8710 atoms, 8880 bonds, 1052 residues, 6 models selected
> select add #6.16
10252 atoms, 10444 bonds, 1241 residues, 7 models selected
> select subtract #6.16
8710 atoms, 8880 bonds, 1052 residues, 6 models selected
> select add #6.28
11564 atoms, 11794 bonds, 1408 residues, 7 models selected
> select add #6.27
14418 atoms, 14708 bonds, 1764 residues, 8 models selected
> select subtract #6.27
11564 atoms, 11794 bonds, 1408 residues, 7 models selected
> select add #6.26
14418 atoms, 14708 bonds, 1764 residues, 8 models selected
> select subtract #6.26
11564 atoms, 11794 bonds, 1408 residues, 7 models selected
> select add #6.25
14418 atoms, 14708 bonds, 1764 residues, 8 models selected
> select subtract #6.25
11564 atoms, 11794 bonds, 1408 residues, 7 models selected
> select add #6.24
12919 atoms, 13182 bonds, 1570 residues, 8 models selected
> select subtract #6.28
10065 atoms, 10268 bonds, 1214 residues, 7 models selected
> select subtract #6.24
8710 atoms, 8880 bonds, 1052 residues, 6 models selected
> select add #6.23
10168 atoms, 10368 bonds, 1227 residues, 7 models selected
> select subtract #6.23
8710 atoms, 8880 bonds, 1052 residues, 6 models selected
> select add #6.22
10252 atoms, 10444 bonds, 1241 residues, 7 models selected
> select subtract #6.22
8710 atoms, 8880 bonds, 1052 residues, 6 models selected
> select add #6.21
10065 atoms, 10268 bonds, 1214 residues, 7 models selected
> select subtract #6.21
8710 atoms, 8880 bonds, 1052 residues, 6 models selected
> select add #6.20
10168 atoms, 10368 bonds, 1227 residues, 7 models selected
> select subtract #6.20
8710 atoms, 8880 bonds, 1052 residues, 6 models selected
> select add #6.27
11564 atoms, 11794 bonds, 1408 residues, 7 models selected
> select subtract #6.27
8710 atoms, 8880 bonds, 1052 residues, 6 models selected
> select add #6.28
11564 atoms, 11794 bonds, 1408 residues, 7 models selected
> select subtract #6.28
8710 atoms, 8880 bonds, 1052 residues, 6 models selected
> select add #6.26
11564 atoms, 11794 bonds, 1408 residues, 7 models selected
> select subtract #6.26
8710 atoms, 8880 bonds, 1052 residues, 6 models selected
> select add #6.25
11564 atoms, 11794 bonds, 1408 residues, 7 models selected
> save /Users/shoichi/Desktop/2nd-template_from_JMB.pdb selectedOnly true
> hide #!6 models
> select clear
> open /Users/shoichi/Desktop/2nd-template_from_JMB.pdb
Summary of feedback from opening /Users/shoichi/Desktop/2nd-
template_from_JMB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 49 1 48
Start residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1
42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
73 messages similar to the above omitted
Chain information for 2nd-template_from_JMB.pdb
---
Chain | Description
18.1/A 18.4/M | No description available
18.2/B 18.5/N | No description available
18.3/C 18.6/O | No description available
18.7/Y | No description available
> combine #18
> matchmaker #17 to #19
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 combination, chain Y (#19) with combination, chain c (#17),
sequence alignment score = 1828.6
RMSD between 356 pruned atom pairs is 0.001 angstroms; (across all 356 pairs:
0.001)
> hide #!18 models
> hide #19 models
> show #!18 models
> hide #!18 models
> show #19 models
> hide #19 models
> hide #17 models
> show #17 models
> close #17
> show #!18 models
> hide #!18 models
> hide #!14 models
> show #!14 models
> hide #!15 models
> show #!15 models
> close #16
> select add #14
7209 atoms, 7354 bonds, 882 residues, 5 models selected
> select add #15
10081 atoms, 10284 bonds, 1228 residues, 8 models selected
> show #!5 models
> hide #!5 models
> show #!4 models
> view matrix models
> #14,1,0,0,3.3676,0,1,0,-0.44796,0,0,1,-0.20608,#15,1,0,0,3.3676,0,1,0,-0.44796,0,0,1,-0.20608
> view matrix models
> #14,1,0,0,6.2868,0,1,0,0.2217,0,0,1,-0.99469,#15,1,0,0,6.2868,0,1,0,0.2217,0,0,1,-0.99469
> view matrix models
> #14,1,0,0,2.3606,0,1,0,0.057463,0,0,1,-1.1217,#15,1,0,0,2.3606,0,1,0,0.057463,0,0,1,-1.1217
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.99999,0.00061754,0.0051091,1.1528,-0.00062903,1,0.0022477,-0.23281,-0.0051077,-0.0022509,0.99998,0.85808,#15,0.99999,0.00061754,0.0051091,1.1528,-0.00062903,1,0.0022477,-0.23281,-0.0051077,-0.0022509,0.99998,0.85808
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #14,1,0,0,2.633,0,1,0,0.17005,0,0,1,-1.182,#15,1,0,0,2.633,0,1,0,0.17005,0,0,1,-1.182
> view matrix models
> #14,1,0,0,3.0941,0,1,0,0.17912,0,0,1,-1.2208,#15,1,0,0,3.0941,0,1,0,0.17912,0,0,1,-1.2208
> view matrix models
> #14,1,0,0,3.0428,0,1,0,-0.8073,0,0,1,-1.045,#15,1,0,0,3.0428,0,1,0,-0.8073,0,0,1,-1.045
> undo
[Repeated 6 time(s)]
> show #!4 models
> view matrix models
> #14,1,0,0,-0.29071,0,1,0,-2.0166,0,0,1,0.11827,#15,1,0,0,-0.29071,0,1,0,-2.0166,0,0,1,0.11827
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.99998,0.0030942,0.0046981,-1.8586,-0.0032499,0.99943,0.033503,-8.1288,-0.0045918,-0.033518,0.99943,7.731,#15,0.99998,0.0030942,0.0046981,-1.8586,-0.0032499,0.99943,0.033503,-8.1288,-0.0045918,-0.033518,0.99943,7.731
> undo
[Repeated 1 time(s)]
> select clear
> show #!12 models
> hide #!12 models
> show #!18 models
> hide #!18 models
> show #!18 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/PflCD_Docking_model_Fig3/REDO/Models/Jack_models/Modify/Cage_PflDC_JMB_Modified.pdb"
Summary of feedback from opening /Volumes/Lab Backup/Jun Liu Lab 2025/Project
files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
refinment/PflCD_Docking_model_Fig3/REDO/Models/Jack_models/Modify/Cage_PflDC_JMB_Modified.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 49 1 48
End residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1 42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
Start residue of secondary structure not found: HELIX 6 6 PRO A 146 ARG A 148
1 3
Start residue of secondary structure not found: HELIX 7 7 LEU A 149 ASP A 154
1 6
59 messages similar to the above omitted
End residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1 42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
Start residue of secondary structure not found: HELIX 6 6 PRO A 146 ARG A 148
1 3
Start residue of secondary structure not found: HELIX 7 7 LEU A 149 ASP A 154
1 6
6 messages similar to the above omitted
Chain information for Cage_PflDC_JMB_Modified.pdb
---
Chain | Description
16.1/A 16.6/A | No description available
16.1/J 16.2/V | No description available
16.1/K 16.3/W | No description available
16.1/L 16.4/X | No description available
16.5/c | No description available
> combine #16
Remapping chain ID 'A' in Cage_PflDC_JMB_Modified.pdb #16.6 to 'B'
> matchmaker #17 to #19
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 combination, chain Y (#19) with combination, chain c (#17),
sequence alignment score = 1828.6
RMSD between 356 pruned atom pairs is 0.001 angstroms; (across all 356 pairs:
0.001)
> hide #17 models
> show #17 models
> hide #!18 models
> show #!6 models
> hide #6.28 models
> show #6.28 models
> hide #!4 models
> hide #!3 models
> show #!3 models
Drag select of 144 residues
> select add #6.7
2479 atoms, 1564 bonds, 303 residues, 6 models selected
> select add #6.8
3723 atoms, 3052 bonds, 452 residues, 6 models selected
> select add #6.9
4933 atoms, 4440 bonds, 597 residues, 6 models selected
> hide #!3 models
> select add #6.19
6230 atoms, 6004 bonds, 756 residues, 6 models selected
> select add #6.20
7480 atoms, 7492 bonds, 905 residues, 6 models selected
> select add #6.21
8710 atoms, 8880 bonds, 1052 residues, 6 models selected
Drag select of 108 residues
> select add #6.27
11564 atoms, 11794 bonds, 1408 residues, 7 models selected
> save /Users/shoichi/Desktop/3rd_template_JMB.pdb selectedOnly true
> open /Users/shoichi/Desktop/3rd_template_JMB.pdb
Summary of feedback from opening /Users/shoichi/Desktop/3rd_template_JMB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 49 1 48
Start residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1
42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
86 messages similar to the above omitted
Chain information for 3rd_template_JMB.pdb
---
Chain | Description
20.1/G 20.4/S | No description available
20.2/H 20.5/T | No description available
20.3/I 20.6/U | No description available
20.7/b | No description available
> combine #20
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/PflCD_Docking_model_Fig3/REDO/Models/Jack_models/Modify/Cage_PflDC_JMB_Modified.pdb"
Summary of feedback from opening /Volumes/Lab Backup/Jun Liu Lab 2025/Project
files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
refinment/PflCD_Docking_model_Fig3/REDO/Models/Jack_models/Modify/Cage_PflDC_JMB_Modified.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 49 1 48
End residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1 42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
Start residue of secondary structure not found: HELIX 6 6 PRO A 146 ARG A 148
1 3
Start residue of secondary structure not found: HELIX 7 7 LEU A 149 ASP A 154
1 6
59 messages similar to the above omitted
End residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1 42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
Start residue of secondary structure not found: HELIX 6 6 PRO A 146 ARG A 148
1 3
Start residue of secondary structure not found: HELIX 7 7 LEU A 149 ASP A 154
1 6
6 messages similar to the above omitted
Chain information for Cage_PflDC_JMB_Modified.pdb
---
Chain | Description
22.1/A 22.6/A | No description available
22.1/J 22.2/V | No description available
22.1/K 22.3/W | No description available
22.1/L 22.4/X | No description available
22.5/c | No description available
> close #22
> combine #16
Remapping chain ID 'A' in Cage_PflDC_JMB_Modified.pdb #16.6 to 'B'
> matchmaker #22 to #21
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 combination, chain b (#21) with combination, chain c (#22),
sequence alignment score = 1828.6
RMSD between 356 pruned atom pairs is 0.001 angstroms; (across all 356 pairs:
0.001)
> select clear
> hide #!6 models
> hide #21 models
> hide #!20 models
> hide #13 models
> hide #!14 models
> show #!14 models
> hide #!15 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #17 models
> show #17 models
> hide #!14 models
> show #!16 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!4 models
> hide #!3 models
> split #22
Split combination (#22) into 9 models
Chain information for combination A #22.1
---
Chain | Description
A | No description available
Chain information for combination B #22.2
---
Chain | Description
B | No description available
Chain information for combination J #22.3
---
Chain | Description
J | No description available
Chain information for combination K #22.4
---
Chain | Description
K | No description available
Chain information for combination L #22.5
---
Chain | Description
L | No description available
Chain information for combination V #22.6
---
Chain | Description
V | No description available
Chain information for combination W #22.7
---
Chain | Description
W | No description available
Chain information for combination X #22.8
---
Chain | Description
X | No description available
Chain information for combination c #22.9
---
Chain | Description
c | No description available
> hide #22.9 models
> show #22.9 models
> hide #22.1 models
> hide #22.3 models
> hide #22.4 models
> hide #22.5 models
> close #22.3-5
> close #22.1
> save /Users/shoichi/Desktop/Docking_models_07232025.cxs includeMaps true
——— End of log from Wed Jul 23 10:13:39 2025 ———
opened ChimeraX session
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/PflCD_Docking_model_Fig3/REDO/Models/Jack_models/One_Cage-
> PflAB_JMB.pdb"
Chain information for One_Cage-PflAB_JMB.pdb
---
Chain | Description
23.1/A 23.2/A 23.3/A 23.4/A | No description available
23.5/A 23.6/A 23.7/A 23.8/A | No description available
23.9/A 23.10/A 23.11/A 23.12/A 23.13/A | No description available
23.1/B 23.2/B 23.3/B 23.4/B | No description available
23.9/B 23.10/B 23.11/B 23.12/B 23.13/B | No description available
23.1/C 23.2/C 23.3/C 23.4/C | No description available
> combine #23
Remapping chain ID 'A' in One_Cage-PflAB_JMB.pdb #23.2 to 'D'
Remapping chain ID 'B' in One_Cage-PflAB_JMB.pdb #23.2 to 'E'
Remapping chain ID 'C' in One_Cage-PflAB_JMB.pdb #23.2 to 'F'
Remapping chain ID 'A' in One_Cage-PflAB_JMB.pdb #23.3 to 'G'
Remapping chain ID 'B' in One_Cage-PflAB_JMB.pdb #23.3 to 'H'
Remapping chain ID 'C' in One_Cage-PflAB_JMB.pdb #23.3 to 'I'
Remapping chain ID 'A' in One_Cage-PflAB_JMB.pdb #23.4 to 'J'
Remapping chain ID 'B' in One_Cage-PflAB_JMB.pdb #23.4 to 'K'
Remapping chain ID 'C' in One_Cage-PflAB_JMB.pdb #23.4 to 'L'
Remapping chain ID 'A' in One_Cage-PflAB_JMB.pdb #23.5 to 'M'
Remapping chain ID 'A' in One_Cage-PflAB_JMB.pdb #23.6 to 'N'
Remapping chain ID 'A' in One_Cage-PflAB_JMB.pdb #23.7 to 'O'
Remapping chain ID 'A' in One_Cage-PflAB_JMB.pdb #23.8 to 'P'
Remapping chain ID 'A' in One_Cage-PflAB_JMB.pdb #23.9 to 'Q'
Remapping chain ID 'B' in One_Cage-PflAB_JMB.pdb #23.9 to 'R'
Remapping chain ID 'A' in One_Cage-PflAB_JMB.pdb #23.10 to 'S'
Remapping chain ID 'B' in One_Cage-PflAB_JMB.pdb #23.10 to 'T'
Remapping chain ID 'A' in One_Cage-PflAB_JMB.pdb #23.11 to 'U'
Remapping chain ID 'B' in One_Cage-PflAB_JMB.pdb #23.11 to 'V'
Remapping chain ID 'A' in One_Cage-PflAB_JMB.pdb #23.12 to 'W'
Remapping chain ID 'B' in One_Cage-PflAB_JMB.pdb #23.12 to 'X'
Remapping chain ID 'A' in One_Cage-PflAB_JMB.pdb #23.13 to 'Y'
Remapping chain ID 'B' in One_Cage-PflAB_JMB.pdb #23.13 to 'Z'
> hide #!23 models
> hide #!24 models
> select add #22
9846 atoms, 10040 bonds, 1201 residues, 6 models selected
> select add #17
26684 atoms, 27206 bonds, 3247 residues, 7 models selected
> select add #16
43522 atoms, 44372 bonds, 5293 residues, 14 models selected
> save /Users/shoichi/Desktop/CagePflCD_modified_JMB.pdb selectedOnly true
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/PflCD_Docking_model_Fig3/REDO/Models/Jack_models/Final-
> Cage_PflDC_JMB_Modified.pdb"
Chain information for Final-Cage_PflDC_JMB_Modified.pdb
---
Chain | Description
25.1/A 25.6/A | No description available
25.1/J 25.2/V | No description available
25.1/K 25.3/W | No description available
25.1/L 25.4/X | No description available
25.5/c | No description available
> hide #!16 models
> hide #17 models
> hide #!22 models
> select clear
> close #25
> show #!22 models
> show #21 models
> hide #21 models
> show #19 models
> show #17 models
> hide #17 models
> show #!15 models
> hide #!15 models
> show #!14 models
> hide #!14 models
> show #13 models
> hide #13 models
> show #17 models
> hide #17 models
> show #!16 models
> select add #16
16838 atoms, 17166 bonds, 2046 residues, 7 models selected
> select add #19
28402 atoms, 28960 bonds, 3454 residues, 8 models selected
> select add #22
38248 atoms, 39000 bonds, 4655 residues, 14 models selected
> hide #19 models
> select subtract #19
26684 atoms, 27206 bonds, 3247 residues, 13 models selected
> select add #21
38248 atoms, 39000 bonds, 4655 residues, 14 models selected
> show #21 models
> hide #21 models
> show #21 models
> select subtract #21
26684 atoms, 27206 bonds, 3247 residues, 13 models selected
> hide #21 models
> show #17 models
> select add #17
43522 atoms, 44372 bonds, 5293 residues, 14 models selected
> save /Users/shoichi/Desktop/Final-Cage-PflCD_JMB_Modified.pdb selectedOnly
> true
> open /Users/shoichi/Desktop/Final-Cage-PflCD_JMB_Modified.pdb
Summary of feedback from opening /Users/shoichi/Desktop/Final-Cage-
PflCD_JMB_Modified.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 49 1 48
End residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1 42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
Start residue of secondary structure not found: HELIX 6 6 PRO A 146 ARG A 148
1 3
Start residue of secondary structure not found: HELIX 7 7 LEU A 149 ASP A 154
1 6
59 messages similar to the above omitted
End residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1 42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
Start residue of secondary structure not found: HELIX 6 6 PRO A 146 ARG A 148
1 3
Start residue of secondary structure not found: HELIX 7 7 LEU A 149 ASP A 154
1 6
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1 42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
Start residue of secondary structure not found: HELIX 6 6 PRO A 146 ARG A 148
1 3
Start residue of secondary structure not found: HELIX 7 7 LEU A 149 ASP A 154
1 6
71 messages similar to the above omitted
Chain information for Final-Cage-PflCD_JMB_Modified.pdb
---
Chain | Description
25.1/A 25.6/A 25.7/A 25.7/B 25.8/B | No description available
25.1/J 25.7/J 25.2/V 25.7/V 25.9/V | No description available
25.1/K 25.7/K 25.3/W 25.7/W 25.10/W | No description available
25.1/L 25.7/L 25.4/X 25.7/X 25.11/X | No description available
25.5/c 25.7/c 25.12/c | No description available
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> close #25
> hide #!16 models
> show #!16 models
> hide #!22 models
> show #!22 models
> hide #17 models
> show #17 models
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!22 models
> show #!22 models
> hide #17 models
> show #17 models
> hide #17 models
> show #17 models
> hide #17 models
> show #17 models
> combine #16
Remapping chain ID 'A' in Cage_PflDC_JMB_Modified.pdb #16.6 to 'B'
> combine #17
> combine #22
> hide #!16 models
> hide #17 models
> hide #!22 models
> select clear
> select add #25
16838 atoms, 17166 bonds, 2046 residues, 1 model selected
> select add #26
33676 atoms, 34332 bonds, 4092 residues, 2 models selected
> select add #27
43522 atoms, 44372 bonds, 5293 residues, 3 models selected
> save /Users/shoichi/Desktop/Final-Cage-PflCD_JMB_Modified.pdb selectedOnly
> true
> select clear
> hide #25 models
> hide #26 models
> hide #27 models
> open /Users/shoichi/Desktop/Final-Cage-PflCD_JMB_Modified.pdb
Summary of feedback from opening /Users/shoichi/Desktop/Final-Cage-
PflCD_JMB_Modified.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 49 1 48
End residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1 42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
Start residue of secondary structure not found: HELIX 6 6 PRO A 146 ARG A 148
1 3
Start residue of secondary structure not found: HELIX 7 7 LEU A 149 ASP A 154
1 6
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1 42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
Start residue of secondary structure not found: HELIX 6 6 PRO A 146 ARG A 148
1 3
Start residue of secondary structure not found: HELIX 7 7 LEU A 149 ASP A 154
1 6
19 messages similar to the above omitted
Chain information for Final-Cage-PflCD_JMB_Modified.pdb
---
Chain | Description
28.1/A 28.2/A 28.1/B 28.2/B 28.3/B | No description available
28.1/J 28.2/J 28.1/V 28.2/V 28.3/V | No description available
28.1/K 28.2/K 28.1/W 28.2/W 28.3/W | No description available
28.1/L 28.2/L 28.1/X 28.2/X 28.3/X | No description available
28.1/c 28.2/c 28.3/c | No description available
> close #25-27
> select add #28
43522 atoms, 44372 bonds, 5293 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> select clear
> combine #28
Remapping chain ID 'A' in Final-Cage-PflCD_JMB_Modified.pdb #28.2 to 'C'
Remapping chain ID 'B' in Final-Cage-PflCD_JMB_Modified.pdb #28.2 to 'D'
Remapping chain ID 'J' in Final-Cage-PflCD_JMB_Modified.pdb #28.2 to 'M'
Remapping chain ID 'K' in Final-Cage-PflCD_JMB_Modified.pdb #28.2 to 'N'
Remapping chain ID 'L' in Final-Cage-PflCD_JMB_Modified.pdb #28.2 to 'O'
Remapping chain ID 'V' in Final-Cage-PflCD_JMB_Modified.pdb #28.2 to 'Y'
Remapping chain ID 'W' in Final-Cage-PflCD_JMB_Modified.pdb #28.2 to 'Z'
Remapping chain ID 'X' in Final-Cage-PflCD_JMB_Modified.pdb #28.2 to 'a'
Remapping chain ID 'c' in Final-Cage-PflCD_JMB_Modified.pdb #28.2 to 'd'
Remapping chain ID 'B' in Final-Cage-PflCD_JMB_Modified.pdb #28.3 to 'E'
Remapping chain ID 'V' in Final-Cage-PflCD_JMB_Modified.pdb #28.3 to 'b'
Remapping chain ID 'W' in Final-Cage-PflCD_JMB_Modified.pdb #28.3 to 'e'
Remapping chain ID 'X' in Final-Cage-PflCD_JMB_Modified.pdb #28.3 to 'f'
Remapping chain ID 'c' in Final-Cage-PflCD_JMB_Modified.pdb #28.3 to 'g'
> show #!24 models
> matchmaker #24 to #25
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 combination, chain c (#25) with combination, chain M (#24),
sequence alignment score = 1828.6
RMSD between 356 pruned atom pairs is 0.001 angstroms; (across all 356 pairs:
0.001)
> hide #!3 models
> show #!4 models
> hide #25 models
> show #25 models
> hide #25 models
> hide #!24 models
> show #!24 models
> select add #24
60311 atoms, 61486 bonds, 5 pseudobonds, 7438 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.87058,0.49184,0.013279,-141.73,-0.49173,0.87068,-0.010718,163.17,-0.016833,0.0028008,0.99985,-72.067
> ui mousemode right "rotate selected models"
> view matrix models
> #24,0.99976,0.01729,0.013741,-87.931,-0.016229,0.99713,-0.073914,14.176,-0.01498,0.073673,0.99717,-85.685
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.99976,0.01729,0.013741,-78.781,-0.016229,0.99713,-0.073914,96.218,-0.01498,0.073673,0.99717,-90.282
> matchmaker #24 to #25
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 combination, chain c (#25) with combination, chain M (#24),
sequence alignment score = 1828.6
RMSD between 356 pruned atom pairs is 0.001 angstroms; (across all 356 pairs:
0.001)
> view matrix models
> #24,0.87058,0.49184,0.013279,-179.73,-0.49173,0.87068,-0.010718,164.3,-0.016833,0.0028008,0.99985,-75.657
> ui mousemode right "rotate selected models"
> view matrix models
> #24,0.99946,-0.030105,0.01296,-116.29,0.030253,0.99948,-0.011403,-19.029,-0.01261,0.011789,0.99985,-78.7
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.99946,-0.030105,0.01296,-79.579,0.030253,0.99948,-0.011403,0.83744,-0.01261,0.011789,0.99985,-78.996
> view matrix models
> #24,0.99946,-0.030105,0.01296,-54.482,0.030253,0.99948,-0.011403,-5.1535,-0.01261,0.011789,0.99985,-87.925
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #24 inMap #4
Fit molecule combination (#24) to map Cage-PflAB.mrc gaussian (#4) using 60311
atoms
average map value = 0.006174, steps = 160
shifted from previous position = 14.8
rotated from previous position = 9.71 degrees
atoms outside contour = 39815, contour level = 0.0013059
Position of combination (#24) relative to Cage-PflAB.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.98824437 -0.01429463 -0.15221278 -8.80734476
0.00813284 0.99912492 -0.04102737 15.79098852
0.15266605 0.03930714 0.98749584 -133.39658319
Axis 0.25415733 -0.96455663 0.07095463
Axis point 854.79901291 0.00000000 -78.90503148
Rotation angle (degrees) 9.09320222
Shift along axis -26.93485970
> fitmap #24 inMap #4
Fit molecule combination (#24) to map Cage-PflAB.mrc gaussian (#4) using 60311
atoms
average map value = 0.006174, steps = 36
shifted from previous position = 0.00634
rotated from previous position = 0.00281 degrees
atoms outside contour = 39814, contour level = 0.0013059
Position of combination (#24) relative to Cage-PflAB.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.98823741 -0.01429693 -0.15225776 -8.79356980
0.00813057 0.99912420 -0.04104537 15.80213354
0.15271123 0.03932463 0.98748815 -133.41457102
Axis 0.25419238 -0.96454897 0.07093318
Axis point 854.66924028 0.00000000 -78.80434462
Rotation angle (degrees) 9.09598705
Shift along axis -26.94070962
> fitmap #24 inMap #4
Fit molecule combination (#24) to map Cage-PflAB.mrc gaussian (#4) using 60311
atoms
average map value = 0.006174, steps = 40
shifted from previous position = 0.00288
rotated from previous position = 0.00501 degrees
atoms outside contour = 39813, contour level = 0.0013059
Position of combination (#24) relative to Cage-PflAB.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.98822490 -0.01433503 -0.15233535 -8.75430498
0.00816568 0.99912384 -0.04104722 15.79083374
0.15279029 0.03931996 0.98747611 -133.43773924
Axis 0.25405846 -0.96456978 0.07112973
Axis point 854.35445149 0.00000000 -78.56573805
Rotation angle (degrees) 9.10050113
Shift along axis -26.94685726
> view matrix models
> #24,0.98822,-0.014335,-0.15234,-13.617,0.0081657,0.99912,-0.041047,74.125,0.15279,0.03932,0.98748,-139.29
> fitmap #24 inMap #4
Fit molecule combination (#24) to map Cage-PflAB.mrc gaussian (#4) using 60311
atoms
average map value = 0.0166, steps = 240
shifted from previous position = 13.5
rotated from previous position = 15.8 degrees
atoms outside contour = 34391, contour level = 0.0013059
Position of combination (#24) relative to Cage-PflAB.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.97475676 -0.22232403 0.02052542 -23.12518483
0.22250786 0.97490485 -0.00712606 -5.27372184
-0.01842604 0.01151324 0.99976394 -69.38349145
Axis 0.04170584 0.08715477 0.99532139
Axis point -13.96754221 -89.20784370 0.00000000
Rotation angle (degrees) 12.91242166
Shift along axis -70.48295846
> fitmap #24 inMap #4
Fit molecule combination (#24) to map Cage-PflAB.mrc gaussian (#4) using 60311
atoms
average map value = 0.0166, steps = 44
shifted from previous position = 0.0384
rotated from previous position = 0.0493 degrees
atoms outside contour = 34392, contour level = 0.0013059
Position of combination (#24) relative to Cage-PflAB.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.97472885 -0.22236547 0.02138398 -23.39716090
0.22255966 0.97489289 -0.00714538 -5.30319048
-0.01925820 0.01172402 0.99974580 -69.11523189
Axis 0.04219684 0.09088635 0.99496688
Axis point -15.02788372 -90.18317417 0.00000000
Rotation angle (degrees) 12.91985606
Shift along axis -70.23664080
> fitmap #24 inMap #4
Fit molecule combination (#24) to map Cage-PflAB.mrc gaussian (#4) using 60311
atoms
average map value = 0.0166, steps = 44
shifted from previous position = 0.0261
rotated from previous position = 0.00945 degrees
atoms outside contour = 34382, contour level = 0.0013059
Position of combination (#24) relative to Cage-PflAB.mrc gaussian (#4)
coordinates:
Matrix rotation and translation
0.97469836 -0.22249848 0.02139025 -23.34719639
0.22269448 0.97486144 -0.00723487 -5.33061284
-0.01924278 0.01181531 0.99974502 -69.14377033
Axis 0.04257507 0.09081038 0.99495771
Axis point -14.85561016 -89.79583919 0.00000000
Rotation angle (degrees) 12.92788946
Shift along axis -70.27321074
> hide #!28 models
> select subtract #24
Nothing selected
> split #24
Split combination (#24) into 26 models
Chain information for combination A #24.1
---
Chain | Description
A | No description available
Chain information for combination B #24.2
---
Chain | Description
B | No description available
Chain information for combination C #24.3
---
Chain | Description
C | No description available
Chain information for combination D #24.4
---
Chain | Description
D | No description available
Chain information for combination E #24.5
---
Chain | Description
E | No description available
Chain information for combination F #24.6
---
Chain | Description
F | No description available
Chain information for combination G #24.7
---
Chain | Description
G | No description available
Chain information for combination H #24.8
---
Chain | Description
H | No description available
Chain information for combination I #24.9
---
Chain | Description
I | No description available
Chain information for combination J #24.10
---
Chain | Description
J | No description available
Chain information for combination K #24.11
---
Chain | Description
K | No description available
Chain information for combination L #24.12
---
Chain | Description
L | No description available
Chain information for combination M #24.13
---
Chain | Description
M | No description available
Chain information for combination N #24.14
---
Chain | Description
N | No description available
Chain information for combination O #24.15
---
Chain | Description
O | No description available
Chain information for combination P #24.16
---
Chain | Description
P | No description available
Chain information for combination Q #24.17
---
Chain | Description
Q | No description available
Chain information for combination R #24.18
---
Chain | Description
R | No description available
Chain information for combination S #24.19
---
Chain | Description
S | No description available
Chain information for combination T #24.20
---
Chain | Description
T | No description available
Chain information for combination U #24.21
---
Chain | Description
U | No description available
Chain information for combination V #24.22
---
Chain | Description
V | No description available
Chain information for combination W #24.23
---
Chain | Description
W | No description available
Chain information for combination X #24.24
---
Chain | Description
X | No description available
Chain information for combination Y #24.25
---
Chain | Description
Y | No description available
Chain information for combination Z #24.26
---
Chain | Description
Z | No description available
> hide #!24.26 models
> show #!24.26 models
> hide #24.25 models
> show #24.25 models
> hide #24.23 models
> show #24.23 models
> hide #!24.20 models
> show #!24.20 models
> hide #24.19 models
> hide #!24.18 models
> hide #24.17 models
> hide #24.16 models
> show #24.16 models
> hide #24.16 models
> hide #24.15 models
> hide #24.14 models
> hide #24.13 models
> show #24.13 models
> hide #24.13 models
> hide #24.12 models
> show #24.12 models
> hide #24.12 models
> hide #24.11 models
> hide #24.10 models
> hide #24.9 models
> hide #24.8 models
> hide #24.7 models
> hide #24.6 models
> hide #24.5 models
> hide #24.4 models
> hide #24.3 models
> hide #24.2 models
> hide #24.1 models
> select add #24.20
5103 atoms, 5196 bonds, 1 pseudobond, 633 residues, 2 models selected
> select add #24.21
6295 atoms, 6414 bonds, 1 pseudobond, 782 residues, 3 models selected
> select add #24.22
11398 atoms, 11610 bonds, 2 pseudobonds, 1415 residues, 5 models selected
> select add #24.23
12590 atoms, 12828 bonds, 2 pseudobonds, 1564 residues, 6 models selected
> select add #24.24
17693 atoms, 18024 bonds, 3 pseudobonds, 2197 residues, 8 models selected
> select add #24.25
18885 atoms, 19242 bonds, 3 pseudobonds, 2346 residues, 9 models selected
> select add #24.26
23988 atoms, 24438 bonds, 4 pseudobonds, 2979 residues, 11 models selected
> save /Users/shoichi/Desktop/PflB_PflAn_JMB.pdb selectedOnly true
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
> refinment/PflCD_Docking_model_Fig3/REDO/Models/Jack_models/PflB_PflAn_JMB.pdb"
Summary of feedback from opening /Volumes/Lab Backup/Jun Liu Lab 2025/Project
files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/Local-
refinment/PflCD_Docking_model_Fig3/REDO/Models/Jack_models/PflB_PflAn_JMB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 49 1 48
Start residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1
42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
86 messages similar to the above omitted
Chain information for PflB_PflAn_JMB.pdb
---
Chain | Description
26.1/T 26.3/V 26.5/X 26.7/Z | No description available
26.2/U 26.4/W 26.6/Y | No description available
> select clear
> hide #!24 models
> show #!28 models
> hide #28.2 models
> show #28.2 models
> split #28
Split Final-Cage-PflCD_JMB_Modified.pdb (#28.1) into 9 models
Split Final-Cage-PflCD_JMB_Modified.pdb (#28.2) into 9 models
Split Final-Cage-PflCD_JMB_Modified.pdb (#28.3) into 5 models
Chain information for Final-Cage-PflCD_JMB_Modified.pdb A #28.1.1
---
Chain | Description
A | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb B #28.1.2
---
Chain | Description
B | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb J #28.1.3
---
Chain | Description
J | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb K #28.1.4
---
Chain | Description
K | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb L #28.1.5
---
Chain | Description
L | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb V #28.1.6
---
Chain | Description
V | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb W #28.1.7
---
Chain | Description
W | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb X #28.1.8
---
Chain | Description
X | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb c #28.1.9
---
Chain | Description
c | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb A #28.2.1
---
Chain | Description
A | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb B #28.2.2
---
Chain | Description
B | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb J #28.2.3
---
Chain | Description
J | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb K #28.2.4
---
Chain | Description
K | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb L #28.2.5
---
Chain | Description
L | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb V #28.2.6
---
Chain | Description
V | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb W #28.2.7
---
Chain | Description
W | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb X #28.2.8
---
Chain | Description
X | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb c #28.2.9
---
Chain | Description
c | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb B #28.3.1
---
Chain | Description
B | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb V #28.3.2
---
Chain | Description
V | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb W #28.3.3
---
Chain | Description
W | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb X #28.3.4
---
Chain | Description
X | No description available
Chain information for Final-Cage-PflCD_JMB_Modified.pdb c #28.3.5
---
Chain | Description
c | No description available
> hide #28.1.2 models
> show #28.1.2 models
> hide #28.1.9 models
> show #28.1.9 models
> color #28.1.9 #7b80ffff
> color #28.2.9 #7b80ffff
> color #28.3.9 #7b80ffff
> hide #28.3.5 models
> show #28.3.5 models
> color #28.3.5 #7b80ffff
> hide #28.1.3 models
> show #28.1.3 models
> hide #!26.1 models
> show #!26.1 models
> hide #26.1.1 models
> show #26.1.1 models
> hide #26.1.1 models
> show #26.1.1 models
> hide #!26.7 models
> show #!26.7 models
> hide #26.6 models
> show #26.6 models
> color #26.6 #ca4949ff models
> color #26.4 #ca4949ff models
> color #26.2 #ca4949ff models
> color #26.3 magenta models
> color #26.7 magenta models
> color #26.5 magenta models
> color #26.1 magenta models
> color #28.1.1 #a7c5d2ff models
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> color #28.2.1 #a7c5d2ff models
> color #28.3.1 #a7c5d2ff models
> color #28.2.2 #a7c5d2ff models
> color #28.1.2 #a7c5d2ff models
> hide #!4 models
> color #28.1.3 #0b6dffff
> hide #28.1.2 models
> show #28.1.2 models
> color #28.1.4 #0b6dffff
> color #28.2.4 #0b6dffff
> color #28.3.4 #0b6dffff
> color #28.3.3 #0b6dffff
> hide #28.3.3 models
> hide #28.1.3 models
> color #28.2.6 #0b6dffff
> color #28.2.7 #0b6dffff
> hide #28.2.6 models
> hide #28.1.4 models
> show #28.1.4 models
> hide #28.3.4 models
> show #28.3.3 models
> show #28.3.4 models
> hide #28.3.4 models
> color #28.3.4 #7b80ffff
> show #28.3.4 models
> color #28.3.4 #adffc1ff
> show #28.1.3 models
> hide #28.1.3 models
> show #28.1.3 models
> color #28.1.3 #20e0ffff
> hide #28.1.7 models
> show #28.1.7 models
> hide #28.1.7 models
> show #28.1.7 models
> color #28.1.7 #20e0ffff
> color #28.1.6 #20e0ffff
> color #28.1.7 #0b6dffff
> hide #!28.3 models
> show #!28.3 models
> hide #28.2.3 models
> show #28.2.3 models
> color #28.2.3 #20e0ffff
> show #28.2.6 models
> hide #28.2.6 models
> show #28.2.6 models
> color #28.2.6 #20e0ffff
> hide #28.3.2 models
> show #28.3.2 models
> color #28.3.2 #20e0ffff
> hide #28.1.1 models
> show #28.1.1 models
> hide #28.1.1 models
> show #28.1.1 models
> split #28.1.1
Did not split Final-Cage-PflCD_JMB_Modified.pdb A, has only one piece
> show #!3 models
> show #!4 models
> color #3-4 #c0c0c080 models
> hide #!3 models
> select add #4
2 models selected
> hide #!26 models
> hide #!28 models
> hide #!4 models
> select subtract #4
Nothing selected
> show #!1 models
> show #!2 models
> save /Users/shoichi/Desktop/Docking_models_07232025.cxs includeMaps true
> ui tool show "Segment Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Segmenting PflCD.mrc, density threshold 0.007034
Only showing 60 of 726 regions.
Showing 60 of 726 region surfaces
15043 watershed regions, grouped to 726 regions
Showing PflCD.seg - 726 regions, 60 surfaces
> hide #!27 models
> show #!28 models
> show #!26 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!27 models
> select #27.5
1 model selected
> select add #27.4
2 models selected
> select add #27.6
3 models selected
> hide #!1 models
Grouped 3 regions
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Opened PflCD_imasked as #29, grid size 200,200,200, pixel 2.14, shown at step
1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/PflC-polished.mrc models #29
Segmenting Cage-PflAB.mrc, density threshold 0.007030
Only showing 60 of 697 regions.
Showing 60 of 697 region surfaces
16352 watershed regions, grouped to 697 regions
Showing Cage-PflAB.seg - 697 regions, 60 surfaces
> select #27.20
1 model selected
Ungrouped to 2 regions
Ungrouped to 12 regions, but did not show all surfaces, see Options
Segmenting Cage-PflAB.mrc, density threshold 0.007030
Only showing 60 of 697 regions.
Showing 60 of 697 region surfaces
16352 watershed regions, grouped to 697 regions
Showing Cage-PflAB.seg - 697 regions, 60 surfaces
Segmenting Cage-PflAB.mrc, density threshold 0.007030
Showing 697 region surfaces
16352 watershed regions, grouped to 697 regions
Showing Cage-PflAB.seg - 697 regions, 697 surfaces
> select #27.20
1 model selected
Ungrouped to 2 regions
> select #27.698
1 model selected
Ungrouped to 9 regions
> select #27.706
1 model selected
> select clear
> select #27.7
1 model selected
Ungrouped to 2 regions
> select #27.708
1 model selected
> select add #27.706
2 models selected
> select clear
> select #27.708
1 model selected
Ungrouped to 5 regions
Ungrouped to 7 regions
Ungrouped to 0 regions
> select #27.713
1 model selected
> select clear
> select #27.706
1 model selected
Opened Cage-PflAB_imasked as #30, grid size 200,200,200, pixel 2.14, shown at
step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/Cage-polished.mrc models #30
> hide #!27 models
> select add #27
717 models selected
> select subtract #27
Nothing selected
> hide #!26 models
> hide #!28 models
> volume gaussian #29 sDev 3
Opened PflC-polished.mrc gaussian as #31, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume gaussian #30 sDev 3
Opened Cage-polished.mrc gaussian as #32, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #31 level 0.001811
> volume #31 level 0.001355
> volume #32 level 0.00135
> hide #!32 models
> ui tool show "Map Eraser"
> volume erase #31 center 310.54,252.16,359.07 radius 202.11 outside true
> volume erase #31 center 86.433,242,485.85 radius 202.11
> volume erase #31 center 495.25,235.77,181.43 radius 202.11
> volume erase #31 center 451.37,446.66,217.02 radius 202.11
> volume erase #31 center 466.42,111.27,194.5 radius 202.11
> volume erase #31 center 210.09,295.03,81.331 radius 202.11
> volume erase #31 center 481.97,351.66,535.14 radius 202.11
> volume erase #31 center 488.2,156.87,534.3 radius 202.11
> hide #!31 models
> show #!32 models
> volume erase #32 center 23.429,216.1,398.49 radius 214
> volume erase #32 center 27.142,270.43,151.6 radius 214
> volume erase #32 center 4.6577,123.48,180.34 radius 214
> volume erase #32 center 19.934,117.11,34.421 radius 214
> volume erase #32 center 60.331,307.21,2.3713 radius 214
> volume erase #32 center 303.24,77.202,533.39 radius 214
> volume erase #32 center 260.38,349.57,533.45 radius 214
> volume erase #32 center 572.58,249.27,290.61 radius 214
> volume erase #32 center 524.32,27.885,356.21 radius 214
> volume erase #32 center 542.87,452.78,219.12 radius 214
> volume erase #32 center 482.13,518.12,8.8554 radius 214
> close #33
> volume erase #32 center 174.93,578.32,93.856 radius 214
> volume erase #32 center 417.68,515.64,393.86 radius 214
> volume erase #32 center 177.66,186.34,-111.3 radius 214
> hide #33 models
> show #!31 models
> surface dust #31-32 size 58.49
> hide #!32 models
> show #33 models
> hide #33 models
> show #33 models
> volume erase #31 center 292.19,164.98,348.83 radius 13.054
> close #33
> show #!32 models
> hide #!32 models
> volume erase #31 center 273.22,397.73,322.99 radius 13.696
> color #31-32 #c0c0c080 models
> hide #!31 models
> show #!31 models
> show #!32 models
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!29 models
> show #!28 models
> show #!27 models
> hide #!27 models
> show #!29 models
> hide #!29 models
> show #!26 models
> save /Users/shoichi/Desktop/Docking_models_07232025.cxs includeMaps true
Drag select of 179 residues
> hide #!26 models
> show #!26 models
> select add #26
23988 atoms, 24438 bonds, 4 pseudobonds, 2979 residues, 12 models selected
> select add #28
67510 atoms, 68810 bonds, 4 pseudobonds, 8272 residues, 39 models selected
> select add #31
67510 atoms, 68810 bonds, 4 pseudobonds, 8272 residues, 41 models selected
> select subtract #31
67510 atoms, 68810 bonds, 4 pseudobonds, 8272 residues, 39 models selected
> select add #31
67510 atoms, 68810 bonds, 4 pseudobonds, 8272 residues, 41 models selected
> select subtract #31
67510 atoms, 68810 bonds, 4 pseudobonds, 8272 residues, 39 models selected
> show sel surfaces
> select clear
Drag select of PflB_PflAn_JMB.pdb_T SES surface, 217184 of 558182 triangles,
226 residues
> hide sel surfaces
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
Drag select of PflB_PflAn_JMB.pdb_T SES surface, 11215 of 558182 triangles, 13
residues
> hide sel surfaces
> hide sel cartoons
Drag select of PflB_PflAn_JMB.pdb_Z SES surface, 239671 of 558246 triangles,
304 residues, 1 pseudobonds, 32 Cage-polished.mrc gaussian
> hide sel cartoons
> hide sel surfaces
> hide sel cartoons
> select add #26
23988 atoms, 24438 bonds, 4 pseudobonds, 2979 residues, 14 models selected
> select add #28
67510 atoms, 68810 bonds, 4 pseudobonds, 8272 residues, 46 models selected
> hide sel cartoons
[Repeated 1 time(s)]
> select clear
> save /Users/shoichi/Desktop/Docking_models_07232025.cxs includeMaps true
Drag select of PflB_PflAn_JMB.pdb_Z SES surface, 35717 of 558246 triangles, 32
Cage-polished.mrc gaussian
> select subtract #32
1 model selected
> hide #!26.1-7#!28.1.1-9#!28.2.1-9#!28.3.1-5 surfaces
> show #!26.1-7#!28.1.1-9#!28.2.1-9#!28.3.1-5 surfaces
> select clear
Drag select of PflB_PflAn_JMB.pdb_Z SES surface, 281564 of 558246 triangles,
32 Cage-polished.mrc gaussian
> select clear
Drag select of PflB_PflAn_JMB.pdb_Y SES surface, 1429 of 176284 triangles,
PflB_PflAn_JMB.pdb_Z SES surface, 312627 of 558246 triangles, 31 PflC-
polished.mrc gaussian , 32 Cage-polished.mrc gaussian
> select #31
2 models selected
Drag select of PflB_PflAn_JMB.pdb_Z SES surface, 164687 of 558246 triangles
> select add #26
23988 atoms, 24438 bonds, 4 pseudobonds, 2979 residues, 15 models selected
> select add #28
67510 atoms, 68810 bonds, 4 pseudobonds, 8272 residues, 48 models selected
> hide sel surfaces
> show sel cartoons
> select clear
Drag select of 382 residues, 1 pseudobonds, 32 Cage-polished.mrc gaussian
> select add #26.6
4262 atoms, 1218 bonds, 1 pseudobond, 529 residues, 5 models selected
> select subtract #26.6
3070 atoms, 1 pseudobond, 380 residues, 4 models selected
> hide sel cartoons
Drag select of 334 residues, 32 Cage-polished.mrc gaussian
> hide sel cartoons
> hide #!28 models
> hide #!31 models
> hide #!32 models
> select add #26
23988 atoms, 24438 bonds, 4 pseudobonds, 2979 residues, 14 models selected
> select subtract #26
7 models selected
Drag select of 2265 residues, 3 pseudobonds
> save /Users/shoichi/Desktop/Cropped_PflAB_Fig3.pdb selectedOnly true
> open /Users/shoichi/Desktop/Cropped_PflAB_Fig3.pdb
Summary of feedback from opening /Users/shoichi/Desktop/Cropped_PflAB_Fig3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 49 1 48
Start residue of secondary structure not found: HELIX 2 2 LEU A 50 GLU A 91 1
42
Start residue of secondary structure not found: HELIX 3 3 ASN A 93 GLU A 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE A 105 PHE A 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU A 112 LYS A 114
1 3
86 messages similar to the above omitted
Chain information for Cropped_PflAB_Fig3.pdb
---
Chain | Description
34.1/T | No description available
34.2/U 34.4/W 34.6/Y | No description available
34.3/V 34.5/X | No description available
34.7/Z | No description available
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> hide #!26 models
> hide #!34.1 models
> show #!34.1 models
> hide #34.2 models
> hide #!34.3 models
> show #!34.3 models
> hide #34.4 models
> hide #!34.5 models
> show #!34.5 models
> hide #34.6 models
> color #34.1 magenta models
> color #34.3 magenta models
> color #34.5 magenta models
> color #34.7 magenta models
> color #34.2 #ca4949ff models
> show #34.2 models
> show #34.4 models
> show #34.6 models
> color #34.4 #ca4949ff models
> color #34.6 #ca4949ff models
> select add #34
18239 atoms, 18574 bonds, 12 pseudobonds, 2265 residues, 12 models selected
> show sel surfaces
> show #!31 models
> show #!32 models
> show #25 models
> select add #25
61761 atoms, 62946 bonds, 12 pseudobonds, 7558 residues, 20 models selected
> show sel surfaces
> select clear
> hide #!25 models
> show #!28 models
> select add #28
43522 atoms, 44372 bonds, 5293 residues, 27 models selected
> show sel surfaces
> select clear
> view orient
> turn x 90
[Repeated 2 time(s)]
> turn y 90
[Repeated 2 time(s)]
> select add #28
43522 atoms, 44372 bonds, 5293 residues, 27 models selected
> hide sel cartoons
> select clear
> save /Users/shoichi/Desktop/Docking_models_07232025.cxs includeMaps true
[Repeated 1 time(s)]
——— End of log from Wed Jul 23 17:25:02 2025 ———
opened ChimeraX session
Showing Cage-PflAB.seg - 716 regions, 716 surfaces
> close session
> open /Users/shoichi/Desktop/Original-map-deposit/L0.12-Wild-
> type_EMD_45507.mrc
Opened L0.12-Wild-type_EMD_45507.mrc as #1, grid size 250,250,250, pixel 4.3,
shown at level 0.262, step 1, values float32
> volume #1 level 0.01067
> ui tool show "Segment Map"
Segmenting L0.12-Wild-type_EMD_45507.mrc, density threshold 0.010668
Showing 1281 region surfaces
12116 watershed regions, grouped to 1281 regions
Showing L0.12-Wild-type_EMD_45507.seg - 1281 regions, 1281 surfaces
> select #2.18
1 model selected
> select add #2.73
2 models selected
> select add #2.37
3 models selected
> select add #2.20
4 models selected
> select add #2.16
5 models selected
> select add #2.42
6 models selected
> select add #2.88
7 models selected
> select add #2.19
8 models selected
> select add #2.38
9 models selected
> select add #2.232
10 models selected
> select add #2.209
11 models selected
> select add #2.17
12 models selected
> select add #2.65
13 models selected
> select add #2.58
14 models selected
> select add #2.21
15 models selected
> select add #2.32
16 models selected
> select add #2.95
17 models selected
> select add #2.336
18 models selected
> select add #2.29
19 models selected
> select add #2.60
20 models selected
> select add #2.51
21 models selected
> select add #2.34
22 models selected
> select add #2.127
23 models selected
> select add #2.472
24 models selected
> select add #2.4
25 models selected
> select add #2.79
26 models selected
> select add #2.461
27 models selected
> select add #2.235
28 models selected
> select add #2.216
29 models selected
> select add #2.693
30 models selected
> select add #2.52
31 models selected
> select add #2.25
32 models selected
Grouped 32 regions
> select add #2.121
2 models selected
> select add #2.663
3 models selected
> select add #2.244
4 models selected
> select add #2.185
5 models selected
> select subtract #2.185
4 models selected
> select add #2.68
5 models selected
Grouped 5 regions
> select add #2.185
2 models selected
> select add #2.379
3 models selected
> select add #2.157
4 models selected
> select add #2.128
5 models selected
> select add #2.901
6 models selected
> select add #2.439
7 models selected
> select add #2.1219
8 models selected
> select subtract #2.1219
7 models selected
> select add #2.137
8 models selected
> select add #2.226
9 models selected
Segmenting L0.12-Wild-type_EMD_45507.mrc, density threshold 0.010668
Showing 1281 region surfaces
12116 watershed regions, grouped to 1281 regions
Showing L0.12-Wild-type_EMD_45507.seg - 1281 regions, 1281 surfaces
> select #2.29
1 model selected
> select add #2.336
2 models selected
> select add #2.95
3 models selected
> select add #2.32
4 models selected
> select add #2.21
5 models selected
> select add #2.58
6 models selected
> select add #2.65
7 models selected
> select add #2.17
8 models selected
> select add #2.209
9 models selected
> select add #2.232
10 models selected
> select add #2.38
11 models selected
> select add #2.19
12 models selected
> select add #2.88
13 models selected
> select add #2.744
14 models selected
> select add #2.42
15 models selected
> select add #2.61
16 models selected
> select add #2.16
17 models selected
> select add #2.90
18 models selected
> select add #2.80
19 models selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #2.240
20 models selected
> select add #2.168
21 models selected
> select add #2.377
22 models selected
> select add #2.137
23 models selected
> select add #2.226
24 models selected
> select add #2.128
25 models selected
> select add #2.439
26 models selected
> select add #2.157
27 models selected
> select add #2.68
28 models selected
> select add #2.185
29 models selected
> select subtract #2.185
28 models selected
> select add #2.60
29 models selected
> select add #2.185
30 models selected
> select add #2.379
31 models selected
> select add #2.51
32 models selected
> select add #2.127
33 models selected
> select add #2.472
34 models selected
> select add #2.34
35 models selected
> select add #2.121
36 models selected
> select add #2.4
37 models selected
> select add #2.79
38 models selected
> select add #2.216
39 models selected
> select add #2.235
40 models selected
> select subtract #2.216
39 models selected
> select add #2.216
40 models selected
> select add #2.52
41 models selected
> select add #2.25
42 models selected
> select add #2.148
43 models selected
> select add #2.18
44 models selected
> select add #2.227
45 models selected
> select add #2.73
46 models selected
> select add #2.37
47 models selected
> select add #2.20
48 models selected
Grouped 48 regions
> hide #!1 models
> select add #2.143
2 models selected
> select add #2.257
3 models selected
> select add #2.693
4 models selected
> select add #2.141
5 models selected
> select add #2.49
6 models selected
> select add #2.75
7 models selected
> select add #2.123
8 models selected
> select add #2.205
9 models selected
> select add #2.173
10 models selected
> select add #2.317
11 models selected
> select add #2.134
12 models selected
> select add #2.208
13 models selected
> select add #2.461
14 models selected
> select add #2.178
15 models selected
> select add #2.119
16 models selected
> select add #2.663
17 models selected
> select add #2.244
18 models selected
> select add #2.188
19 models selected
> select add #2.159
20 models selected
> select add #2.115
21 models selected
> select add #2.901
22 models selected
> select add #2.196
23 models selected
> select add #2.217
24 models selected
> select add #2.432
25 models selected
> select add #2.243
26 models selected
> select add #2.189
27 models selected
> select add #2.236
28 models selected
> select add #2.234
29 models selected
> select add #2.200
30 models selected
> select add #2.433
31 models selected
> select add #2.266
32 models selected
> select add #2.851
33 models selected
> select add #2.655
34 models selected
> select add #2.455
35 models selected
> select add #2.353
36 models selected
> select add #2.402
37 models selected
> select add #2.506
38 models selected
> select add #2.281
39 models selected
> select add #2.401
40 models selected
> select add #2.467
41 models selected
> select add #2.565
42 models selected
> select add #2.300
43 models selected
> select add #2.420
44 models selected
> select add #2.423
45 models selected
Grouped 45 regions
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #2.81
1 model selected
> select add #2.35
2 models selected
Ungrouped to 12 regions
Ungrouped to 27 regions
Ungrouped to 21 regions
> select #2.19
1 model selected
Ungrouped to 3 regions
Ungrouped to 0 regions
> select #2.65
1 model selected
> select add #2.42
2 models selected
> select add #2.51
3 models selected
Grouped 3 regions
> select add #2.4
2 models selected
Grouped 2 regions
> select #2.39
1 model selected
> select add #2.197
2 models selected
Ungrouped to 6 regions
Ungrouped to 15 regions
Ungrouped to 24 regions
Ungrouped to 8 regions
Ungrouped to 0 regions
> select #2.4
1 model selected
> select #2.234
1 model selected
> select add #2.4
2 models selected
Grouped 2 regions
> select #2.125
1 model selected
> select add #2.99
2 models selected
Ungrouped to 5 regions
Ungrouped to 13 regions
Ungrouped to 21 regions
Ungrouped to 7 regions
Ungrouped to 0 regions
> select #2.506
1 model selected
> select add #2.467
2 models selected
Grouped 2 regions
> select add #2.4
2 models selected
Grouped 2 regions
> select #2.67
1 model selected
Ungrouped to 5 regions
Ungrouped to 13 regions
Ungrouped to 11 regions
Ungrouped to 8 regions
Ungrouped to 0 regions
Ungrouped to 1615 regions
Ungrouped to 3322 regions
Ungrouped to 6024 regions
> select #2.655
1 model selected
> select #2.1312
1 model selected
> select add #2.1311
2 models selected
Grouped 2 regions
> select add #2.4
2 models selected
> select add #2.9151
3 models selected
> select add #2.9152
4 models selected
Grouped 4 regions
> select #2.3638
1 model selected
> select add #2.5286
2 models selected
> select add #2.3
3 models selected
> select add #2.5194
4 models selected
> select add #2.5977
5 models selected
> select add #2.5399
6 models selected
> select subtract #2.5399
5 models selected
> select add #2.714
6 models selected
> select add #2.5189
7 models selected
> select add #2.5121
8 models selected
> select add #2.4974
9 models selected
> select add #2.3725
10 models selected
> select add #2.8295
11 models selected
> select subtract #2.3638
10 models selected
> select subtract #2.5286
9 models selected
> select add #2.5150
10 models selected
> select add #2.5498
11 models selected
> select add #2.5399
12 models selected
> select add #2.709
13 models selected
> select add #2.8881
14 models selected
> select subtract #2.8881
13 models selected
> select add #2.3638
14 models selected
> select add #2.3910
15 models selected
> select add #2.8223
16 models selected
> select add #2.402
17 models selected
> select add #2.5100
18 models selected
Grouped 18 regions
Opened L0.12-Wild-type_EMD_45507_imasked as #3, grid size 250,250,250, pixel
4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/Original-map-deposit/Seg/OM.mrc models #3
Opened L0.12-Wild-type_EMD_45507_imasked as #4, grid size 250,250,250, pixel
4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Segmenting L0.12-Wild-type_EMD_45507_imasked, density threshold 0.010668
Showing 1191 region surfaces
11278 watershed regions, grouped to 1191 regions
Showing L0.seg - 1191 regions, 1191 surfaces
> hide #!3 models
> hide #!4 models
> select #2.25
1 model selected
> select add #2.40
2 models selected
> select add #2.66
3 models selected
> select add #2.251
4 models selected
> select add #2.880
5 models selected
> select add #2.921
6 models selected
> select add #2.565
7 models selected
> select add #2.364
8 models selected
> select add #2.583
9 models selected
> select add #2.941
10 models selected
> select add #2.27
11 models selected
> select add #2.105
12 models selected
> select add #2.107
13 models selected
Grouped 13 regions
> select add #2.47
2 models selected
> select add #2.43
3 models selected
> select add #2.52
4 models selected
> select add #2.71
5 models selected
> select subtract #2.52
4 models selected
> select add #2.52
5 models selected
> select add #2.41
6 models selected
> select add #2.134
7 models selected
> select add #2.17
8 models selected
Grouped 8 regions
> select add #2.166
2 models selected
> select add #2.898
3 models selected
> select add #2.330
4 models selected
> select add #2.530
5 models selected
> select add #2.506
6 models selected
> select add #2.553
7 models selected
> select add #2.905
8 models selected
> select add #2.519
9 models selected
> select add #2.526
10 models selected
> select add #2.537
11 models selected
> select add #2.328
12 models selected
> select add #2.888
13 models selected
> select add #2.271
14 models selected
> select add #2.541
15 models selected
> select add #2.883
16 models selected
> select add #2.49
17 models selected
> select add #2.42
18 models selected
> select subtract #2.42
17 models selected
> select add #2.42
18 models selected
> select add #2.54
19 models selected
> select add #2.34
20 models selected
> select add #2.20
21 models selected
> select add #2.24
22 models selected
> select add #2.119
23 models selected
> select add #2.21
24 models selected
> select add #2.116
25 models selected
> select add #2.50
26 models selected
> select add #2.45
27 models selected
> select add #2.138
28 models selected
> select add #2.305
29 models selected
> select add #2.193
30 models selected
> select add #2.33
31 models selected
> select add #2.16
32 models selected
> select add #2.151
33 models selected
> select add #2.135
34 models selected
> select add #2.23
35 models selected
> select add #2.46
36 models selected
> select add #2.39
37 models selected
> select add #2.53
38 models selected
> select add #2.148
39 models selected
> select add #2.560
40 models selected
> select add #2.789
41 models selected
> select add #2.600
42 models selected
> select add #2.809
43 models selected
> select add #2.836
44 models selected
> select add #2.415
45 models selected
> select add #2.597
46 models selected
> select add #2.807
47 models selected
> select add #2.544
48 models selected
> select add #2.656
49 models selected
> select add #2.804
50 models selected
> select add #2.606
51 models selected
> select add #2.796
52 models selected
> select add #2.912
53 models selected
> select add #2.551
54 models selected
> select add #2.621
55 models selected
> select add #2.756
56 models selected
> select add #2.339
57 models selected
> select add #2.548
58 models selected
> select add #2.517
59 models selected
> select add #2.778
60 models selected
> select add #2.542
61 models selected
> select add #2.287
62 models selected
> select add #2.211
63 models selected
> select add #2.244
64 models selected
> select add #2.379
65 models selected
> select add #2.308
66 models selected
> select add #2.291
67 models selected
> select add #2.697
68 models selected
> select add #2.277
69 models selected
> select add #2.738
70 models selected
> select add #2.378
71 models selected
> select add #2.397
72 models selected
> select add #2.712
73 models selected
> select add #2.505
74 models selected
> select add #2.665
75 models selected
> select add #2.767
76 models selected
> select add #2.424
77 models selected
> select add #2.803
78 models selected
> select add #2.609
79 models selected
> select add #2.247
80 models selected
> select add #2.728
81 models selected
> select add #2.441
82 models selected
> select add #2.270
83 models selected
> select add #2.275
84 models selected
> select add #2.215
85 models selected
> select add #2.693
86 models selected
> select add #2.392
87 models selected
> select add #2.635
88 models selected
> select add #2.800
89 models selected
> select add #2.401
90 models selected
> select add #2.706
91 models selected
> select add #2.303
92 models selected
> select add #2.189
93 models selected
> select add #2.430
94 models selected
> select add #2.731
95 models selected
> select add #2.374
96 models selected
> select add #2.726
97 models selected
> select add #2.715
98 models selected
> select add #2.306
99 models selected
> select add #2.224
100 models selected
> select subtract #2.224
99 models selected
> select add #2.224
100 models selected
> select add #2.213
101 models selected
> select add #2.680
102 models selected
> select add #2.533
103 models selected
> select add #2.249
104 models selected
> select add #2.310
105 models selected
> select add #2.443
106 models selected
> select add #2.552
107 models selected
> select add #2.237
108 models selected
> select add #2.214
109 models selected
> select add #2.429
110 models selected
> select add #2.676
111 models selected
> select add #2.388
112 models selected
> select add #2.901
113 models selected
> select add #2.690
114 models selected
> select add #2.256
115 models selected
> select subtract #2.256
114 models selected
> select add #2.256
115 models selected
> select add #2.798
116 models selected
> select add #2.521
117 models selected
> select add #2.748
118 models selected
> select add #2.217
119 models selected
> select add #2.234
120 models selected
> select add #2.437
121 models selected
> select add #2.716
122 models selected
> select add #2.525
123 models selected
> select add #2.338
124 models selected
> select add #2.599
125 models selected
> select add #2.673
126 models selected
> select add #2.141
127 models selected
> select add #2.220
128 models selected
> select add #2.875
129 models selected
> select add #2.642
130 models selected
> select add #2.702
131 models selected
> select add #2.444
132 models selected
> select add #2.805
133 models selected
> select add #2.337
134 models selected
> select add #2.529
135 models selected
> select add #2.351
136 models selected
> select subtract #2.351
135 models selected
> select add #2.351
136 models selected
> select add #2.520
137 models selected
> select add #2.555
138 models selected
> select add #2.260
139 models selected
> select add #2.273
140 models selected
> select add #2.297
141 models selected
> select add #2.762
142 models selected
> select add #2.813
143 models selected
> select add #2.408
144 models selected
> select add #2.669
145 models selected
> select add #2.696
146 models selected
> select add #2.452
147 models selected
> select subtract #2.452
146 models selected
> select add #2.299
147 models selected
> select add #2.452
148 models selected
> select add #2.546
149 models selected
> select add #2.188
150 models selected
> select add #2.231
151 models selected
> select add #2.730
152 models selected
> select add #2.607
153 models selected
> select add #2.373
154 models selected
> select add #2.512
155 models selected
> select add #2.516
156 models selected
> select add #2.879
157 models selected
> select add #2.679
158 models selected
> select add #2.341
159 models selected
> select add #2.399
160 models selected
> select add #2.278
161 models selected
> select add #2.112
162 models selected
> select add #2.703
163 models selected
> select add #2.395
164 models selected
> select add #2.645
165 models selected
> select add #2.409
166 models selected
> select add #2.396
167 models selected
> select add #2.681
168 models selected
> select add #2.754
169 models selected
> select add #2.788
170 models selected
> select add #2.601
171 models selected
> select add #2.769
172 models selected
> select subtract #2.112
171 models selected
Grouped 171 regions
> select clear
> select #2.1060
1 model selected
> select #2.1060
1 model selected
> select #2.16
1 model selected
> ui tool show "Side View"
Opened L0_imasked as #5, grid size 250,250,250, pixel 4.3, shown at step 1,
values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/Original-map-deposit/Seg/Basal_disk.mrc models
> #5
Opened L0_imasked as #6, grid size 250,250,250, pixel 4.3, shown at step 1,
values float32
Segmenting L0_imasked, density threshold 0.010668
Showing 1000 region surfaces
9960 watershed regions, grouped to 1000 regions
Showing L0_imasked.seg - 1000 regions, 1000 surfaces
> hide #!5 models
> hide #!6 models
> select #2.537
1 model selected
> select add #2.563
2 models selected
> select add #2.577
3 models selected
> select add #2.588
4 models selected
> select add #2.484
5 models selected
> select add #2.468
6 models selected
> select add #2.476
7 models selected
> select add #2.467
8 models selected
> select add #2.490
9 models selected
> select add #2.559
10 models selected
> select add #2.592
11 models selected
> select add #2.471
12 models selected
> select add #2.568
13 models selected
> select add #2.500
14 models selected
> select add #2.469
15 models selected
> select add #2.239
16 models selected
> select add #2.451
17 models selected
> select add #2.480
18 models selected
> select add #2.582
19 models selected
> select add #2.692
20 models selected
> select add #2.591
21 models selected
> select add #2.474
22 models selected
> select add #2.585
23 models selected
> select add #2.556
24 models selected
> select add #2.355
25 models selected
> select add #2.574
26 models selected
> select add #2.499
27 models selected
> select add #2.461
28 models selected
> select add #2.584
29 models selected
> select add #2.570
30 models selected
> select add #2.496
31 models selected
> select add #2.320
32 models selected
Grouped 32 regions
> select clear
> select #2.865
1 model selected
> select add #2.820
2 models selected
Showing 969 region surfaces
Grouped 2 regions
> select clear
> select #2.239
1 model selected
Showing 968 region surfaces
> select clear
> select #2.239
1 model selected
Opened L0_imasked_imasked as #7, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/Original-map-deposit/Seg/LP-ring.mrc models #7
Opened L0_imasked_imasked as #8, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
Segmenting L0_imasked_imasked, density threshold 0.010668
Showing 965 region surfaces
9863 watershed regions, grouped to 965 regions
Showing L0_imasked_imasked.seg - 965 regions, 965 surfaces
> hide #!7 models
> hide #!8 models
> close #7-8
Segmenting L0_imasked, density threshold 0.010668
Showing 1000 region surfaces
9960 watershed regions, grouped to 1000 regions
Showing L0_imasked.seg - 1000 regions, 1000 surfaces
> select #2.481
1 model selected
> select add #2.239
2 models selected
> select add #2.451
3 models selected
> select add #2.691
4 models selected
> select add #2.582
5 models selected
> select add #2.585
6 models selected
> select add #2.474
7 models selected
> select add #2.591
8 models selected
> select add #2.355
9 models selected
> select add #2.499
10 models selected
> select add #2.574
11 models selected
> select subtract #2.574
10 models selected
> select add #2.556
11 models selected
> select add #2.574
12 models selected
> select add #2.584
13 models selected
> select add #2.461
14 models selected
> select add #2.570
15 models selected
> select add #2.496
16 models selected
> select add #2.320
17 models selected
> select add #2.469
18 models selected
> select add #2.500
19 models selected
> select add #2.568
20 models selected
> select add #2.471
21 models selected
> select add #2.592
22 models selected
> select add #2.490
23 models selected
> select add #2.559
24 models selected
> select add #2.468
25 models selected
> select add #2.537
26 models selected
> select add #2.476
27 models selected
> select add #2.467
28 models selected
> select add #2.563
29 models selected
> select add #2.577
30 models selected
> select add #2.484
31 models selected
> select add #2.588
32 models selected
Grouped 32 regions
> select add #2.869
2 models selected
> select add #2.820
3 models selected
Grouped 3 regions
> select clear
> select #2.239
1 model selected
Opened L0_imasked_imasked as #7, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/Original-map-deposit/Seg/LP-ring.mrc models #7
Opened L0_imasked_imasked as #8, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
Segmenting L0_imasked_imasked, density threshold 0.010668
Showing 965 region surfaces
9861 watershed regions, grouped to 965 regions
Showing L0_imasked_imasked.seg - 965 regions, 965 surfaces
> hide #!7 models
> select #2.98
1 model selected
> select add #2.209
2 models selected
> select add #2.228
3 models selected
> select add #2.110
4 models selected
> select add #2.347
5 models selected
> select add #2.241
6 models selected
> select add #2.87
7 models selected
> select add #2.351
8 models selected
> select add #2.237
9 models selected
> select add #2.166
10 models selected
> select add #2.146
11 models selected
> select add #2.231
12 models selected
> select add #2.121
13 models selected
> select add #2.447
14 models selected
> select add #2.723
15 models selected
> select add #2.226
16 models selected
> select add #2.114
17 models selected
> select add #2.360
18 models selected
> select add #2.214
19 models selected
> select add #2.99
20 models selected
> select add #2.238
21 models selected
> select add #2.442
22 models selected
> select add #2.93
23 models selected
> select add #2.344
24 models selected
> select add #2.239
25 models selected
> select add #2.96
26 models selected
> select add #2.453
27 models selected
> select add #2.717
28 models selected
> select add #2.208
29 models selected
> select add #2.112
30 models selected
> select add #2.444
31 models selected
> select add #2.113
32 models selected
> select add #2.233
33 models selected
> select add #2.357
34 models selected
> select add #2.207
35 models selected
> select add #2.167
36 models selected
> select add #2.153
37 models selected
> select add #2.119
38 models selected
> select add #2.242
39 models selected
> select add #2.369
40 models selected
> select add #2.85
41 models selected
> select add #2.212
42 models selected
> select add #2.446
43 models selected
> select add #2.227
44 models selected
> select add #2.108
45 models selected
> select add #2.346
46 models selected
> select add #2.240
47 models selected
> select add #2.210
48 models selected
> select add #2.268
49 models selected
> select add #2.353
50 models selected
> select add #2.235
51 models selected
> select add #2.714
52 models selected
> select add #2.456
53 models selected
> select add #2.117
54 models selected
> select add #2.667
55 models selected
> hide #!8 models
> show #!8 models
> select add #2.588
56 models selected
> select add #2.637
57 models selected
> select add #2.449
58 models selected
> select add #2.639
59 models selected
> select add #2.591
60 models selected
> hide #!8 models
> select #2.453
1 model selected
> select add #2.344
2 models selected
> select add #2.442
3 models selected
> select add #2.360
4 models selected
> select add #2.447
5 models selected
> select add #2.146
6 models selected
> select add #2.351
7 models selected
> select add #2.347
8 models selected
> select add #2.449
9 models selected
> select add #2.456
10 models selected
> select add #2.353
11 models selected
> select add #2.446
12 models selected
> select add #2.346
13 models selected
> select add #2.369
14 models selected
> select add #2.153
15 models selected
> select add #2.357
16 models selected
> select add #2.444
17 models selected
Ungrouped to 40 regions
> select #2.972
1 model selected
> select add #2.988
2 models selected
> select add #2.998
3 models selected
> select add #2.1003
4 models selected
> select #2.1003
1 model selected
Ungrouped to 2 regions
> select clear
> select #2.146
1 model selected
> select add #2.998
2 models selected
> select add #2.988
3 models selected
> select add #2.972
4 models selected
> select add #2.966
5 models selected
> select add #2.973
6 models selected
> select add #2.991
7 models selected
> select add #2.976
8 models selected
> select add #2.999
9 models selected
> select add #2.978
10 models selected
> select add #2.969
11 models selected
> select add #2.981
12 models selected
> select add #2.985
13 models selected
> select add #2.993
14 models selected
Grouped 14 regions
> select clear
> select #2.989
1 model selected
> select add #2.1005
2 models selected
> select add #2.996
3 models selected
Ungrouped to 7 regions
> select clear
> select #2.353
1 model selected
> select add #2.344
2 models selected
> select add #2.347
3 models selected
> select add #2.146
4 models selected
Grouped 4 regions
> select clear
[Repeated 1 time(s)]Drag select of 14375, 19792 of 22604 triangles, 14273,
14276, 14450, 14288, 14470, 14280, 14286, 14397, 14377, 14272, 14281, 14560,
17270 of 18064 triangles, 14380, 14330, 14306, 14098, 13665, 13679, 14559,
13654, 13839, 14147, 14123, 14145, 13657, 13660, 13667, 13685, 14152, 13686,
13688, 13670, 13652, 10880, 13610, 13621, 12155, 12207, 12170, 8109, 8080,
8089, 8096, 8097, 8104, 8087, 8102, 8103, 8131, 8108, 8128, 8090, 8118, 8085,
8084, 8082, 13512, 8110, 8115, 10873, 8078, 8132, 8111, 8079, 8098, 8112,
8123, 8125, 8121, 8093
Grouped 71 regions
Showing 907 region surfaces
> select #2.600
1 model selected
> select add #2.650
2 models selected
> select add #2.603
3 models selected
> select add #2.718
4 models selected
> select add #2.675
5 models selected
> select add #2.85
6 models selected
Grouped 6 regions
> select #2.190
1 model selected
> select add #2.178
2 models selected
> select add #2.189
3 models selected
Ungrouped to 9 regions
> select #2.110
1 model selected
> select add #2.113
2 models selected
> select add #2.98
3 models selected
> select add #2.99
4 models selected
> select add #2.93
5 models selected
> select add #2.87
6 models selected
Ungrouped to 13 regions
> select #2.119
1 model selected
> select add #2.121
2 models selected
> select add #2.208
3 models selected
> select add #2.209
4 models selected
> select add #2.190
5 models selected
Grouped 5 regions
> select add #2.207
2 models selected
Grouped 2 regions
> select #2.191
1 model selected
> select add #2.177
2 models selected
> select add #2.182
3 models selected
> select add #2.174
4 models selected
> select add #2.180
5 models selected
Ungrouped to 13 regions
Ungrouped to 20 regions
> select clear
> select #2.233
1 model selected
> select add #2.226
2 models selected
> select add #2.227
3 models selected
> select add #2.180
4 models selected
> select add #2.182
5 models selected
> select add #2.228
6 models selected
> select add #2.231
7 models selected
> select add #2.268
8 models selected
> select add #2.344
9 models selected
> select add #2.242
10 models selected
> select subtract #2.242
9 models selected
Grouped 9 regions
> select add #2.87
2 models selected
Showing 921 region surfaces
> select add #2.85
3 models selected
Grouped 3 regions
> select clear
> select #2.85
1 model selected
> select #2.186
1 model selected
> select add #2.181
2 models selected
> select add #2.184
3 models selected
> select add #2.175
4 models selected
> select add #2.187
5 models selected
> select add #2.188
6 models selected
> select add #2.176
7 models selected
> select add #2.183
8 models selected
> select add #2.193
9 models selected
Ungrouped to 26 regions
Ungrouped to 35 regions
Ungrouped to 15 regions
> select #2.970
1 model selected
> select add #2.971
2 models selected
> select add #2.210
3 models selected
> select add #2.226
4 models selected
> select add #2.442
5 models selected
> select add #2.444
6 models selected
> select add #2.446
7 models selected
> select add #2.447
8 models selected
> select add #2.717
9 models selected
> select add #2.718
10 models selected
> select add #2.188
11 models selected
> select add #2.193
12 models selected
> select add #2.456
13 models selected
> select add #2.588
14 models selected
> select add #2.591
15 models selected
> select add #2.600
16 models selected
> select add #2.98
17 models selected
> select add #2.99
18 models selected
Grouped 18 regions
Showing 946 region surfaces
> select add #2.85
2 models selected
Grouped 2 regions
Opened L0_imasked_imasked_imasked as #9, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/Original-map-deposit/Seg/PflC.mrc models #9
Opened L0_imasked_imasked_imasked as #10, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
Segmenting L0_imasked_imasked_imasked, density threshold 0.010668
Showing 917 region surfaces
9268 watershed regions, grouped to 917 regions
Showing L0_imasked_imasked_imasked.seg - 917 regions, 917 surfaces
> hide #!9 models
> show #!9 models
> select #2.564
1 model selected
> select add #2.563
2 models selected
> select add #2.579
3 models selected
> select add #2.572
4 models selected
> select add #2.569
5 models selected
> select add #2.576
6 models selected
> select add #2.565
7 models selected
> select add #2.574
8 models selected
> select add #2.571
9 models selected
> select add #2.585
10 models selected
> select add #2.559
11 models selected
> select add #2.587
12 models selected
> select add #2.581
13 models selected
> select add #2.592
14 models selected
> select add #2.562
15 models selected
> select add #2.549
16 models selected
> select add #2.561
17 models selected
Grouped 17 regions
> hide #!9 models
Opened L0_imasked_imasked_imasked_imasked as #11, grid size 250,250,250, pixel
4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/Original-map-deposit/Seg/PflD.mrc models #11
Opened L0_imasked_imasked_imasked_imasked as #12, grid size 250,250,250, pixel
4.3, shown at step 1, values float32
Segmenting L0_imasked_imasked_imasked_imasked, density threshold 0.010668
Showing 900 region surfaces
9251 watershed regions, grouped to 900 regions
Showing L0_imasked_imasked_imasked_imasked.seg - 900 regions, 900 surfaces
> select #2.112
1 model selected
> select add #2.110
2 models selected
> select add #2.155
3 models selected
> select add #2.142
4 models selected
> select add #2.138
5 models selected
> select add #2.253
6 models selected
> select add #2.103
7 models selected
> select add #2.165
8 models selected
> select add #2.145
9 models selected
> select add #2.136
10 models selected
Grouped 10 regions
> hide #!10 models
> hide #!11 models
> hide #!12 models
> select add #2.428
2 models selected
> select add #2.382
3 models selected
> select add #2.101
4 models selected
> select add #2.166
5 models selected
> select add #2.121
6 models selected
> select add #2.510
7 models selected
> select add #2.424
8 models selected
> select add #2.488
9 models selected
> select add #2.519
10 models selected
> select add #2.394
11 models selected
> select add #2.77
12 models selected
> select add #2.105
13 models selected
> select add #2.160
14 models selected
> select add #2.109
15 models selected
> select add #2.182
16 models selected
> select add #2.422
17 models selected
> select add #2.460
18 models selected
> select add #2.477
19 models selected
> select add #2.176
20 models selected
> select add #2.576
21 models selected
> select add #2.94
22 models selected
> select add #2.386
23 models selected
> select add #2.106
24 models selected
> select add #2.122
25 models selected
> select add #2.139
26 models selected
> select add #2.113
27 models selected
> select add #2.87
28 models selected
> select add #2.192
29 models selected
> select add #2.111
30 models selected
> select add #2.126
31 models selected
> select add #2.71
32 models selected
> select add #2.67
33 models selected
> select add #2.41
34 models selected
> select add #2.123
35 models selected
> select add #2.148
36 models selected
> select add #2.193
37 models selected
> select add #2.404
38 models selected
> select add #2.197
39 models selected
> select add #2.196
40 models selected
> select add #2.190
41 models selected
> select add #2.169
42 models selected
> select add #2.278
43 models selected
> select add #2.634
44 models selected
> select add #2.189
45 models selected
> select add #2.537
46 models selected
> select add #2.239
47 models selected
> select add #2.313
48 models selected
> select add #2.689
49 models selected
> select add #2.173
50 models selected
> select add #2.164
51 models selected
> select add #2.302
52 models selected
> select add #2.181
53 models selected
> select add #2.177
54 models selected
> select add #2.174
55 models selected
> select add #2.156
56 models selected
> select add #2.408
57 models selected
> select add #2.346
58 models selected
> select add #2.180
59 models selected
> select add #2.124
60 models selected
> select add #2.207
61 models selected
> select add #2.503
62 models selected
> select add #2.443
63 models selected
> select add #2.282
64 models selected
> select add #2.602
65 models selected
> select add #2.401
66 models selected
> select add #2.331
67 models selected
> select add #2.269
68 models selected
> select add #2.195
69 models selected
> select add #2.586
70 models selected
> select add #2.558
71 models selected
> select add #2.298
72 models selected
> select add #2.221
73 models selected
> select add #2.479
74 models selected
> select add #2.625
75 models selected
> select add #2.262
76 models selected
> select add #2.535
77 models selected
> select add #2.660
78 models selected
> select add #2.450
79 models selected
> select add #2.161
80 models selected
> select add #2.661
81 models selected
> select add #2.399
82 models selected
> select add #2.521
83 models selected
> select add #2.255
84 models selected
> select add #2.297
85 models selected
> select add #2.179
86 models selected
> select add #2.406
87 models selected
> select add #2.413
88 models selected
> select add #2.261
89 models selected
> select add #2.526
90 models selected
> select add #2.590
91 models selected
> select add #2.525
92 models selected
> select add #2.250
93 models selected
> select add #2.529
94 models selected
> select add #2.266
95 models selected
> select add #2.599
96 models selected
> select add #2.459
97 models selected
> select add #2.186
98 models selected
> select add #2.426
99 models selected
> select add #2.191
100 models selected
> select add #2.421
101 models selected
> select add #2.326
102 models selected
> select add #2.385
103 models selected
> select add #2.163
104 models selected
> select add #2.396
105 models selected
> select add #2.354
106 models selected
> select add #2.457
107 models selected
> select add #2.621
108 models selected
> select add #2.380
109 models selected
> select add #2.225
110 models selected
> select add #2.317
111 models selected
> select add #2.184
112 models selected
> select add #2.361
113 models selected
> select add #2.387
114 models selected
> select add #2.199
115 models selected
> select add #2.336
116 models selected
> select add #2.447
117 models selected
> select add #2.158
118 models selected
> select add #2.411
119 models selected
> select add #2.570
120 models selected
> select add #2.468
121 models selected
Drag select of 13339, 21 of 52168 triangles, 13401, 16 of 51284 triangles,
12911, 43 of 17832 triangles, 13455, 31 of 15944 triangles, 5274, 6 of 5364
triangles, 13542, 59 of 9548 triangles, 12832, 15 of 5244 triangles, 13388, 19
of 5120 triangles
> select add #2.275
130 models selected
> select add #2.449
131 models selected
> select subtract #2.453
130 models selected
> select add #2.453
131 models selected
> select subtract #2.431
130 models selected
> select subtract #2.6
129 models selected
> select add #2.431
130 models selected
> select subtract #2.11
129 models selected
> select subtract #2.431
128 models selected
Showing 891 region surfaces
> select clear
Drag select of 13304, 37356 of 37380 triangles, 13358, 29953 of 30572
triangles, 13364, 27403 of 30864 triangles, 13477, 15431 of 26464 triangles,
13500, 12563, 18598 of 24212 triangles, 13337, 12534, 9841 of 19672 triangles,
13320, 13483, 19006 of 24376 triangles, 12583, 11018 of 21688 triangles,
13577, 12820, 12578, 13281, 13282, 13256 of 22308 triangles, 12696, 11405 of
18696 triangles, 13342, 13467, 13523, 5294 of 18688 triangles, 13619, 172 of
15900 triangles, 13300, 10414 of 17236 triangles, 13481, 13306, 13406, 13474,
12556, 12871 of 13420 triangles, 13493, 13353, 15759 of 16180 triangles,
12785, 11504 of 12336 triangles, 13287, 13646, 13101 of 17524 triangles,
13568, 8865 of 14668 triangles, 13645, 12531, 3782 of 11396 triangles, 12560,
13354, 13494, 13366, 12693, 6454 of 11680 triangles, 13565, 13575, 13330,
13312, 13322, 6210 of 14824 triangles, 13571, 13471, 6337 of 12228 triangles,
13545, 13405, 6593 of 13360 triangles, 13487, 13925 of 14032 triangles, 13439,
1596 of 12416 triangles, 13605, 12636, 10955 of 13388 triangles, 13498, 13254,
13661, 13413, 13352, 8927 of 11472 triangles, 13280, 12846, 13475, 13269, 1910
of 8804 triangles, 13562, 12491, 13509, 1026 of 8528 triangles, 12524, 11745,
12688, 13628, 12694, 12810, 13594, 12903, 12508, 12529, 13634, 3876 of 9280
triangles, 12562, 2194 of 6232 triangles, 12836, 2290 of 7052 triangles,
13567, 3927 of 8540 triangles, 13464, 12796, 12805, 13485, 11053, 12860,
12108, 12516, 12832, 13164, 13640, 11070, 11906, 5095 of 5332 triangles,
11122, 13470, 12808, 13045, 5151 of 5256 triangles, 11511, 11040, 10941,
13606, 2040 of 5700 triangles, 12690, 1649 of 4968 triangles, 12672, 5485 of
5508 triangles, 13309, 12766, 12855, 11877, 1846 of 3788 triangles, 11045,
13187, 13220, 3226 of 4596 triangles, 10924, 4057 of 4156 triangles, 12638,
12448, 10940, 13031, 12080, 10953, 492, 13681
Grouped 118 regions
Drag select of 13302, 13283, 12854, 13116, 12819, 11481
Grouped 7 regions
Showing 768 region surfaces
> select clear
> select #2.41
1 model selected
Opened L0_imasked_imasked_imasked_imasked_imasked as #13, grid size
250,250,250, pixel 4.3, shown at step 1, values float32
Segmenting L0_imasked_imasked_imasked_imasked_imasked, density threshold
0.010668
Showing 768 region surfaces
6984 watershed regions, grouped to 768 regions
Showing L0_imasked_imasked_imasked_imasked_imasked.seg - 768 regions, 768
surfaces
Drag select of 10178, 10095, 10170, 79 of 56104 triangles, 10052, 71186 of
71560 triangles, 10000, 10099, 10137, 10139, 10284, 10181, 8323, 4325 of 11168
triangles, 10093, 3805 of 9260 triangles, 9498, 3311 of 8832 triangles, 10097,
8337, 1360 of 6568 triangles, 9921, 9250, 998 of 5700 triangles, 10167, 24 of
5116 triangles, 9387, 62 of 3216 triangles, 9391, 38 of 3016 triangles, 10159,
10122, 10160, 9997, 10224, 10019, 9400, 10229, 10126, 10132, 10244, 9557,
10215, 10243, 10311, 10276, 10172, 10087, 10266, 10189, 10207, 9759, 10183,
9527, 10029, 9406, 9410, 10200, 10098, 10184, 10163, 10202, 9737, 6448, 10114,
10038, 630 of 1492 triangles, 10130, 536 of 1276 triangles, 10186, 10145,
9285, 10146, 10064, 10102, 10004, 9005, 10119, 9300, 7598, 8759, 9776, 9293,
10287, 10055, 10173, 10205, 10109, 9568, 138 of 744 triangles, 10147, 10191,
392 of 980 triangles, 6916, 10115, 166 of 752 triangles, 6419, 9598, 10124,
375 of 692 triangles, 5878, 10142, 10112, 248 of 552 triangles, 6557, 10121,
10106, 127 of 540 triangles, 5883, 10156, 10231, 6650, 5886, 8618, 10316,
5880, 6606, 10157, 10107, 351 of 452 triangles, 9558, 10162, 10100, 9530,
6608, 6891, 9653, 10171, 160 of 340 triangles, 6610, 10111, 6607, 10150, 6949,
96 of 188 triangles, 6787, 9669, 10161, 6752, 9672, 9476, 5898, 6902, 36 of
180 triangles, 9553, 9123, 10131, 6915, 6743, 6750, 6563, 6623, 6832, 6847,
10168, 6644, 6913, 6672, 6852, 6849, 6807, 74 of 112 triangles, 6809, 10129,
6520, 5895, 6638, 6624, 6570, 6579, 6643, 6435, 6605, 6755, 6666, 6747, 6636,
6838, 52 of 56 triangles, 13 L0_imasked_imasked_imasked_imasked_imasked
> hide #!13 models
> select subtract #13
155 models selected
> select add #2.394
156 models selected
> select add #2.362
157 models selected
> select add #2.414
158 models selected
> select add #2.425
159 models selected
> select add #2.376
160 models selected
> select add #2.409
161 models selected
> select add #2.206
162 models selected
> select add #2.386
163 models selected
> select add #2.374
164 models selected
> select add #2.230
165 models selected
> select add #2.492
166 models selected
> select add #2.393
167 models selected
> select add #2.363
168 models selected
> select add #2.222
169 models selected
> select add #2.398
170 models selected
> select add #2.387
171 models selected
> select add #2.144
172 models selected
> select add #2.523
173 models selected
> select add #2.396
174 models selected
> select add #2.460
175 models selected
> select add #2.339
176 models selected
> select add #2.350
177 models selected
> select add #2.427
178 models selected
> select add #2.385
179 models selected
> select add #2.364
180 models selected
> select add #2.499
181 models selected
> select add #2.451
182 models selected
> select add #2.449
183 models selected
> select add #2.218
184 models selected
> select add #2.384
185 models selected
> select add #2.391
186 models selected
> select subtract #2.391
185 models selected
> select add #2.314
186 models selected
> select add #2.391
187 models selected
> select add #2.435
188 models selected
> select add #2.380
189 models selected
> select add #2.397
190 models selected
> select add #2.16
191 models selected
Grouped 191 regions
> select add #2.156
2 models selected
> select add #2.160
3 models selected
> select add #2.148
4 models selected
> select add #2.161
5 models selected
> select add #2.162
6 models selected
> select add #2.152
7 models selected
> select add #2.154
8 models selected
> select add #2.165
9 models selected
> select add #2.170
10 models selected
> select add #2.155
11 models selected
> select add #2.159
12 models selected
> select add #2.164
13 models selected
> select add #2.158
14 models selected
> select add #2.157
15 models selected
> select add #2.153
16 models selected
> select add #2.151
17 models selected
> select add #2.163
18 models selected
Grouped 18 regions
> select add #2.90
2 models selected
> select add #2.72
3 models selected
> select add #2.80
4 models selected
> select add #2.73
5 models selected
> select add #2.93
6 models selected
> select add #2.97
7 models selected
> select add #2.92
8 models selected
> select add #2.96
9 models selected
> select add #2.74
10 models selected
> select add #2.78
11 models selected
> select add #2.81
12 models selected
> select add #2.77
13 models selected
> select add #2.79
14 models selected
> select add #2.88
15 models selected
> select add #2.86
16 models selected
> select add #2.85
17 models selected
> select add #2.89
18 models selected
> select add #2.122
19 models selected
> select add #2.121
20 models selected
> select add #2.124
21 models selected
> select add #2.109
22 models selected
> select add #2.102
23 models selected
> select add #2.111
24 models selected
> select add #2.103
25 models selected
> select add #2.120
26 models selected
> select add #2.127
27 models selected
> select add #2.118
28 models selected
> select add #2.117
29 models selected
> select add #2.123
30 models selected
> select add #2.113
31 models selected
> select add #2.112
32 models selected
> select add #2.116
33 models selected
> select add #2.110
34 models selected
> select add #2.115
35 models selected
Grouped 35 regions
> select add #2.3
2 models selected
> select add #2.43
3 models selected
> select add #2.40
4 models selected
> select add #2.46
5 models selected
> select add #2.49
6 models selected
> select add #2.45
7 models selected
> select add #2.55
8 models selected
> select add #2.36
9 models selected
> select add #2.59
10 models selected
> select add #2.35
11 models selected
> select add #2.38
12 models selected
> select add #2.34
13 models selected
> select add #2.50
14 models selected
> select add #2.32
15 models selected
> select add #2.47
16 models selected
> select add #2.53
17 models selected
> select add #2.41
18 models selected
> select add #2.44
19 models selected
> select add #2.294
20 models selected
> select add #2.183
21 models selected
> select add #2.296
22 models selected
> select add #2.191
23 models selected
> select add #2.310
24 models selected
> select add #2.221
25 models selected
> select subtract #2.221
24 models selected
> select add #2.184
25 models selected
> select add #2.221
26 models selected
> select add #2.214
27 models selected
> select add #2.301
28 models selected
> select add #2.194
29 models selected
> select add #2.288
30 models selected
> select add #2.220
31 models selected
> select add #2.229
32 models selected
> select add #2.210
33 models selected
> select add #2.198
34 models selected
> select add #2.285
35 models selected
> select add #2.196
36 models selected
> select add #2.37
37 models selected
> select add #2.75
38 models selected
> select add #2.61
39 models selected
> select add #2.64
40 models selected
> select add #2.56
41 models selected
> select add #2.66
42 models selected
> select add #2.54
43 models selected
> select add #2.63
44 models selected
> select add #2.71
45 models selected
> select add #2.67
46 models selected
> select add #2.62
47 models selected
> select add #2.68
48 models selected
> select add #2.51
49 models selected
> select add #2.39
50 models selected
> select add #2.52
51 models selected
> select add #2.76
52 models selected
> select add #2.58
53 models selected
> select add #2.185
54 models selected
> select add #2.186
55 models selected
> select add #2.188
56 models selected
> select add #2.173
57 models selected
> select add #2.179
58 models selected
> select add #2.177
59 models selected
> select add #2.180
60 models selected
> select add #2.190
61 models selected
> select add #2.182
62 models selected
> select add #2.150
63 models selected
> select add #2.181
64 models selected
> select add #2.172
65 models selected
> select add #2.171
66 models selected
> select add #2.146
67 models selected
> select add #2.200
68 models selected
> select add #2.189
69 models selected
> select add #2.192
70 models selected
> select add #2.249
71 models selected
> select add #2.265
72 models selected
> select add #2.266
73 models selected
> select add #2.234
74 models selected
> select add #2.228
75 models selected
> select add #2.291
76 models selected
> select add #2.255
77 models selected
> select add #2.224
78 models selected
> select add #2.258
79 models selected
> select add #2.280
80 models selected
> select add #2.243
81 models selected
> select add #2.283
82 models selected
> select add #2.290
83 models selected
> select add #2.223
84 models selected
> select add #2.275
85 models selected
> select add #2.226
86 models selected
> select add #2.254
87 models selected
> select add #2.279
88 models selected
> select add #2.231
89 models selected
> select add #2.241
90 models selected
> select add #2.244
91 models selected
> select add #2.289
92 models selected
> select add #2.211
93 models selected
> select add #2.287
94 models selected
> select add #2.263
95 models selected
> select add #2.260
96 models selected
> select add #2.236
97 models selected
> select add #2.257
98 models selected
> select add #2.292
99 models selected
> select add #2.235
100 models selected
> select add #2.237
101 models selected
> select add #2.269
102 models selected
> select add #2.262
103 models selected
> select add #2.232
104 models selected
> select add #2.84
105 models selected
> select add #2.100
106 models selected
> select add #2.94
107 models selected
> select add #2.57
108 models selected
> select add #2.315
109 models selected
> select add #2.335
110 models selected
> select add #2.166
111 models selected
> select add #2.82
112 models selected
> select add #2.91
113 models selected
> select add #2.65
114 models selected
> select add #2.322
115 models selected
> select add #2.99
116 models selected
> select add #2.125
117 models selected
> select add #2.31
118 models selected
> select add #2.129
119 models selected
> select add #2.205
120 models selected
> select add #2.69
121 models selected
> select add #2.114
122 models selected
> select add #2.135
123 models selected
> select add #2.119
124 models selected
> select add #2.495
125 models selected
> select add #2.98
126 models selected
> select add #2.197
127 models selected
> select add #2.105
128 models selected
> select add #2.134
129 models selected
> select add #2.104
130 models selected
> select add #2.187
131 models selected
> select subtract #2.187
130 models selected
> select add #2.187
131 models selected
> select add #2.278
132 models selected
> select add #2.87
133 models selected
> select add #2.328
134 models selected
> select add #2.256
135 models selected
Grouped 135 regions
> select add #2.277
2 models selected
> select add #2.297
3 models selected
> select add #2.307
4 models selected
> select add #2.251
5 models selected
> select add #2.274
6 models selected
> select add #2.252
7 models selected
> select add #2.282
8 models selected
> select add #2.286
9 models selected
> select add #2.239
10 models selected
> select add #2.253
11 models selected
> select add #2.273
12 models selected
> select add #2.281
13 models selected
> select add #2.272
14 models selected
> select add #2.259
15 models selected
> select add #2.299
16 models selected
> select add #2.267
17 models selected
> select add #2.240
18 models selected
Grouped 18 regions
> select clear
> select #2.83
1 model selected
> select add #2.137
2 models selected
> select add #2.95
3 models selected
> select add #2.101
4 models selected
> select add #2.268
5 models selected
> select add #2.130
6 models selected
> select add #2.107
7 models selected
> select add #2.511
8 models selected
Grouped 8 regions
Showing 369 region surfaces
> select add #2.1
2 models selected
Grouped 2 regions
> select clear
> select #2.20
1 model selected
> select add #2.208
2 models selected
> select add #2.306
3 models selected
Drag select of 9578, 14 of 10576 triangles, 9416, 14 of 6092 triangles, 9426,
6 of 4972 triangles, 10324, 13 of 1743064 triangles
> select add #2.276
6 models selected
> select clear
> select #2.264
1 model selected
> select add #2.139
2 models selected
> select add #2.106
3 models selected
> select subtract #2.106
2 models selected
> select add #2.106
3 models selected
> select add #2.227
4 models selected
> select add #2.126
5 models selected
> select add #2.217
6 models selected
> select add #2.250
7 models selected
> select add #2.176
8 models selected
> select add #2.333
9 models selected
> select add #2.128
10 models selected
> select add #2.138
11 models selected
> select add #2.141
12 models selected
Grouped 12 regions
> select #2.1
1 model selected
> select add #2.12
2 models selected
> select add #2.30
3 models selected
> select add #2.17
4 models selected
> select add #2.24
5 models selected
> select add #2.25
6 models selected
> select add #2.4
7 models selected
> select add #2.29
8 models selected
> select add #2.19
9 models selected
> select add #2.26
10 models selected
> select add #2.28
11 models selected
> select add #2.14
12 models selected
> select add #2.7
13 models selected
> select add #2.21
14 models selected
> select add #2.27
15 models selected
> select add #2.22
16 models selected
> select add #2.9
17 models selected
> select add #2.13
18 models selected
> select add #2.11
19 models selected
> select add #2.6
20 models selected
> select add #2.10
21 models selected
> select add #2.8
22 models selected
> select add #2.23
23 models selected
> select add #2.20
24 models selected
Grouped 24 regions
> select clear
> select #2.1
1 model selected
Showing 334 region surfaces
Opened L0_imasked_imasked_imasked_imasked_imasked_imasked as #14, grid size
250,250,250, pixel 4.3, shown at step 1, values float32
Segmenting L0_imasked_imasked_imasked_imasked_imasked_imasked, density
threshold 0.010668
Showing 425 region surfaces
3855 watershed regions, grouped to 425 regions
Showing L0_imasked_imasked_imasked_imasked_imasked_imasked.seg - 425 regions,
425 surfaces
> select #2.14
1 model selected
> select add #2.7
2 models selected
> select add #2.21
3 models selected
> select add #2.22
4 models selected
> select add #2.9
5 models selected
> select add #2.13
6 models selected
> select add #2.11
7 models selected
> select add #2.6
8 models selected
> select add #2.10
9 models selected
> select add #2.8
10 models selected
> select add #2.5
11 models selected
> select add #2.12
12 models selected
> select add #2.17
13 models selected
> select add #2.25
14 models selected
> select add #2.4
15 models selected
> select add #2.19
16 models selected
> select add #2.28
17 models selected
Ungrouped to 63 regions
> select clear
> select #2.478
1 model selected
> select add #2.477
2 models selected
> select #2.477
1 model selected
Ungrouped to 5 regions
> select clear
> select #2.7
1 model selected
> select add #2.478
2 models selected
> hide #!14 models
Grouped 2 regions
> select #2.443
1 model selected
> select add #2.444
2 models selected
Ungrouped to 7 regions
> select clear
> select #2.11
1 model selected
> select add #2.9
2 models selected
> select add #2.12
3 models selected
> select add #2.7
4 models selected
Grouped 4 regions
> select #2.436
1 model selected
> select #2.435
1 model selected
Ungrouped to 7 regions
> select clear
> select #2.19
1 model selected
> select add #2.436
2 models selected
> select add #2.7
3 models selected
Grouped 3 regions
> select #2.486
1 model selected
Ungrouped to 4 regions
> select #2.435
1 model selected
> select add #2.488
2 models selected
> select add #2.7
3 models selected
Grouped 3 regions
> select #2.453
1 model selected
Ungrouped to 6 regions
> select clear
> select #2.486
1 model selected
> select add #2.452
2 models selected
> select add #2.7
3 models selected
Grouped 3 regions
> select #2.467
1 model selected
> select add #2.466
2 models selected
> select add #2.7
3 models selected
Grouped 3 regions
> select #2.469
1 model selected
> select add #2.470
2 models selected
> select #2.470
1 model selected
Ungrouped to 6 regions
> select #2.488
1 model selected
> select add #2.469
2 models selected
> select add #2.7
3 models selected
> select clear
> select #2.469
1 model selected
> select add #2.488
2 models selected
Grouped 2 regions
> select #2.428
1 model selected
> select add #2.429
2 models selected
> select #2.429
1 model selected
Ungrouped to 4 regions
> select clear
> select #2.470
1 model selected
> select add #2.428
2 models selected
Grouped 2 regions
> select #2.475
1 model selected
> select #2.474
1 model selected
Ungrouped to 5 regions
> select clear
> select #2.493
1 model selected
> select add #2.475
2 models selected
Grouped 2 regions
> select #2.483
1 model selected
Ungrouped to 5 regions
> select clear
> select #2.494
1 model selected
> select add #2.482
2 models selected
Grouped 2 regions
> select #2.460
1 model selected
> select add #2.456
2 models selected
> select clear
> select #2.456
1 model selected
Ungrouped to 6 regions
> select clear
> select #2.499
1 model selected
> select add #2.460
2 models selected
Grouped 2 regions
> select clear
> select #2.446
1 model selected
> select #2.445
1 model selected
Ungrouped to 6 regions
> select clear
> select #2.501
1 model selected
> select add #2.446
2 models selected
Grouped 2 regions
> select #2.438
1 model selected
> select add #2.434
2 models selected
> select add #2.442
3 models selected
> select add #2.447
4 models selected
> select add #2.454
5 models selected
Ungrouped to 22 regions
> select clear
> select #2.516
1 model selected
> select add #2.520
2 models selected
> select add #2.437
3 models selected
Grouped 3 regions
> select clear
> select add #2.430
1 model selected
> select add #2.434
2 models selected
> select add #2.441
3 models selected
> select add #2.501
4 models selected
> select add #2.448
5 models selected
> select add #2.509
6 models selected
> select add #2.455
7 models selected
> select add #2.524
8 models selected
Grouped 8 regions
> select clear
> select #2.430
1 model selected
> select add #2.7
2 models selected
> select add #2.469
3 models selected
> select add #2.428
4 models selected
> select add #2.474
5 models selected
> select add #2.482
6 models selected
> select add #2.456
7 models selected
> select add #2.445
8 models selected
> select #2.430
1 model selected
> select #2.428
1 model selected
> select clear
> select #2.428
1 model selected
> select add #2.7
2 models selected
> select add #2.482
3 models selected
> select add #2.456
4 models selected
> select add #2.445
5 models selected
> select add #2.430
6 models selected
Ungrouped to 19 regions
> select #2.527
1 model selected
> select add #2.501
2 models selected
> select add #2.524
3 models selected
> select add #2.528
4 models selected
> select add #2.516
5 models selected
> select add #2.434
6 models selected
Ungrouped to 22 regions
Ungrouped to 18 regions
> select clear
> select #2.546
1 model selected
> select add #2.553
2 models selected
> select add #2.456
3 models selected
> select add #2.541
4 models selected
> select add #2.533
5 models selected
> select add #2.536
6 models selected
> select add #2.534
7 models selected
> select add #2.537
8 models selected
> select add #2.524
9 models selected
> select add #2.528
10 models selected
> select add #2.535
11 models selected
> select add #2.545
12 models selected
> select add #2.549
13 models selected
> select add #2.554
14 models selected
> select add #2.555
15 models selected
> select add #2.556
16 models selected
> select add #2.548
17 models selected
> select add #2.445
18 models selected
Grouped 18 regions
Ungrouped to 18 regions
> select clear
> select #2.430
1 model selected
Ungrouped to 0 regions
> select #2.539
1 model selected
Ungrouped to 0 regions
> select #2.524
1 model selected
> select add #2.538
2 models selected
> select add #2.535
3 models selected
> select add #2.536
4 models selected
> select add #2.543
5 models selected
> select add #2.534
6 models selected
> select add #2.545
7 models selected
> select add #2.546
8 models selected
> select add #2.541
9 models selected
Drag select of 3903, 24 of 4808 triangles, 1426, 22 of 2176 triangles
> select clear
> select #2.544
1 model selected
> select add #2.456
2 models selected
> select add #2.482
3 models selected
> select #2.445
1 model selected
> select add #2.532
2 models selected
> select add #2.537
3 models selected
> select add #2.533
4 models selected
> select add #2.430
5 models selected
> select clear
> select #2.428
1 model selected
> select add #2.528
2 models selected
> select add #2.542
3 models selected
> select clear
> select #2.539
1 model selected
Ungrouped to 0 regions
> select clear
Drag select of 5545, 5547, 4834, 427, 4420, 4550, 4829, 4840, 3903, 5543,
45241 of 45264 triangles, 4842, 3920, 4547, 4259, 3891, 269, 603, 443, 5912 of
6428 triangles, 592, 472, 3955, 418, 559, 346, 520, 379, 431, 365
Grouped 28 regions
> select clear
Showing 523 region surfaces
> select #2.7
1 model selected
Opened L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked as #15, grid
size 250,250,250, pixel 4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/Original-map-deposit/Seg/PilM.mrc models #15
Opened L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked as #16, grid
size 250,250,250, pixel 4.3, shown at step 1, values float32
Segmenting L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked, density
threshold 0.010668
Showing 427 region surfaces
3773 watershed regions, grouped to 427 regions
Showing L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg - 427
regions, 427 surfaces
> hide #!15 models
> hide #!16 models
Segmenting L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked, density
threshold 0.010668
Showing 427 region surfaces
3773 watershed regions, grouped to 427 regions
Showing L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg - 427
regions, 427 surfaces
> select #2.16
1 model selected
Ungrouped to 6 regions
Ungrouped to 13 regions
> select #2.438
1 model selected
> select #2.436
1 model selected
> select add #2.437
2 models selected
> select add #2.439
3 models selected
> select add #2.442
4 models selected
> select add #2.440
5 models selected
> select add #2.441
6 models selected
> select add #2.443
7 models selected
> select add #2.435
8 models selected
> select add #2.444
9 models selected
Grouped 9 regions
> select clear
> select #2.438
1 model selected
> select add #2.430
2 models selected
> select clear
> select #2.108
1 model selected
> select add #2.85
2 models selected
> select add #2.133
3 models selected
> select add #2.97
4 models selected
> select add #2.292
5 models selected
> select add #2.103
6 models selected
> select add #2.223
7 models selected
> select add #2.129
8 models selected
> select add #2.428
9 models selected
> select add #2.16
10 models selected
> select add #2.434
11 models selected
> select add #2.445
12 models selected
Grouped 12 regions
Opened L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#17, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/Original-map-deposit/Seg/Exp_ATP.mrc models #17
Opened L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#18, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
Segmenting L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.010668
Showing 420 region surfaces
3728 watershed regions, grouped to 420 regions
Showing L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 420 regions, 420 surfaces
> hide #!17 models
> hide #!18 models
> select #2.98
1 model selected
> select add #2.66
2 models selected
> select add #2.91
3 models selected
> select add #2.83
4 models selected
> select add #2.58
5 models selected
> select add #2.148
6 models selected
> select add #2.94
7 models selected
> select add #2.245
8 models selected
> select add #2.248
9 models selected
> select add #2.99
10 models selected
> select add #2.84
11 models selected
Drag select of 5205, 27 of 18376 triangles, 5023, 42 of 14808 triangles, 5165,
31 of 13920 triangles, 4664, 32 of 4880 triangles, 5221, 45 of 6280 triangles
> select add #2.206
15 models selected
> select add #2.102
16 models selected
> select add #2.162
17 models selected
> select add #2.103
18 models selected
> select add #2.125
19 models selected
> select add #2.170
20 models selected
> select add #2.97
21 models selected
> select add #2.115
22 models selected
> select add #2.126
23 models selected
> select add #2.110
24 models selected
> select add #2.70
25 models selected
> select add #2.123
26 models selected
> select add #2.173
27 models selected
> select add #2.29
28 models selected
> select add #2.121
29 models selected
Grouped 29 regions
> select add #2.84
2 models selected
> select add #2.222
3 models selected
> select add #2.280
4 models selected
Grouped 4 regions
> select #2.161
1 model selected
> select add #2.163
2 models selected
> select add #2.152
3 models selected
> select add #2.154
4 models selected
> select add #2.153
5 models selected
> select add #2.155
6 models selected
Ungrouped to 13 regions
Ungrouped to 2 regions
> select #2.29
1 model selected
Showing 397 region surfaces
> select clear
> select #2.29
1 model selected
> select add #2.246
2 models selected
Grouped 2 regions
> select add #2.196
2 models selected
> select add #2.98
3 models selected
> select add #2.97
4 models selected
> select add #2.221
5 models selected
> select add #2.94
6 models selected
> select add #2.91
7 models selected
> select add #2.70
8 models selected
> select add #2.66
9 models selected
> select add #2.102
10 models selected
> select add #2.99
11 models selected
> select add #2.165
12 models selected
> select add #2.157
13 models selected
> select add #2.132
14 models selected
> select add #2.156
15 models selected
> select add #2.151
16 models selected
> select add #2.150
17 models selected
> select add #2.129
18 models selected
> select add #2.172
19 models selected
> select add #2.164
20 models selected
> select add #2.167
21 models selected
> select add #2.160
22 models selected
> select add #2.46
23 models selected
> select add #2.103
24 models selected
> select add #2.110
25 models selected
> select add #2.87
26 models selected
> select add #2.84
27 models selected
> select add #2.215
28 models selected
> select add #2.238
29 models selected
> select add #2.242
30 models selected
> select add #2.201
31 models selected
> select add #2.219
32 models selected
> select add #2.202
33 models selected
> select add #2.226
34 models selected
> select add #2.229
35 models selected
> select add #2.195
36 models selected
> select add #2.203
37 models selected
> select add #2.218
38 models selected
> select add #2.225
39 models selected
> select add #2.217
40 models selected
> select add #2.209
41 models selected
> select add #2.239
42 models selected
Grouped 42 regions
> select clear
> select #2.68
1 model selected
Ungrouped to 2 regions
Ungrouped to 6 regions
> select #2.70
1 model selected
> select add #2.87
2 models selected
Grouped 2 regions
> select #2.63
1 model selected
> select add #2.69
2 models selected
> select add #2.52
3 models selected
> select add #2.39
4 models selected
> select add #2.54
5 models selected
> select add #2.77
6 models selected
> select add #2.83
7 models selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #2.59
8 models selected
> select subtract #2.83
7 models selected
> select add #2.37
8 models selected
> select add #2.76
9 models selected
> select add #2.62
10 models selected
> select add #2.65
11 models selected
> select add #2.53
12 models selected
> select add #2.67
13 models selected
> select add #2.56
14 models selected
> select add #2.64
15 models selected
> select add #2.72
16 models selected
> select add #2.46
17 models selected
Ungrouped to 46 regions
> select subtract #2.157
45 models selected
> select subtract #2.160
44 models selected
Ungrouped to 99 regions
Ungrouped to 116 regions
Ungrouped to 29 regions
Ungrouped to 0 regions
> select #2.148
1 model selected
> select add #2.565
2 models selected
> select add #2.566
3 models selected
> select add #2.440
4 models selected
> select add #2.439
5 models selected
> select add #2.157
6 models selected
> select add #2.160
7 models selected
> select add #2.115
8 models selected
> select add #2.123
9 models selected
> select add #2.126
10 models selected
> select add #2.53
11 models selected
> select add #2.52
12 models selected
> select add #2.422
13 models selected
> select add #2.568
14 models selected
> select add #2.567
15 models selected
> select add #2.91
16 models selected
> select add #2.84
17 models selected
> select add #2.221
18 models selected
> select add #2.226
19 models selected
> select add #2.129
20 models selected
> select add #2.56
21 models selected
> select add #2.54
22 models selected
> select add #2.72
23 models selected
> select add #2.480
24 models selected
> select add #2.425
25 models selected
> select add #2.427
26 models selected
> select add #2.520
27 models selected
> select add #2.522
28 models selected
> select add #2.426
29 models selected
> select add #2.69
30 models selected
> select add #2.576
31 models selected
> select add #2.452
32 models selected
> select add #2.451
33 models selected
> select add #2.573
34 models selected
> select add #2.87
35 models selected
> select add #2.99
36 models selected
> select add #2.575
37 models selected
> select add #2.97
38 models selected
> select add #2.436
39 models selected
> select add #2.434
40 models selected
> select add #2.433
41 models selected
> select add #2.457
42 models selected
> select add #2.458
43 models selected
> select add #2.435
44 models selected
> select add #2.500
45 models selected
> select add #2.498
46 models selected
> select add #2.531
47 models selected
> select add #2.532
48 models selected
> select add #2.540
49 models selected
> select add #2.499
50 models selected
> select add #2.239
51 models selected
> select add #2.242
52 models selected
> select add #2.556
53 models selected
> select add #2.557
54 models selected
> select add #2.558
55 models selected
> select add #2.245
56 models selected
> select add #2.247
57 models selected
> select add #2.544
58 models selected
> select add #2.543
59 models selected
> select add #2.225
60 models selected
> select add #2.454
61 models selected
> select add #2.456
62 models selected
> select add #2.550
63 models selected
> select add #2.536
64 models selected
> select add #2.508
65 models selected
> select add #2.83
66 models selected
> select add #2.535
67 models selected
> select add #2.475
68 models selected
> select add #2.529
69 models selected
> select add #2.509
70 models selected
> select add #2.470
71 models selected
> select add #2.548
72 models selected
> select add #2.443
73 models selected
> select add #2.467
74 models selected
> select add #2.547
75 models selected
> select add #2.441
76 models selected
> select add #2.569
77 models selected
> select add #2.570
78 models selected
> select add #2.514
79 models selected
> select add #2.515
80 models selected
> select add #2.564
81 models selected
> select add #2.563
82 models selected
> select add #2.485
83 models selected
> select add #2.463
84 models selected
> select subtract #2.463
83 models selected
> select add #2.463
84 models selected
> select add #2.201
85 models selected
> select add #2.76
86 models selected
> select add #2.219
87 models selected
> select add #2.196
88 models selected
> select add #2.203
89 models selected
> select add #2.154
90 models selected
> select add #2.153
91 models selected
> select add #2.161
92 models selected
> select add #2.165
93 models selected
> select add #2.561
94 models selected
> select add #2.164
95 models selected
> select add #2.562
96 models selected
> select add #2.445
97 models selected
> select add #2.503
98 models selected
> select add #2.502
99 models selected
> select add #2.504
100 models selected
> select add #2.492
101 models selected
> select add #2.491
102 models selected
> select add #2.430
103 models selected
> select add #2.494
104 models selected
> select add #2.493
105 models selected
Grouped 105 regions
> select add #2.206
2 models selected
Grouped 2 regions
Showing 446 region surfaces
> select add #2.29
2 models selected
> select #2.29
1 model selected
> select clear
> select #2.29
1 model selected
Ungrouped to 42 regions
Ungrouped to 32 regions
Ungrouped to 8 regions
> select #2.91
1 model selected
Ungrouped to 29 regions
> select clear
> select #2.242
1 model selected
Ungrouped to 5 regions
> select #2.520
1 model selected
> select add #2.512
2 models selected
> select add #2.514
3 models selected
> select add #2.91
4 models selected
> select add #2.515
5 models selected
> select clear
Drag select of 5353, 142720 of 176292 triangles, 432, 181, 426, 442, 439, 175,
160, 493, 185, 438, 190, 191, 188, 166, 174, 490, 434, 492, 437, 186, 146,
424, 169, 441, 155, 407, 421, 5819 of 6528 triangles, 440, 192, 498, 478, 419,
427, 425, 483, 4567 of 4816 triangles, 182, 481, 416, 418, 463, 406, 165, 467,
388, 839, 433, 431, 414, 413, 472, 2753 of 3224 triangles, 417, 4606 of 4792
triangles, 164, 458, 462, 408, 409, 405, 5023, 284, 5035, 516, 411, 6018 of
6216 triangles, 210, 95, 5047, 5162, 5013, 4664, 5157, 12982 of 13792
triangles, 4174, 5044, 5076, 5126, 4945, 5276, 10913 of 11100 triangles, 5150,
5165, 5148, 5031, 9816 of 10084 triangles, 17, 5129, 5160, 5086, 4681, 5757 of
5896 triangles, 5022, 8840 of 8924 triangles, 4742, 5151, 5281, 5164, 4134,
5029
Grouped 92 regions
> select clear
> select #2.29
1 model selected
Showing 451 region surfaces
> select clear
> select #2.29
1 model selected
Showing 451 region surfaces
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#19, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/Original-map-deposit/Seg/C-ring-stators.mrc
> models #19
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked as
#20, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
Segmenting
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.010668
Showing 355 region surfaces
3376 watershed regions, grouped to 355 regions
Showing
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 355 regions, 355 surfaces
> hide #!19 models
> hide #!20 models
> select #2.156
1 model selected
> select add #2.196
2 models selected
> select add #2.203
3 models selected
> select add #2.142
4 models selected
> select add #2.153
5 models selected
> select add #2.158
6 models selected
Drag select of 4775, 7 of 20572 triangles, 4628, 7 of 7720 triangles, 4726, 12
of 5384 triangles, 4305, 16 of 5224 triangles
Drag select of 4695, 30 of 71560 triangles, 4762, 10 of 20120 triangles, 4713,
4 of 19980 triangles, 4560, 7 of 7840 triangles
> select #2.158
1 model selected
> select add #2.141
2 models selected
> select add #2.143
3 models selected
> select add #2.148
4 models selected
> select add #2.164
5 models selected
> select add #2.175
6 models selected
> select add #2.157
7 models selected
> select add #2.169
8 models selected
> select add #2.167
9 models selected
> select add #2.153
10 models selected
> select add #2.174
11 models selected
> select add #2.142
12 models selected
> select add #2.166
13 models selected
> select add #2.203
14 models selected
> select add #2.196
15 models selected
> select add #2.168
16 models selected
> select add #2.156
17 models selected
> select add #2.152
18 models selected
> select add #2.146
19 models selected
> select add #2.173
20 models selected
Drag select of 4733, 17 of 21208 triangles, 4603, 18 of 7732 triangles, 4104,
19 of 5384 triangles
> select add #2.171
24 models selected
> select add #2.135
25 models selected
> select subtract #2.30
24 models selected
> select add #2.162
25 models selected
> select add #2.160
26 models selected
> select add #2.159
27 models selected
> select add #2.150
28 models selected
> select add #2.149
29 models selected
> select add #2.176
30 models selected
> select add #2.165
31 models selected
> select add #2.151
32 models selected
> select add #2.147
33 models selected
> select add #2.161
34 models selected
> select add #2.163
35 models selected
> select add #2.155
36 models selected
Grouped 36 regions
> select clear
> select #2.118
1 model selected
> select #2.118
1 model selected
Ungrouped to 36 regions
> select subtract #2.196
35 models selected
Grouped 35 regions
Showing 321 region surfaces
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #21, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/Original-map-deposit/Seg/C-Vring.mrc models #21
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #22, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
Segmenting
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.010668
Showing 320 region surfaces
3316 watershed regions, grouped to 320 regions
Showing
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 320 regions, 320 surfaces
> hide #!21 models
> hide #!22 models
> select #2.18
1 model selected
> select add #2.9
2 models selected
> select #2.58
1 model selected
> select add #2.63
2 models selected
> select add #2.62
3 models selected
> select add #2.61
4 models selected
> select clear
Drag select of 2, 1
Drag select of 4496, 32 of 4668 triangles, 4666, 3350 of 3396 triangles, 4667,
4619, 4472, 153 of 1580 triangles, 4515, 1050 of 1208 triangles, 4676, 496 of
704 triangles, 4278, 467 of 684 triangles, 2219, 3675, 176 of 440 triangles,
2231
> select subtract #2.174
12 models selected
> select add #2.174
13 models selected
> select add #2.178
14 models selected
> select add #2.179
15 models selected
Drag select of 4698, 3411 of 3552 triangles, 4385, 4697, 2164 of 3016
triangles, 4726, 1744 of 2292 triangles, 2211, 2213
Drag select of 4668, 2949 of 3596 triangles, 4666, 88 of 3396 triangles
> select add #2.189
22 models selected
> select add #2.234
23 models selected
> select add #2.199
24 models selected
> select add #2.207
25 models selected
> select add #2.224
26 models selected
> select add #2.253
27 models selected
Drag select of 4598, 296 of 94920 triangles, 4597, 315 of 71560 triangles,
4737, 104 of 992 triangles, 4611, 665 of 1052 triangles, 4623, 355 of 1092
triangles, 4639, 2983, 81 of 384 triangles, 4671, 565 of 616 triangles, 4599,
210 of 452 triangles, 4390, 3224, 258 of 260 triangles, 3120, 4411, 4589, 152
of 208 triangles, 3165, 3180, 3005, 2976
> select subtract #2.2
44 models selected
> select subtract #2.14
43 models selected
Drag select of 4604, 286 of 94960 triangles, 4597, 38 of 71560 triangles,
4714, 88 of 884 triangles, 4743, 132 of 792 triangles, 4624, 259 of 1132
triangles, 4603, 104 of 1260 triangles, 4647, 380 of 892 triangles, 4631, 590
of 980 triangles, 4655, 226 of 692 triangles, 4715, 397 of 728 triangles,
3987, 315 of 368 triangles, 2939, 4648, 172 of 500 triangles, 4359, 227 of 340
triangles, 2941, 4735, 248 of 356 triangles, 4608, 148 of 460 triangles, 2943,
2940, 4620, 4622, 2956, 3185, 3246, 4 of 120 triangles, 3142, 2903, 3080, 3171
> select subtract #2.1
70 models selected
> select add #2.2
71 models selected
> select subtract #2.2
70 models selected
> select subtract #2.14
69 models selected
Drag select of 4598, 68 of 94920 triangles, 4607, 211 of 1492 triangles, 4615,
947 of 1276 triangles, 4420, 4746, 13 of 528 triangles, 4614, 4617, 4636,
4642, 180 of 340 triangles, 3085, 71 of 196 triangles, 3235, 3076, 99 of 156
triangles, 3140, 3182, 2999, 38 of 56 triangles
> select subtract #2.2
83 models selected
Drag select of 4597, 215 of 71560 triangles, 4646, 3249, 114 of 476 triangles,
4381, 193 of 736 triangles, 4605, 4335, 155 of 328 triangles, 4338, 3083,
4742, 80 of 128 triangles, 2971, 41 of 80 triangles, 2957, 73 of 80 triangles,
4644, 28 of 84 triangles
> select subtract #2.14
94 models selected
Drag select of 4596, 189 of 220 triangles, 4740, 48 of 248 triangles, 2977
Grouped 97 regions
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #23, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
Segmenting
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.010668
Showing 223 region surfaces
3017 watershed regions, grouped to 223 regions
Showing
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 223 regions, 223 surfaces
> select #2.68
1 model selected
> select add #2.66
2 models selected
> select add #2.69
3 models selected
> select add #2.67
4 models selected
> select add #2.54
5 models selected
> select add #2.59
6 models selected
> select add #2.53
7 models selected
> select add #2.65
8 models selected
> select add #2.64
9 models selected
> select add #2.61
10 models selected
> select add #2.62
11 models selected
> select add #2.63
12 models selected
> select add #2.58
13 models selected
> select add #2.56
14 models selected
> select add #2.60
15 models selected
> select add #2.57
16 models selected
> select add #2.55
17 models selected
Ungrouped to 47 regions
Ungrouped to 70 regions
Ungrouped to 64 regions
Ungrouped to 17 regions
Ungrouped to 0 regions
> select #2.86
1 model selected
> select add #2.83
2 models selected
> select #2.301
1 model selected
> select add #2.300
2 models selected
> select add #2.299
3 models selected
> hide #!23 models
Grouped 3 regions
Ungrouped to 3 regions
Ungrouped to 0 regions
> select #2.240
1 model selected
> select #2.247
1 model selected
> select add #2.240
2 models selected
> select add #2.236
3 models selected
> select add #2.83
4 models selected
> select #2.83
1 model selected
Ungrouped to 3 regions
> select #2.84
1 model selected
> select add #2.78
2 models selected
> select add #2.74
3 models selected
Ungrouped to 11 regions
Ungrouped to 4 regions
Ungrouped to 0 regions
> select #2.79
1 model selected
> select add #2.76
2 models selected
> select add #2.77
3 models selected
> select add #2.85
4 models selected
> select add #2.80
5 models selected
> select add #2.81
6 models selected
> select add #2.87
7 models selected
> select add #2.82
8 models selected
> select add #2.71
9 models selected
> select add #2.75
10 models selected
> select add #2.70
11 models selected
> select add #2.73
12 models selected
> select add #2.86
13 models selected
> select add #2.265
14 models selected
> select subtract #2.265
13 models selected
Ungrouped to 43 regions
Ungrouped to 13 regions
Ungrouped to 0 regions
> select #2.374
1 model selected
> select add #2.238
2 models selected
> select add #2.288
3 models selected
> select add #2.292
4 models selected
> select add #2.306
5 models selected
Grouped 5 regions
> select #2.371
1 model selected
> select add #2.370
2 models selected
> select add #2.346
3 models selected
> select add #2.347
4 models selected
> select add #2.315
5 models selected
Grouped 5 regions
> select #2.379
1 model selected
> select add #2.376
2 models selected
> select add #2.356
3 models selected
> select add #2.283
4 models selected
> select add #2.389
5 models selected
> select add #2.266
6 models selected
> select add #2.269
7 models selected
> select add #2.312
8 models selected
Grouped 8 regions
> select add #2.288
2 models selected
Grouped 2 regions
> select #2.77
1 model selected
> select add #2.79
2 models selected
> select add #2.75
3 models selected
> select add #2.339
4 models selected
> select add #2.277
5 models selected
> select add #2.80
6 models selected
> select add #2.81
7 models selected
> select add #2.333
8 models selected
> select add #2.272
9 models selected
> select add #2.273
10 models selected
> select add #2.318
11 models selected
> select add #2.301
12 models selected
> select add #2.341
13 models selected
> select add #2.278
14 models selected
> select add #2.275
15 models selected
> select add #2.287
16 models selected
> select add #2.335
17 models selected
> select add #2.231
18 models selected
> select add #2.230
19 models selected
> select add #2.59
20 models selected
> select add #2.70
21 models selected
> select add #2.71
22 models selected
> select add #2.349
23 models selected
> select add #2.351
24 models selected
> select add #2.348
25 models selected
> select add #2.293
26 models selected
> select add #2.82
27 models selected
> select subtract #2.82
26 models selected
> select add #2.82
27 models selected
> select add #2.85
28 models selected
> select add #2.337
29 models selected
> select add #2.338
30 models selected
> select add #2.68
31 models selected
> select add #2.368
32 models selected
> select add #2.366
33 models selected
> select add #2.282
34 models selected
> select add #2.281
35 models selected
> select add #2.279
36 models selected
> select add #2.363
37 models selected
> select add #2.362
38 models selected
> select add #2.261
39 models selected
> select add #2.263
40 models selected
> select add #2.271
41 models selected
Drag select of 4256, 16 of 42652 triangles, 4243, 16 of 19312 triangles, 4269,
27 of 19980 triangles, 4072, 12 of 7776 triangles, 1667, 17 of 4228 triangles
> select add #2.86
47 models selected
> select add #2.286
48 models selected
> select subtract #2.101
47 models selected
> select subtract #2.49
46 models selected
> select add #2.284
47 models selected
> select add #2.290
48 models selected
> select add #2.316
49 models selected
Drag select of 4256, 12 of 42652 triangles, 4233, 34 of 20120 triangles, 3442,
4 of 5396 triangles, 1578, 18 of 4388 triangles, 1747, 22 of 2792 triangles,
1815, 7 of 4608 triangles, 1992, 7 of 2268 triangles, 1602, 16 of 4224
triangles
> select add #2.326
54 models selected
> select subtract #2.46
53 models selected
> select subtract #2.36
52 models selected
> select subtract #2.61
51 models selected
> select subtract #2.344
50 models selected
> select subtract #2.303
49 models selected
> select add #2.316
50 models selected
> select add #2.327
51 models selected
> select add #2.62
52 models selected
> select add #2.78
53 models selected
> select add #2.74
54 models selected
> select add #2.83
55 models selected
> select add #2.328
56 models selected
> select add #2.330
57 models selected
> select add #2.54
58 models selected
> select add #2.317
59 models selected
> select add #2.84
60 models selected
> select add #2.245
61 models selected
> select add #2.67
62 models selected
> select add #2.63
63 models selected
> select add #2.320
64 models selected
> select add #2.265
65 models selected
> select add #2.236
66 models selected
> select add #2.240
67 models selected
> select add #2.247
68 models selected
Grouped 68 regions
> select #2.238
1 model selected
> select add #2.266
2 models selected
> select add #2.54
3 models selected
> select #2.54
1 model selected
Ungrouped to 68 regions
> select subtract #2.71
67 models selected
Grouped 67 regions
> select add #2.238
2 models selected
> select add #2.266
3 models selected
> select subtract #2.238
2 models selected
Grouped 2 regions
> select clear
Showing 306 region surfaces
> select #2.238
1 model selected
> select #2.58
1 model selected
Ungrouped to 0 regions
> select #2.20
1 model selected
Ungrouped to 5 regions
Ungrouped to 22 regions
Ungrouped to 20 regions
Ungrouped to 0 regions
> select #2.13
1 model selected
> select #2.275
1 model selected
> select add #2.238
2 models selected
Grouped 2 regions
> select clear
> select #2.20
1 model selected
> select add #2.54
2 models selected
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #24, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/Original-map-deposit/Seg/Cage-C17.mrc models #24
> select clear
> select #2.20
1 model selected
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #25, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/Original-map-deposit/Seg/Cage-Mono-Good.mrc
> models #25
> select clear
> select #2.54
1 model selected
> select add #2.20
2 models selected
> hide #!2 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> hide #!25 models
> show #!2 models
> select clear
> select #2.54
1 model selected
> select add #2.20
2 models selected
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #26, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
Segmenting
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.010668
Showing 240 region surfaces
2931 watershed regions, grouped to 240 regions
Showing
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 240 regions, 240 surfaces
> select #2.155
1 model selected
> select add #2.165
2 models selected
> select add #2.154
3 models selected
> select add #2.150
4 models selected
> show #!25 models
> select add #2.157
5 models selected
> select add #2.162
6 models selected
> select add #2.153
7 models selected
> select add #2.149
8 models selected
> select add #2.158
9 models selected
> select add #2.164
10 models selected
> select add #2.161
11 models selected
> select add #2.152
12 models selected
> select add #2.160
13 models selected
> select add #2.159
14 models selected
> select add #2.166
15 models selected
> select add #2.163
16 models selected
> select add #2.156
17 models selected
Ungrouped to 0 regions
> select #2.155
1 model selected
> select add #2.150
2 models selected
> select add #2.157
3 models selected
> select add #2.162
4 models selected
> select add #2.165
5 models selected
> select add #2.154
6 models selected
> select add #2.156
7 models selected
> select add #2.163
8 models selected
> select add #2.153
9 models selected
> select add #2.149
10 models selected
> select add #2.158
11 models selected
> select add #2.164
12 models selected
> select add #2.161
13 models selected
> select add #2.152
14 models selected
> select add #2.160
15 models selected
> select add #2.159
16 models selected
> select add #2.166
17 models selected
> hide #!26 models
Grouped 17 regions
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #27, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichi/Desktop/Original-map-deposit/Seg/MotB.mrc models #27
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #28, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
Segmenting
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.010668
Showing 220 region surfaces
2914 watershed regions, grouped to 220 regions
Showing
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 220 regions, 220 surfaces
> hide #!27 models
> hide #!28 models
> select #2.83
1 model selected
Ungrouped to 2 regions
[Repeated 2 time(s)]Ungrouped to 0 regions
> select #2.222
1 model selected
> select add #2.224
2 models selected
> select add #2.221
3 models selected
> select #2.53
1 model selected
Ungrouped to 2 regions
Ungrouped to 5 regions
Ungrouped to 4 regions
Ungrouped to 0 regions
> select #2.230
1 model selected
> select add #2.227
2 models selected
> select add #2.221
3 models selected
> select add #2.224
4 models selected
> select add #2.222
5 models selected
Grouped 5 regions
> select #2.223
1 model selected
Ungrouped to 0 regions
> select #2.53
1 model selected
> hide #!25 models
> select #2.229
1 model selected
> select add #2.83
2 models selected
> select add #2.78
3 models selected
> select subtract #2.78
2 models selected
> select #2.231
1 model selected
> select add #2.53
2 models selected
Grouped 2 regions
Ungrouped to 2 regions
> select #2.221
1 model selected
Ungrouped to 0 regions
> select #2.222
1 model selected
> select add #2.221
2 models selected
Showing 225 region surfaces
> select #2.222
1 model selected
Ungrouped to 5 regions
> select #2.227
1 model selected
Ungrouped to 0 regions
> show #!24 models
> show #!27 models
> hide #!27 models
> hide #!24 models
Showing 229 region surfaces
> select #2.224
1 model selected
> select add #2.226
2 models selected
> select add #2.230
3 models selected
> select add #2.53
4 models selected
> select add #2.227
5 models selected
> select subtract #2.226
4 models selected
Grouped 4 regions
> select add #2.226
2 models selected
> save /Users/shoichi/Desktop/Original-map-deposit/Seg/Segmentation.cxs
> includeMaps true
> select #2.78
1 model selected
> select add #2.229
2 models selected
> select add #2.83
3 models selected
> select add #2.225
4 models selected
> select #2.78
1 model selected
Ungrouped to 2 regions
> select #2.224
1 model selected
> select add #2.221
2 models selected
> select add #2.229
3 models selected
> select add #2.83
4 models selected
> select #2.89
1 model selected
> select #2.228
1 model selected
> save /Users/shoichi/Desktop/Original-map-deposit/Seg/Segmentation.cxs
> includeMaps true
——— End of log from Fri Jul 25 14:31:14 2025 ———
opened ChimeraX session
Showing
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 227 regions, 227 surfaces
> select #2.206
1 model selected
> select subtract #2.206
Nothing selected
> select add #2.166
1 model selected
> select add #2.206
2 models selected
> select add #2.115
3 models selected
> select add #2.203
4 models selected
> select add #2.122
5 models selected
> select add #2.100
6 models selected
> select add #2.170
7 models selected
> select add #2.200
8 models selected
> select add #2.14
9 models selected
> select add #2.60
10 models selected
> select add #2.205
11 models selected
Grouped 11 regions
> select add #2.32
2 models selected
> select add #2.64
3 models selected
> select add #2.66
4 models selected
Grouped 4 regions
> select add #2.173
2 models selected
> select clear
> select #2.173
1 model selected
Ungrouped to 14 regions
> select #2.166
1 model selected
> select add #2.191
2 models selected
Grouped 2 regions
> select add #2.170
2 models selected
> select add #2.122
3 models selected
> select add #2.153
4 models selected
> select clear
> select #2.153
1 model selected
Ungrouped to 18 regions
> select #2.143
1 model selected
> select add #2.86
2 models selected
> select add #2.16
3 models selected
> select add #2.124
4 models selected
> select #2.238
1 model selected
> select add #2.194
2 models selected
Ungrouped to 13 regions
Ungrouped to 37 regions
> select #2.278
1 model selected
> select add #2.260
2 models selected
> select add #2.290
3 models selected
> select add #2.258
4 models selected
> select add #2.272
5 models selected
> select add #2.237
6 models selected
> select add #2.274
7 models selected
> select add #2.273
8 models selected
> select add #2.267
9 models selected
Grouped 9 regions
> select #2.235
1 model selected
Ungrouped to 5 regions
> select #2.248
1 model selected
> select add #2.291
2 models selected
> select add #2.194
3 models selected
> select add #2.173
4 models selected
> select add #2.236
5 models selected
> select subtract #2.173
4 models selected
Grouped 4 regions
> select add #2.14
2 models selected
Grouped 2 regions
> select clear
> select #2.173
1 model selected
Ungrouped to 7 regions
Ungrouped to 13 regions
> select #2.267
1 model selected
> select add #2.256
2 models selected
> select add #2.255
3 models selected
> select add #2.173
4 models selected
> select add #2.278
5 models selected
> select add #2.260
6 models selected
> select add #2.14
7 models selected
> select add #2.274
8 models selected
> select add #2.238
9 models selected
> select add #2.239
10 models selected
Grouped 10 regions
> select add #2.153
2 models selected
Grouped 2 regions
> select add #2.257
2 models selected
Grouped 2 regions
> select #2.205
1 model selected
> select add #2.166
2 models selected
> select #2.166
1 model selected
Ungrouped to 2 regions
Ungrouped to 22 regions
Ungrouped to 47 regions
> select #2.300
1 model selected
> select add #2.313
2 models selected
> select add #2.331
3 models selected
> select add #2.173
4 models selected
> select add #2.153
5 models selected
> select add #2.310
6 models selected
> select subtract #2.310
5 models selected
> select add #2.200
6 models selected
> select add #2.310
7 models selected
> select add #2.311
8 models selected
> select add #2.337
9 models selected
> select add #2.335
10 models selected
> select add #2.334
11 models selected
> select add #2.330
12 models selected
> select add #2.332
13 models selected
> select add #2.321
14 models selected
> select add #2.115
15 models selected
> select add #2.315
16 models selected
Grouped 16 regions
> select add #2.336
2 models selected
> select add #2.338
3 models selected
> select add #2.14
4 models selected
Grouped 4 regions
> select #2.170
1 model selected
> select add #2.307
2 models selected
> select add #2.268
3 models selected
Grouped 3 regions
> select add #2.14
2 models selected
Grouped 2 regions
> select add #2.122
2 models selected
> select add #2.151
3 models selected
> select add #2.314
4 models selected
> select add #2.205
5 models selected
> select add #2.312
6 models selected
> select add #2.301
7 models selected
> select add #2.303
8 models selected
> select add #2.302
9 models selected
> select add #2.333
10 models selected
> select add #2.304
11 models selected
> select add #2.270
12 models selected
> select add #2.277
13 models selected
> select add #2.259
14 models selected
> select add #2.258
15 models selected
> select add #2.276
16 models selected
Grouped 16 regions
> select clear
> select #2.14
1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> select #2.14
1 model selected
Ungrouped to 16 regions
Ungrouped to 53 regions
Ungrouped to 122 regions
> select #2.363
1 model selected
Ungrouped to 2 regions
[Repeated 1 time(s)]Ungrouped to 19 regions
> select #2.331
1 model selected
Ungrouped to 2 regions
Ungrouped to 8 regions
Ungrouped to 29 regions
Ungrouped to 51 regions
Ungrouped to 82 regions
Ungrouped to 94 regions
Ungrouped to 49 regions
Ungrouped to 0 regions
> select #2.330
1 model selected
Ungrouped to 25 regions
Ungrouped to 57 regions
Ungrouped to 33 regions
Ungrouped to 0 regions
> select clear
Drag select of 2134, 646 of 1164 triangles, 2157, 184 of 480 triangles, 2136,
18 of 208 triangles, 2206, 2270, 2192, 2306, 2255, 2287, 2217, 125 of 212
triangles, 2230, 285 of 288 triangles
Drag select of 3887, 50 of 32680 triangles, 2253, 2168, 416 of 504 triangles,
2149, 118 of 664 triangles
> select subtract #2.451
14 models selected
> select add #2.451
15 models selected
> select subtract #2.451
14 models selected
Drag select of 2846, 2861, 96 of 100 triangles, 2906, 2895, 2907, 66 of 80
triangles, 3769, 77 of 1564 triangles, 2866, 25 of 80 triangles
> select subtract #2.411
20 models selected
Drag select of 2903, 2902, 2844, 119 of 264 triangles, 2893, 114 of 224
triangles, 2914, 2894, 2824, 2904, 2823, 2790, 2789, 2875, 32 of 196 triangles
Grouped 32 regions
Drag select of 2842, 4163, 240 of 38128 triangles, 2803, 3717, 38 of 1544
triangles, 2788, 2899, 2898, 2686, 100 of 236 triangles
> select subtract #2.416
8 models selected
> select clear
[Repeated 1 time(s)]Drag select of 3759, 13 of 3948 triangles, 1932, 1929,
1941, 1958, 1943, 1961, 1950, 1931, 1917, 1937, 1979, 1926, 1927, 1930, 1915,
1963, 1944, 1965, 1949, 1948, 1964, 1987, 1980, 1995, 1994, 1953, 1955, 1945,
1989, 1986, 1924, 1916, 1914, 1936, 1962, 1946, 1952, 1954, 1947, 1970, 1951,
1971, 1960, 1966, 1968, 1918, 1942, 1978, 1985, 1993, 1959, 1957, 2009, 319 of
1352 triangles, 1983, 1967, 1969, 1934, 1919, 2008, 503 of 2396 triangles,
2005, 1128 of 1468 triangles, 2011, 826 of 1532 triangles, 2042, 685 of 1608
triangles, 2041, 530 of 1332 triangles, 2001, 3009 of 4812 triangles, 1999,
3884 of 5484 triangles, 2019, 15 of 1068 triangles, 1984, 1991, 1992, 2018,
376 of 1536 triangles, 2015, 629 of 2064 triangles, 2034, 546 of 1292
triangles, 2045, 87 of 1696 triangles, 2054, 359 of 2100 triangles, 1976,
1975, 2016, 323 of 2124 triangles, 1973, 1972, 1977, 1974, 1982, 1990, 1998,
5283 of 6072 triangles, 1988, 1981, 1920, 1933, 2020, 251 of 4748 triangles,
2022, 209 of 1996 triangles, 2003, 3804 of 4272 triangles, 2014, 505 of 1296
triangles, 1996, 5206 of 6132 triangles, 2044, 111 of 1444 triangles, 2004,
2260 of 3664 triangles, 2000, 4488 of 6468 triangles, 2043, 456 of 1960
triangles, 2017, 765 of 4084 triangles, 2006, 679 of 1672 triangles, 2007, 509
of 1244 triangles, 2040, 707 of 1872 triangles, 2013, 708 of 1036 triangles,
1997, 4320 of 4764 triangles, 2021, 289 of 4780 triangles, 2012, 664 of 1836
triangles, 2033, 382 of 868 triangles, 2010, 836 of 2120 triangles, 2032, 559
of 1060 triangles
Grouped 109 regions
> select #2.451
1 model selected
Ungrouped to 20 regions
Ungrouped to 34 regions
> select #2.517
1 model selected
> select add #2.520
2 models selected
> select add #2.482
3 models selected
> select add #2.507
4 models selected
> select add #2.506
5 models selected
> select add #2.362
6 models selected
> select subtract #2.362
5 models selected
> select add #2.519
6 models selected
> select add #2.598
7 models selected
> select add #2.702
8 models selected
> select add #2.577
9 models selected
> select add #2.663
10 models selected
> select add #2.362
11 models selected
> select subtract #2.362
10 models selected
> select clear
> select #2.362
1 model selected
Ungrouped to 16 regions
Ungrouped to 21 regions
> select clear
[Repeated 1 time(s)]
> select #2.551
1 model selected
> select clear
> select #2.338
1 model selected
Drag select of 2207, 915 of 2828 triangles, 2267, 82 of 2000 triangles, 2205,
637 of 1484 triangles, 2127, 1696 of 2468 triangles, 2246, 215 of 1748
triangles, 2204, 1029 of 2616 triangles, 2244, 235 of 1900 triangles, 2101,
1796 of 2524 triangles, 2111, 1626 of 2368 triangles, 2077, 2114, 1819 of 2544
triangles, 2095, 2272, 25 of 1112 triangles, 2265, 210 of 2556 triangles,
2094, 2073, 3412, 2268 of 2968 triangles, 2161, 1383 of 2096 triangles, 2103,
2098, 2268 of 3096 triangles, 2100, 3218, 159 of 3636 triangles, 3725, 904 of
4604 triangles, 2139, 2138, 2203, 764 of 1816 triangles, 2221, 288 of 924
triangles, 3877, 262 of 21936 triangles, 3495, 2947 of 3972 triangles, 3537,
1208 of 4924 triangles, 2099, 2102, 2174, 1030 of 1876 triangles, 3057, 555 of
3912 triangles, 2084, 2239, 260 of 2052 triangles, 2163, 814 of 1040
triangles, 2105, 2162, 1157 of 1916 triangles, 2082, 2504 of 3552 triangles,
2197, 742 of 1664 triangles, 2116, 1835 of 2604 triangles, 2104, 2237, 381 of
1888 triangles, 2235, 314 of 1472 triangles, 2236, 325 of 1940 triangles,
2277, 65 of 2228 triangles, 2280, 159 of 2984 triangles, 2196, 867 of 1544
triangles, 2248, 222 of 1352 triangles, 2209, 649 of 1712 triangles, 2133,
1739 of 2396 triangles, 2155, 1959 of 2504 triangles, 2152, 2120 of 2980
triangles, 2171, 628 of 1540 triangles, 2247, 297 of 2168 triangles, 2273, 53
of 1676 triangles, 2274, 169 of 1632 triangles, 2068, 2067, 2065, 2093, 2023,
2049, 2039, 2066, 2063, 2026, 2036, 2154, 838 of 1456 triangles, 2112, 1559 of
2244 triangles, 2079, 2122, 1485 of 2332 triangles, 2088, 2097, 2048, 2035,
2037, 2052, 2050, 2051, 2028, 2030, 2046, 2092, 2029, 2091, 2047, 2038, 2072,
2125, 1513 of 1760 triangles, 2024, 2172, 870 of 1232 triangles, 2194, 964 of
1384 triangles, 2064, 2061, 2153, 1934 of 2784 triangles, 2170, 661 of 916
triangles, 2059, 2074, 2053, 2083, 2055, 2076, 1835 of 2684 triangles, 2078,
2031, 2027, 2090, 2201, 451 of 616 triangles, 2108, 2022 of 2236 triangles,
2056, 2025, 2062, 2489 of 2680 triangles, 2086, 2202, 655 of 1032 triangles,
2057, 2058, 2109, 2110, 2060, 2137, 2069, 2342 of 2348 triangles, 2262, 172 of
1840 triangles, 2185, 559 of 1536 triangles, 2187, 768 of 2344 triangles,
2219, 506 of 1216 triangles, 3385, 2893 of 4476 triangles, 2087, 2233, 226 of
1332 triangles, 2222, 406 of 1868 triangles, 2148, 1229 of 2536 triangles,
2085, 2075, 1876 of 2688 triangles, 2243, 20 of 2236 triangles, 2145, 1017 of
2040 triangles, 2160, 1201 of 2248 triangles, 2158, 1220 of 2148 triangles,
2113, 2200 of 3032 triangles, 2191, 704 of 1352 triangles, 2263, 43 of 1144
triangles, 2131, 1003 of 1464 triangles, 2200, 581 of 1276 triangles, 2269,
158 of 2376 triangles, 3205, 40 of 3552 triangles, 3834, 2375 of 3076
triangles
Grouped 146 regions
Drag select of 2275, 2292, 2266, 2406, 677 of 704 triangles, 2418, 997 of 2592
triangles, 2445, 223 of 1580 triangles, 2392, 878 of 2072 triangles, 2394, 763
of 1852 triangles, 2991, 28 of 2332 triangles, 2260, 2382, 1216 of 1572
triangles, 3141, 16 of 2840 triangles, 2492, 275 of 2348 triangles, 2409, 792
of 900 triangles, 2408, 730 of 816 triangles, 3208, 1453 of 2324 triangles,
2295, 2380, 1069 of 1760 triangles, 2381, 738 of 872 triangles, 2407, 785 of
828 triangles, 2495, 651 of 2424 triangles, 2427, 925 of 1788 triangles, 2429,
965 of 2440 triangles, 2434, 1058 of 1880 triangles, 2498, 448 of 2132
triangles, 2405, 1143 of 1820 triangles, 2428, 851 of 1496 triangles, 2430,
1318 of 3396 triangles, 2425, 1030 of 1688 triangles, 2379, 1437 of 2060
triangles, 2493, 391 of 2872 triangles, 2404, 1118 of 1928 triangles, 2494,
542 of 3696 triangles, 2467, 464 of 812 triangles, 2426, 979 of 4276
triangles, 2484, 125 of 2144 triangles, 2261, 2486, 9 of 2760 triangles, 2369,
936 of 1940 triangles, 2396, 856 of 1952 triangles, 3140, 2122 of 3520
triangles, 2290, 2344, 634 of 1080 triangles, 3240, 1956 of 2976 triangles,
2291, 2391, 410 of 708 triangles, 3241, 1917 of 3736 triangles, 2485, 69 of
2684 triangles, 2361, 755 of 1560 triangles, 2416, 287 of 648 triangles, 2527,
579 of 2632 triangles, 2431, 629 of 724 triangles, 2420, 544 of 876 triangles,
2371, 1109 of 1396 triangles, 2293, 1765 of 1808 triangles, 2375, 1032 of 1908
triangles, 2374, 810 of 884 triangles, 3678, 3924 of 12112 triangles, 2378,
1381 of 1464 triangles, 2294
Grouped 61 regions
> select add #2.537
2 models selected
> select add #2.536
3 models selected
> select add #2.516
4 models selected
> select add #2.451
5 models selected
> select add #2.390
6 models selected
> select add #2.393
7 models selected
> select add #2.389
8 models selected
> select add #2.388
9 models selected
> select add #2.380
10 models selected
> select add #2.378
11 models selected
> select add #2.377
12 models selected
> select add #2.383
13 models selected
> select add #2.384
14 models selected
> select add #2.464
15 models selected
> select add #2.381
16 models selected
> select add #2.303
17 models selected
> select add #2.382
18 models selected
> select add #2.379
19 models selected
> select add #2.751
20 models selected
> select add #2.762
21 models selected
> select add #2.563
22 models selected
> select add #2.356
23 models selected
> select add #2.359
24 models selected
> select add #2.363
25 models selected
> select add #2.613
26 models selected
> select add #2.542
27 models selected
> select add #2.760
28 models selected
Grouped 28 regions
> select add #2.392
2 models selected
> select add #2.466
3 models selected
> select add #2.422
4 models selected
> select add #2.771
5 models selected
> select add #2.756
6 models selected
> select add #2.759
7 models selected
> select add #2.439
8 models selected
Grouped 8 regions
> select add #2.763
2 models selected
> select add #2.450
3 models selected
> select add #2.410
4 models selected
> select add #2.415
5 models selected
> select add #2.769
6 models selected
> select add #2.711
7 models selected
> select add #2.710
8 models selected
> select add #2.770
9 models selected
> select add #2.740
10 models selected
> select add #2.350
11 models selected
> select add #2.765
12 models selected
> select add #2.764
13 models selected
> select add #2.731
14 models selected
> select add #2.727
15 models selected
> select add #2.732
16 models selected
> select add #2.534
17 models selected
> select add #2.568
18 models selected
> select add #2.761
19 models selected
> select add #2.704
20 models selected
> select add #2.412
21 models selected
Grouped 21 regions
> select add #2.700
2 models selected
> select add #2.707
3 models selected
> select add #2.730
4 models selected
> select add #2.714
5 models selected
> select add #2.713
6 models selected
> select add #2.778
7 models selected
> select add #2.703
8 models selected
> select add #2.741
9 models selected
> select add #2.742
10 models selected
> select add #2.775
11 models selected
> select add #2.773
12 models selected
> select add #2.733
13 models selected
> select add #2.774
14 models selected
> select add #2.425
15 models selected
> select add #2.766
16 models selected
> select add #2.767
17 models selected
> select add #2.768
18 models selected
> select add #2.715
19 models selected
> select add #2.706
20 models selected
> select add #2.777
21 models selected
> select add #2.712
22 models selected
Grouped 22 regions
> select add #2.418
2 models selected
> select add #2.442
3 models selected
> select add #2.735
4 models selected
> select add #2.752
5 models selected
> select add #2.737
6 models selected
> select add #2.734
7 models selected
> select add #2.736
8 models selected
> select add #2.726
9 models selected
> select add #2.436
10 models selected
> select add #2.717
11 models selected
> select add #2.411
12 models selected
> select add #2.424
13 models selected
> select add #2.456
14 models selected
Grouped 14 regions
> select add #2.728
2 models selected
> select add #2.330
3 models selected
> select add #2.471
4 models selected
> select add #2.441
5 models selected
> select add #2.429
6 models selected
> select add #2.423
7 models selected
> select add #2.401
8 models selected
> select add #2.427
9 models selected
> select add #2.151
10 models selected
> select add #2.421
11 models selected
Grouped 11 regions
> select add #2.470
2 models selected
> select add #2.431
3 models selected
> select add #2.370
4 models selected
> select add #2.417
5 models selected
> select add #2.433
6 models selected
> select add #2.122
7 models selected
> select add #2.449
8 models selected
> select subtract #2.449
7 models selected
> select add #2.426
8 models selected
> select add #2.413
9 models selected
> select add #2.420
10 models selected
> select add #2.447
11 models selected
> select add #2.371
12 models selected
> select add #2.153
13 models selected
> select add #2.406
14 models selected
> select add #2.405
15 models selected
> select add #2.404
16 models selected
> select add #2.361
17 models selected
> select add #2.360
18 models selected
> select add #2.387
19 models selected
> select add #2.386
20 models selected
Grouped 20 regions
> select add #2.449
2 models selected
> select add #2.419
3 models selected
> select add #2.444
4 models selected
> select add #2.428
5 models selected
> select add #2.448
6 models selected
> select subtract #2.448
5 models selected
> select add #2.448
6 models selected
> select add #2.409
7 models selected
> select add #2.440
8 models selected
> select add #2.432
9 models selected
> select add #2.445
10 models selected
> select add #2.414
11 models selected
> select add #2.446
12 models selected
> select add #2.434
13 models selected
> select add #2.435
14 models selected
> select add #2.385
15 models selected
Grouped 15 regions
> select add #2.560
2 models selected
> select add #2.554
3 models selected
> select add #2.430
4 models selected
> select add #2.437
5 models selected
> select add #2.558
6 models selected
> select add #2.416
7 models selected
> select add #2.673
8 models selected
> select add #2.776
9 models selected
Grouped 9 regions
> select clear
Showing 351 region surfaces
> select #2.61
1 model selected
> select add #2.78
2 models selected
> select add #2.59
3 models selected
> select add #2.42
4 models selected
> select add #2.45
5 models selected
> select add #2.197
6 models selected
> select add #2.36
7 models selected
Ungrouped to 14 regions
Ungrouped to 10 regions
> select #2.38
1 model selected
> select add #2.37
2 models selected
> select add #2.43
3 models selected
> select add #2.41
4 models selected
Ungrouped to 8 regions
> select #2.53
1 model selected
> select add #2.44
2 models selected
> select add #2.49
3 models selected
Ungrouped to 7 regions
Ungrouped to 2 regions
Ungrouped to 0 regions
> select #2.14
1 model selected
> select add #2.161
2 models selected
Grouped 2 regions
> select clear
> select #2.270
1 model selected
> select add #2.151
2 models selected
> select add #2.200
3 models selected
> select add #2.42
4 models selected
> select add #2.78
5 models selected
> select add #2.255
6 models selected
> select add #2.238
7 models selected
> select add #2.267
8 models selected
> select add #2.166
9 models selected
> select add #2.49
10 models selected
> select add #2.278
11 models selected
> select add #2.43
12 models selected
> select add #2.38
13 models selected
> select add #2.258
14 models selected
> select add #2.256
15 models selected
> select add #2.59
16 models selected
> select add #2.235
17 models selected
Ungrouped to 0 regions
> select #2.14
1 model selected
Showing 371 region surfaces
> select clear
> select #2.192
1 model selected
> select clear
> select #2.192
1 model selected
Ungrouped to 12 regions
Ungrouped to 39 regions
Ungrouped to 41 regions
Ungrouped to 8 regions
> select #2.14
1 model selected
> select add #2.154
2 models selected
> ui tool show "Side View"
> select #2.154
1 model selected
Ungrouped to 15 regions
> select clear
> select #2.356
1 model selected
> select add #2.397
2 models selected
> select add #2.418
3 models selected
> select add #2.414
4 models selected
> select add #2.14
5 models selected
> select add #2.351
6 models selected
Grouped 6 regions
> select clear
> select #2.14
1 model selected
Showing 446 region surfaces
> select clear
> select #2.14
1 model selected
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #29, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/Rod.mrc models #29
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #30, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Segmenting
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.010668
Showing 224 region surfaces
2302 watershed regions, grouped to 224 regions
Showing
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 224 regions, 224 surfaces
> hide #!29 models
> hide #!30 models
Drag select of 3226, 3212, 3256, 3027, 3227, 3233, 3261, 3250, 3090, 3224,
3201, 3202, 3272, 3066, 3239, 3232, 3032, 3217, 3216, 3207, 3203, 3039, 3263,
3236, 3243, 3244, 3253, 2719, 3285, 3237, 3282, 3140, 2156, 3254, 3260, 3123,
3241, 2929, 2844, 2646, 3163, 3258, 2136, 2193, 3221, 3252, 3257, 2957, 2279,
2195, 2200, 2190, 2146, 2208, 2248, 2215
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #31, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
Segmenting
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.010668
Showing 168 region surfaces
1897 watershed regions, grouped to 168 regions
Showing
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 168 regions, 168 surfaces
> select #2.84
1 model selected
> select add #2.91
2 models selected
> select add #2.66
3 models selected
> select add #2.83
4 models selected
> select add #2.50
5 models selected
> select add #2.73
6 models selected
> select add #2.93
7 models selected
> select add #2.52
8 models selected
> select add #2.48
9 models selected
> select add #2.75
10 models selected
> select add #2.43
11 models selected
> select #2.70
1 model selected
> select add #2.87
2 models selected
> select add #2.88
3 models selected
> select add #2.72
4 models selected
> select add #2.76
5 models selected
> select add #2.94
6 models selected
> select add #2.97
7 models selected
> select add #2.77
8 models selected
> select add #2.86
9 models selected
> select add #2.90
10 models selected
> select add #2.82
11 models selected
> select add #2.81
12 models selected
> select add #2.74
13 models selected
> select add #2.71
14 models selected
> select add #2.89
15 models selected
> select add #2.80
16 models selected
> select add #2.85
17 models selected
Grouped 17 regions
> hide #!31 models
> select #2.45
1 model selected
> select add #2.58
2 models selected
> select add #2.57
3 models selected
> select add #2.60
4 models selected
> select add #2.121
5 models selected
> select add #2.134
6 models selected
> select add #2.53
7 models selected
> select add #2.64
8 models selected
> select add #2.110
9 models selected
> select add #2.112
10 models selected
> select add #2.67
11 models selected
> select add #2.43
12 models selected
> select add #2.122
13 models selected
> select add #2.44
14 models selected
> select add #2.56
15 models selected
> select add #2.47
16 models selected
> select add #2.49
17 models selected
Ungrouped to 40 regions
> select #2.74
1 model selected
> select add #2.70
2 models selected
> select add #2.188
3 models selected
> select add #2.88
4 models selected
> select add #2.90
5 models selected
> select add #2.85
6 models selected
> select add #2.170
7 models selected
> select add #2.184
8 models selected
> select add #2.80
9 models selected
> select add #2.190
10 models selected
> select add #2.177
11 models selected
> select add #2.174
12 models selected
> select add #2.183
13 models selected
> select add #2.76
14 models selected
Grouped 14 regions
> select #2.97
1 model selected
> select add #2.180
2 models selected
> select add #2.192
3 models selected
> select add #2.179
4 models selected
Ungrouped to 10 regions
> select clear
> select #2.60
1 model selected
> select add #2.57
2 models selected
> select add #2.47
3 models selected
> select add #2.45
4 models selected
> select add #2.43
5 models selected
Grouped 5 regions
> select clear
> select #2.43
1 model selected
> select #2.84
1 model selected
> select add #2.178
2 models selected
> select add #2.99
3 models selected
> select add #2.96
4 models selected
> select add #2.98
5 models selected
> select add #2.191
6 models selected
> select add #2.78
7 models selected
> select add #2.181
8 models selected
> select add #2.75
9 models selected
> select add #2.48
10 models selected
> select add #2.52
11 models selected
> select add #2.93
12 models selected
> select add #2.73
13 models selected
> select add #2.50
14 models selected
> select add #2.83
15 models selected
> select add #2.66
16 models selected
> select add #2.91
17 models selected
Ungrouped to 35 regions
> select #2.76
1 model selected
> select add #2.121
2 models selected
> select add #2.174
3 models selected
> select add #2.110
4 models selected
> select add #2.88
5 models selected
> select add #2.195
6 models selected
> select add #2.45
7 models selected
> select add #2.60
8 models selected
> select add #2.97
9 models selected
> select add #2.196
10 models selected
> select add #2.193
11 models selected
> select add #2.170
12 models selected
> select add #2.74
13 models selected
> select add #2.198
14 models selected
> select add #2.183
15 models selected
> select add #2.188
16 models selected
> select add #2.180
17 models selected
Grouped 17 regions
> select clear
> select #2.45
1 model selected
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #32, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/FliL.mrc models #32
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #33, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
> hide #!32 models
> hide #!33 models
Segmenting
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.010668
Showing 171 region surfaces
1880 watershed regions, grouped to 171 regions
Showing
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 171 regions, 171 surfaces
> show #!32 models
> show #!29 models
> show #!27 models
> show #!25 models
> hide #!25 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!25 models
> hide #!25 models
> hide #!27 models
> hide #!29 models
> hide #!32 models
> select #2.152
1 model selected
> select add #2.138
2 models selected
> select add #2.154
3 models selected
> select add #2.139
4 models selected
> select add #2.149
5 models selected
> select add #2.147
6 models selected
> select add #2.50
7 models selected
> select add #2.97
8 models selected
> select add #2.105
9 models selected
> select add #2.141
10 models selected
> select add #2.146
11 models selected
> select add #2.153
12 models selected
> select add #2.142
13 models selected
Ungrouped to 26 regions
Ungrouped to 15 regions
Ungrouped to 2 regions
Ungrouped to 0 regions
> select #2.194
1 model selected
> select add #2.141
2 models selected
> select add #2.180
3 models selected
> select add #2.152
4 models selected
> select add #2.97
5 models selected
> select add #2.154
6 models selected
> select add #2.198
7 models selected
> select add #2.146
8 models selected
> select add #2.138
9 models selected
> select add #2.174
10 models selected
> select add #2.182
11 models selected
> select add #2.192
12 models selected
> select add #2.197
13 models selected
> select add #2.177
14 models selected
> select add #2.191
15 models selected
> select add #2.178
16 models selected
> select add #2.185
17 models selected
> select add #2.85
18 models selected
> select add #2.71
19 models selected
> select add #2.77
20 models selected
> select add #2.81
21 models selected
> select add #2.75
22 models selected
> select add #2.74
23 models selected
> select add #2.69
24 models selected
> select add #2.67
25 models selected
> select add #2.80
26 models selected
> select add #2.73
27 models selected
> select add #2.76
28 models selected
> select add #2.66
29 models selected
> select add #2.78
30 models selected
> select add #2.79
31 models selected
> select add #2.68
32 models selected
> select add #2.70
33 models selected
> select add #2.83
34 models selected
Grouped 34 regions
> select add #2.143
2 models selected
> select add #2.158
3 models selected
> select add #2.119
4 models selected
> select add #2.148
5 models selected
> select add #2.144
6 models selected
> select add #2.101
7 models selected
> select add #2.160
8 models selected
> select add #2.161
9 models selected
> select add #2.168
10 models selected
> select add #2.140
11 models selected
> select add #2.145
12 models selected
> select add #2.157
13 models selected
> select add #2.136
14 models selected
> select add #2.135
15 models selected
> select add #2.162
16 models selected
> select add #2.150
17 models selected
> select add #2.151
18 models selected
> select add #2.176
19 models selected
> select add #2.190
20 models selected
> select add #2.179
21 models selected
> select add #2.184
22 models selected
> select add #2.195
23 models selected
> select add #2.139
24 models selected
> select add #2.172
25 models selected
> select add #2.149
26 models selected
> select add #2.50
27 models selected
> select add #2.153
28 models selected
> select add #2.199
29 models selected
> select add #2.142
30 models selected
> select add #2.173
31 models selected
> select add #2.175
32 models selected
> select add #2.183
33 models selected
> select add #2.193
34 models selected
> select add #2.196
35 models selected
> select subtract #2.176
34 models selected
> select subtract #2.190
33 models selected
> select add #2.190
34 models selected
> select subtract #2.190
33 models selected
> select add #2.176
34 models selected
> select add #2.190
35 models selected
> select add #2.167
36 models selected
> select add #2.156
37 models selected
> select add #2.165
38 models selected
> select add #2.163
39 models selected
> select add #2.170
40 models selected
> select add #2.155
41 models selected
> select add #2.108
42 models selected
> select add #2.1
43 models selected
> select add #2.117
44 models selected
> select add #2.164
45 models selected
> select add #2.169
46 models selected
> select add #2.159
47 models selected
> select add #2.129
48 models selected
> select add #2.166
49 models selected
> select clear
> select #2.1
1 model selected
Ungrouped to 12 regions
Ungrouped to 39 regions
Ungrouped to 41 regions
> select #2.232
1 model selected
> select add #2.215
2 models selected
> select add #2.233
3 models selected
> select add #2.185
4 models selected
> select add #2.70
5 models selected
> select add #2.219
6 models selected
> select add #2.78
7 models selected
> select add #2.211
8 models selected
> select #2.228
1 model selected
> select add #2.231
2 models selected
> select add #2.230
3 models selected
> select add #2.229
4 models selected
> select add #2.73
5 models selected
> select add #2.75
6 models selected
> select add #2.237
7 models selected
> select add #2.235
8 models selected
> select add #2.223
9 models selected
> select add #2.224
10 models selected
> select add #2.138
11 models selected
> select add #2.226
12 models selected
> select add #2.239
13 models selected
> select add #2.240
14 models selected
> select add #2.212
15 models selected
> select add #2.79
16 models selected
> select add #2.220
17 models selected
> select add #2.71
18 models selected
> select add #2.178
19 models selected
> select add #2.182
20 models selected
> select add #2.213
21 models selected
> select add #2.214
22 models selected
> select add #2.154
23 models selected
> select add #2.174
24 models selected
> select add #2.177
25 models selected
> select add #2.77
26 models selected
> select add #2.76
27 models selected
> select add #2.238
28 models selected
> select add #2.236
29 models selected
> select add #2.225
30 models selected
> select add #2.227
31 models selected
> select add #2.69
32 models selected
> select add #2.216
33 models selected
> select add #2.234
34 models selected
> select clear
> select add #2.74
1 model selected
> select add #2.147
2 models selected
> select add #2.68
3 models selected
> select add #2.204
4 models selected
> select add #2.194
5 models selected
> select add #2.218
6 models selected
> select add #2.80
7 models selected
> select add #2.202
8 models selected
> select add #2.198
9 models selected
> select add #2.187
10 models selected
> select add #2.189
11 models selected
> select add #2.188
12 models selected
> select add #2.85
13 models selected
> select add #2.97
14 models selected
> select add #2.222
15 models selected
> select add #2.209
16 models selected
> select add #2.210
17 models selected
> select #2.161
1 model selected
> select add #2.168
2 models selected
> select add #2.140
3 models selected
> select add #2.117
4 models selected
> select add #2.164
5 models selected
> select add #2.221
6 models selected
> select add #2.160
7 models selected
> select add #2.101
8 models selected
> select add #2.159
9 models selected
> select add #2.129
10 models selected
> select add #2.144
11 models selected
> select add #2.166
12 models selected
> select add #2.119
13 models selected
> select add #2.148
14 models selected
> select add #2.167
15 models selected
> select add #2.156
16 models selected
> select add #2.158
17 models selected
> select add #2.143
18 models selected
> select add #2.165
19 models selected
> select add #2.151
20 models selected
> select add #2.1
21 models selected
> select add #2.163
22 models selected
> select add #2.155
23 models selected
> select add #2.217
24 models selected
> select subtract #2.151
23 models selected
> select add #2.150
24 models selected
> select add #2.151
25 models selected
> select add #2.162
26 models selected
> select add #2.135
27 models selected
> select add #2.108
28 models selected
> select add #2.67
29 models selected
> select add #2.136
30 models selected
> select add #2.157
31 models selected
> select add #2.145
32 models selected
> select add #2.199
33 models selected
> select add #2.153
34 models selected
> select add #2.50
35 models selected
> select add #2.149
36 models selected
> select add #2.172
37 models selected
> select add #2.139
38 models selected
> select add #2.195
39 models selected
> select add #2.184
40 models selected
> select add #2.179
41 models selected
> select add #2.190
42 models selected
> select add #2.176
43 models selected
> select add #2.196
44 models selected
> select add #2.193
45 models selected
> select add #2.183
46 models selected
> select add #2.175
47 models selected
Grouped 47 regions
> select add #2.173
2 models selected
> select add #2.142
3 models selected
Grouped 3 regions
> select clear
> select #2.169
1 model selected
> select add #2.170
2 models selected
> select add #2.1
3 models selected
Grouped 3 regions
Showing 172 region surfaces
> select clear
> select #2.1
1 model selected
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #34, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/MS-ring.mrc models #34
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #35, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
Segmenting
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.010668
Showing 141 region surfaces
1780 watershed regions, grouped to 141 regions
Showing
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 141 regions, 141 surfaces
> hide #!34 models
> hide #!35 models
> show #!34 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> close #34-35
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Segmenting
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.010668
Showing 171 region surfaces
1880 watershed regions, grouped to 171 regions
Showing
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 171 regions, 171 surfaces
> select #2.139
1 model selected
> select add #2.154
2 models selected
> select add #2.138
3 models selected
> select add #2.152
4 models selected
> select add #2.142
5 models selected
> select add #2.153
6 models selected
> select add #2.146
7 models selected
> select add #2.141
8 models selected
> select add #2.105
9 models selected
> select add #2.97
10 models selected
> select add #2.50
11 models selected
> select add #2.147
12 models selected
> select add #2.149
13 models selected
Ungrouped to 26 regions
Ungrouped to 15 regions
Ungrouped to 2 regions
Ungrouped to 0 regions
Ungrouped to 160 regions
> select #2.180
1 model selected
> select add #2.194
2 models selected
> select add #2.176
3 models selected
> select add #2.192
4 models selected
> select add #2.174
5 models selected
> select add #2.182
6 models selected
> select add #2.190
7 models selected
> select add #2.184
8 models selected
> select add #2.188
9 models selected
> select add #2.178
10 models selected
> select add #2.50
11 models selected
> select add #2.139
12 models selected
> select add #2.105
13 models selected
> select add #2.153
14 models selected
> select add #2.142
15 models selected
> select add #2.172
16 models selected
> select add #2.198
17 models selected
Grouped 17 regions
> select add #2.149
2 models selected
Grouped 2 regions
> select add #2.181
2 models selected
> select add #2.199
3 models selected
> select add #2.173
4 models selected
> select add #2.147
5 models selected
> select add #2.154
6 models selected
> select add #2.138
7 models selected
> select add #2.141
8 models selected
> select add #2.97
9 models selected
> select add #2.152
10 models selected
> select subtract #2.152
9 models selected
> select add #2.185
10 models selected
> select add #2.189
11 models selected
> select add #2.191
12 models selected
> select add #2.183
13 models selected
> select add #2.175
14 models selected
> select add #2.193
15 models selected
> select add #2.177
16 models selected
> select add #2.195
17 models selected
> select add #2.85
18 models selected
> select add #2.71
19 models selected
> select add #2.297
20 models selected
> select add #2.353
21 models selected
> select add #2.75
22 models selected
> select add #2.74
23 models selected
> select add #2.69
24 models selected
> select add #2.67
25 models selected
> select add #2.80
26 models selected
> select add #2.280
27 models selected
> select add #2.76
28 models selected
> select add #2.287
29 models selected
> select add #2.341
30 models selected
> select add #2.79
31 models selected
> select add #2.68
32 models selected
> select add #2.70
33 models selected
> select add #2.299
34 models selected
> select add #2.152
35 models selected
> select add #2.136
36 models selected
> select add #2.135
37 models selected
> select add #2.162
38 models selected
> select add #2.150
39 models selected
> select add #2.151
40 models selected
> select add #2.143
41 models selected
> select add #2.158
42 models selected
> select add #2.119
43 models selected
> select add #2.148
44 models selected
> select add #2.144
45 models selected
> select add #2.207
46 models selected
> select add #2.208
47 models selected
> select add #2.160
48 models selected
> select add #2.161
49 models selected
> select add #2.168
50 models selected
> select add #2.140
51 models selected
> select add #2.157
52 models selected
> select add #2.145
53 models selected
> select add #2.167
54 models selected
> select add #2.166
55 models selected
> select add #2.230
56 models selected
> select add #2.229
57 models selected
> select add #2.159
58 models selected
> select add #2.169
59 models selected
> select add #2.164
60 models selected
> select add #2.228
61 models selected
> select add #2.227
62 models selected
> select add #2.108
63 models selected
> select add #2.155
64 models selected
> select add #2.170
65 models selected
> select add #2.163
66 models selected
> select add #2.165
67 models selected
> select add #2.156
68 models selected
> select add #2.301
69 models selected
> select add #2.311
70 models selected
> select add #2.308
71 models selected
> select add #2.303
72 models selected
> select #2.308
1 model selected
Ungrouped to 4 regions
Ungrouped to 5 regions
> select clear
> select #2.3
1 model selected
> select add #2.9
2 models selected
> select add #2.10
3 models selected
> select add #2.6
4 models selected
> select add #2.8
5 models selected
> select add #2.2
6 models selected
> select #2.311
1 model selected
> select add #2.301
2 models selected
Ungrouped to 5 regions
Ungrouped to 4 regions
Ungrouped to 0 regions
> select #2.4
1 model selected
> select add #2.14
2 models selected
> select add #2.12
3 models selected
> select add #2.17
4 models selected
> select add #2.18
5 models selected
> select clear
> select #2.303
1 model selected
Ungrouped to 3 regions
> select clear
> select #2.20
1 model selected
Ungrouped to 2 regions
> select clear
> select #2.22
1 model selected
> select add #2.11
2 models selected
> select add #2.13
3 models selected
> select clear
> select #2.163
1 model selected
> select subtract #2.163
Nothing selected
> select #2.156
1 model selected
> select add #2.165
2 models selected
> select add #2.163
3 models selected
> select add #2.170
4 models selected
> select add #2.155
5 models selected
> select add #2.108
6 models selected
> select add #2.227
7 models selected
> select add #2.228
8 models selected
> select add #2.164
9 models selected
> select add #2.169
10 models selected
> select add #2.159
11 models selected
> select add #2.229
12 models selected
> select add #2.230
13 models selected
> select add #2.166
14 models selected
> select add #2.167
15 models selected
Grouped 15 regions
> select add #2.16
2 models selected
> select add #2.5
3 models selected
> select add #2.158
4 models selected
> select add #2.119
5 models selected
> select add #2.23
6 models selected
> select add #2.7
7 models selected
> select add #2.143
8 models selected
> select add #2.151
9 models selected
> select add #2.150
10 models selected
> select add #2.162
11 models selected
> select add #2.135
12 models selected
> select subtract #2.135
11 models selected
> select add #2.135
12 models selected
> select add #2.136
13 models selected
> select add #2.157
14 models selected
> select add #2.145
15 models selected
> select subtract #2.145
14 models selected
> select add #2.145
15 models selected
> select add #2.140
16 models selected
> select add #2.168
17 models selected
> select add #2.161
18 models selected
> select add #2.160
19 models selected
> select add #2.208
20 models selected
> select add #2.207
21 models selected
> select add #2.144
22 models selected
> select add #2.148
23 models selected
> select add #2.1
24 models selected
Grouped 24 regions
> select clear
> select #2.1
1 model selected
> select clear
[Repeated 1 time(s)]
> select #2.1
1 model selected
Showing 264 region surfaces
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #34, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/MS-ring.mrc models #34
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #35, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
Segmenting
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.010668
Showing 140 region surfaces
1779 watershed regions, grouped to 140 regions
Showing
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 140 regions, 140 surfaces
> hide #!34 models
> hide #!35 models
> select #2.72
1 model selected
> select add #2.76
2 models selected
> select add #2.65
3 models selected
> select add #2.77
4 models selected
> select add #2.78
5 models selected
> select add #2.67
6 models selected
> select add #2.69
7 models selected
> select add #2.82
8 models selected
> select add #2.84
9 models selected
> select add #2.70
10 models selected
> select add #2.75
11 models selected
> select add #2.80
12 models selected
> select add #2.74
13 models selected
> select add #2.73
14 models selected
> select add #2.68
15 models selected
> select add #2.66
16 models selected
> select add #2.79
17 models selected
Ungrouped to 43 regions
Ungrouped to 36 regions
Ungrouped to 14 regions
Ungrouped to 0 regions
> select #2.79
1 model selected
> select add #2.152
2 models selected
> select #2.183
1 model selected
> select #2.70
1 model selected
> select add #2.183
2 models selected
Grouped 2 regions
Ungrouped to 2 regions
Ungrouped to 0 regions
> select #2.146
1 model selected
> select add #2.158
2 models selected
> select add #2.143
3 models selected
> select add #2.84
4 models selected
Ungrouped to 0 regions
> select #2.79
1 model selected
> select add #2.178
2 models selected
> select add #2.68
3 models selected
> select add #2.190
4 models selected
> select add #2.146
5 models selected
> select add #2.158
6 models selected
> select add #2.143
7 models selected
> select add #2.84
8 models selected
> select add #2.77
9 models selected
> select add #2.78
10 models selected
> select add #2.200
11 models selected
> select add #2.198
12 models selected
> select add #2.165
13 models selected
> select add #2.160
14 models selected
> select add #2.151
15 models selected
> select add #2.174
16 models selected
> select add #2.187
17 models selected
> select subtract #2.79
16 models selected
> select add #2.79
17 models selected
Ungrouped to 0 regions
> select #2.79
1 model selected
> select add #2.187
2 models selected
> select add #2.174
3 models selected
> select add #2.151
4 models selected
> select add #2.160
5 models selected
> select add #2.165
6 models selected
> select add #2.198
7 models selected
> select add #2.200
8 models selected
> select add #2.78
9 models selected
> select add #2.77
10 models selected
> select add #2.84
11 models selected
> select add #2.143
12 models selected
> select add #2.158
13 models selected
> select add #2.146
14 models selected
> select add #2.190
15 models selected
> select add #2.68
16 models selected
> select add #2.178
17 models selected
Grouped 17 regions
> select add #2.113
2 models selected
> select add #2.116
3 models selected
> select add #2.105
4 models selected
> select add #2.115
5 models selected
> select add #2.138
6 models selected
> select add #2.135
7 models selected
> select add #2.136
8 models selected
> select add #2.134
9 models selected
> select add #2.139
10 models selected
> select add #2.133
11 models selected
> select add #2.137
12 models selected
> select add #2.117
13 models selected
Grouped 13 regions
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #36, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/E-ring.mrc models #36
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #37, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
Segmenting
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.010668
Showing 128 region surfaces
1745 watershed regions, grouped to 128 regions
Showing
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 128 regions, 128 surfaces
> hide #!36 models
> hide #!37 models
> show #!32 models
> show #!25 models
> hide #!25 models
> select #2.73
1 model selected
> select add #2.47
2 models selected
Ungrouped to 5 regions
Ungrouped to 6 regions
Ungrouped to 0 regions
> select #2.133
1 model selected
> select add #2.73
2 models selected
Grouped 2 regions
> show #!24 models
> hide #!24 models
> show #!25 models
> select #2.61
1 model selected
> select #2.124
1 model selected
> select #2.47
1 model selected
Ungrouped to 0 regions
> select #2.73
1 model selected
> select add #2.47
2 models selected
> select add #2.124
3 models selected
> select add #2.135
4 models selected
> select add #2.129
5 models selected
> select add #2.96
6 models selected
> select add #2.134
7 models selected
> select #2.39
1 model selected
Ungrouped to 3 regions
Ungrouped to 5 regions
Ungrouped to 8 regions
Ungrouped to 5 regions
> select #2.140
1 model selected
Showing 147 region surfaces
> select add #2.47
2 models selected
> select add #2.73
3 models selected
> select add #2.124
4 models selected
> select add #2.135
5 models selected
> select add #2.129
6 models selected
> select add #2.134
7 models selected
> select add #2.96
8 models selected
> hide #!25 models
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #38, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/1unit_PflAB_FliL.mrc models #38
> select clear
> select #2.73
1 model selected
> select add #2.140
2 models selected
> select add #2.47
3 models selected
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #39, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/FliL_out.mrc models #39
> select #2.47
1 model selected
> select add #2.124
2 models selected
> select add #2.135
3 models selected
> select add #2.134
4 models selected
> select add #2.61
5 models selected
> select subtract #2.61
4 models selected
> select add #2.61
5 models selected
> select subtract #2.61
4 models selected
> select clear
> select #2.61
1 model selected
> select clear
> select #2.124
1 model selected
> select add #2.47
2 models selected
> select add #2.135
3 models selected
> select add #2.129
4 models selected
> select add #2.73
5 models selected
> select add #2.96
6 models selected
> select add #2.134
7 models selected
> select add #2.61
8 models selected
> select clear
> select #2.61
1 model selected
Ungrouped to 2 regions
> select #2.134
1 model selected
> select add #2.124
2 models selected
> select add #2.135
3 models selected
> select add #2.47
4 models selected
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #40, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/1unit_rim.mrc models #40
> select #2.129
1 model selected
> select add #2.96
2 models selected
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #41, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/1unit_PflA.mrc models #41
> select clear
> select #2.73
1 model selected
> select add #2.120
2 models selected
> select add #2.47
3 models selected
> select add #2.129
4 models selected
> select add #2.135
5 models selected
> select add #2.96
6 models selected
> select add #2.134
7 models selected
> select add #2.124
8 models selected
> select add #2.92
9 models selected
> select add #2.105
10 models selected
> select add #2.115
11 models selected
> select add #2.62
12 models selected
> select add #2.99
13 models selected
> select add #2.86
14 models selected
> select add #2.79
15 models selected
> select add #2.88
16 models selected
> select add #2.87
17 models selected
> select add #2.78
18 models selected
> select add #2.103
19 models selected
> select add #2.126
20 models selected
> select add #2.60
21 models selected
> select add #2.114
22 models selected
> select add #2.49
23 models selected
> select add #2.89
24 models selected
> select add #2.85
25 models selected
> select add #2.127
26 models selected
> select add #2.95
27 models selected
> select add #2.116
28 models selected
> select add #2.91
29 models selected
> select add #2.94
30 models selected
> select add #2.56
31 models selected
> select add #2.104
32 models selected
> select add #2.121
33 models selected
> select add #2.122
34 models selected
> select add #2.52
35 models selected
> select add #2.101
36 models selected
> select add #2.113
37 models selected
> select add #2.54
38 models selected
> select add #2.97
39 models selected
> select add #2.117
40 models selected
> select add #2.53
41 models selected
> select add #2.108
42 models selected
> select add #2.118
43 models selected
> select add #2.45
44 models selected
> select add #2.106
45 models selected
> select add #2.123
46 models selected
> select add #2.44
47 models selected
> select add #2.98
48 models selected
> select add #2.119
49 models selected
> select add #2.51
50 models selected
> select add #2.90
51 models selected
> select add #2.125
52 models selected
> select add #2.48
53 models selected
> select add #2.102
54 models selected
> hide #!32 models
> hide #!38 models
> hide #!39 models
> hide #!40 models
> select add #2.93
55 models selected
Grouped 55 regions
> select #2.141
1 model selected
Grouped 1 regions
Showing 94 region surfaces
> select subtract #2.45
Nothing selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #2.45
1 model selected
> select add #2.44
2 models selected
Grouped 2 regions
> select #2.44
1 model selected
> select #2.58
1 model selected
Ungrouped to 3 regions
> select #2.47
1 model selected
> select add #2.45
2 models selected
> select add #2.44
3 models selected
Grouped 3 regions
> select #2.43
1 model selected
Ungrouped to 3 regions
> select #2.47
1 model selected
> select add #2.44
2 models selected
Grouped 2 regions
> select #2.66
1 model selected
Ungrouped to 3 regions
> select #2.44
1 model selected
> select add #2.47
2 models selected
> select add #2.43
3 models selected
Grouped 3 regions
> select #2.67
1 model selected
Ungrouped to 3 regions
> select #2.44
1 model selected
> select add #2.43
2 models selected
Grouped 2 regions
> select add #2.59
2 models selected
> select #2.59
1 model selected
Ungrouped to 3 regions
> select #2.53
1 model selected
> select add #2.44
2 models selected
> select add #2.43
3 models selected
Grouped 3 regions
> select #2.64
1 model selected
> select add #2.46
2 models selected
Ungrouped to 7 regions
> select #2.61
1 model selected
> select add #2.53
2 models selected
> select add #2.58
3 models selected
> select add #2.43
4 models selected
Grouped 4 regions
> select #2.55
1 model selected
Ungrouped to 3 regions
> select #2.53
1 model selected
> select add #2.46
2 models selected
> select add #2.43
3 models selected
Grouped 3 regions
> select #2.57
1 model selected
Ungrouped to 3 regions
Ungrouped to 2 regions
> select #2.53
1 model selected
> select add #2.46
2 models selected
> select add #2.43
3 models selected
Grouped 3 regions
> select #2.63
1 model selected
Ungrouped to 3 regions
Ungrouped to 0 regions
> select #2.55
1 model selected
> select add #2.43
2 models selected
Grouped 2 regions
> select #2.69
1 model selected
Ungrouped to 2 regions
> select #2.62
1 model selected
> select add #2.43
2 models selected
Grouped 2 regions
> select #2.68
1 model selected
Ungrouped to 2 regions
> select #2.63
1 model selected
> select add #2.43
2 models selected
Grouped 2 regions
> select #2.50
1 model selected
Ungrouped to 3 regions
Ungrouped to 2 regions
> select #2.66
1 model selected
> select add #2.63
2 models selected
> select add #2.43
3 models selected
Grouped 3 regions
> select #2.72
1 model selected
Ungrouped to 2 regions
[Repeated 1 time(s)]
> select #2.64
1 model selected
> select add #2.43
2 models selected
Grouped 2 regions
> select add #2.30
2 models selected
> select #2.43
1 model selected
> select #2.65
1 model selected
Ungrouped to 3 regions
Ungrouped to 2 regions
> select #2.69
1 model selected
> select add #2.63
2 models selected
> select add #2.43
3 models selected
Grouped 3 regions
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #42, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/C17_proximal-disk.mrc models #42
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #43, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
Segmenting
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked,
density threshold 0.010668
Showing 76 region surfaces
1581 watershed regions, grouped to 76 regions
Showing
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked.seg
- 76 regions, 76 surfaces
> hide #!41 models
> hide #!42 models
> hide #!43 models
> select #2.28
1 model selected
> select add #2.26
2 models selected
> select add #2.35
3 models selected
> select add #2.32
4 models selected
> select add #2.36
5 models selected
> select add #2.37
6 models selected
> select add #2.19
7 models selected
> select add #2.38
8 models selected
> select subtract #2.19
7 models selected
> select subtract #2.38
6 models selected
> select add #2.19
7 models selected
> select add #2.29
8 models selected
> select add #2.40
9 models selected
Grouped 9 regions
> select add #2.38
2 models selected
> select add #2.42
3 models selected
> select add #2.31
4 models selected
> select add #2.27
5 models selected
> select add #2.41
6 models selected
> select add #2.30
7 models selected
> select add #2.39
8 models selected
> select add #2.34
9 models selected
Grouped 9 regions
Drag select of 2173, 1966, 6813 of 7104 triangles, 1965, 1976, 1947, 6356 of
6868 triangles, 1924, 1938, 3854 of 6956 triangles, 2065, 3596 of 6388
triangles, 1837, 5873 of 6204 triangles, 1672, 2076, 6011 of 6220 triangles,
2098, 4727 of 5832 triangles, 1610, 3955 of 5396 triangles, 1831, 5195 of 5548
triangles, 2052, 5648 of 5704 triangles, 1933, 5575 of 5660 triangles, 1985,
1687, 5481 of 5484 triangles
Grouped 19 regions
> select add #2.61
2 models selected
> select add #2.65
3 models selected
> select add #2.46
4 models selected
> select add #2.70
5 models selected
> select add #2.68
6 models selected
> select add #2.51
7 models selected
> select add #2.64
8 models selected
> select add #2.43
9 models selected
> select add #2.67
10 models selected
> select add #2.60
11 models selected
> select add #2.66
12 models selected
> select add #2.56
13 models selected
> select add #2.59
14 models selected
> select add #2.58
15 models selected
> select add #2.62
16 models selected
> select add #2.63
17 models selected
Grouped 17 regions
> select #2.17
1 model selected
> select add #2.20
2 models selected
> select add #2.14
3 models selected
> select add #2.33
4 models selected
> select add #2.15
5 models selected
> select add #2.24
6 models selected
> select add #2.5
7 models selected
> select add #2.12
8 models selected
> select add #2.22
9 models selected
> select add #2.6
10 models selected
> select add #2.16
11 models selected
> select add #2.21
12 models selected
> select add #2.10
13 models selected
> select add #2.8
14 models selected
> select add #2.4
15 models selected
> select add #2.9
16 models selected
> select add #2.3
17 models selected
> select add #2.2
18 models selected
> select add #2.18
19 models selected
> select add #2.11
20 models selected
> select add #2.25
21 models selected
> select add #2.13
22 models selected
> select add #2.23
23 models selected
> select add #2.7
24 models selected
> select subtract #2.7
23 models selected
> select add #2.7
24 models selected
Ungrouped to 79 regions
> select subtract #2.19
78 models selected
> select subtract #2.87
77 models selected
> select subtract #2.54
76 models selected
> select subtract #2.45
75 models selected
> select subtract #2.28
74 models selected
> select add #2.28
75 models selected
> select subtract #2.104
74 models selected
> select subtract #2.81
73 models selected
> select subtract #2.95
72 models selected
> select subtract #2.47
71 models selected
Ungrouped to 268 regions
Ungrouped to 643 regions
Ungrouped to 499 regions
Ungrouped to 0 regions
Ungrouped to 4 regions
Ungrouped to 36 regions
Drag select of 10, 40, 134, 112 of 236 triangles, 19, 13, 119, 94 of 168
triangles, 97, 205 of 716 triangles, 1, 27, 88, 390 of 696 triangles, 107, 116
of 392 triangles, 20, 1064 of 1684 triangles, 145, 38 of 604 triangles, 141,
119 of 1296 triangles, 38, 192 of 468 triangles, 25, 156 of 160 triangles, 80,
354 of 440 triangles, 17, 50, 116 of 600 triangles, 51, 15 of 1608 triangles,
64, 478 of 664 triangles, 142, 125 of 228 triangles, 46, 379 of 452 triangles,
21, 47, 583 of 1332 triangles, 81, 374 of 420 triangles, 122, 226 of 668
triangles, 26, 1010 of 1480 triangles, 140, 75 of 364 triangles, 174, 13 of
316 triangles, 68, 178 of 180 triangles, 7, 8, 36, 615 of 1248 triangles, 37,
494 of 592 triangles, 120, 205 of 4436 triangles, 84, 14, 60, 42 of 428
triangles, 91, 89 of 276 triangles, 3, 5, 41, 679 of 864 triangles, 15, 9, 31,
65 of 516 triangles, 100, 537 of 1176 triangles, 63, 841 of 868 triangles, 24,
65, 898 of 1640 triangles, 61, 123, 199 of 244 triangles, 110, 8 of 80
triangles, 39, 448 of 1524 triangles, 170, 78 of 724 triangles, 86, 429 of 500
triangles, 101, 321 of 664 triangles, 143, 87 of 96 triangles, 106, 200 of 636
triangles, 2, 151 of 552 triangles, 49, 128 of 836 triangles, 109, 37 of 596
triangles, 96, 89 of 420 triangles, 79, 199 of 376 triangles, 18, 127, 28 of
756 triangles, 172, 45 of 400 triangles, 103, 405 of 844 triangles, 137, 25 of
588 triangles, 85, 461 of 492 triangles, 126, 308 of 600 triangles, 166, 15 of
268 triangles
Drag select of 35, 299 of 504 triangles, 12, 77, 132 of 192 triangles, 16,
124, 72 of 696 triangles, 44, 375 of 564 triangles, 125, 10 of 1424 triangles,
271, 46 of 1112 triangles, 214, 210 of 1024 triangles, 153, 315 of 1276
triangles, 30, 18 of 136 triangles, 11, 257 of 588 triangles, 274, 173 of 2996
triangles, 83, 246 of 364 triangles, 98, 137 of 160 triangles, 193, 624 of 904
triangles, 360, 25 of 1840 triangles, 147, 23, 305 of 332 triangles, 32, 79 of
532 triangles, 4, 433 of 596 triangles, 173, 662 of 1272 triangles, 28, 791 of
2164 triangles, 182, 26 of 1932 triangles, 43, 400 of 468 triangles, 131, 140
of 420 triangles, 22, 282 of 976 triangles, 55, 102 of 1208 triangles, 162,
486 of 1088 triangles, 237, 351 of 2300 triangles, 176, 367 of 480 triangles,
201, 402 of 648 triangles, 138, 22 of 56 triangles, 111, 578 of 680 triangles,
191, 631 of 1104 triangles, 240, 363 of 5172 triangles, 161, 141 of 948
triangles, 92, 409 of 448 triangles, 154, 132 of 200 triangles, 62, 691 of
1468 triangles, 42, 429 of 488 triangles, 54, 21 of 344 triangles, 158, 279,
136 of 1276 triangles, 95, 73 of 80 triangles, 74, 575 of 1396 triangles, 242,
471 of 1304 triangles, 33, 56, 287 of 436 triangles, 179, 358 of 660
triangles, 209, 208, 259 of 724 triangles, 149, 297 of 2028 triangles, 116, 45
of 464 triangles, 82, 379 of 380 triangles, 163, 93 of 392 triangles, 121, 259
of 524 triangles, 66, 44 of 1092 triangles, 29, 296 of 724 triangles, 202, 434
of 1632 triangles, 205, 398 of 1648 triangles, 177, 321, 161 of 460 triangles,
318, 276 of 2068 triangles, 278, 214 of 2840 triangles, 244, 441 of 824
triangles, 160, 210 of 680 triangles, 159, 230 of 644 triangles, 34, 208 of
584 triangles, 57, 150 of 1144 triangles, 78, 5 of 216 triangles, 52, 708 of
1080 triangles, 235, 145 of 3672 triangles, 270, 12 of 300 triangles, 99, 304
of 692 triangles, 45, 183 of 404 triangles, 364, 9 of 1588 triangles, 59, 288
of 972 triangles, 58, 466 of 1252 triangles, 212, 254 of 2236 triangles, 150,
221 of 364 triangles, 250, 142 of 624 triangles, 290, 138 of 3772 triangles,
291, 10 of 976 triangles, 322, 62 of 856 triangles, 280, 213 of 3872
triangles, 136, 441 of 2104 triangles, 239, 262 of 1672 triangles, 282, 359 of
1168 triangles, 283, 136 of 3160 triangles, 135, 421 of 1468 triangles, 313,
220 of 840 triangles, 6, 392 of 480 triangles, 315, 15 of 1128 triangles, 241,
135 of 188 triangles, 249, 190 of 416 triangles, 253, 5 of 532 triangles, 216,
13 of 4072 triangles, 139, 242 of 572 triangles, 200, 435 of 708 triangles,
284, 212 of 1680 triangles, 164, 102 of 576 triangles, 189, 360 of 820
triangles, 180, 134 of 1468 triangles, 256, 6 of 1368 triangles, 326, 29 of
1048 triangles, 325, 78 of 4324 triangles, 195, 446 of 728 triangles, 243, 371
of 1716 triangles, 192, 428 of 2648 triangles, 197, 488 of 1564 triangles,
281, 227 of 696 triangles
Drag select of 2195, 694 of 309624 triangles, 76, 52 of 56 triangles, 48, 180
of 496 triangles, 351, 145 of 4372 triangles, 411, 221 of 504 triangles, 190,
197 of 1036 triangles, 72, 25 of 236 triangles, 269, 86 of 952 triangles, 102,
28 of 80 triangles, 219, 493 of 920 triangles, 71, 104 of 1228 triangles, 73,
129 of 732 triangles, 353, 93, 25 of 56 triangles, 502, 91 of 864 triangles,
358, 612 of 3084 triangles, 378, 405 of 2868 triangles, 70, 133 of 1388
triangles, 327, 642 of 7304 triangles, 53, 122 of 184 triangles, 94, 246 of
1024 triangles, 117, 51 of 56 triangles, 157, 10 of 988 triangles, 511, 149 of
3000 triangles, 468, 305 of 496 triangles, 186, 71 of 748 triangles, 133, 180
of 508 triangles, 508, 111 of 2712 triangles, 155, 323 of 380 triangles, 420,
1006 of 3276 triangles, 390, 371 of 2724 triangles, 331, 480, 127 of 644
triangles, 183, 403 of 596 triangles, 221, 258 of 772 triangles, 156, 102 of
612 triangles, 227, 113 of 768 triangles, 224, 78 of 880 triangles, 231, 6 of
148 triangles, 69, 191 of 1220 triangles, 366, 356 of 1076 triangles, 436, 692
of 4728 triangles, 467, 533 of 1448 triangles, 104, 55 of 580 triangles, 296,
493 of 2656 triangles, 447, 41 of 1084 triangles, 341, 23 of 3192 triangles,
165, 232 of 704 triangles, 234, 157 of 596 triangles, 232, 282 of 1584
triangles, 473, 386 of 1084 triangles, 342, 75 of 512 triangles, 333, 512, 93
of 2128 triangles, 328, 408 of 1296 triangles, 506, 38 of 5116 triangles, 226,
66 of 468 triangles, 354, 25 of 6592 triangles, 308, 159 of 3916 triangles,
223, 222 of 1136 triangles, 419, 611 of 4292 triangles, 339, 119 of 304
triangles, 336, 143 of 1552 triangles, 418, 295 of 484 triangles, 75, 66 of 80
triangles, 509, 165 of 2632 triangles, 340, 41 of 1900 triangles, 259, 275 of
664 triangles, 255, 337, 176 of 464 triangles, 87, 4 of 188 triangles, 67, 132
of 1124 triangles, 518, 18 of 228 triangles, 225, 85 of 564 triangles, 267,
406 of 1236 triangles, 236, 265 of 2832 triangles, 384, 210 of 244 triangles,
437, 479 of 1644 triangles, 393, 398 of 3164 triangles, 510, 174 of 2680
triangles, 355, 74 of 420 triangles, 356, 61 of 2328 triangles, 412, 9 of 1496
triangles, 268, 355 of 1268 triangles, 300, 119 of 1184 triangles, 471, 227 of
2528 triangles, 181, 254 of 292 triangles, 218, 418 of 876 triangles, 167, 59
of 1088 triangles, 472, 475 of 1152 triangles, 423, 622 of 2468 triangles,
263, 76 of 2164 triangles, 272, 363 of 1320 triangles, 332, 227 of 4892
triangles
> select subtract #2.1
277 models selected
> select add #2.924
278 models selected
> select add #2.744
279 models selected
> select add #2.490
280 models selected
> select add #2.729
281 models selected
> select add #2.149
282 models selected
> select add #2.732
283 models selected
> select add #2.462
284 models selected
> select add #2.1152
285 models selected
> select add #2.1301
286 models selected
> select add #2.371
287 models selected
> select add #2.370
288 models selected
> select add #2.931
289 models selected
> select add #2.880
290 models selected
> select add #2.663
291 models selected
Grouped 291 regions
Drag select of 1581, 1558, 150 of 380 triangles, 1559, 230 of 308 triangles,
1578, 1575, 1572, 1580, 1570, 1577, 1569, 1571, 1579, 1574, 1568, 1556, 41 of
348 triangles, 1560, 197 of 228 triangles, 1563, 85 of 144 triangles, 1576,
1567, 1562, 155 of 168 triangles, 1573, 1561, 244 of 308 triangles, 1565,
1564, 1566
Grouped 26 regions
> select add #2.83
2 models selected
> select add #2.561
3 models selected
> select add #2.1033
4 models selected
> select add #2.132
5 models selected
> select add #2.259
6 models selected
> select add #2.680
7 models selected
> select add #2.195
8 models selected
> select add #2.305
9 models selected
> select add #2.775
10 models selected
> select add #2.297
11 models selected
Grouped 11 regions
Opened
L0_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked_imasked
as #44, grid size 250,250,250, pixel 4.3, shown at step 1, values float32
> hide #!2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/tmp/IM.mrc models #44
> save /Users/shoichitachiyama/Desktop/tmp/Segmentation.cxs includeMaps true
> close session
> open /Users/shoichitachiyama/Desktop/tmp/C17_proximal-disk.mrc
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
level 0.0101, step 1, values float32
> open /Users/shoichitachiyama/Desktop/tmp/1unit_rim.mrc
Opened 1unit_rim.mrc as #2, grid size 250,250,250, pixel 4.3, shown at level
0.00909, step 1, values float32
> open /Users/shoichitachiyama/Desktop/tmp/Rod.mrc
Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0124,
step 1, values float32
> volume #2 level 0.01227
> volume #1 level 0.01376
> volume #3 level 0.01368
> view orient
> turn z 21.17647 models #2 center #3
> volume copy #2
Opened 1unit_rim.mrc copy as #4, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #2 show
> turn z 21.17647 models #2 center #3
> volume copy #2
Opened 1unit_rim.mrc copy as #5, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #2 show
> turn z 21.17647 models #2 center #3
> volume copy #2
Opened 1unit_rim.mrc copy as #6, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #2 show
> turn z 21.17647 models #2 center #3
> volume copy #2
Opened 1unit_rim.mrc copy as #7, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #2 show
> turn z 21.17647 models #2 center #3
> volume copy #2
Opened 1unit_rim.mrc copy as #8, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #2 show
> turn z 21.17647 models #2 center #3
> volume copy #2
Opened 1unit_rim.mrc copy as #9, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #2 show
> turn z 21.17647 models #2 center #3
> volume copy #2
Opened 1unit_rim.mrc copy as #10, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #2 show
> turn z 21.17647 models #2 center #3
> volume copy #2
Opened 1unit_rim.mrc copy as #11, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #2 show
> turn z 21.17647 models #2 center #3
> volume copy #2
Opened 1unit_rim.mrc copy as #12, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #2 show
> turn z 21.17647 models #2 center #3
> volume copy #2
Opened 1unit_rim.mrc copy as #13, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #2 show
> turn z 21.17647 models #2 center #3
> volume copy #2
Opened 1unit_rim.mrc copy as #14, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #2 show
> turn z 21.17647 models #2 center #3
> volume copy #2
Opened 1unit_rim.mrc copy as #15, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #2 show
> turn z 21.17647 models #2 center #3
> volume copy #2
Opened 1unit_rim.mrc copy as #16, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #2 show
> turn z 21.17647 models #2 center #3
> volume copy #2
Opened 1unit_rim.mrc copy as #17, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #2 show
> turn z 21.17647 models #2 center #3
> volume copy #2
Opened 1unit_rim.mrc copy as #18, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #2 show
> turn z 21.17647 models #2 center #3
> volume copy #2
Opened 1unit_rim.mrc copy as #19, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #2 show
> turn z 21.17647 models #2 center #3
> volume copy #2
Opened 1unit_rim.mrc copy as #20, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #2 show
> hide #!2 models
> hide #!20 models
> close #4-20
> show #!2 models
> volume gaussian #2 sDev 3
Opened 1unit_rim.mrc gaussian as #4, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> volume #4 level 0.008185
> turn z 21.17647 models #4 center #3
> volume copy #4
Opened 1unit_rim.mrc gaussian copy as #5, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #4 show
> turn z 21.17647 models #4 center #3
> volume copy #4
Opened 1unit_rim.mrc gaussian copy as #6, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #4 show
> turn z 21.17647 models #4 center #3
> volume copy #4
Opened 1unit_rim.mrc gaussian copy as #7, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #4 show
> turn z 21.17647 models #4 center #3
> volume copy #4
Opened 1unit_rim.mrc gaussian copy as #8, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #4 show
> turn z 21.17647 models #4 center #3
> volume copy #4
Opened 1unit_rim.mrc gaussian copy as #9, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #4 show
> turn z 21.17647 models #4 center #3
> volume copy #4
Opened 1unit_rim.mrc gaussian copy as #10, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #4 show
> turn z 21.17647 models #4 center #3
> volume copy #4
Opened 1unit_rim.mrc gaussian copy as #11, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #4 show
> turn z 21.17647 models #4 center #3
> volume copy #4
Opened 1unit_rim.mrc gaussian copy as #12, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #4 show
> turn z 21.17647 models #4 center #3
> volume copy #4
Opened 1unit_rim.mrc gaussian copy as #13, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #4 show
> turn z 21.17647 models #4 center #3
> volume copy #4
Opened 1unit_rim.mrc gaussian copy as #14, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #4 show
> turn z 21.17647 models #4 center #3
> volume copy #4
Opened 1unit_rim.mrc gaussian copy as #15, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #4 show
> turn z 21.17647 models #4 center #3
> volume copy #4
Opened 1unit_rim.mrc gaussian copy as #16, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #4 show
> turn z 21.17647 models #4 center #3
> volume copy #4
Opened 1unit_rim.mrc gaussian copy as #17, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #4 show
> turn z 21.17647 models #4 center #3
> volume copy #4
Opened 1unit_rim.mrc gaussian copy as #18, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #4 show
> turn z 21.17647 models #4 center #3
> volume copy #4
Opened 1unit_rim.mrc gaussian copy as #19, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #4 show
> turn z 21.17647 models #4 center #3
> volume copy #4
Opened 1unit_rim.mrc gaussian copy as #20, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #4 show
> hide #!4 models
> open /Users/shoichitachiyama/Desktop/tmp/1unit_PflA.mrc
Opened 1unit_PflA.mrc as #21, grid size 250,250,250, pixel 4.3, shown at level
0.00904, step 1, values float32
> turn z 21.17647 models #21 center #3
> volume copy #21
Opened 1unit_PflA.mrc copy as #22, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #21 show
> turn z 21.17647 models #21 center #3
> volume copy #21
Opened 1unit_PflA.mrc copy as #23, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #21 show
> turn z 21.17647 models #21 center #3
> volume copy #21
Opened 1unit_PflA.mrc copy as #24, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #21 show
> turn z 21.17647 models #21 center #3
> volume copy #21
Opened 1unit_PflA.mrc copy as #25, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #21 show
> turn z 21.17647 models #21 center #3
> volume copy #21
Opened 1unit_PflA.mrc copy as #26, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #21 show
> turn z 21.17647 models #21 center #3
> volume copy #21
Opened 1unit_PflA.mrc copy as #27, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #21 show
> turn z 21.17647 models #21 center #3
> volume copy #21
Opened 1unit_PflA.mrc copy as #28, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #21 show
> turn z 21.17647 models #21 center #3
> volume copy #21
Opened 1unit_PflA.mrc copy as #29, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #21 show
> turn z 21.17647 models #21 center #3
> volume copy #21
Opened 1unit_PflA.mrc copy as #30, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #21 show
> turn z 21.17647 models #21 center #3
> volume copy #21
Opened 1unit_PflA.mrc copy as #31, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #21 show
> turn z 21.17647 models #21 center #3
> volume copy #21
Opened 1unit_PflA.mrc copy as #32, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #21 show
> turn z 21.17647 models #21 center #3
> volume copy #21
Opened 1unit_PflA.mrc copy as #33, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #21 show
> turn z 21.17647 models #21 center #3
> volume copy #21
Opened 1unit_PflA.mrc copy as #34, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #21 show
> turn z 21.17647 models #21 center #3
> volume copy #21
Opened 1unit_PflA.mrc copy as #35, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #21 show
> turn z 21.17647 models #21 center #3
> volume copy #21
Opened 1unit_PflA.mrc copy as #36, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #21 show
> turn z 21.17647 models #21 center #3
> volume copy #21
Opened 1unit_PflA.mrc copy as #37, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #21 show
> turn z 21.17647 models #21 center #3
> volume copy #21
Opened 1unit_PflA.mrc copy as #38, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #21 show
> hide #!21 models
> open /Users/shoichitachiyama/Desktop/tmp/FliL_out.mrc
Opened FliL_out.mrc as #39, grid size 250,250,250, pixel 4.3, shown at level
0.00908, step 1, values float32
> hide #!38 models
> hide #!37 models
> hide #!36 models
> hide #!35 models
> hide #!34 models
> hide #!33 models
> hide #!31 models
> hide #!32 models
> hide #!30 models
> hide #!29 models
> hide #!27 models
> hide #!28 models
> hide #!26 models
> hide #!25 models
> hide #!24 models
> hide #!23 models
> hide #!22 models
> hide #!20 models
> hide #!18 models
> hide #!19 models
> hide #!17 models
> hide #!16 models
> hide #!15 models
> hide #!14 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume gaussian #39 sDev 2
Opened FliL_out.mrc gaussian as #40, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> turn z 21.17647 models #40 center #3
> volume copy #40
Opened FliL_out.mrc gaussian copy as #41, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #40 show
> turn z 21.17647 models #40 center #3
> volume copy #40
Opened FliL_out.mrc gaussian copy as #42, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #40 show
> turn z 21.17647 models #40 center #3
> volume copy #40
Opened FliL_out.mrc gaussian copy as #43, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #40 show
> turn z 21.17647 models #40 center #3
> volume copy #40
Opened FliL_out.mrc gaussian copy as #44, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #40 show
> turn z 21.17647 models #40 center #3
> volume copy #40
Opened FliL_out.mrc gaussian copy as #45, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #40 show
> turn z 21.17647 models #40 center #3
> volume copy #40
Opened FliL_out.mrc gaussian copy as #46, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #40 show
> turn z 21.17647 models #40 center #3
> volume copy #40
Opened FliL_out.mrc gaussian copy as #47, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #40 show
> turn z 21.17647 models #40 center #3
> volume copy #40
Opened FliL_out.mrc gaussian copy as #48, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #40 show
> turn z 21.17647 models #40 center #3
> volume copy #40
Opened FliL_out.mrc gaussian copy as #49, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #40 show
> turn z 21.17647 models #40 center #3
> volume copy #40
Opened FliL_out.mrc gaussian copy as #50, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #40 show
> turn z 21.17647 models #40 center #3
> volume copy #40
Opened FliL_out.mrc gaussian copy as #51, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #40 show
> turn z 21.17647 models #40 center #3
> volume copy #40
Opened FliL_out.mrc gaussian copy as #52, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #40 show
> turn z 21.17647 models #40 center #3
> volume copy #40
Opened FliL_out.mrc gaussian copy as #53, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #40 show
> turn z 21.17647 models #40 center #3
> volume copy #40
Opened FliL_out.mrc gaussian copy as #54, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #40 show
> turn z 21.17647 models #40 center #3
> volume copy #40
Opened FliL_out.mrc gaussian copy as #55, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #40 show
> turn z 21.17647 models #40 center #3
> volume copy #40
Opened FliL_out.mrc gaussian copy as #56, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #40 show
> turn z 21.17647 models #40 center #3
> volume copy #40
Opened FliL_out.mrc gaussian copy as #57, grid size 250,250,250, pixel 4.3,
shown at step 1, values float32
> volume #40 show
> open /Users/shoichitachiyama/Desktop/tmp/FliL.mrc
Opened FliL.mrc as #58, grid size 250,250,250, pixel 4.3, shown at level
0.00921, step 1, values float32
> close #40-58
> hide #!1 models
> show #!39 models
> ui tool show "Map Eraser"
Can only have one displayed volume when erasing
[Repeated 1 time(s)]
> hide #!3 models
> volume erase #39 center 850.21,719.14,614.23 radius 179.9
Opened FliL_out.mrc copy as #41, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> close #40
> show #!3 models
> close #39
> view orient
> turn z 21.17647 models #41 center #3
> volume copy #41
Opened FliL_out.mrc copy as #39, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #41 show
> turn z 21.17647 models #41 center #3
> volume copy #41
Opened FliL_out.mrc copy as #40, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #41 show
> turn z 21.17647 models #41 center #3
> volume copy #41
Opened FliL_out.mrc copy as #42, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #41 show
> turn z 21.17647 models #41 center #3
> volume copy #41
Opened FliL_out.mrc copy as #43, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #41 show
> turn z 21.17647 models #41 center #3
> volume copy #41
Opened FliL_out.mrc copy as #44, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #41 show
> turn z 21.17647 models #41 center #3
> volume copy #41
Opened FliL_out.mrc copy as #45, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #41 show
> turn z 21.17647 models #41 center #3
> volume copy #41
Opened FliL_out.mrc copy as #46, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #41 show
> turn z 21.17647 models #41 center #3
> volume copy #41
Opened FliL_out.mrc copy as #47, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #41 show
> turn z 21.17647 models #41 center #3
> volume copy #41
Opened FliL_out.mrc copy as #48, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #41 show
> turn z 21.17647 models #41 center #3
> volume copy #41
Opened FliL_out.mrc copy as #49, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #41 show
> turn z 21.17647 models #41 center #3
> volume copy #41
Opened FliL_out.mrc copy as #50, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #41 show
> turn z 21.17647 models #41 center #3
> volume copy #41
Opened FliL_out.mrc copy as #51, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #41 show
> turn z 21.17647 models #41 center #3
> volume copy #41
Opened FliL_out.mrc copy as #52, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #41 show
> turn z 21.17647 models #41 center #3
> volume copy #41
Opened FliL_out.mrc copy as #53, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #41 show
> turn z 21.17647 models #41 center #3
> volume copy #41
Opened FliL_out.mrc copy as #54, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #41 show
> turn z 21.17647 models #41 center #3
> volume copy #41
Opened FliL_out.mrc copy as #55, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #41 show
> turn z 21.17647 models #41 center #3
> volume copy #41
Opened FliL_out.mrc copy as #56, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #41 show
> open /Users/shoichitachiyama/Desktop/tmp/FliL.mrc
Opened FliL.mrc as #57, grid size 250,250,250, pixel 4.3, shown at level
0.00921, step 1, values float32
> view orient
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/07252025/Original-map-deposit/Seg/Cage-Mono-Good.mrc"
Opened Cage-Mono-Good.mrc as #58, grid size 250,250,250, pixel 4.3, shown at
level 0.00905, step 1, values float32
> view orient
> turn z 21.17647 models #58 center #3
> volume copy #58
Opened Cage-Mono-Good.mrc copy as #59, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> volume #58 show
> turn z 21.17647 models #58 center #3
> volume copy #58
Opened Cage-Mono-Good.mrc copy as #60, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> volume #58 show
> turn z 21.17647 models #58 center #3
> volume copy #58
Opened Cage-Mono-Good.mrc copy as #61, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> volume #58 show
> turn z 21.17647 models #58 center #3
> volume copy #58
Opened Cage-Mono-Good.mrc copy as #62, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> volume #58 show
> turn z 21.17647 models #58 center #3
> volume copy #58
Opened Cage-Mono-Good.mrc copy as #63, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> volume #58 show
> turn z 21.17647 models #58 center #3
> volume copy #58
Opened Cage-Mono-Good.mrc copy as #64, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> volume #58 show
> turn z 21.17647 models #58 center #3
> volume copy #58
Opened Cage-Mono-Good.mrc copy as #65, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> volume #58 show
> turn z 21.17647 models #58 center #3
> volume copy #58
Opened Cage-Mono-Good.mrc copy as #66, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> volume #58 show
> turn z 21.17647 models #58 center #3
> volume copy #58
Opened Cage-Mono-Good.mrc copy as #67, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> volume #58 show
> turn z 21.17647 models #58 center #3
> volume copy #58
Opened Cage-Mono-Good.mrc copy as #68, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> volume #58 show
> turn z 21.17647 models #58 center #3
> volume copy #58
Opened Cage-Mono-Good.mrc copy as #69, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> volume #58 show
> turn z 21.17647 models #58 center #3
> volume copy #58
Opened Cage-Mono-Good.mrc copy as #70, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> volume #58 show
> turn z 21.17647 models #58 center #3
> volume copy #58
Opened Cage-Mono-Good.mrc copy as #71, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> volume #58 show
> turn z 21.17647 models #58 center #3
> volume copy #58
Opened Cage-Mono-Good.mrc copy as #72, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> volume #58 show
> turn z 21.17647 models #58 center #3
> volume copy #58
Opened Cage-Mono-Good.mrc copy as #73, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> volume #58 show
> turn z 21.17647 models #58 center #3
> volume copy #58
Opened Cage-Mono-Good.mrc copy as #74, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> volume #58 show
> turn z 21.17647 models #58 center #3
> volume copy #58
Opened Cage-Mono-Good.mrc copy as #75, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> volume #58 show
> surface dust #1-58 size 30
> volume #75 level 0.01374
> volume #1-75 level 0.01374
> view orient
> open /Users/shoichitachiyama/Desktop/tmp/MS-ring.mrc
Opened MS-ring.mrc as #76, grid size 250,250,250, pixel 4.3, shown at level
0.00931, step 1, values float32
> open /Users/shoichitachiyama/Desktop/tmp/E-ring.mrc
Opened E-ring.mrc as #77, grid size 250,250,250, pixel 4.3, shown at level
0.00927, step 1, values float32
> volume gaussian #77 sDev 2
Opened E-ring.mrc gaussian as #78, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> close #77
> volume #1-77 level 0.01374
> volume #1-78 level 0.01374
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 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 #!16 models
> show #!17 models
> show #!18 models
> show #!19 models
> show #!20 models
> show #!2 models
> hide #!2 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #!20
> hide #!20 models
> show #!20 models
> hide #20.1 models
> show #20.1 models
> hide #!4 models
> show #!4 models
> hide #4.1 models
> show #4.1 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!4 models
> show #!2 models
> hide #!2 models
> close #4
> volume gaussian #2 sDev 3
Opened 1unit_rim.mrc gaussian as #4, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> volume #1-78 level 0.01374
> show #!21 models
> show #!22 models
> show #!23 models
> show #!24 models
> show #!25 models
> show #!26 models
> show #!27 models
> show #!28 models
> show #!38 models
> show #!37 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
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/07252025/Original-map-deposit/Seg/Basal_disk.mrc"
Opened Basal_disk.mrc as #77, grid size 250,250,250, pixel 4.3, shown at level
0.128, step 1, values float32
> volume #77 level 0.0137
> volume gaussian #77 sDev 3
Opened Basal_disk.mrc gaussian as #79, grid size 250,250,250, pixel 4.3, shown
at step 1, values float32
> close #77
> volume #79 level 0.0137
> volume #79 level 0.02553
> volume #79 level 0.05953
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/07252025/Original-map-deposit/Seg/C-ring-stators.mrc"
Opened C-ring-stators.mrc as #77, grid size 250,250,250, pixel 4.3, shown at
level 0.0725, step 1, values float32
> volume #77 level 0.0595
> volume #77 level 0.0137
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/07252025/Original-map-deposit/Seg/C-Vring.mrc"
Opened C-Vring.mrc as #80, grid size 250,250,250, pixel 4.3, shown at level
0.00961, step 1, values float32
> volume #80 level 0.0137
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/07252025/Original-map-deposit/Seg/Exp_ATP.mrc"
Opened Exp_ATP.mrc as #81, grid size 250,250,250, pixel 4.3, shown at level
0.00943, step 1, values float32
> volume #81 level 0.0137
> volume gaussian #81 sDev 4
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> close #81
> volume #82 level 0.0137
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/07252025/Original-map-deposit/Seg/LP-ring.mrc"
Opened LP-ring.mrc as #81, grid size 250,250,250, pixel 4.3, shown at level
0.00947, step 1, values float32
> volume gaussian #81 sDev 3
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #83 level 0.0137
> close #81
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/07252025/Original-map-deposit/Seg/MotB.mrc"
Opened MotB.mrc as #81, grid size 250,250,250, pixel 4.3, shown at level
0.00929, step 1, values float32
> volume #81 level 0.0137
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/07252025/Original-map-deposit/Seg/PflC.mrc"
Opened PflC.mrc as #84, grid size 250,250,250, pixel 4.3, shown at level
0.0179, step 1, values float32
> volume gaussian #84 sDev 3
Opened PflC.mrc gaussian as #85, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> volume #85 level 0.0137
> volume #85 level 0.03146
> volume #85 level 0.06343
> volume #85 level 0.04389
> surface dust #85\ size 50
Missing or invalid "surfaces" argument: only initial part "#85" of atom
specifier valid
> surface dust #85 size 50
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/07252025/Original-map-deposit/Seg/PflD.mrc"
Opened PflD.mrc as #86, grid size 250,250,250, pixel 4.3, shown at level
0.00914, step 1, values float32
> volume #86 level 0.0137
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/07252025/Original-map-deposit/Seg/PilM.mrc"
Opened PilM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level
0.00952, step 1, values float32
> close #84
> volume gaussian #85 sDev 3
Opened PflC.mrc gaussian as #84, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> show #!85 models
> hide #!84 models
> close #84
> volume gaussian #87 sDev 3
Opened PilM.mrc gaussian as #84, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
> close #87
> volume #84 level 0.0137
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/07252025/Original-map-deposit/Seg/OM.mrc"
Opened OM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.132,
step 1, values float32
> volume #87 level 0.02428
> volume gaussian #87 sDev 7
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at step
1, values float32
> volume #88 level 0.02703
> close #87
> open /Users/shoichitachiyama/Desktop/tmp/IM.mrc
Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
step 1, values float32
> volume gaussian #87 sDev 9
Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at step
1, values float32
> volume #89 level 0.01114
> ui tool show "Side View"
> view orient
> hide #!85 models
> lighting soft
[Repeated 1 time(s)]
> lighting flat
[Repeated 1 time(s)]
> lighting soft
> graphics silhouettes false
> color #21 #eba384ff models
> color #21 #eb9275ff models
> hide #!21 models
> show #!21 models
> hide #!22 models
> show #!22 models
> color #22 #eb3718ff models
> color #22 #eb3d1cff models
> color #22 #eb1334ff models
> color #22-38 #eb1334ff models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> color #78 #ffc6ffff models
> color #78 #ffe0fdff models
> color #78 #ffd2fbff models
> color #78 #fdd8ffff models
> color #76 #3eff23ff models
> color #76 #1d7710ff models
> color #3 #929292ff models
> color #3 #919191ff models
> color #3 #797979ff models
> color #81 #ff8e21ff models
> color #81 #ff871cff models
> color #81 #ba6315ff models
> volume #89 level 0.006427
> color #86 #2cc9ebff models
> color #58 #24aaffff models
> color #58 #35bdffff models
> color #59 #4496ffff models
> color #59 #488fffff models
> color #59 #2da3ffff models
> color #59 #2698ffff models
> color #59 #2c93ffff models
> color #59-75 #2c93ffff models
> color #4 #ff41fcff models
> color #4 #f046ffff models
> color #4 #fe3dffff models
> color #4-20 #fe3dffff models
> hide #!81 models
> view orient
> color #89 #ffeffbff models
> color #89 #a5ffadff models
> color #89 #466c49ff models
> color #89 #3a5a3dff models
> color #89 #365338ff models
> view orient
> turn x 90
[Repeated 2 time(s)]
> color #75 #2c93fffc models
> color #75 #2c93ffff models
> color #84 #2c93ffff models
> show #!85 models
> color #85 #abe2aeff models
> volume #71 level 0.01374
> volume #74 level 0.007489
> volume #74 level 0.002801
> volume #74 level 0.0137
> volume #89 level 0.01665
> color #44 #fff7b8ff models
> color #44 #ffe68bff models
> color #44 #ffe776ff models
> color #44 #ffe877ff models
> color #44 #e9d46dff models
> color #39-56 #e9d46dff models
> color #77 #919191ff models
> color #77 #797979ff models
> color #82 #797979ff models
> color #80 #797979ff models
> color #88 #4f8f00ff models
> color #88 #008f00ff models
> color #88 #009051ff models
> color #88 #559050ff models
> color #88 #477743ff models
> color #88 #2e4e2cff models
> color #89 #2e4e2cff models
> view orient
> turn x 90
[Repeated 2 time(s)]
> turn y 90
[Repeated 5 time(s)]
> turn y -10
[Repeated 1 time(s)]
> turn x 90
> hide #!85 models
> hide #!86 models
> show #!86 models
> show #!85 models
> hide #!85 models
> show #!81 models
> color #79 #797979ff models
> hide #!79 models
> color #83 #d4fb79ff models
> color #83 #b5fb6cff models
> color #83 #d2fbbfff models
> color #83 #d2fbbbff models
> color #83 #b4fba8ff models
> color #83 #c2fbafff models
> color #83 #c1fbafff models
> hide #!83 models
> volume #78 level 0.0273
> volume #78 level 0.0137
> volume #76 level 0.01374
> volume #76 level 0.006688
> volume #76 level 0.0137
> volume #78 level 0.2392
> volume #78 level 0.1137
> save /Users/shoichitachiyama/Desktop/tmp/Figure-1.cxs includeMaps true
——— End of log from Fri Jul 25 22:07:01 2025 ———
opened ChimeraX session
> ui tool show "Side View"
> save /Users/shoichi/Desktop/For_Composition-maps/Global_Segment_Fig1.cxs
> includeMaps true
——— End of log from Tue Sep 9 09:30:49 2025 ———
opened ChimeraX session
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> hide #!21 models
> hide #!16 models
> hide #!22 models
> hide #!22-57 models
> hide #!88 models
> hide #!89 models
> open "/Users/shoichi/Desktop/For_Composition-maps/Segmented for
> Compositions/Resegment_for-C17_FlgY/C17-FlgY_New.mrc"
Opened C17-FlgY_New.mrc as #90, grid size 256,256,256, pixel 2.14, shown at
level 0.0212, step 1, values float32
> select add #90
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #90,1,0,0,245.65,0,1,0,1.0032,0,0,1,74.641
> view matrix models #90,1,0,0,184.1,0,1,0,167.05,0,0,1,228.41
> view matrix models #90,1,0,0,271.38,0,1,0,269.89,0,0,1,245.5
> view matrix models #90,1,0,0,244.99,0,1,0,277.14,0,0,1,184.64
> ui tool show "Fit in Map"
> fitmap #90 inMap #78
Fit map C17-FlgY_New.mrc in map E-ring.mrc gaussian using 167766 points
correlation = 0.1097, correlation about mean = 0.1148, overlap = 135.6
steps = 320, shift = 15.1, angle = 1.23 degrees
Position of C17-FlgY_New.mrc (#90) relative to E-ring.mrc gaussian (#78)
coordinates:
Matrix rotation and translation
0.99982891 -0.00230575 0.01835296 226.46472726
0.00250823 0.99993617 -0.01101686 275.00777671
-0.01832639 0.01106101 0.99977087 181.62569917
Axis 0.51247229 0.85140226 0.11174234
Axis point 7675.61342484 0.00000000 -1922.49036663
Rotation angle (degrees) 1.23427829
Shift along axis 370.49441986
> view matrix models
> #90,0.99983,-0.0023058,0.018353,248.02,0.0025082,0.99994,-0.011017,262.05,-0.018326,0.011061,0.99977,185.52
> view matrix models
> #90,0.99983,-0.0023058,0.018353,253.83,0.0025082,0.99994,-0.011017,271.25,-0.018326,0.011061,0.99977,188.02
> ui mousemode right "rotate selected models"
> view matrix models
> #90,0.99448,0.10449,0.0096588,228.95,-0.10438,0.99447,-0.011667,302.12,-0.010824,0.010595,0.99989,186.06
> ui mousemode right "translate selected models"
> view matrix models
> #90,0.99448,0.10449,0.0096588,229.04,-0.10438,0.99447,-0.011667,285.58,-0.010824,0.010595,0.99989,187.22
> fitmap #90 inMap #78
Fit map C17-FlgY_New.mrc in map E-ring.mrc gaussian using 167766 points
correlation = 0.6839, correlation about mean = 0.321, overlap = 935.3
steps = 64, shift = 13.7, angle = 4.51 degrees
Position of C17-FlgY_New.mrc (#90) relative to E-ring.mrc gaussian (#78)
coordinates:
Matrix rotation and translation
0.98351554 0.18082356 0.00011815 217.33566048
-0.18082356 0.98351555 0.00001166 316.52533809
-0.00011410 -0.00003283 0.99999999 179.33555985
Axis -0.00012301 0.00064219 -0.99999979
Axis point 1845.32525184 -1033.57351932 0.00000000
Rotation angle (degrees) 10.41773572
Shift along axis -179.15898502
> fitmap #90 inMap #78
Fit map C17-FlgY_New.mrc in map E-ring.mrc gaussian using 167766 points
correlation = 0.6836, correlation about mean = 0.3202, overlap = 934.5
steps = 28, shift = 0.134, angle = 0.000421 degrees
Position of C17-FlgY_New.mrc (#90) relative to E-ring.mrc gaussian (#78)
coordinates:
Matrix rotation and translation
0.98351572 0.18082259 0.00011753 217.33678736
-0.18082259 0.98351573 0.00000441 316.52723110
-0.00011479 -0.00002559 0.99999999 179.19963162
Axis -0.00008294 0.00064239 -0.99999979
Axis point 1845.34897778 -1033.62473418 0.00000000
Rotation angle (degrees) 10.41767902
Shift along axis -179.01428601
> fitmap #90 inMap #78
Fit map C17-FlgY_New.mrc in map E-ring.mrc gaussian using 167766 points
correlation = 0.6839, correlation about mean = 0.3209, overlap = 935.1
steps = 28, shift = 0.105, angle = 0.00708 degrees
Position of C17-FlgY_New.mrc (#90) relative to E-ring.mrc gaussian (#78)
coordinates:
Matrix rotation and translation
0.98349340 0.18094397 0.00011842 217.30906338
-0.18094397 0.98349341 0.00001137 316.56441860
-0.00011441 -0.00003261 0.99999999 179.30672010
Axis -0.00012152 0.00064339 -0.99999979
Axis point 1844.35230864 -1032.60313161 0.00000000
Rotation angle (degrees) 10.42475041
Shift along axis -179.12941598
> fitmap #90 inMap #78
Fit map C17-FlgY_New.mrc in map E-ring.mrc gaussian using 167766 points
correlation = 0.6839, correlation about mean = 0.3209, overlap = 935.2
steps = 24, shift = 0.00918, angle = 0.00599 degrees
Position of C17-FlgY_New.mrc (#90) relative to E-ring.mrc gaussian (#78)
coordinates:
Matrix rotation and translation
0.98351231 0.18084116 0.00011826 217.33198706
-0.18084116 0.98351232 0.00001196 316.53064101
-0.00011415 -0.00003315 0.99999999 179.31597535
Axis -0.00012470 0.00064260 -0.99999979
Axis point 1845.18083989 -1033.43111010 0.00000000
Rotation angle (degrees) 10.41876093
Shift along axis -179.13963772
> fitmap #90 inMap #78
Fit map C17-FlgY_New.mrc in map E-ring.mrc gaussian using 167766 points
correlation = 0.6839, correlation about mean = 0.3209, overlap = 935.2
steps = 24, shift = 0.000454, angle = 0.000298 degrees
Position of C17-FlgY_New.mrc (#90) relative to E-ring.mrc gaussian (#78)
coordinates:
Matrix rotation and translation
0.98351325 0.18083604 0.00011821 217.33313816
-0.18083604 0.98351326 0.00001201 316.52893273
-0.00011409 -0.00003319 0.99999999 179.31642449
Axis -0.00012498 0.00064231 -0.99999979
Axis point 1845.22172311 -1033.47232911 0.00000000
Rotation angle (degrees) 10.41846272
Shift along axis -179.14023835
> open "/Users/shoichi/Desktop/For_Composition-maps/Segmented for
> Compositions/Resegment_for-C17_FlgY/MS-ring_New.mrc"
Opened MS-ring_New.mrc as #91, grid size 256,256,256, pixel 2.14, shown at
level 0.0165, step 1, values float32
> select subtract #90
Nothing selected
> select add #91
2 models selected
> view matrix models #91,1,0,0,291.47,0,1,0,121.38,0,0,1,153.39
> view matrix models #91,1,0,0,259.76,0,1,0,253.65,0,0,1,124.48
> view matrix models #91,1,0,0,266.47,0,1,0,253.28,0,0,1,170.43
> view matrix models #91,1,0,0,260.49,0,1,0,263.72,0,0,1,170.63
> fitmap #91 inMap #76
Fit map MS-ring_New.mrc in map MS-ring.mrc using 167703 points
correlation = 0.7299, correlation about mean = 0.3966, overlap = 644.1
steps = 56, shift = 6.57, angle = 0.63 degrees
Position of MS-ring_New.mrc (#91) relative to MS-ring.mrc (#76) coordinates:
Matrix rotation and translation
0.99993954 -0.01099523 -0.00014578 265.54423379
0.01099524 0.99993955 0.00001435 259.52130179
0.00014562 -0.00001595 0.99999999 176.74014177
Axis -0.00137748 -0.01324995 0.99991127
Axis point -23677.83582371 24302.71072857 0.00000000
Rotation angle (degrees) 0.63004917
Shift along axis 172.92003226
> fitmap #91 inMap #76
Fit map MS-ring_New.mrc in map MS-ring.mrc using 167703 points
correlation = 0.7298, correlation about mean = 0.3962, overlap = 644.3
steps = 40, shift = 0.0436, angle = 0.404 degrees
Position of MS-ring_New.mrc (#91) relative to MS-ring.mrc (#76) coordinates:
Matrix rotation and translation
0.99983748 -0.01802647 0.00025465 267.36720617
0.01802647 0.99983751 0.00001754 257.63185173
-0.00025492 -0.00001295 0.99999997 176.88955347
Axis -0.00084577 0.01413266 0.99989977
Axis point -14015.61177085 14966.74136379 0.00000000
Rotation angle (degrees) 1.03300013
Shift along axis 180.28671713
> fitmap #91 inMap #76
Fit map MS-ring_New.mrc in map MS-ring.mrc using 167703 points
correlation = 0.7297, correlation about mean = 0.3958, overlap = 644.7
steps = 48, shift = 0.064, angle = 0.0699 degrees
Position of MS-ring_New.mrc (#91) relative to MS-ring.mrc (#76) coordinates:
Matrix rotation and translation
0.99981486 -0.01924111 0.00016948 267.72835743
0.01924110 0.99981487 0.00010263 257.27485766
-0.00017142 -0.00009935 0.99999998 176.95402408
Axis -0.00524842 0.00885831 0.99994699
Axis point -13153.68310891 14089.46165095 0.00000000
Rotation angle (degrees) 1.10256055
Shift along axis 177.81851213
> fitmap #91 inMap #76
Fit map MS-ring_New.mrc in map MS-ring.mrc using 167703 points
correlation = 0.7298, correlation about mean = 0.3963, overlap = 644.2
steps = 48, shift = 0.0759, angle = 0.0477 degrees
Position of MS-ring_New.mrc (#91) relative to MS-ring.mrc (#76) coordinates:
Matrix rotation and translation
0.99979850 -0.02007278 0.00019300 267.95352720
0.02007277 0.99979852 0.00008478 257.05746254
-0.00019466 -0.00008089 0.99999998 176.87940534
Axis -0.00412629 0.00965567 0.99994487
Axis point -12584.90928667 13512.07043080 0.00000000
Rotation angle (degrees) 1.15022591
Shift along axis 178.24606312
> fitmap #91 inMap #76
Fit map MS-ring_New.mrc in map MS-ring.mrc using 167703 points
correlation = 0.7297, correlation about mean = 0.3959, overlap = 644.6
steps = 40, shift = 0.0654, angle = 0.0573 degrees
Position of MS-ring_New.mrc (#91) relative to MS-ring.mrc (#76) coordinates:
Matrix rotation and translation
0.99981759 -0.01909930 -0.00003711 267.75321626
0.01909930 0.99981759 0.00007701 257.32313906
0.00003563 -0.00007771 1.00000000 176.88069568
Axis -0.00405033 -0.00190407 0.99998998
Axis point -13354.92044279 14183.73056555 0.00000000
Rotation angle (degrees) 1.09438682
Shift along axis 175.30447343
> hide #!76 models
> show #!76 models
> select subtract #91
Nothing selected
> hide #!91 models
> show #!91 models
> hide #!76 models
> open "/Users/shoichi/Desktop/For_Composition-maps/Segmented for
> Compositions/Single_Cage_unit.mrc"
Opened Single_Cage_unit.mrc as #92, grid size 200,200,200, pixel 2.14, shown
at level 0.00107, step 1, values float32
> hide #!78 models
> select add #92
2 models selected
> view matrix models #92,1,0,0,704.7,0,1,0,201.74,0,0,1,279.53
> volume #92 level 0.001585
> surface dust #92 size 21.4
> view matrix models #92,1,0,0,603.05,0,1,0,250.24,0,0,1,261.5
> view matrix models #92,1,0,0,598.33,0,1,0,250.84,0,0,1,244.9
> view matrix models #92,1,0,0,575.39,0,1,0,253.1,0,0,1,244.59
> fitmap #92 inMap #73
Fit map Single_Cage_unit.mrc in map Cage-Mono-Good.mrc copy using 34592 points
correlation = 0.894, correlation about mean = 0.8133, overlap = 137.7
steps = 204, shift = 16.6, angle = 11.3 degrees
Position of Single_Cage_unit.mrc (#92) relative to Cage-Mono-Good.mrc copy
(#73) coordinates:
Matrix rotation and translation
0.85084055 -0.52520357 -0.01521737 688.24289033
0.52349429 0.84984002 -0.06103828 395.07505258
0.04498985 0.04396764 0.99801942 212.17994558
Axis 0.09946944 -0.05703277 0.99340480
Axis point -389.02391770 1372.29633513 0.00000000
Rotation angle (degrees) 31.85895864
Shift along axis 256.70748721
> fitmap #92 inMap #73
Fit map Single_Cage_unit.mrc in map Cage-Mono-Good.mrc copy using 34592 points
correlation = 0.8937, correlation about mean = 0.8129, overlap = 137.7
steps = 44, shift = 0.14, angle = 0.132 degrees
Position of Single_Cage_unit.mrc (#92) relative to Cage-Mono-Good.mrc copy
(#73) coordinates:
Matrix rotation and translation
0.85111163 -0.52478264 -0.01456634 687.93682375
0.52300606 0.84998400 -0.06318116 395.78421808
0.04553753 0.04615593 0.99789577 211.64041367
Axis 0.10361828 -0.05696018 0.99298479
Axis point -391.71924113 1370.91624424 0.00000000
Rotation angle (degrees) 31.84313889
Shift along axis 258.89460578
> hide #!73 models
> hide #!84 models
> select clear
> open "/Users/shoichi/Desktop/For_Composition-maps/Segmented for
> Compositions/Single_MotBpg_unit.mrc"
Opened Single_MotBpg_unit.mrc as #93, grid size 200,200,200, pixel 2.14, shown
at level 0.000906, step 1, values float32
> open "/Users/shoichi/Desktop/For_Composition-maps/Segmented for
> Compositions/Single_Cage_unit.mrc"
Opened Single_Cage_unit.mrc as #94, grid size 200,200,200, pixel 2.14, shown
at level 0.00107, step 1, values float32
> select add #93
2 models selected
> select add #94
4 models selected
> view matrix models
> #93,1,0,0,423.77,0,1,0,326.57,0,0,1,-198.88,#94,1,0,0,423.77,0,1,0,326.57,0,0,1,-198.88
> view matrix models
> #93,1,0,0,553.22,0,1,0,257.53,0,0,1,-173.52,#94,1,0,0,553.22,0,1,0,257.53,0,0,1,-173.52
> view matrix models
> #93,1,0,0,633.8,0,1,0,242.26,0,0,1,163.41,#94,1,0,0,633.8,0,1,0,242.26,0,0,1,163.41
> view matrix models
> #93,1,0,0,584.51,0,1,0,253.75,0,0,1,164.38,#94,1,0,0,584.51,0,1,0,253.75,0,0,1,164.38
> view matrix models
> #93,1,0,0,584.09,0,1,0,250.32,0,0,1,244.11,#94,1,0,0,584.09,0,1,0,250.32,0,0,1,244.11
> view matrix models
> #93,1,0,0,568.99,0,1,0,264.34,0,0,1,246.68,#94,1,0,0,568.99,0,1,0,264.34,0,0,1,246.68
> close #94
> surface dust #93 size 21.4
> fitmap #93 inMap #81
Fit map Single_MotBpg_unit.mrc in map MotB.mrc using 79697 points
correlation = 0.6163, correlation about mean = 0.7395, overlap = 76.2
steps = 1036, shift = 18.9, angle = 15.8 degrees
Position of Single_MotBpg_unit.mrc (#93) relative to MotB.mrc (#81)
coordinates:
Matrix rotation and translation
0.96291147 0.21432700 0.16390679 496.18471925
-0.21988562 0.97538880 0.01633999 323.01791718
-0.15637075 -0.05177472 0.98634049 282.69998534
Axis -0.12524856 0.58892269 -0.79842524
Axis point 1945.55949190 -1921.35819287 0.00000000
Rotation angle (degrees) 15.77843975
Shift along axis -97.62864004
> fitmap #93 inMap #81
Fit map Single_MotBpg_unit.mrc in map MotB.mrc using 79697 points
correlation = 0.6164, correlation about mean = 0.7397, overlap = 76.2
steps = 64, shift = 0.179, angle = 0.0698 degrees
Position of Single_MotBpg_unit.mrc (#93) relative to MotB.mrc (#81)
coordinates:
Matrix rotation and translation
0.96261273 0.21530646 0.16437718 496.05703745
-0.22080365 0.97519165 0.01571595 323.41930659
-0.15691551 -0.05142346 0.98627235 282.85027814
Axis -0.12300460 0.58863307 -0.79898747
Axis point 1937.21793975 -1912.35827810 0.00000000
Rotation angle (degrees) 15.83775503
Shift along axis -96.63582434
> hide #!81 models
> select clear
> show #!85 models
> save "/Users/shoichi/Desktop/For_Composition-maps/Segmented for
> Compositions/Building_Composition.cxs" includeMaps true
——— End of log from Tue Sep 9 10:34:35 2025 ———
opened ChimeraX session
> hide #!58-82 models
> open "/Users/shoichi/Desktop/For_Composition-maps/Segmented for
> Compositions/Resegment-PflABCD/1unit_PflABCD.mrc"
Opened 1unit_PflABCD.mrc as #94, grid size 200,200,200, pixel 2.14, shown at
level 0.0254, step 1, values float32
> volume #94 level 0.006399
> show #!73 models
> select add #94
2 models selected
> view matrix models #94,1,0,0,134.96,0,1,0,267.28,0,0,1,-152.38
> view matrix models #94,1,0,0,616.66,0,1,0,273.81,0,0,1,250.99
> view matrix models #94,1,0,0,614.55,0,1,0,260.12,0,0,1,251.89
> view matrix models #94,1,0,0,563.09,0,1,0,258.63,0,0,1,232.09
> ui mousemode right "rotate selected models"
> view matrix models
> #94,0.98847,0.15032,0.017943,537.22,-0.15005,0.98855,-0.015814,295.14,-0.020114,0.012939,0.99971,234.24
> ui mousemode right "translate selected models"
> view matrix models
> #94,0.98847,0.15032,0.017943,545.83,-0.15005,0.98855,-0.015814,312.83,-0.020114,0.012939,0.99971,240.63
> ui tool show "Fit in Map"
> fitmap #94 inMap #73
Fit map 1unit_PflABCD.mrc in map Cage-Mono-Good.mrc copy using 172147 points
correlation = 0.3775, correlation about mean = 0.2345, overlap = 170.4
steps = 64, shift = 7.13, angle = 1.7 degrees
Position of 1unit_PflABCD.mrc (#94) relative to Cage-Mono-Good.mrc copy (#73)
coordinates:
Matrix rotation and translation
0.84722403 -0.53100503 0.01565581 683.75620450
0.53108654 0.84731663 -0.00127003 378.56488217
-0.01259103 0.00939059 0.99987663 237.53110681
Axis 0.01003334 0.02658474 0.99959621
Axis point -305.96006063 1370.88620298 0.00000000
Rotation angle (degrees) 32.09064827
Shift along axis 254.35960048
> fitmap #94 inMap #73
Fit map 1unit_PflABCD.mrc in map Cage-Mono-Good.mrc copy using 172147 points
correlation = 0.3775, correlation about mean = 0.2345, overlap = 170.4
steps = 40, shift = 0.0474, angle = 0.0132 degrees
Position of 1unit_PflABCD.mrc (#94) relative to Cage-Mono-Good.mrc copy (#73)
coordinates:
Matrix rotation and translation
0.84715231 -0.53111398 0.01584006 683.73927411
0.53119663 0.84724769 -0.00122224 378.49374197
-0.01277131 0.00944961 0.99987379 237.58259702
Axis 0.01004173 0.02692202 0.99958710
Axis point -305.53002615 1370.48324286 0.00000000
Rotation angle (degrees) 32.09838562
Shift along axis 254.54024033
> fitmap #94 inMap #73
Fit map 1unit_PflABCD.mrc in map Cage-Mono-Good.mrc copy using 172147 points
correlation = 0.3775, correlation about mean = 0.2345, overlap = 170.4
steps = 44, shift = 0.0335, angle = 0.016 degrees
Position of 1unit_PflABCD.mrc (#94) relative to Cage-Mono-Good.mrc copy (#73)
coordinates:
Matrix rotation and translation
0.84703176 -0.53130938 0.01573358 683.84612052
0.53138952 0.84712689 -0.00110162 378.40957007
-0.01274304 0.00929377 0.99987561 237.60613942
Axis 0.00977809 0.02678562 0.99959338
Axis point -305.09112739 1370.25341209 0.00000000
Rotation angle (degrees) 32.11129691
Shift along axis 254.33216755
> close #93
> open "/Users/shoichi/Desktop/For_Composition-maps/Segmented for
> Compositions/Resegment-PflABCD/1xMotBpg-09092025.mrc"
Opened 1xMotBpg-09092025.mrc as #93, grid size 200,200,200, pixel 2.14, shown
at level 0.00231, step 1, values float32
> select subtract #94
Nothing selected
> select add #93
2 models selected
> view matrix models #93,1,0,0,321.52,0,1,0,-29.634,0,0,1,-6.3464
> view matrix models #93,1,0,0,590.01,0,1,0,120.49,0,0,1,62.951
> hide #!85 models
> view matrix models #93,1,0,0,612.95,0,1,0,203.95,0,0,1,215.29
> view matrix models #93,1,0,0,562.32,0,1,0,257.83,0,0,1,248.36
> view matrix models #93,1,0,0,563.74,0,1,0,271.47,0,0,1,236.73
> fitmap #93 inMap #94
Fit map 1xMotBpg-09092025.mrc in map 1unit_PflABCD.mrc using 77865 points
correlation = 0.9993, correlation about mean = 0.9993, overlap = 14.25
steps = 188, shift = 17, angle = 10.3 degrees
Position of 1xMotBpg-09092025.mrc (#93) relative to 1unit_PflABCD.mrc (#94)
coordinates:
Matrix rotation and translation
0.99999961 -0.00039220 0.00078983 0.04468720
0.00039242 0.99999989 -0.00027317 0.02089191
-0.00078972 0.00027348 0.99999965 0.02286352
Axis 0.29605513 0.85544384 0.42493199
Axis point 7.00681634 0.00000000 -41.27533441
Rotation angle (degrees) 0.05289726
Shift along axis 0.04081717
> surface dust #93 size 21.4
> save /Users/shoichi/Desktop/For_Composition-maps/Building_Composition.cxs
> includeMaps true
> select subtract #93
Nothing selected
> open "/Users/shoichi/Desktop/For_Composition-maps/Segmented for
> Compositions/Resegment-PflABCD/1xPflD.mrc"
Opened 1xPflD.mrc as #95, grid size 200,200,200, pixel 2.14, shown at level
0.00228, step 1, values float32
> select add #94
2 models selected
> select subtract #94
Nothing selected
> hide #!86 models
> hide #!73 models
> select add #95
2 models selected
> view matrix models #95,1,0,0,360.08,0,1,0,557.3,0,0,1,108.22
> view matrix models #95,1,0,0,511.15,0,1,0,235.1,0,0,1,234
> view matrix models #95,1,0,0,548.26,0,1,0,280.14,0,0,1,227.15
> view matrix models #95,1,0,0,568.63,0,1,0,254.58,0,0,1,233.42
> view matrix models #95,1,0,0,573.08,0,1,0,261.87,0,0,1,235.11
> fitmap #95 inMap #94
Fit map 1xPflD.mrc in map 1unit_PflABCD.mrc using 78846 points
correlation = 0.8209, correlation about mean = 0.8407, overlap = 5.624
steps = 2000, shift = 238, angle = 106 degrees
Position of 1xPflD.mrc (#95) relative to 1unit_PflABCD.mrc (#94) coordinates:
Matrix rotation and translation
0.44871392 -0.03658823 -0.89292616 442.77007253
-0.88403945 0.12815784 -0.44949952 586.83714695
0.13088188 0.99107864 0.02516077 54.01643407
Axis 0.73498676 -0.52234955 -0.43237184
Axis point 0.00000000 421.79210823 482.25137983
Rotation angle (degrees) 101.47753696
Shift along axis -4.45916358
> fitmap #95 inMap #94
Fit map 1xPflD.mrc in map 1unit_PflABCD.mrc using 78846 points
correlation = 0.8598, correlation about mean = 0.8825, overlap = 5.862
steps = 2000, shift = 181, angle = 78.1 degrees
Position of 1xPflD.mrc (#95) relative to 1unit_PflABCD.mrc (#94) coordinates:
Matrix rotation and translation
-0.02391511 -0.78326783 -0.62122426 657.29982054
-0.79318482 -0.36337187 0.48869083 375.16815684
-0.60851123 0.50443275 -0.61258607 573.31264207
Axis 0.69858872 -0.56417411 -0.44009246
Axis point 0.00000000 450.69566568 495.19894104
Rotation angle (degrees) 179.35443813
Shift along axis -4.78849562
> volume #95 level 0.002032
> ui mousemode right "rotate selected models"
> view matrix models
> #95,0.98255,0.0020586,0.186,681.77,0.042772,-0.97564,-0.21515,727.54,0.18102,0.21935,-0.95871,774.82
> view matrix models
> #95,0.93452,-0.2697,0.23225,740.01,-0.25906,-0.96288,-0.075776,759.41,0.24407,0.010648,-0.9697,808.17
> view matrix models
> #95,0.95575,-0.2707,0.11518,760.63,-0.2702,-0.96259,-0.020269,749.9,0.11635,-0.011749,-0.99314,845.12
> ui mousemode right "translate selected models"
> view matrix models
> #95,0.95575,-0.2707,0.11518,635.07,-0.2702,-0.96259,-0.020269,809.33,0.11635,-0.011749,-0.99314,807.67
> view matrix models
> #95,0.95575,-0.2707,0.11518,636.37,-0.2702,-0.96259,-0.020269,771.31,0.11635,-0.011749,-0.99314,834.5
> view matrix models
> #95,0.95575,-0.2707,0.11518,627.99,-0.2702,-0.96259,-0.020269,758.59,0.11635,-0.011749,-0.99314,823.54
> view matrix models
> #95,0.95575,-0.2707,0.11518,609.79,-0.2702,-0.96259,-0.020269,772.68,0.11635,-0.011749,-0.99314,826.49
> fitmap #95 inMap #94
Fit map 1xPflD.mrc in map 1unit_PflABCD.mrc using 114776 points
correlation = 0.6933, correlation about mean = 0.7102, overlap = 5.309
steps = 2000, shift = 130, angle = 50.4 degrees
Position of 1xPflD.mrc (#95) relative to 1unit_PflABCD.mrc (#94) coordinates:
Matrix rotation and translation
0.52455209 -0.11161180 0.84403075 -102.83118592
-0.15504536 -0.98731516 -0.03420095 486.03876715
0.83714159 -0.11292287 -0.53520312 260.07931488
Axis -0.87301496 0.07639984 -0.48167204
Axis point 0.00000000 241.88964464 152.13052619
Rotation angle (degrees) 177.41587276
Shift along axis 1.63351334
> close #95
> open "/Users/shoichi/Desktop/For_Composition-maps/Segmented for
> Compositions/Resegment-PflABCD/1xPflD.mrc"
Opened 1xPflD.mrc as #95, grid size 200,200,200, pixel 2.14, shown at level
0.00228, step 1, values float32
> open "/Users/shoichi/Desktop/For_Composition-maps/Segmented for
> Compositions/Resegment-PflABCD/1unit_PflABCD.mrc"
Opened 1unit_PflABCD.mrc as #96, grid size 200,200,200, pixel 2.14, shown at
level 0.0254, step 1, values float32
> select add #95
2 models selected
> view matrix models #95,1,0,0,658.55,0,1,0,85.496,0,0,1,168.29
> undo
> select add #96
4 models selected
> view matrix models
> #95,1,0,0,626.4,0,1,0,50.751,0,0,1,154.84,#96,1,0,0,626.4,0,1,0,50.751,0,0,1,154.84
> view matrix models
> #95,1,0,0,592.4,0,1,0,246.58,0,0,1,207.61,#96,1,0,0,592.4,0,1,0,246.58,0,0,1,207.61
> view matrix models
> #95,1,0,0,591.84,0,1,0,256.22,0,0,1,244.02,#96,1,0,0,591.84,0,1,0,256.22,0,0,1,244.02
> view matrix models
> #95,1,0,0,575.69,0,1,0,261.67,0,0,1,234.11,#96,1,0,0,575.69,0,1,0,261.67,0,0,1,234.11
> view matrix models
> #95,1,0,0,575.88,0,1,0,260.53,0,0,1,234.52,#96,1,0,0,575.88,0,1,0,260.53,0,0,1,234.52
> view matrix models
> #95,1,0,0,575.38,0,1,0,263.66,0,0,1,233.96,#96,1,0,0,575.38,0,1,0,263.66,0,0,1,233.96
> view matrix models
> #95,1,0,0,575.14,0,1,0,258.24,0,0,1,239.73,#96,1,0,0,575.14,0,1,0,258.24,0,0,1,239.73
> ui mousemode right "rotate selected models"
> view matrix models
> #95,0.99997,2.0466e-05,0.0077597,573.49,-3.7193e-05,1,0.0021554,257.79,-0.0077596,-0.0021556,0.99997,241.85,#96,0.99997,2.0466e-05,0.0077597,573.49,-3.7193e-05,1,0.0021554,257.79,-0.0077596,-0.0021556,0.99997,241.85
> undo
> view matrix models
> #95,0.97176,0.23585,-0.0074376,532.52,-0.23555,0.97144,0.028666,308.37,0.013986,-0.026104,0.99956,242.4,#96,0.97176,0.23585,-0.0074376,532.52,-0.23555,0.97144,0.028666,308.37,0.013986,-0.026104,0.99956,242.4
> ui mousemode right "translate selected models"
> view matrix models
> #95,0.97176,0.23585,-0.0074376,541.01,-0.23555,0.97144,0.028666,323.91,0.013986,-0.026104,0.99956,240.71,#96,0.97176,0.23585,-0.0074376,541.01,-0.23555,0.97144,0.028666,323.91,0.013986,-0.026104,0.99956,240.71
> view matrix models
> #95,0.97176,0.23585,-0.0074376,541.48,-0.23555,0.97144,0.028666,322.49,0.013986,-0.026104,0.99956,240.86,#96,0.97176,0.23585,-0.0074376,541.48,-0.23555,0.97144,0.028666,322.49,0.013986,-0.026104,0.99956,240.86
> view matrix models
> #95,0.97176,0.23585,-0.0074376,543.62,-0.23555,0.97144,0.028666,335.39,0.013986,-0.026104,0.99956,239.37,#96,0.97176,0.23585,-0.0074376,543.62,-0.23555,0.97144,0.028666,335.39,0.013986,-0.026104,0.99956,239.37
> view orient
> ui mousemode right "rotate selected models"
> view matrix models
> #95,0.99866,0.050244,-0.012661,578.52,-0.049891,0.9984,0.026772,290.52,0.013986,-0.026104,0.99956,239.37,#96,0.99866,0.050244,-0.012661,578.52,-0.049891,0.9984,0.026772,290.52,0.013986,-0.026104,0.99956,239.37
> ui mousemode right "translate selected models"
> view matrix models
> #95,0.99866,0.050244,-0.012661,561.81,-0.049891,0.9984,0.026772,290.83,0.013986,-0.026104,0.99956,239.37,#96,0.99866,0.050244,-0.012661,561.81,-0.049891,0.9984,0.026772,290.83,0.013986,-0.026104,0.99956,239.37
> ui mousemode right "rotate selected models"
> view matrix models
> #95,0.98842,0.15143,-0.0098752,541.85,-0.15111,0.98812,0.02792,314.32,0.013986,-0.026104,0.99956,239.37,#96,0.98842,0.15143,-0.0098752,541.85,-0.15111,0.98812,0.02792,314.32,0.013986,-0.026104,0.99956,239.37
> ui mousemode right "translate selected models"
> view matrix models
> #95,0.98842,0.15143,-0.0098752,547.66,-0.15111,0.98812,0.02792,301.69,0.013986,-0.026104,0.99956,239.37,#96,0.98842,0.15143,-0.0098752,547.66,-0.15111,0.98812,0.02792,301.69,0.013986,-0.026104,0.99956,239.37
> fitmap #96 inMap #94
Fit map 1unit_PflABCD.mrc in map 1unit_PflABCD.mrc using 79988 points
correlation = 1, correlation about mean = 1, overlap = 160.9
steps = 84, shift = 3.24, angle = 2.99 degrees
Position of 1unit_PflABCD.mrc (#96) relative to 1unit_PflABCD.mrc (#94)
coordinates:
Matrix rotation and translation
0.99999999 0.00012179 -0.00002993 -0.00800089
-0.00012179 0.99999999 -0.00008588 0.02768822
0.00002992 0.00008588 1.00000000 -0.01306696
Axis 0.56501331 -0.19686455 -0.80125171
Axis point 228.14078409 68.02211020 0.00000000
Rotation angle (degrees) 0.00870895
Shift along axis 0.00049848
> fitmap #95 inMap #94
Fit map 1xPflD.mrc in map 1unit_PflABCD.mrc using 78846 points
correlation = 0.8501, correlation about mean = 0.8718, overlap = 5.79
steps = 2000, shift = 294, angle = 167 degrees
Position of 1xPflD.mrc (#95) relative to 1unit_PflABCD.mrc (#94) coordinates:
Matrix rotation and translation
-0.04205809 -0.56541269 -0.82373515 678.34340473
-0.82611959 -0.44401593 0.34695285 446.71743157
-0.56192307 0.69509592 -0.44842404 467.46909136
Axis 0.68578189 -0.51572470 -0.51354768
Axis point 0.00000000 434.70163018 529.49245281
Rotation angle (degrees) 165.29577328
Shift along axis -5.25525907
> select subtract #96
2 models selected
> surface dust #95 size 21.4
> view matrix models
> #95,0.98842,0.15143,-0.0098752,547.97,-0.15111,0.98812,0.02792,301.11,0.013986,-0.026104,0.99956,236.65
> hide #!95 models
> show #!95 models
> view matrix models
> #95,0.98842,0.15143,-0.0098752,547.84,-0.15111,0.98812,0.02792,301.06,0.013986,-0.026104,0.99956,237.57
> hide #!95 models
> show #!95 models
> hide #!95 models
> show #!95 models
> ui mousemode right "rotate selected models"
> view matrix models
> #95,0.98973,0.14292,0.00076463,545.98,-0.14287,0.98949,-0.022312,313.97,-0.0039455,0.021974,0.99975,232.44
> hide #!95 models
> show #!95 models
> hide #!95 models
> show #!95 models
> select subtract #95
Nothing selected
> close #96
> save /Users/shoichi/Desktop/For_Composition-maps/Building_Composition.cxs
> includeMaps true
> open "/Users/shoichi/Desktop/For_Composition-maps/Segmented for
> Compositions/Resegment-PflABCD/1xPflC.mrc"
Opened 1xPflC.mrc as #96, grid size 200,200,200, pixel 2.14, shown at level
0.00265, step 1, values float32
> select add #96
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #96,1,0,0,47.658,0,1,0,167.48,0,0,1,-32.861
> view matrix models #96,1,0,0,398.68,0,1,0,90.654,0,0,1,177.19
> view matrix models #96,1,0,0,401.83,0,1,0,160.82,0,0,1,160.74
> hide #!90 models
> view matrix models #96,1,0,0,592.48,0,1,0,257.09,0,0,1,202.08
> view matrix models #96,1,0,0,565.28,0,1,0,293.67,0,0,1,244.67
> ui mousemode right "rotate selected models"
> view matrix models
> #96,0.93537,0.34387,-0.082687,523.43,-0.34961,0.93434,-0.069212,396.82,0.053457,0.093647,0.99417,214.59
> view matrix models
> #96,0.97814,0.19907,0.060063,514.76,-0.19581,0.97904,-0.056063,351.76,-0.069964,0.043077,0.99662,251.11
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #96,0.93537,0.34387,-0.082687,556.57,-0.34961,0.93434,-0.069212,391.56,0.053457,0.093647,0.99417,208.33
> fitmap #96 inMap #94
Fit map 1xPflC.mrc in map 1unit_PflABCD.mrc using 78535 points
correlation = 0.9996, correlation about mean = 0.9994, overlap = 49.99
steps = 220, shift = 16.6, angle = 11.8 degrees
Position of 1xPflC.mrc (#96) relative to 1unit_PflABCD.mrc (#94) coordinates:
Matrix rotation and translation
0.99999792 0.00180027 0.00095518 -0.61225302
-0.00180227 0.99999618 0.00209512 -0.27012088
-0.00095141 -0.00209684 0.99999735 0.43871009
Axis -0.71695761 0.32608723 -0.61614845
Axis point 0.00000000 232.71942073 141.89223067
Rotation angle (degrees) 0.16750063
Shift along axis 0.08056595
> fitmap #96 inMap #94
Fit map 1xPflC.mrc in map 1unit_PflABCD.mrc using 78535 points
correlation = 0.9996, correlation about mean = 0.9994, overlap = 50
steps = 44, shift = 0.0391, angle = 0.00304 degrees
Position of 1xPflC.mrc (#96) relative to 1unit_PflABCD.mrc (#94) coordinates:
Matrix rotation and translation
0.99999790 0.00179596 0.00098457 -0.61146150
-0.00179798 0.99999628 0.00205106 -0.29518315
-0.00098088 -0.00205282 0.99999741 0.44410267
Axis -0.70776292 0.33896566 -0.61981766
Axis point 0.00000000 233.48955235 153.83532488
Rotation angle (degrees) 0.16611180
Shift along axis 0.05745015
> select subtract #96
Nothing selected
> open "/Users/shoichi/Desktop/For_Composition-maps/Segmented for
> Compositions/Resegment-PflABCD/Single-MotA-ring.mrc"
Opened Single-MotA-ring.mrc as #97, grid size 200,200,200, pixel 2.14, shown
at level 0.00252, step 1, values float32
> select add #97
2 models selected
> view matrix models #97,1,0,0,559.27,0,1,0,54.882,0,0,1,225.63
> view matrix models #97,1,0,0,550.32,0,1,0,274.63,0,0,1,233.61
> fitmap #97 inMap #94
Fit map Single-MotA-ring.mrc in map 1unit_PflABCD.mrc using 78731 points
correlation = 0.9998, correlation about mean = 0.9997, overlap = 12.79
steps = 228, shift = 17.3, angle = 10.3 degrees
Position of Single-MotA-ring.mrc (#97) relative to 1unit_PflABCD.mrc (#94)
coordinates:
Matrix rotation and translation
1.00000000 0.00004806 0.00006055 -0.00771370
-0.00004807 1.00000000 0.00005679 0.02316086
-0.00006055 -0.00005679 1.00000000 0.04060887
Axis -0.59202396 0.63123982 -0.50104283
Axis point 661.04108577 0.00000000 138.75851289
Rotation angle (degrees) 0.00549622
Shift along axis -0.00116003
> surface dust #97 size 21.4
> select add #96
4 models selected
> surface dust #96 size 21.4
> surface dust #97 size 21.4
> select clear
> open "/Users/shoichi/Desktop/For_Composition-maps/Segmented for
> Compositions/1xPflAB_region.mrc"
Opened 1xPflAB_region.mrc as #98, grid size 200,200,200, pixel 2.14, shown at
level 0.00102, step 1, values float32
> select add #98
2 models selected
> view matrix models #98,1,0,0,436.2,0,1,0,351.41,0,0,1,126.63
> view matrix models #98,1,0,0,523.29,0,1,0,319.09,0,0,1,220.28
> ui mousemode right "rotate selected models"
> view matrix models
> #98,0.87364,0.48391,-0.050772,457.98,-0.48465,0.87471,-0.0024665,449.48,0.043217,0.026762,0.99871,205.66
> view matrix models
> #98,0.95152,0.29602,-0.08357,488.38,-0.29459,0.95518,0.029281,385.12,0.088492,-0.0032432,0.99607,202.97
> ui mousemode right "translate selected models"
> view matrix models
> #98,0.95152,0.29602,-0.08357,505.6,-0.29459,0.95518,0.029281,327,0.088492,-0.0032432,0.99607,203.92
> view matrix models
> #98,0.95152,0.29602,-0.08357,517.91,-0.29459,0.95518,0.029281,320,0.088492,-0.0032432,0.99607,212.98
> view matrix models
> #98,0.95152,0.29602,-0.08357,534.13,-0.29459,0.95518,0.029281,316.29,0.088492,-0.0032432,0.99607,225.17
> view matrix models
> #98,0.95152,0.29602,-0.08357,530.43,-0.29459,0.95518,0.029281,315.24,0.088492,-0.0032432,0.99607,227.07
> fitmap #98 inMap #94
Fit map 1xPflAB_region.mrc in map 1unit_PflABCD.mrc using 76608 points
correlation = 0.5966, correlation about mean = 0.4565, overlap = 29.71
steps = 664, shift = 32.6, angle = 44.6 degrees
Position of 1xPflAB_region.mrc (#98) relative to 1unit_PflABCD.mrc (#94)
coordinates:
Matrix rotation and translation
0.95592663 0.29045115 0.04292326 -42.30141462
-0.23646452 0.67495658 0.69894073 -91.79425743
0.17403680 -0.67828589 0.71389036 192.50582055
Axis -0.93030712 -0.08856630 -0.35592791
Axis point 0.00000000 180.78761442 218.07439158
Rotation angle (degrees) 47.74845368
Shift along axis -21.03501029
> fitmap #98 inMap #94
Fit map 1xPflAB_region.mrc in map 1unit_PflABCD.mrc using 76608 points
correlation = 0.5966, correlation about mean = 0.4565, overlap = 29.71
steps = 64, shift = 0.00184, angle = 0.00355 degrees
Position of 1xPflAB_region.mrc (#98) relative to 1unit_PflABCD.mrc (#94)
coordinates:
Matrix rotation and translation
0.95592836 0.29044793 0.04290646 -42.29555535
-0.23644047 0.67492038 0.69898382 -91.80116532
0.17405995 -0.67832328 0.71384918 192.51794182
Axis -0.93031831 -0.08858917 -0.35589297
Axis point 0.00000000 180.78184164 218.07817843
Rotation angle (degrees) 47.75138103
Shift along axis -21.03486420
> surface dust #98 size 21.4
> hide #!91 models
> hide #!92 models
> hide #!93 models
> hide #!94 models
> show #!94 models
> hide #!95 models
> hide #!96 models
> hide #!97 models
> ui mousemode right "rotate selected models"
> view matrix models
> #98,0.80298,0.1547,0.57559,457.97,-0.051244,0.98007,-0.19192,297.88,-0.59381,0.12461,0.7949,371.39
> view matrix models
> #98,0.77375,0.41156,0.48159,426.82,-0.30633,0.9085,-0.28423,388,-0.55451,0.072402,0.82902,367.4
> view matrix models
> #98,0.72563,0.66601,0.17291,453.53,-0.61766,0.74121,-0.26288,483.34,-0.30324,0.083957,0.94921,285.18
> ui mousemode right "translate selected models"
> view matrix models
> #98,0.72563,0.66601,0.17291,436.66,-0.61766,0.74121,-0.26288,498.09,-0.30324,0.083957,0.94921,281.71
> ui mousemode right "rotate selected models"
> view matrix models
> #98,0.93121,0.34943,-0.10363,539.57,-0.36429,0.90125,-0.2346,403.49,0.011419,0.25621,0.96655,174.89
> ui mousemode right "translate selected models"
> view matrix models
> #98,0.93121,0.34943,-0.10363,549.55,-0.36429,0.90125,-0.2346,419.89,0.011419,0.25621,0.96655,195.07
> view matrix models
> #98,0.93121,0.34943,-0.10363,540.04,-0.36429,0.90125,-0.2346,424.51,0.011419,0.25621,0.96655,196.08
> fitmap #98 inMap #94
Fit map 1xPflAB_region.mrc in map 1unit_PflABCD.mrc using 76608 points
correlation = 0.8837, correlation about mean = 0.8256, overlap = 43.6
steps = 436, shift = 9.7, angle = 18.1 degrees
Position of 1xPflAB_region.mrc (#98) relative to 1unit_PflABCD.mrc (#94)
coordinates:
Matrix rotation and translation
0.99999726 0.00117357 0.00202402 -0.58103994
-0.00117078 0.99999836 -0.00138321 0.48246498
-0.00202564 0.00138083 0.99999699 0.27982521
Axis 0.50859335 0.74515350 -0.43136882
Axis point 125.65966211 0.00000000 272.99145858
Rotation angle (degrees) 0.15569221
Shift along axis -0.05671046
> fitmap #98 inMap #94
Fit map 1xPflAB_region.mrc in map 1unit_PflABCD.mrc using 76608 points
correlation = 0.8837, correlation about mean = 0.8255, overlap = 43.59
steps = 48, shift = 0.0196, angle = 0.00692 degrees
Position of 1xPflAB_region.mrc (#98) relative to 1unit_PflABCD.mrc (#94)
coordinates:
Matrix rotation and translation
0.99999727 0.00115967 0.00202834 -0.57775370
-0.00115711 0.99999853 -0.00126335 0.43180142
-0.00202980 0.00126100 0.99999714 0.30530944
Axis 0.47529436 0.76407878 -0.43620969
Axis point 133.30782771 0.00000000 266.77772187
Rotation angle (degrees) 0.15215337
Shift along axis -0.07785171
> save /Users/shoichi/Desktop/For_Composition-maps/Building_Composition.cxs
> includeMaps true
——— End of log from Tue Sep 9 11:45:50 2025 ———
opened ChimeraX session
> open "/Users/shoichi/Desktop/For_Composition-maps/Segmented for
> Compositions/Resegment-PflABCD/1xFliL.mrc"
Opened 1xFliL.mrc as #99, grid size 200,200,200, pixel 2.14, shown at level
0.00238, step 1, values float32
> select add #99
2 models selected
> view matrix models #99,1,0,0,412.15,0,1,0,194.7,0,0,1,-151.37
> view matrix models #99,1,0,0,540.78,0,1,0,141.7,0,0,1,232.01
> view matrix models #99,1,0,0,549.52,0,1,0,285.14,0,0,1,213.45
> view matrix models #99,1,0,0,567.09,0,1,0,290.51,0,0,1,228.84
> view matrix models #99,1,0,0,572.06,0,1,0,276.29,0,0,1,237.15
> ui tool show "Fit in Map"
> fitmap #99 inMap #94
Fit map 1xFliL.mrc in map 1unit_PflABCD.mrc using 79950 points
correlation = 0.8654, correlation about mean = 0.8142, overlap = 14.02
steps = 228, shift = 6.94, angle = 10.3 degrees
Position of 1xFliL.mrc (#99) relative to 1unit_PflABCD.mrc (#94) coordinates:
Matrix rotation and translation
0.99999941 0.00067094 -0.00085062 -0.10891124
-0.00067114 0.99999975 -0.00022852 0.34103581
0.00085047 0.00022909 0.99999961 -0.19995192
Axis 0.20663599 -0.76813768 -0.60602481
Axis point 351.42628630 0.00000000 -88.61247436
Rotation angle (degrees) 0.06344247
Shift along axis -0.16329161
> fitmap #99 inMap #94
Fit map 1xFliL.mrc in map 1unit_PflABCD.mrc using 79950 points
correlation = 0.8654, correlation about mean = 0.8146, overlap = 14
steps = 84, shift = 0.04, angle = 0.0091 degrees
Position of 1xFliL.mrc (#99) relative to 1unit_PflABCD.mrc (#94) coordinates:
Matrix rotation and translation
0.99999946 0.00066514 -0.00080258 -0.14033314
-0.00066545 0.99999971 -0.00037983 0.40263590
0.00080232 0.00038036 0.99999961 -0.20619691
Axis 0.34257713 -0.72324753 -0.59962815
Axis point 418.11929545 0.00000000 -83.09150205
Rotation angle (degrees) 0.06357029
Shift along axis -0.21563887
> surface dust #99 size 21.4
> show #!95 models
> hide #!94 models
> show #!93 models
> show #!96 models
> show #!97 models
> show #!92 models
> show #!3 models
> hide #!3 models
> volume gaussian #92 sDev 2
Opened Single_Cage_unit.mrc gaussian as #100, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> close #100
> volume gaussian #92 sDev 2.5
Opened Single_Cage_unit.mrc gaussian as #100, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> surface dust #100 size 58.49
> volume #100 level 0.0004746
> select subtract #99
Nothing selected
> volume gaussian #93 sDev 2.5
Opened 1xMotBpg-09092025.mrc gaussian as #101, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> surface dust #101 size 58.49
> volume #101 level 0.000475
> surface dust #101 size 70
> surface dust #101 size 60
> hide #!95 models
> hide #!96 models
> hide #!97 models
> hide #!98 models
> hide #!99 models
> hide #!100 models
> ui tool show "Map Eraser"
> close #101
> volume gaussian #93 sDev 2
Opened 1xMotBpg-09092025.mrc gaussian as #101, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume erase #101 center 829.76,424.5,513.44 radius 61.846 outside true
> volume erase #101 center 808.45,419.45,496.48 radius 61.846 outside true
> volume erase #101 center 728.23,397.72,499.08 radius 61.846
> volume erase #101 center 764.6,385.97,450.86 radius 61.846
> volume erase #101 center 841.25,386.46,417.05 radius 61.846
> volume erase #101 center 873.63,489.27,496.79 radius 61.846
> close #100
> hide #!101 models
> volume gaussian #92 sDev 2
Opened Single_Cage_unit.mrc gaussian as #100, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume erase #100 center 895.5,406.58,415.67 radius 139.1 outside true
> volume erase #100 center 968.62,589.51,395.09 radius 139.1
> volume erase #100 center 772.1,254.71,380.84 radius 139.1
> volume erase #100 center 1062.1,403.04,504.48 radius 139.1
> volume erase #100 center 1010.4,257.36,382.45 radius 139.1
> volume erase #100 center 1041.3,320.67,445.97 radius 139.1
> volume erase #100 center 710.6,460.67,350.75 radius 139.1
> volume erase #100 center 866.66,228.8,548.32 radius 139.1
> volume #100 level 0.0005759
> surface dust #100 size 70
> show #!101 models
> volume gaussian #95 sDev 2
Opened 1xPflD.mrc gaussian as #103, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> hide #!100 models
> hide #!101 models
> volume erase #103 center 871.21,481.94,542.43 radius 46.652 outside true
> volume erase #103 center 908.86,413.45,538.4 radius 46.652
> volume gaussian #96 sDev 2
Opened 1xPflC.mrc gaussian as #104, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> hide #!103 models
> show #!103 models
> hide #!103 models
> volume erase #104 center 785.1,444.43,565.63 radius 173.13 outside true
> volume erase #104 center 723.77,506.03,771.26 radius 173.13
> volume erase #104 center 679.19,265.08,669.9 radius 173.13
> volume erase #104 center 712.3,653.46,453.51 radius 173.13
> volume erase #104 center 933.46,435.63,382.11 radius 173.13
> volume erase #104 center 686.53,436.27,325.5 radius 173.13
> volume erase #104 center 919.63,250.56,604.23 radius 173.13
> volume erase #104 center 898.54,244.83,603.89 radius 173.13
[Repeated 1 time(s)]
> volume erase #104 center 680.09,206.07,598.64 radius 173.13
> volume erase #104 center 895.71,248.28,603.49 radius 173.13
> volume erase #104 center 681.24,655.87,555.01 radius 173.13
> volume erase #104 center 820.74,703.21,533.09 radius 173.13
> volume erase #104 center 870.76,722.05,585.21 radius 173.13
> volume erase #104 center 959.91,689.99,485.26 radius 173.13
> volume erase #104 center 535.57,456.82,733.8 radius 173.13
> volume erase #104 center 742.24,477.25,675.98 radius 91.378
> volume erase #104 center 707.14,403.77,596.19 radius 33.17
> volume erase #104 center 614.96,420.41,513.49 radius 33.17
> volume erase #104 center 736.63,433.42,613.02 radius 33.17
> volume erase #104 center 834.45,555.87,590.53 radius 33.17
> show #!103 models
> show #!98 models
> hide #!98 models
> volume gaussian #98 sDev 2
Opened 1xPflAB_region.mrc gaussian as #105, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> hide #!103 models
> hide #!104 models
> close #105
> volume gaussian #98 sDev 1.5
Opened 1xPflAB_region.mrc gaussian as #105, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume erase #105 center 781.9,485.71,512.43 radius 147.45 outside true
> volume erase #105 center 758.02,633.26,590.41 radius 147.45
> volume erase #105 center 695.55,312.58,428.26 radius 147.45
> volume erase #105 center 950.23,321.56,442.66 radius 147.45
> volume erase #105 center 793.41,400.92,664.64 radius 147.45
> volume erase #105 center 735.08,553.48,317.21 radius 147.45
> volume erase #105 center 807.62,404.1,298.54 radius 147.45
> volume #105 level 0.0006923
> volume erase #105 center 817.59,488.09,548.79 radius 45.796
> close #105
> volume gaussian #98 sDev 1.5
Opened 1xPflAB_region.mrc gaussian as #105, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume erase #105 center 781.31,461.6,497.58 radius 148.73 outside true
> volume erase #105 center 791.02,318.44,601.06 radius 148.73
> volume erase #105 center 745.49,326.98,361.1 radius 148.73
> volume erase #105 center 759.36,497.86,295.72 radius 148.73
> volume erase #105 center 789.13,543.88,682.73 radius 148.73
> volume erase #105 center 733.56,666.85,457.34 radius 148.73
> volume erase #105 center 961.03,325.33,517.64 radius 148.73
> volume #105 level 0.0009229
> hide #102 models
> show #!99 models
> volume gaussian #99 sDev 2
Opened 1xFliL.mrc gaussian as #106, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> hide #!105 models
> show #102 models
> volume erase #106 center 813.72,389.77,462.24 radius 81.32 outside true
> volume erase #106 center 822.6,364.5,336.25 radius 81.32
> volume erase #106 center 758.13,418.61,344.41 radius 81.32
> volume erase #106 center 697.35,350.59,412.64 radius 81.32
> volume erase #106 center 764.38,274.6,414.23 radius 81.32
> volume erase #106 center 919.39,299.8,428.71 radius 81.32
> volume erase #106 center 690.31,438.35,408.57 radius 81.32
> volume erase #106 center 802.55,400.1,569.96 radius 81.32
> volume erase #106 center 840,286.64,550.41 radius 81.32
> volume erase #106 center 864.62,409.05,368.26 radius 50.076
> volume erase #106 center 870.87,331.2,485.64 radius 50.076
> hide #102 models
> show #!101 models
> show #!103 models
> show #!104 models
> show #!105 models
> show #!100 models
> show #!3 models
> view orient
> save /Users/shoichi/Desktop/For_Composition-maps/Building_Composition.cxs
> includeMaps true
> turn z 21.176471 models #100 center #3
> volume copy #100
Opened Single_Cage_unit.mrc gaussian copy as #107, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #100 show
> turn z 21.176471 models #100 center #3
> volume copy #100
Opened Single_Cage_unit.mrc gaussian copy as #108, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #100 show
> turn z 21.176471 models #100 center #3
> volume copy #100
Opened Single_Cage_unit.mrc gaussian copy as #109, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #100 show
> turn z 21.176471 models #100 center #3
> volume copy #100
Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #100 show
> turn z 21.176471 models #100 center #3
> volume copy #100
Opened Single_Cage_unit.mrc gaussian copy as #111, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #100 show
> turn z 21.176471 models #100 center #3
> volume copy #100
Opened Single_Cage_unit.mrc gaussian copy as #112, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #100 show
> turn z 21.176471 models #100 center #3
> volume copy #100
Opened Single_Cage_unit.mrc gaussian copy as #113, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #100 show
> turn z 21.176471 models #100 center #3
> volume copy #100
Opened Single_Cage_unit.mrc gaussian copy as #114, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #100 show
> turn z 21.176471 models #100 center #3
> volume copy #100
Opened Single_Cage_unit.mrc gaussian copy as #115, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #100 show
> turn z 21.176471 models #100 center #3
> volume copy #100
Opened Single_Cage_unit.mrc gaussian copy as #116, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #100 show
> turn z 21.176471 models #100 center #3
> volume copy #100
Opened Single_Cage_unit.mrc gaussian copy as #117, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #100 show
> turn z 21.176471 models #100 center #3
> volume copy #100
Opened Single_Cage_unit.mrc gaussian copy as #118, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #100 show
> turn z 21.176471 models #100 center #3
> volume copy #100
Opened Single_Cage_unit.mrc gaussian copy as #119, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #100 show
> turn z 21.176471 models #100 center #3
> volume copy #100
Opened Single_Cage_unit.mrc gaussian copy as #120, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #100 show
> turn z 21.176471 models #100 center #3
> volume copy #100
Opened Single_Cage_unit.mrc gaussian copy as #121, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #100 show
> turn z 21.176471 models #100 center #3
> volume copy #100
Opened Single_Cage_unit.mrc gaussian copy as #122, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #100 show
> turn z 21.176471 models #100 center #3
> volume copy #100
Opened Single_Cage_unit.mrc gaussian copy as #123, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #100 show
> turn z 21.176471 models #101 center #3
> volume copy #101
Opened 1xMotBpg-09092025.mrc gaussian copy as #124, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #101 show
> turn z 21.176471 models #101 center #3
> volume copy #101
Opened 1xMotBpg-09092025.mrc gaussian copy as #125, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #101 show
> turn z 21.176471 models #101 center #3
> volume copy #101
Opened 1xMotBpg-09092025.mrc gaussian copy as #126, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #101 show
> turn z 21.176471 models #101 center #3
> volume copy #101
Opened 1xMotBpg-09092025.mrc gaussian copy as #127, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #101 show
> turn z 21.176471 models #101 center #3
> volume copy #101
Opened 1xMotBpg-09092025.mrc gaussian copy as #128, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #101 show
> turn z 21.176471 models #101 center #3
> volume copy #101
Opened 1xMotBpg-09092025.mrc gaussian copy as #129, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #101 show
> turn z 21.176471 models #101 center #3
> volume copy #101
Opened 1xMotBpg-09092025.mrc gaussian copy as #130, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #101 show
> turn z 21.176471 models #101 center #3
> volume copy #101
Opened 1xMotBpg-09092025.mrc gaussian copy as #131, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #101 show
> turn z 21.176471 models #101 center #3
> volume copy #101
Opened 1xMotBpg-09092025.mrc gaussian copy as #132, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #101 show
> turn z 21.176471 models #101 center #3
> volume copy #101
Opened 1xMotBpg-09092025.mrc gaussian copy as #133, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #101 show
> turn z 21.176471 models #101 center #3
> volume copy #101
Opened 1xMotBpg-09092025.mrc gaussian copy as #134, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #101 show
> turn z 21.176471 models #101 center #3
> volume copy #101
Opened 1xMotBpg-09092025.mrc gaussian copy as #135, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #101 show
> turn z 21.176471 models #101 center #3
> volume copy #101
Opened 1xMotBpg-09092025.mrc gaussian copy as #136, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #101 show
> turn z 21.176471 models #101 center #3
> volume copy #101
Opened 1xMotBpg-09092025.mrc gaussian copy as #137, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #101 show
> turn z 21.176471 models #101 center #3
> volume copy #101
Opened 1xMotBpg-09092025.mrc gaussian copy as #138, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #101 show
> turn z 21.176471 models #101 center #3
> volume copy #101
Opened 1xMotBpg-09092025.mrc gaussian copy as #139, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #101 show
> turn z 21.176471 models #101 center #3
> volume copy #101
Opened 1xMotBpg-09092025.mrc gaussian copy as #140, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #101 show
> turn z 21.176471 models #103 center #3
> volume copy #103
Opened 1xPflD.mrc gaussian copy as #141, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #103 show
> turn z 21.176471 models #103 center #3
> volume copy #103
Opened 1xPflD.mrc gaussian copy as #142, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #103 show
> turn z 21.176471 models #103 center #3
> volume copy #103
Opened 1xPflD.mrc gaussian copy as #143, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #103 show
> turn z 21.176471 models #103 center #3
> volume copy #103
Opened 1xPflD.mrc gaussian copy as #144, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #103 show
> turn z 21.176471 models #103 center #3
> volume copy #103
Opened 1xPflD.mrc gaussian copy as #145, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #103 show
> turn z 21.176471 models #103 center #3
> volume copy #103
Opened 1xPflD.mrc gaussian copy as #146, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #103 show
> turn z 21.176471 models #103 center #3
> volume copy #103
Opened 1xPflD.mrc gaussian copy as #147, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #103 show
> turn z 21.176471 models #103 center #3
> volume copy #103
Opened 1xPflD.mrc gaussian copy as #148, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #103 show
> turn z 21.176471 models #103 center #3
> volume copy #103
Opened 1xPflD.mrc gaussian copy as #149, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #103 show
> turn z 21.176471 models #103 center #3
> volume copy #103
Opened 1xPflD.mrc gaussian copy as #150, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #103 show
> turn z 21.176471 models #103 center #3
> volume copy #103
Opened 1xPflD.mrc gaussian copy as #151, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #103 show
> turn z 21.176471 models #103 center #3
> volume copy #103
Opened 1xPflD.mrc gaussian copy as #152, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #103 show
> turn z 21.176471 models #103 center #3
> volume copy #103
Opened 1xPflD.mrc gaussian copy as #153, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #103 show
> turn z 21.176471 models #103 center #3
> volume copy #103
Opened 1xPflD.mrc gaussian copy as #154, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #103 show
> turn z 21.176471 models #103 center #3
> volume copy #103
Opened 1xPflD.mrc gaussian copy as #155, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #103 show
> turn z 21.176471 models #103 center #3
> volume copy #103
Opened 1xPflD.mrc gaussian copy as #156, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #103 show
> turn z 21.176471 models #103 center #3
> volume copy #103
Opened 1xPflD.mrc gaussian copy as #157, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #103 show
> turn z 21.176471 models #104 center #3
> volume copy #104
Opened 1xPflC.mrc gaussian copy as #158, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #104 show
> turn z 21.176471 models #104 center #3
> volume copy #104
Opened 1xPflC.mrc gaussian copy as #159, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #104 show
> turn z 21.176471 models #104 center #3
> volume copy #104
Opened 1xPflC.mrc gaussian copy as #160, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #104 show
> turn z 21.176471 models #104 center #3
> volume copy #104
Opened 1xPflC.mrc gaussian copy as #161, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #104 show
> turn z 21.176471 models #104 center #3
> volume copy #104
Opened 1xPflC.mrc gaussian copy as #162, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #104 show
> turn z 21.176471 models #104 center #3
> volume copy #104
Opened 1xPflC.mrc gaussian copy as #163, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #104 show
> turn z 21.176471 models #104 center #3
> volume copy #104
Opened 1xPflC.mrc gaussian copy as #164, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #104 show
> turn z 21.176471 models #104 center #3
> volume copy #104
Opened 1xPflC.mrc gaussian copy as #165, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #104 show
> turn z 21.176471 models #104 center #3
> volume copy #104
Opened 1xPflC.mrc gaussian copy as #166, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #104 show
> turn z 21.176471 models #104 center #3
> volume copy #104
Opened 1xPflC.mrc gaussian copy as #167, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #104 show
> turn z 21.176471 models #104 center #3
> volume copy #104
Opened 1xPflC.mrc gaussian copy as #168, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #104 show
> turn z 21.176471 models #104 center #3
> volume copy #104
Opened 1xPflC.mrc gaussian copy as #169, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #104 show
> turn z 21.176471 models #104 center #3
> volume copy #104
Opened 1xPflC.mrc gaussian copy as #170, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #104 show
> turn z 21.176471 models #104 center #3
> volume copy #104
Opened 1xPflC.mrc gaussian copy as #171, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #104 show
> turn z 21.176471 models #104 center #3
> volume copy #104
Opened 1xPflC.mrc gaussian copy as #172, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #104 show
> turn z 21.176471 models #104 center #3
> volume copy #104
Opened 1xPflC.mrc gaussian copy as #173, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #104 show
> turn z 21.176471 models #104 center #3
> volume copy #104
Opened 1xPflC.mrc gaussian copy as #174, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #104 show
> turn z 21.176471 models #106 center #3
> volume copy #106
Opened 1xFliL.mrc gaussian copy as #175, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #106 show
> turn z 21.176471 models #106 center #3
> volume copy #106
Opened 1xFliL.mrc gaussian copy as #176, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #106 show
> turn z 21.176471 models #106 center #3
> volume copy #106
Opened 1xFliL.mrc gaussian copy as #177, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #106 show
> turn z 21.176471 models #106 center #3
> volume copy #106
Opened 1xFliL.mrc gaussian copy as #178, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #106 show
> turn z 21.176471 models #106 center #3
> volume copy #106
Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #106 show
> turn z 21.176471 models #106 center #3
> volume copy #106
Opened 1xFliL.mrc gaussian copy as #180, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #106 show
> turn z 21.176471 models #106 center #3
> volume copy #106
Opened 1xFliL.mrc gaussian copy as #181, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #106 show
> turn z 21.176471 models #106 center #3
> volume copy #106
Opened 1xFliL.mrc gaussian copy as #182, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #106 show
> turn z 21.176471 models #106 center #3
> volume copy #106
Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #106 show
> turn z 21.176471 models #106 center #3
> volume copy #106
Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #106 show
> turn z 21.176471 models #106 center #3
> volume copy #106
Opened 1xFliL.mrc gaussian copy as #185, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #106 show
> turn z 21.176471 models #106 center #3
> volume copy #106
Opened 1xFliL.mrc gaussian copy as #186, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #106 show
> turn z 21.176471 models #106 center #3
> volume copy #106
Opened 1xFliL.mrc gaussian copy as #187, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #106 show
> turn z 21.176471 models #106 center #3
> volume copy #106
Opened 1xFliL.mrc gaussian copy as #188, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #106 show
> turn z 21.176471 models #106 center #3
> volume copy #106
Opened 1xFliL.mrc gaussian copy as #189, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #106 show
> turn z 21.176471 models #106 center #3
> volume copy #106
Opened 1xFliL.mrc gaussian copy as #190, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #106 show
> turn z 21.176471 models #106 center #3
> volume copy #106
Opened 1xFliL.mrc gaussian copy as #191, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
> volume #106 show
> show #!79 models
> hide #!79 models
> show #!79 models
> volume #79 level 0.1628
> volume #79 level 0.1593
> surface dust #3 size 43
> surface dust #79 size 43
> surface dust #101 size 21.4
> surface dust #100 size 21.4
> surface dust #103 size 21.4
> surface dust #104 size 21.4
> surface dust #105 size 21.4
> surface dust #106 size 21.4
> surface dust #107 size 21.4
> surface dust #108 size 21.4
> surface dust #109 size 21.4
> surface dust #110 size 21.4
> surface dust #111 size 21.4
> surface dust #112 size 21.4
> surface dust #113 size 21.4
> surface dust #114 size 21.4
> surface dust #115 size 21.4
> surface dust #116 size 21.4
> surface dust #117 size 21.4
> surface dust #118 size 21.4
> surface dust #119 size 21.4
> surface dust #120 size 21.4
> surface dust #121 size 21.4
> surface dust #122 size 21.4
> surface dust #123 size 21.4
> surface dust #124 size 21.4
> surface dust #125 size 21.4
> surface dust #126 size 21.4
> surface dust #127 size 21.4
> surface dust #128 size 21.4
> surface dust #129 size 21.4
> surface dust #130 size 21.4
> surface dust #131 size 21.4
> surface dust #132 size 21.4
> surface dust #133 size 21.4
> surface dust #134 size 21.4
> surface dust #135 size 21.4
> surface dust #136 size 21.4
> surface dust #137 size 21.4
> surface dust #138 size 21.4
> surface dust #139 size 21.4
> surface dust #140 size 21.4
> surface dust #141 size 21.4
> surface dust #142 size 21.4
> surface dust #143 size 21.4
> surface dust #144 size 21.4
> surface dust #145 size 21.4
> surface dust #146 size 21.4
> surface dust #147 size 21.4
> surface dust #148 size 21.4
> surface dust #149 size 21.4
> surface dust #150 size 21.4
> surface dust #151 size 21.4
> surface dust #152 size 21.4
> surface dust #153 size 21.4
> surface dust #154 size 21.4
> surface dust #155 size 21.4
> surface dust #156 size 21.4
> surface dust #157 size 21.4
> surface dust #158 size 21.4
> surface dust #159 size 21.4
> surface dust #160 size 21.4
> surface dust #161 size 21.4
> surface dust #162 size 21.4
> surface dust #163 size 21.4
> surface dust #164 size 21.4
> surface dust #165 size 21.4
> surface dust #166 size 21.4
> surface dust #167 size 21.4
> surface dust #168 size 21.4
> surface dust #169 size 21.4
> surface dust #170 size 21.4
> surface dust #171 size 21.4
> surface dust #172 size 21.4
> surface dust #173 size 21.4
> surface dust #174 size 21.4
> surface dust #175 size 21.4
> surface dust #176 size 21.4
> surface dust #177 size 21.4
> surface dust #178 size 21.4
> surface dust #179 size 21.4
> surface dust #180 size 21.4
> surface dust #181 size 21.4
> surface dust #182 size 21.4
> surface dust #183 size 21.4
> surface dust #184 size 21.4
> surface dust #185 size 21.4
> surface dust #186 size 21.4
> surface dust #187 size 21.4
> surface dust #188 size 21.4
> surface dust #189 size 21.4
> surface dust #190 size 21.4
> surface dust #191 size 21.4
> show #!90 models
> save /Users/shoichi/Desktop/For_Composition-maps/Building_Composition.cxs
> includeMaps true
> show #!97 models
> hide #!97 models
> hide #!90 models
> hide #!100-191 models
> hide #!3 models
> hide #!79 models
> show #!97 models
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-review/PDB/From_PDB/6ykm-
> MotA-only.pdb"
Chain information for 6ykm-MotA-only.pdb #192
---
Chain | Description
A B C D E | No description available
> select add #192
9770 atoms, 9945 bonds, 1275 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> color #97 #737259ff models
> color #97 #737259a6 models
> ui mousemode right "translate selected models"
> view matrix models #192,1,0,0,310.87,0,1,0,-71.092,0,0,1,-263.17
> view matrix models #192,1,0,0,391.76,0,1,0,95.092,0,0,1,29.173
> view matrix models #192,1,0,0,519.88,0,1,0,106.67,0,0,1,-21.308
> view matrix models #192,1,0,0,516.85,0,1,0,73.428,0,0,1,-24.051
> view matrix models #192,1,0,0,517.91,0,1,0,71.221,0,0,1,-27.42
> ui tool show "Fit in Map"
> fitmap #192 inMap #97
Fit molecule 6ykm-MotA-only.pdb (#192) to map Single-MotA-ring.mrc (#97) using
9770 atoms
average map value = 0.01292, steps = 92
shifted from previous position = 2.78
rotated from previous position = 16.5 degrees
atoms outside contour = 2537, contour level = 0.0025221
Position of 6ykm-MotA-only.pdb (#192) relative to Single-MotA-ring.mrc (#97)
coordinates:
Matrix rotation and translation
0.93131251 -0.36421870 -0.00132323 101.07630370
0.35563891 0.90857781 0.21910574 -362.60912716
-0.07860015 -0.20452651 0.97570022 -161.37208721
Axis -0.50502926 0.09212496 0.85817157
Axis point 909.62525032 -203.15588010 0.00000000
Rotation angle (degrees) 24.79756955
Shift along axis -222.93678080
> fitmap #192 inMap #97
Fit molecule 6ykm-MotA-only.pdb (#192) to map Single-MotA-ring.mrc (#97) using
9770 atoms
average map value = 0.01292, steps = 48
shifted from previous position = 0.00729
rotated from previous position = 0.0262 degrees
atoms outside contour = 2539, contour level = 0.0025221
Position of 6ykm-MotA-only.pdb (#192) relative to Single-MotA-ring.mrc (#97)
coordinates:
Matrix rotation and translation
0.93120884 -0.36448253 -0.00160501 101.30546334
0.35597140 0.90850003 0.21888822 -362.59823396
-0.07832278 -0.20440199 0.97574862 -161.50864836
Axis -0.50444835 0.09142700 0.85858777
Axis point 909.38164504 -202.21982554 0.00000000
Rotation angle (degrees) 24.80665576
Shift along axis -222.92399207
> fitmap #192 inMap #97
Fit molecule 6ykm-MotA-only.pdb (#192) to map Single-MotA-ring.mrc (#97) using
9770 atoms
average map value = 0.01292, steps = 40
shifted from previous position = 0.01
rotated from previous position = 0.015 degrees
atoms outside contour = 2536, contour level = 0.0025221
Position of 6ykm-MotA-only.pdb (#192) relative to Single-MotA-ring.mrc (#97)
coordinates:
Matrix rotation and translation
0.93129340 -0.36426674 -0.00152769 101.17469277
0.35573768 0.90856941 0.21898022 -362.58654619
-0.07837920 -0.20447829 0.97572810 -161.46755438
Axis -0.50482262 0.09161791 0.85834741
Axis point 909.74182257 -202.73730925 0.00000000
Rotation angle (degrees) 24.79754405
Shift along axis -222.88995165
> mlp sel
Map values for surface "6ykm-MotA-only.pdb_A SES surface": minimum -26.09,
mean -2.55, maximum 24.94
Map values for surface "6ykm-MotA-only.pdb_B SES surface": minimum -27.18,
mean -2.418, maximum 22.6
Map values for surface "6ykm-MotA-only.pdb_C SES surface": minimum -26.36,
mean -2.366, maximum 24.6
Map values for surface "6ykm-MotA-only.pdb_D SES surface": minimum -26.03,
mean -2.469, maximum 23.72
Map values for surface "6ykm-MotA-only.pdb_E SES surface": minimum -26.34,
mean -2.365, maximum 23.11
To also show corresponding color key, enter the above mlp command and add key
true
> ui tool show "Map Eraser"
> show #102 models
> view matrix models
> #192,0.97885,-0.19883,0.048188,384.41,0.18517,0.96116,0.20465,-13.223,-0.087008,-0.1914,0.97765,12.45
> undo
> select clear
> select add #102
1 model selected
> view matrix models #102,1,0,0,788.35,0,1,0,256.25,0,0,1,288.69
> view matrix models #102,1,0,0,784.54,0,1,0,305.75,0,0,1,416.73
> view matrix models #102,1,0,0,718.1,0,1,0,348.68,0,0,1,409.91
> view matrix models #102,1,0,0,731.08,0,1,0,362.38,0,0,1,395.61
> view matrix models #102,1,0,0,734.14,0,1,0,360.72,0,0,1,396.43
> volume erase #97 center 734.14,360.72,396.43 radius 57.78
> view matrix models #102,1,0,0,759.05,0,1,0,325.9,0,0,1,411.92
> view matrix models #102,1,0,0,747.75,0,1,0,328.06,0,0,1,382.84
> view matrix models #102,1,0,0,757.86,0,1,0,330.48,0,0,1,382.37
> volume erase #97 center 757.86,330.48,382.37 radius 57.78
> view matrix models #102,1,0,0,786.76,0,1,0,312.14,0,0,1,387.44
> view matrix models #102,1,0,0,803.59,0,1,0,313.69,0,0,1,379.29
> view matrix models #102,1,0,0,804.48,0,1,0,337.58,0,0,1,373.35
> view matrix models #102,1,0,0,818.78,0,1,0,337.73,0,0,1,376.33
> view matrix models #102,1,0,0,792.94,0,1,0,334.51,0,0,1,371.06
> view matrix models #102,1,0,0,793.98,0,1,0,338.04,0,0,1,370.31
> volume erase #97 center 793.98,338.04,370.31 radius 34.026
> view matrix models #102,1,0,0,830.25,0,1,0,321.5,0,0,1,375.05
> view matrix models #102,1,0,0,828.35,0,1,0,333.31,0,0,1,377.56
> view matrix models #102,1,0,0,825.74,0,1,0,335.74,0,0,1,372.92
> volume erase #97 center 825.74,335.74,372.92 radius 34.026
> view matrix models #102,1,0,0,901.77,0,1,0,340.29,0,0,1,357.06
> view matrix models #102,1,0,0,900.5,0,1,0,433.21,0,0,1,350.14
> view matrix models #102,1,0,0,865.47,0,1,0,457.69,0,0,1,353.3
> view matrix models #102,1,0,0,860.08,0,1,0,465.23,0,0,1,366.42
> view matrix models #102,1,0,0,865.43,0,1,0,455.46,0,0,1,363.77
> view matrix models #102,1,0,0,865.17,0,1,0,456.67,0,0,1,368.81
> view matrix models #102,1,0,0,864.49,0,1,0,455.82,0,0,1,367.83
> volume erase #97 center 864.49,455.82,367.83 radius 34.026
> view matrix models #102,1,0,0,867.81,0,1,0,480.17,0,0,1,444.3
> select subtract #102
Nothing selected
> hide #102 models
> hide #!97 models
> show #!97 models
> volume gaussian #97 sDev 3
Opened Single-MotA-ring.mrc gaussian as #193, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> close #192
> show #102 models
> select add #102
1 model selected
> view matrix models #102,1,0,0,887.49,0,1,0,431.5,0,0,1,364.44
> view matrix models #102,1,0,0,868.09,0,1,0,448.32,0,0,1,341.15
> view matrix models #102,1,0,0,807.1,0,1,0,406.62,0,0,1,348.07
> close #193
> volume gaussian #97 sDev 2.5
Opened Single-MotA-ring.mrc gaussian as #192, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> view matrix models #102,1,0,0,803.3,0,1,0,389.04,0,0,1,345.78
> view matrix models #102,1,0,0,803.04,0,1,0,388.19,0,0,1,344.76
> volume erase #192 center 803.04,388.19,344.76 radius 95.872 outside true
> view matrix models #102,1,0,0,880.05,0,1,0,312.71,0,0,1,375.72
> view matrix models #102,1,0,0,911.02,0,1,0,290.22,0,0,1,367.19
> view matrix models #102,1,0,0,903.26,0,1,0,290.16,0,0,1,356.47
> volume erase #192 center 903.26,290.16,356.47 radius 95.872
> view matrix models #102,1,0,0,704.54,0,1,0,494.29,0,0,1,454.96
> view matrix models #102,1,0,0,920.06,0,1,0,337.52,0,0,1,465.3
> view matrix models #102,1,0,0,954.27,0,1,0,349.71,0,0,1,390.14
> view matrix models #102,1,0,0,937.78,0,1,0,341.52,0,0,1,354.61
> volume erase #192 center 937.78,341.52,354.61 radius 95.872
> view matrix models #102,1,0,0,666.62,0,1,0,406.86,0,0,1,403.15
> view matrix models #102,1,0,0,660.26,0,1,0,395.83,0,0,1,351.92
> view matrix models #102,1,0,0,661.04,0,1,0,391.4,0,0,1,351.38
> volume erase #192 center 661.04,391.4,351.38 radius 95.872
> view matrix models #102,1,0,0,676.12,0,1,0,484.84,0,0,1,354.56
> view matrix models #102,1,0,0,702.87,0,1,0,477.99,0,0,1,428.6
> view matrix models #102,1,0,0,700.58,0,1,0,477.63,0,0,1,427.48
> volume erase #192 center 700.58,477.63,427.48 radius 95.872
> view matrix models #102,1,0,0,883.6,0,1,0,474.85,0,0,1,475.41
> view matrix models #102,1,0,0,932.14,0,1,0,438.27,0,0,1,440.71
> volume erase #192 center 932.14,438.27,440.71 radius 95.872
> view matrix models #102,1,0,0,768.92,0,1,0,240.95,0,0,1,416.7
> view matrix models #102,1,0,0,793.99,0,1,0,270.9,0,0,1,420.59
> volume erase #192 center 793.99,270.9,420.59 radius 95.872
> view matrix models #102,1,0,0,676.43,0,1,0,405.35,0,0,1,378.69
> view matrix models #102,1,0,0,782.9,0,1,0,435.12,0,0,1,230.53
> view matrix models #102,1,0,0,765.87,0,1,0,440.24,0,0,1,190.93
> view matrix models #102,1,0,0,743.92,0,1,0,443.98,0,0,1,207.31
> volume erase #192 center 743.92,443.98,207.31 radius 95.872
> view matrix models #102,1,0,0,925.02,0,1,0,347.27,0,0,1,398.05
> view matrix models #102,1,0,0,935.11,0,1,0,333.41,0,0,1,394.61
> view matrix models #102,1,0,0,933.41,0,1,0,336.1,0,0,1,396.05
> volume erase #192 center 933.41,336.1,396.05 radius 95.872
> view matrix models #102,1,0,0,870.11,0,1,0,279.66,0,0,1,377.67
> view matrix models #102,1,0,0,870.66,0,1,0,278.42,0,0,1,378.1
> view matrix models #102,1,0,0,879.46,0,1,0,272.12,0,0,1,393.49
> view matrix models #102,1,0,0,859.15,0,1,0,261.05,0,0,1,400.57
> view matrix models #102,1,0,0,842.56,0,1,0,273,0,0,1,410.65
> view matrix models #102,1,0,0,844.02,0,1,0,277.85,0,0,1,413.99
> volume erase #192 center 844.02,277.85,413.99 radius 95.872
> volume #192 level 0.0009973
> view matrix models #102,1,0,0,693.07,0,1,0,376.22,0,0,1,306.54
> view matrix models #102,1,0,0,654.03,0,1,0,430.61,0,0,1,272.39
> view matrix models #102,1,0,0,683.58,0,1,0,476.06,0,0,1,279.66
> view matrix models #102,1,0,0,686.22,0,1,0,476.68,0,0,1,282.82
> volume erase #192 center 686.22,476.68,282.82 radius 95.872
> view matrix models #102,1,0,0,643.64,0,1,0,373.51,0,0,1,242.64
> select subtract #102
Nothing selected
> hide #102 models
> show #!3 models
> view orient
> turn z 21.176471 models #192 center #3
> volume copy #192
Opened Single-MotA-ring.mrc gaussian copy as #193, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #192 show
> turn z 21.176471 models #192 center #3
> volume copy #192
Opened Single-MotA-ring.mrc gaussian copy as #194, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #192 show
> turn z 21.176471 models #192 center #3
> volume copy #192
Opened Single-MotA-ring.mrc gaussian copy as #195, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #192 show
> turn z 21.176471 models #192 center #3
> volume copy #192
Opened Single-MotA-ring.mrc gaussian copy as #196, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #192 show
> turn z 21.176471 models #192 center #3
> volume copy #192
Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #192 show
> turn z 21.176471 models #192 center #3
> volume copy #192
Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #192 show
> turn z 21.176471 models #192 center #3
> volume copy #192
Opened Single-MotA-ring.mrc gaussian copy as #199, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #192 show
> turn z 21.176471 models #192 center #3
> volume copy #192
Opened Single-MotA-ring.mrc gaussian copy as #200, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #192 show
> turn z 21.176471 models #192 center #3
> volume copy #192
Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #192 show
> turn z 21.176471 models #192 center #3
> volume copy #192
Opened Single-MotA-ring.mrc gaussian copy as #202, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #192 show
> turn z 21.176471 models #192 center #3
> volume copy #192
Opened Single-MotA-ring.mrc gaussian copy as #203, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #192 show
> turn z 21.176471 models #192 center #3
> volume copy #192
Opened Single-MotA-ring.mrc gaussian copy as #204, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #192 show
> turn z 21.176471 models #192 center #3
> volume copy #192
Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #192 show
> turn z 21.176471 models #192 center #3
> volume copy #192
Opened Single-MotA-ring.mrc gaussian copy as #206, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #192 show
> turn z 21.176471 models #192 center #3
> volume copy #192
Opened Single-MotA-ring.mrc gaussian copy as #207, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #192 show
> turn z 21.176471 models #192 center #3
> volume copy #192
Opened Single-MotA-ring.mrc gaussian copy as #208, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #192 show
> turn z 21.176471 models #192 center #3
> volume copy #192
Opened Single-MotA-ring.mrc gaussian copy as #209, grid size 200,200,200,
pixel 2.14, shown at step 1, values float32
> volume #192 show
> save /Users/shoichi/Desktop/For_Composition-maps/Building_Composition.cxs
> includeMaps true
> hide #!192 models
> hide #!192-209 models
> show #!98 models
> show #!90 models
> color #98 #b2ffffe5 models
> color #98 #b2ffff75 models
> color #98 #b2fffff5 models
> ui tool show "Segment Map"
Segmenting 1xPflAB_region.mrc, density threshold 0.001017
Showing 675 region surfaces
23655 watershed regions, grouped to 675 regions
Showing 1xPflAB_region.seg - 675 regions, 675 surfaces
> select add #102
676 models selected
> select clear
> select #102.5
1 model selected
> select add #102.3
2 models selected
> select add #102.1
3 models selected
> select add #102.6
4 models selected
> select add #102.2
5 models selected
> select add #102.7
6 models selected
> select add #102.4
7 models selected
> select add #102.8
8 models selected
Opened 1xPflAB_region_imasked as #210, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
Segmenting 1xPflAB_region_imasked, density threshold 0.001017
Showing 8 region surfaces
648 watershed regions, grouped to 8 regions
Showing 1xPflAB_region_imasked.seg - 8 regions, 8 surfaces
> select add #102
9 models selected
> view matrix models #102,1,0,0,566.55,0,1,0,259.03,0,0,1,150.41
> view matrix models #102,1,0,0,578.08,0,1,0,255.38,0,0,1,143.97
> view matrix models #102,1,0,0,577.11,0,1,0,271.9,0,0,1,244.58
> view matrix models #102,1,0,0,588.42,0,1,0,262.38,0,0,1,243.75
> ui mousemode right "rotate selected models"
> view matrix models
> #102,0.97772,0.20961,-0.010793,550.06,-0.20924,0.97745,0.028377,302.47,0.016498,-0.025486,0.99954,246.07
> ui mousemode right "translate selected models"
> view matrix models
> #102,0.97772,0.20961,-0.010793,538.58,-0.20924,0.97745,0.028377,319.31,0.016498,-0.025486,0.99954,246.45
> ui mousemode right "rotate selected models"
> view matrix models
> #102,0.98149,0.19125,-0.010081,541.64,-0.19094,0.98126,0.025775,315.43,0.014822,-0.023373,0.99962,246.3
> select clear
> select #102.4
1 model selected
> select add #102.7
2 models selected
> select add #102.8
3 models selected
> select add #102.2
4 models selected
> select add #102.6
5 models selected
> select add #102.1
6 models selected
Grouped 6 regions
> hide #!98 models
> show #!98 models
> hide #!98 models
> hide #!210 models
> show #!210 models
> hide #!210 models
Opened 1xPflAB_region_imasked_imasked as #211, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> save "/Users/shoichi/Desktop/For_Composition-maps/Segmented for
> Compositions/Resegment-PflABCD/PflAB_wout_FlgYoverlap.mrc" models #211
> close #210-211
> hide #!102 models
> select add #102
4 models selected
> show #!98 models
> open "/Users/shoichi/Desktop/For_Composition-maps/Segmented for
> Compositions/Resegment-PflABCD/PflAB_wout_FlgYoverlap.mrc"
Opened PflAB_wout_FlgYoverlap.mrc as #210, grid size 200,200,200, pixel 2.14,
shown at level 0.000859, step 1, values float32
> select subtract #102
Nothing selected
> select add #210
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #210,1,0,0,578.72,0,1,0,299.37,0,0,1,-24.019
> view matrix models #210,1,0,0,597.07,0,1,0,372.63,0,0,1,194.65
> view matrix models #210,1,0,0,582.41,0,1,0,264.41,0,0,1,235.27
> view matrix models #210,1,0,0,582.02,0,1,0,269.07,0,0,1,236.36
> ui mousemode right "rotate selected models"
> view matrix models
> #210,0.99419,0.10498,0.023912,555.81,-0.10552,0.99417,0.022294,288.03,-0.021432,-0.024687,0.99947,246.29
> ui mousemode right "translate selected models"
> view matrix models
> #210,0.99419,0.10498,0.023912,549.46,-0.10552,0.99417,0.022294,288.68,-0.021432,-0.024687,0.99947,247.85
> ui mousemode right "rotate selected models"
> view matrix models
> #210,0.97904,0.19809,0.04735,527.87,-0.20002,0.97897,0.040111,308.25,-0.038409,-0.048742,0.99807,256.89
> ui mousemode right "translate selected models"
> view matrix models
> #210,0.97904,0.19809,0.04735,523.15,-0.20002,0.97897,0.040111,316.32,-0.038409,-0.048742,0.99807,259.68
> ui tool show "Fit in Map"
> fitmap #210 inMap #98
Fit map PflAB_wout_FlgYoverlap.mrc in map 1xPflAB_region.mrc using 78673
points
correlation = 0.9999, correlation about mean = 0.9999, overlap = 42.54
steps = 116, shift = 4.67, angle = 3.81 degrees
Position of PflAB_wout_FlgYoverlap.mrc (#210) relative to 1xPflAB_region.mrc
(#98) coordinates:
Matrix rotation and translation
0.99999941 0.00097539 -0.00048027 -0.15166260
-0.00097521 0.99999945 0.00038164 0.17245805
0.00048065 -0.00038117 0.99999981 -0.04876032
Axis -0.33103101 -0.41700049 -0.84648040
Axis point 185.12467932 148.96149283 0.00000000
Rotation angle (degrees) 0.06601510
Shift along axis 0.01956459
> hide #!98 models
> hide #!90 models
> show #!90 models
> hide #!90 models
> hide #!3 models
> save /Users/shoichi/Desktop/For_Composition-maps/Building_Composition.cxs
> includeMaps true
> ui tool show "Map Eraser"
> volume erase #210 center 835.67,491,484.11 radius 101.9 outside true
Opened PflAB_wout_FlgYoverlap.mrc copy as #212, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume erase #212 center 823.89,475.9,348.44 radius 101.86
> volume erase #212 center 801.02,500.32,620.78 radius 101.86
> volume erase #212 center 829.94,495.06,519.59 radius 24.396
> volume erase #212 center 841.94,492.69,530.53 radius 24.396
> volume erase #212 center 827.71,490.99,487.99 radius 14.124
> volume erase #212 center 783.67,459.74,522.55 radius 14.124
> volume erase #212 center 789.67,438.9,515.7 radius 14.124
> volume erase #212 center 755.55,439.13,496.87 radius 14.124
[Repeated 1 time(s)]
> volume erase #212 center 787.55,562.02,481.72 radius 44.512
> volume erase #212 center 728.45,527.69,481.76 radius 44.512
> volume erase #212 center 798.57,566.03,524.86 radius 44.512
> volume erase #212 center 929.77,486.91,451.38 radius 44.512
> volume erase #212 center 903.46,411.82,475.64 radius 44.512
> volume erase #212 center 878.86,414.21,523.76 radius 44.512
> volume erase #212 center 843.04,448.66,511.91 radius 14.124
> volume erase #212 center 809.36,484.73,510.77 radius 14.124
> volume erase #212 center 845.37,512.41,449.17 radius 14.124
[Repeated 1 time(s)]
> hide #211 models
> show #!210 models
> hide #!210 models
> select subtract #210
Nothing selected
> view orient
> show #!3 models
> view orient
> turn z 21.176471 models #212 center #3
> volume copy #212
Opened PflAB_wout_FlgYoverlap.mrc copy as #213, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #212 show
> turn z 21.176471 models #212 center #3
> volume copy #212
Opened PflAB_wout_FlgYoverlap.mrc copy as #214, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #212 show
> turn z 21.176471 models #212 center #3
> volume copy #212
Opened PflAB_wout_FlgYoverlap.mrc copy as #215, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #212 show
> turn z 21.176471 models #212 center #3
> volume copy #212
Opened PflAB_wout_FlgYoverlap.mrc copy as #216, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #212 show
> turn z 21.176471 models #212 center #3
> volume copy #212
Opened PflAB_wout_FlgYoverlap.mrc copy as #217, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #212 show
> turn z 21.176471 models #212 center #3
> volume copy #212
Opened PflAB_wout_FlgYoverlap.mrc copy as #218, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #212 show
> turn z 21.176471 models #212 center #3
> volume copy #212
Opened PflAB_wout_FlgYoverlap.mrc copy as #219, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #212 show
> turn z 21.176471 models #212 center #3
> volume copy #212
Opened PflAB_wout_FlgYoverlap.mrc copy as #220, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #212 show
> turn z 21.176471 models #212 center #3
> volume copy #212
Opened PflAB_wout_FlgYoverlap.mrc copy as #221, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #212 show
> turn z 21.176471 models #212 center #3
> volume copy #212
Opened PflAB_wout_FlgYoverlap.mrc copy as #222, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #212 show
> turn z 21.176471 models #212 center #3
> volume copy #212
Opened PflAB_wout_FlgYoverlap.mrc copy as #223, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #212 show
> turn z 21.176471 models #212 center #3
> volume copy #212
Opened PflAB_wout_FlgYoverlap.mrc copy as #224, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #212 show
> turn z 21.176471 models #212 center #3
> volume copy #212
Opened PflAB_wout_FlgYoverlap.mrc copy as #225, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #212 show
> turn z 21.176471 models #212 center #3
> volume copy #212
Opened PflAB_wout_FlgYoverlap.mrc copy as #226, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #212 show
> turn z 21.176471 models #212 center #3
> volume copy #212
Opened PflAB_wout_FlgYoverlap.mrc copy as #227, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #212 show
> turn z 21.176471 models #212 center #3
> volume copy #212
Opened PflAB_wout_FlgYoverlap.mrc copy as #228, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #212 show
> turn z 21.176471 models #212 center #3
> volume copy #212
Opened PflAB_wout_FlgYoverlap.mrc copy as #229, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #212 show
> show #!90 models
> surface dust #3 size 43
> surface dust #90 size 21.4
> surface dust #212 size 21.4
> surface dust #213 size 21.4
> surface dust #214 size 21.4
> surface dust #215 size 21.4
> surface dust #216 size 21.4
> surface dust #217 size 21.4
> surface dust #218 size 21.4
> surface dust #219 size 21.4
> surface dust #220 size 21.4
> surface dust #221 size 21.4
> surface dust #222 size 21.4
> surface dust #223 size 21.4
> surface dust #224 size 21.4
> surface dust #225 size 21.4
> surface dust #226 size 21.4
> surface dust #227 size 21.4
> surface dust #228 size 21.4
> surface dust #229 size 21.4
> close #213-229
> volume gaussian #212 sDev 2
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian as #213, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #213 level 0.000211
> close #213
> volume gaussian #212 sDev 1.5
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian as #213, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #213 level 0.0002265
> surface dust #3 size 43
> surface dust #90 size 21.4
> surface dust #213 size 21.4
> view orient
> turn z 21.176471 models #213 center #3
> volume copy #213
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #214, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #213 show
> turn z 21.176471 models #213 center #3
> volume copy #213
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #215, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #213 show
> turn z 21.176471 models #213 center #3
> volume copy #213
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #213 show
> turn z 21.176471 models #213 center #3
> volume copy #213
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #213 show
> turn z 21.176471 models #213 center #3
> volume copy #213
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #213 show
> turn z 21.176471 models #213 center #3
> volume copy #213
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #219, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #213 show
> turn z 21.176471 models #213 center #3
> volume copy #213
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #220, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #213 show
> turn z 21.176471 models #213 center #3
> volume copy #213
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #221, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #213 show
> turn z 21.176471 models #213 center #3
> volume copy #213
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #222, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #213 show
> turn z 21.176471 models #213 center #3
> volume copy #213
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #223, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #213 show
> turn z 21.176471 models #213 center #3
> volume copy #213
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #224, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #213 show
> turn z 21.176471 models #213 center #3
> volume copy #213
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #225, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #213 show
> turn z 21.176471 models #213 center #3
> volume copy #213
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #213 show
> turn z 21.176471 models #213 center #3
> volume copy #213
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #213 show
> turn z 21.176471 models #213 center #3
> volume copy #213
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #213 show
> turn z 21.176471 models #213 center #3
> volume copy #213
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #213 show
> turn z 21.176471 models #213 center #3
> volume copy #213
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size
200,200,200, pixel 2.14, shown at step 1, values float32
> volume #213 show
> surface dust #213-230 size 58.49
> surface dust #213-230 size 70.49
> surface dust #213-230 size 90.49
> volume #228 level 0.0004499
> volume #213-230 level 0.0004499
> save /Users/shoichi/Desktop/For_Composition-maps/Building_Composition.cxs
> includeMaps true
> volume #90 level 0.01875
> volume #90 level 0.01518
> volume #90 level 0.02124
> volume #90 level 0.02053
> volume gaussian #90 sDev 1.5
Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14,
shown at step 1, values float32
> close #231
> volume #90 level 0.01518
> volume gaussian #90 sDev 1
Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14,
shown at step 1, values float32
> close #231
> volume gaussian #90 sDev 1.5
Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14,
shown at step 1, values float32
> volume #231 level 0.01124
> save /Users/shoichi/Desktop/For_Composition-maps/Building_Composition.cxs
> includeMaps true
> show #!91 models
> volume #91 level 0.001924
> hide #!213 models
> hide #!213-231 models
> ui tool show "Segment Map"
Segmenting MS-ring_New.mrc, density threshold 0.001924
Showing 111 region surfaces
5377 watershed regions, grouped to 111 regions
Showing MS-ring_New.seg - 111 regions, 111 surfaces
> select add #102
112 models selected
> ui mousemode right "translate selected models"
> view matrix models #102,1,0,0,134.06,0,1,0,22.057,0,0,1,235.23
> view matrix models #102,1,0,0,216.74,0,1,0,265.66,0,0,1,164.2
> view matrix models #102,1,0,0,61,0,1,0,246.94,0,0,1,179.32
> view matrix models #102,1,0,0,59.391,0,1,0,246.74,0,0,1,178.18
> hide #!91 models
> show #!91 models
> hide #!91 models
> show #!91 models
> select clear
> select #102.43
1 model selected
> select add #102.30
2 models selected
> select #102.43
1 model selected
> select add #102.60
2 models selected
> select add #102.22
3 models selected
Grouped 3 regions
> select #102.22
1 model selected
Ungrouped to 3 regions
> select #102.112
1 model selected
Ungrouped to 2 regions
Ungrouped to 13 regions
> select subtract #102.114
12 models selected
Grouped 12 regions
> select add #102.60
2 models selected
> select add #102.30
3 models selected
> select #102.30
1 model selected
Ungrouped to 2 regions
> select subtract #102.113
1 model selected
> select #102.113
1 model selected
Ungrouped to 9 regions
> select subtract #102.118
8 models selected
Grouped 8 regions
> select add #102.112
2 models selected
> select add #102.60
3 models selected
> select add #102.22
4 models selected
> select add #102.24
5 models selected
Grouped 5 regions
> select add #102.43
2 models selected
> select add #102.34
3 models selected
> select add #102.37
4 models selected
Grouped 4 regions
> select #102.81
1 model selected
Ungrouped to 2 regions
Ungrouped to 11 regions
> select subtract #102.117
10 models selected
Grouped 10 regions
> select #102.117
1 model selected
Ungrouped to 2 regions
> select subtract #102.34
1 model selected
> select add #102.24
2 models selected
> select add #102.22
3 models selected
Grouped 3 regions
> select #102.114
1 model selected
Ungrouped to 3 regions
Ungrouped to 0 regions
> select #102.30
1 model selected
> select add #102.22
2 models selected
> select #102.30
1 model selected
> select #102.74
1 model selected
> select add #102.18
2 models selected
Ungrouped to 5 regions
Ungrouped to 39 regions
Ungrouped to 113 regions
> select subtract #102.247
112 models selected
> select subtract #102.43
111 models selected
Grouped 111 regions
> select #102.129
1 model selected
> select add #102.130
2 models selected
> select #102.60
1 model selected
> select add #102.130
2 models selected
> select add #102.129
3 models selected
> select add #102.151
4 models selected
Grouped 4 regions
> select #102.16
1 model selected
> select #102.80
1 model selected
> select add #102.60
2 models selected
> select #102.80
1 model selected
> select add #102.60
2 models selected
Grouped 2 regions
> select add #102.41
2 models selected
> select add #102.32
3 models selected
> select add #102.52
4 models selected
> select #102.52
1 model selected
Ungrouped to 2 regions
Ungrouped to 13 regions
> select subtract #102.81
12 models selected
Grouped 12 regions
> select add #102.82
2 models selected
> select #102.32
1 model selected
> select add #102.36
2 models selected
> select #102.36
1 model selected
> select #102.36
1 model selected
Ungrouped to 2 regions
Ungrouped to 17 regions
> select subtract #102.119
16 models selected
Grouped 16 regions
> select add #102.32
2 models selected
> select add #102.52
3 models selected
> select add #102.35
4 models selected
> select add #102.22
5 models selected
Grouped 5 regions
> select #102.82
1 model selected
Ungrouped to 2 regions
Ungrouped to 10 regions
Ungrouped to 37 regions
> select #102.52
1 model selected
> select add #102.22
2 models selected
> select #102.22
1 model selected
> select #102.16
1 model selected
> select add #102.41
2 models selected
> select #102.41
1 model selected
> select add #102.22
2 models selected
Grouped 2 regions
> select add #102.60
2 models selected
Grouped 2 regions
> select #102.16
1 model selected
Ungrouped to 3 regions
Ungrouped to 26 regions
Ungrouped to 83 regions
> select subtract #102.216
82 models selected
> select subtract #102.217
81 models selected
Grouped 81 regions
> select add #102.22
2 models selected
Grouped 2 regions
Drag select of 4720, 858 of 940 triangles, 4879, 4874, 4882, 4881, 4936, 4935,
4934, 4889, 4718, 700 of 764 triangles, 4710, 946 of 1008 triangles, 4876,
4711, 854 of 896 triangles, 4705, 722 of 756 triangles
Grouped 15 regions
Opened MS-ring_New_imasked as #211, grid size 256,256,256, pixel 2.14, shown
at step 1, values float32
> save "/Users/shoichi/Desktop/For_Composition-maps/Segmented for
> Compositions/Resegment_for-C17_FlgY/MS-ring_New_polished.mrc" models #211
> hide #!102 models
> select add #102
147 models selected
> select subtract #102
Nothing selected
> select add #211
2 models selected
> hide #!91 models
> volume gaussian #211 sDev 2
Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel
2.14, shown at step 1, values float32
> close #232
> volume gaussian #211 sDev 1.5
Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel
2.14, shown at step 1, values float32
> volume #232 level 0.009738
> save /Users/shoichi/Desktop/For_Composition-maps/Building_Composition.cxs
> includeMaps true
> select subtract #211
Nothing selected
> show #!212 models
> show #!212-231 models
> close #211
> hide #!212 models
> show #!212 models
> hide #!230 models
> hide #!229 models
> show #!230 models
> show #!229 models
> hide #!212 models
> hide #!229 models
> show #!229 models
> hide #!213 models
> hide #!230 models
> show #!230 models
> hide #!230 models
> show #!230 models
> hide #!230 models
> hide #!229 models
> hide #!228 models
> show #!230 models
> show #!229 models
> show #!228 models
> hide #!214 models
> show #!214 models
> hide #!214 models
> show #!214 models
> hide #!214 models
> hide #!230 models
> show #!230 models
> hide #!215 models
> show #!215 models
> show #!214 models
> show #!213 models
> close #213
> show #!212 models
> hide #!212 models
> show #!212 models
> hide #!212 models
> close #212
> show #!210 models
> hide #!210 models
> close #210
> show #!209 models
> show #!192-208 models
> hide #!209 models
> hide #!192 models
> show #!192 models
> hide #!208 models
> show #!208 models
> show #!209 models
> hide #!209 models
> close #209
> show #!175-191 models
> hide #!175 models
> hide #!191 models
> show #!191 models
> show #!175 models
> show #!168-174 models
> show #!158-174 models
> hide #!158 models
> show #!158 models
> hide #!174 models
> show #!174 models
> show #!141-157 models
> hide #!141 models
> show #!141 models
> hide #!157 models
> show #!157 models
> hide #!141 models
> show #!141 models
> show #!124 models
> show #!140 models
> show #!125-139 models
> show #!107 models
> show #!123 models
> show #!108-122 models
> show #!79 models
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/07252025/Original-map-deposit/Seg/Basal_disk.mrc"
Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at
level 0.128, step 1, values float32
> volume #209 level 0.1571
> close #79
> color #209 #797979ff models
> close #4-76
> show #!80 models
> show #!77 models
> hide #!77 models
> show #!82 models
> hide #!82 models
> show #!82 models
> close #81
> close #78
> show #!77 models
> show #!83 models
> close #84-86
> show #!87 models
> hide #!87 models
> show #!88 models
> hide #!88 models
> show #!90 models
> close #90-106
> show #!88 models
> show #!89 models
> color #88 #70887aff models
> color #89 #70887aff models
> save /Users/shoichi/Desktop/For_Composition-
> maps/Cleanup_Building_Composition.cxs includeMaps true
——— End of log from Tue Sep 9 13:34:58 2025 ———
opened ChimeraX session
> open "/Users/shoichi/Desktop/For_Composition-maps/Segmented for
> Compositions/WT_Deposited_Maps/C-Vrings.mrc"
Opened C-Vrings.mrc as #4, grid size 250,250,250, pixel 4.3, shown at level
0.0283, step 1, values float32
> open "/Users/shoichi/Desktop/For_Composition-maps/Segmented for
> Compositions/WT_Deposited_Maps/C-Vrings.mrc"
Opened C-Vrings.mrc as #5, grid size 250,250,250, pixel 4.3, shown at level
0.0283, step 1, values float32
> hide #!80 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> hide #!5 models
> hide #!77 models
> show #!77 models
> close #77
> show #!4 models
> close #5,80
> close #2
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!107 models
> color #4 #797979ff models
> hide #!107-232 models
> hide #!89 models
> hide #!83 models
> hide #!82 models
> hide #!4 models
> hide #!3 models
> ui tool show "Map Eraser"
> volume erase #88 center 101.29,313.39,686.09 radius 138.91
> close #2
> show #!107-232 models
> show #!89 models
> show #!3 models
> show #!4 models
> show #!82 models
> save /Users/shoichi/Desktop/For_Composition-
> maps/Cleanup_Building_Composition.cxs includeMaps true
> view orient
> turn x 90
[Repeated 2 time(s)]
> color #158-174 #7b80ffff models
> color #141-157 #adffc1ff models
> color #107-123 #0b6dffff models
> view orient
> ui tool show "Side View"
> color #214-230 #ff0002ff models
> color #231 #dbb3e2ff models
> color #232 #348e42ff models
> color #175-191 #e2cf7bff models
> color #192-208 #a69b32ff models
> color #124-140 #be41c5ff models
> color #124-140 #b86006ff models
> save /Users/shoichi/Desktop/For_Composition-
> maps/Cleanup_Building_Composition.cxs includeMaps true
> hide #!4 models
> hide #!4-209 models
> hide #!231 models
> hide #!232 models
> ui tool show "Surface Color"
> color radial #214.1 palette #ff0000:#ffffff:#0000ff
> color radial #214.1 palette 337.7,#ff0000:429.9,#ffffff:522,#0000ff center
> 821.11,612.79,486.31
Surface Color: could not parse center "0" as 3 numbers
> color radial #214.1 palette #ff0000:#ffffff:#0000ff
Surface Color: could not parse center "0" as 3 numbers
> color radial #214.1 palette #ff0000:#ffffff:#0000ff
Surface Color: could not parse center "0" as 3 numbers
> color radial #214.1 palette 337.7,#ff0000:429.9,#ffffff:522,#0000ff
Surface Color: could not parse center "0" as 3 numbers
> color radial #214.1 palette 337.7,#ff0000:429.9,#ffffff:522,#0000ff
> color radial #214.1 palette 337.7,#ff0000:429.9,#ffffff:522,#0000ff center
> 821.11,612.79,486.31
> color radial #214.1 palette 137.7,#ff0000:429.9,#ffffff:522,#0000ff center
> 821.11,612.79,486.31
[Repeated 1 time(s)]
> color radial #214.1 palette 137.7,#ff0000:129.9,#ffffff:122,#0000ff center
> 821.11,612.79,486.31
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette 137.7,#ff0000:129.9,#ffffff:122,#0000ff
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette 137.7,#ff0000:129.9,#ffffff:122,#0000ff
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette 17.7,#ff0000:129.9,#ffffff:122,#0000ff
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette 97.7,#ff0000:129.9,#ffffff:122,#0000ff
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette 117.7,#ff0000:129.9,#ffffff:122,#0000ff
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette 117.7,#ff0000:129.9,#ffffff:122,#0000ff
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette #ff0000:#ffffff:#0000ff
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette #ff0000:#ffffff:#0000ff
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette #ff0000:#ffffff:#0000ff:#808080:#808080:#808080
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette
> 337.7,#ff0000:374.6,#ff0000:411.4,#0000ff:448.3,#808080:485.1,#808080:522,#808080
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette
> 337.7,#ff0000:374.6,#ff0000:411.4,#ff0000:448.3,#808080:485.1,#808080:522,#808080
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette
> 337.7,#ff0000:374.6,#ff0000:411.4,#ff0000:448.3,#808080:485.1,#808080:522,#808080
Surface Color: could not parse center "" as 3 numbers
> color cylindrical #214.1 palette
> 337.7,#ff0000:374.6,#ff0000:411.4,#ff0000:448.3,#808080:485.1,#808080:522,#808080
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette
> 337.7,#ff0000:374.6,#ff0000:411.4,#ff0000:448.3,#808080:485.1,#808080:522,#808080
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette
> 337.7,#ff0000:374.6,#ff0000:390.4,#ff0000:448.3,#808080:485.1,#808080:522,#808080
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette
> 337.7,#ff0000:374.6,#ff0000:400.4,#ff0000:448.3,#808080:485.1,#808080:522,#808080
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette
> 337.7,#ff0000:374.6,#ff0000:410.4,#ff0000:448.3,#808080:485.1,#808080:522,#808080
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette
> 337.7,#ff0000:374.6,#ff0000:410.4,#ff0000:448.3,#808080:485.1,#808080:522,#808080
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette
> 337.7,#ff0000:374.6,#ff0000:410.4,#ff0000:448.3,#923e6f:485.1,#808080:522,#808080
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette
> 337.7,#ff0000:374.6,#ff0000:410.4,#ff0000:448.3,#923e6f:485.1,#ff40ff:522,#ff40ff
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette
> 337.7,#ff0000:374.6,#ff0000:405.4,#ff0000:448.3,#923e6f:485.1,#ff40ff:522,#ff40ff
Surface Color: could not parse center "" as 3 numbers
> color radial #214.1 palette
> 337.7,#ff0000:374.6,#ff0000:405.4,#ff0000:448.3,#923e6f:485.1,#ff40ff:522,#ff40ff
> color radial #214.1 palette
> 337.7,#ff0000:374.6,#ff0000:405.4,#ff0000:448.3,#923e6f:485.1,#ff40ff:522,#ff40ff
> center 614.38,336.59,237.88
[Repeated 2 time(s)]
> color radial #214.1 palette
> 337.7,#ff0000:374.6,#ff0000:405.4,#ff0000:448.3,#923e6f:485.1,#ff40ff:522,#ff40ff
> center 537.21,536.85,714.3
> color radial #214.1 palette
> 337.7,#ff0000:374.6,#ff0000:405.4,#ff0000:448.3,#923e6f center
> 537.21,536.85,714.3
[Repeated 1 time(s)]
> color radial #214.1 palette
> 337.7,#ff0000:374.6,#ff0000:405.4,#ff40ff:448.3,#923e6f center
> 537.21,536.85,714.3
> color cylindrical #214.1 palette
> 337.7,#ff0000:374.6,#ff0000:405.4,#ff40ff:448.3,#923e6f center
> 537.21,536.85,714.3
> color cylindrical #214.1 palette
> 337.7,#ff0000:374.6,#ff0000:405.4,#ff40ff:448.3,#923e6f center
> 537.21,536.85,714.3 axis 0,0,0
> color cylindrical #214.1 palette
> 337.7,#ff0000:374.6,#ff0000:405.4,#ff40ff:448.3,#923e6f center
> 537.21,536.85,714.3 axis 0,0,-1
> color cylindrical #214.1 palette
> 337.7,#ff0000:354.6,#ff0000:405.4,#ff40ff:448.3,#923e6f center
> 537.21,536.85,714.3 axis 0,0,-1
> color cylindrical #214.1 palette
> 337.7,#ff0000:354.6,#ff0000:405.4,#ff40ff:448.3,#923e6f center
> 537.21,536.85,714.3 axis 0,-1,-1
> color cylindrical #214.1 palette
> 337.7,#ff0000:354.6,#ff0000:405.4,#ff40ff:448.3,#923e6f center
> 537.21,536.85,714.3 axis 0,-0.5,-1
> color cylindrical #214.1 palette
> 337.7,#ff0000:354.6,#ff0000:405.4,#ff40ff:448.3,#923e6f center
> 537.21,536.85,714.3 axis 0,1,-1
> color cylindrical #214.1 palette
> 337.7,#ff0000:354.6,#ff0000:415.4,#ff40ff:448.3,#923e6f center
> 537.21,536.85,714.3 axis 0,1,-1
> color radial #214.1 palette
> 337.7,#ff0000:354.6,#ff0000:415.4,#ff40ff:448.3,#923e6f center
> 537.21,536.85,714.3
[Repeated 2 time(s)]
> color radial #214.1 palette
> 337.7,#ff0000:354.6,#ff0000:415.4,#ff40ff:448.3,#923e6f center
> 821.11,612.79,486.31
> show #!232 models
> color radial #214.1 palette
> 337.7,#ff0000:354.6,#ff0000:415.4,#ff40ff:448.3,#923e6f center
> 536.27,535.94,464.54
> color radial #214.1 palette 337.7,#ff0000:354.6,#ff0000:415.4,#ff40ff center
> 536.27,535.94,464.54
[Repeated 1 time(s)]
> color radial #214.1 palette 137.7,#ff0000:354.6,#ff0000:415.4,#ff40ff center
> 536.27,535.94,464.54
[Repeated 1 time(s)]
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> hide #!215 models
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> show #!215 models
> show #!216 models
> show #!217 models
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[Repeated 1 time(s)]
> hide #!215 models
> hide #!216 models
> hide #!217 models
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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> showTool true
> ui mousemode right "color key"
> help help:user/tools/surfacecolor.html
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[Repeated 1 time(s)]
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[Repeated 2 time(s)]
> color cylindrical #214.1 palette
> #ff0000:#ff0000:#ff0000:#e13e63:#ff40ff:#ff40ff:#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
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> center 536.27,535.94,464.54 axis 0,0,0
> color radial #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:306.8,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54
[Repeated 2 time(s)]
> color radial #214.1 palette
> #ff0000:#ff0000:#ff0000:#ff0000:#ff40ff:#ff40ff:#ff40ff center
> 536.27,535.94,464.54
> color radial #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:306.8,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54
[Repeated 1 time(s)]
> color radial #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:300.8,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54
> color cylindrical #214.1 palette
> #ff0000:#ff0000:#ff0000:#ff0000:#ff40ff:#ff40ff:#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:306.8,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:286.8,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:289.8,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,0
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:290,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,0
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:299,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,0
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:310,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:290,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:290,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,-1
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:290,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:290,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,2
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:290,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,3
[Repeated 2 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:290,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,-3
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:290,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,-2
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:290,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,0
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,-2,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,2,0
[Repeated 2 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,4,0
[Repeated 2 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,2,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,5,0
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,4,0
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,-2,0
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,-5,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,5,0
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,2,0
[Repeated 4 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,0
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,-2,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,2,0
[Repeated 4 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,2,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,-2,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 1,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis -1,0,0
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,0
> select ~sel & ##selected
Nothing selected
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis -1,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis -2,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 2,0,0
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,-2
[Repeated 2 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,-2,-2
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,2,-2
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,-2
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,10,-2
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,-100,-2
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,-2
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,-100,-2
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,-2
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,-10
[Repeated 2 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,0
[Repeated 2 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,100
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,-10
> color cylindrical #214.1 palette
> 213.6,#ff0000:244.6,#ff0000:275.7,#ff0000:285,#ff0000:337.9,#ff40ff:369,#ff40ff:400,#ff40ff
> center 536.27,535.94,464.54 axis 0,0,0
[Repeated 2 time(s)]
> color cylindrical #214.1 palette 213.6,#ff0000:244.6,#ff0000:275.7,#ed00e2
> center 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette 213.6,#ff0000:244.6,#ff0000:305.7,#ed00e2
> center 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette 213.6,#ff0000:244.6,#ff0000:505.7,#ed00e2
> center 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette 213.6,#ff0000:244.6,#ff0000:405.7,#ed00e2
> center 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette 213.6,#ff0000:244.6,#ff0000:355.7,#ed00e2
> center 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette #ff0000:#ff0000:#ed00e2:#ff0000 center
> 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:275.7,#ff0000:337.9,#ff0000:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:275.7,#ff0000:30.9,#ff0000:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:275.7,#ff0000:300.9,#ff0000:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:275.7,#ff0000:280.9,#ff0000:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:235.7,#ff0000:280.9,#ff0000:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:235.7,#ff0000:240.9,#ff0000:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:235.7,#ff0000:250.9,#ff0000:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:235.7,#ff0000:260.9,#ff0000:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
[Repeated 2 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:235.7,#ff0000:270.9,#ff0000:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
[Repeated 2 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:235.7,#ff0000:280.9,#ff0000:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:235.7,#ff0000:280.9,#ff40ff:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:235.7,#ff0000:380.9,#ff40ff:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:235.7,#ff0000:480.9,#ff40ff:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:235.7,#ff0000:480.9,#ff40ff:500,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:235.7,#ff0000:450.9,#ff40ff:500,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
> color cylindrical #214.1 palette
> 213.6,#ff0000:235.7,#ff0000:420.9,#ff40ff:500,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
> color radial #214.1 palette
> 213.6,#ff0000:235.7,#ff0000:420.9,#ff40ff:500,#ff40ff center
> 536.27,535.94,464.54
[Repeated 7 time(s)]
> color radial #214.1 palette #ff0000:#ff0000:#ff40ff:#ff40ff center
> 536.27,535.94,464.54
[Repeated 1 time(s)]
> color radial #214.1 palette
> 213.6,#ff0000:275.7,#ff0000:337.9,#ff40ff:400,#ff40ff center
> 536.27,535.94,464.54
[Repeated 1 time(s)]
> color radial #214.1 palette
> 213.6,#ff0000:285.7,#ff0000:337.9,#ff40ff:400,#ff40ff center
> 536.27,535.94,464.54
> color radial #214.1 palette
> 213.6,#ff0000:285,#ff0000:337.9,#ff40ff:400,#ff40ff center
> 536.27,535.94,464.54
> color radial #214.1 palette
> 213.6,#ff0000:285,#ff0000:347.9,#ff40ff:400,#ff40ff center
> 536.27,535.94,464.54
> color radial #214.1 palette
> 213.6,#ff0000:285,#ff0000:335.9,#ff40ff:400,#ff40ff center
> 536.27,535.94,464.54
> color radial #214.1 palette
> 213.6,#ff0000:285,#ff0000:333.9,#ff40ff:400,#ff40ff center
> 536.27,535.94,464.54
[Repeated 1 time(s)]
> color radial #214.1 palette
> 213.6,#ff0000:288,#ff0000:333.9,#ff40ff:400,#ff40ff center
> 536.27,535.94,464.54
> color cylindrical #214.1 palette
> 213.6,#ff0000:288,#ff0000:333.9,#ff40ff:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,-1
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:288,#ff0000:333.9,#ff40ff:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,-2
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:288,#ff0000:333.9,#ff40ff:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,2
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:288,#ff0000:333.9,#ff40ff:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,5
[Repeated 3 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:280,#ff0000:333.9,#ff40ff:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,5
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:270,#ff0000:333.9,#ff40ff:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,5
> color cylindrical #214.1 palette
> 213.6,#ff0000:270,#ff0000:333.9,#ff40ff:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
[Repeated 1 time(s)]
> color cylindrical #214.1 palette #ff0000:#ff0000:#ff40ff:#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 213.6,#ff0000:275.7,#ff0000:337.9,#ff40ff:400,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
[Repeated 1 time(s)]
> color cylindrical #214.1 palette #ff0000:#ff0000:#ff40ff:#ff40ff center
> 536.27,535.94,464.54 axis 0,0,10
> close #2
> ui mousemode right "map eraser"
> color cylindrical #214.1 palette
> 211.8,#ff0000:274,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
[Repeated 1 time(s)]
> color cylindrical #214.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
[Repeated 1 time(s)]
> color cylindrical #215.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54 axis 0,0,0
> show #!215 models
> show #!216 models
> show #!217 models
> color radial #214.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54
[Repeated 1 time(s)]
> color radial #230.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54
> color radial #231.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54
> color radial #229.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54
> color radial #228.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54
> color radial #227.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54
> color radial #226.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54
> color radial #225.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54
> color radial #224.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54
> color radial #223.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54
> color radial #222.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54
> color radial #221.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54
> color radial #220.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54
> color radial #219.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54
> color radial #218.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54
> color radial #217.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54
> color radial #216.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54
> color radial #215.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54
> color radial #214.1 palette
> 211.8,#ff0000:278,#ff0000:336.1,#ff40ff:398.2,#ff40ff center
> 536.27,535.94,464.54
> show #!231 models
> color #231 #dbb3e2ff models
> color #231 #ff0002ff models
> hide #!231 models
> show #!231 models
> color radial #231.1 palette
> 211.8,#dbb3e2:278,#dbb3e2:336.1,#ff0002:398.2,#ff0002 center
> 534.95,535.83,501.33
> color radial #231.1 palette #dbb3e2:#dbb3e2:#ff0002:#ff0002 center
> 534.95,535.83,501.33
> color radial #231.1 palette
> 69.6,#dbb3e2:126.8,#dbb3e2:184,#ff0002:241.3,#ff0002 center
> 534.95,535.83,501.33
> color radial #231.1 palette
> 69.6,#f6d9ff:126.8,#f6d9ff:184,#ff0002:241.3,#ff0002 center
> 534.95,535.83,501.33
[Repeated 1 time(s)]
> color #231 orchid models
> color radial #231.1 palette
> 69.6,#f6d9ff:126.8,#fbbdff:184,#ff0002:241.3,#ff0002 center
> 534.95,535.83,501.33
> color radial #231.1 palette
> 69.6,#fdd5f8:126.8,#fbbdff:184,#ff0002:241.3,#ff0002 center
> 534.95,535.83,501.33
[Repeated 2 time(s)]
> color radial #231.1 palette
> 69.6,#fdd5f8:126.8,#fdd5f8:184,#ff0002:241.3,#ff0002 center
> 534.95,535.83,501.33
> color radial #231.1 palette
> 69.6,#fdd5f8:136.8,#fdd5f8:184,#ff0002:241.3,#ff0002 center
> 534.95,535.83,501.33
[Repeated 1 time(s)]
> color radial #231.1 palette
> 69.6,#fdd5f8:140.8,#fdd5f8:184,#ff0002:241.3,#ff0002 center
> 534.95,535.83,501.33
[Repeated 1 time(s)]
> color radial #231.1 palette
> 69.6,#fdd5f8:145.8,#fdd5f8:184,#ff0002:241.3,#ff0002 center
> 534.95,535.83,501.33
> color radial #231.1 palette
> 69.6,#fdd5f8:155.8,#fdd5f8:184,#ff0002:241.3,#ff0002 center
> 534.95,535.83,501.33
> color radial #231.1 palette
> 69.6,#fdd5f8:160.8,#fdd5f8:184,#ff0002:241.3,#ff0002 center
> 534.95,535.83,501.33
> color radial #231.1 palette
> 69.6,#fdd5f8:160.8,#fdd5f8:184,#ed92a9:241.3,#ff0002 center
> 534.95,535.83,501.33
> color radial #231.1 palette
> 69.6,#fdd5f8:155.8,#fdd5f8:184,#ed92a9:241.3,#ff0002 center
> 534.95,535.83,501.33
[Repeated 2 time(s)]
> color radial #231.1 palette
> 69.6,#fdd5f8:155.8,#fdd5f8:180,#ed92a9:241.3,#ff0002 center
> 534.95,535.83,501.33
> color radial #231.1 palette
> 69.6,#fdd5f8:155.8,#fdd5f8:170,#ed92a9:241.3,#ff0002 center
> 534.95,535.83,501.33
> show #!209 models
> show #!208 models
> show #!207 models
> show #!206 models
> show #!107-205 models
> show #!89 models
> show #!88 models
> show #!4 models
> save /Users/shoichi/Desktop/For_Composition-
> maps/Cleanup2_Building_Composition.cxs includeMaps true
> view orient
> turn x 90
[Repeated 2 time(s)]
> save /Users/shoichi/Desktop/Composition1.png supersample 2
> transparentBackground true
> turn x 20
> turn x -20
> turn x 10
> hide #!3 models
> show #!3 models
> hide #!88 models
> show #!82 models
> hide #!82 models
> show #!88 models
> view orient
> turn x 90
[Repeated 2 time(s)]
> turn x 10
> save /Users/shoichi/Desktop/Composition2.png supersample 2
> transparentBackground true
> turn x -10
> turn y 90
[Repeated 3 time(s)]
> turn y 10
[Repeated 8 time(s)]
> turn x 10
> save /Users/shoichi/Desktop/Composition2.png supersample 2
> transparentBackground true
> hide #!4 models
> hide #!88 models
> hide #!89 models
> hide #!107-140 models
> hide #!209 models
> turn x 10
> show #!88-140 models
> show #!83 models
> turn x -10
[Repeated 1 time(s)]
> turn x 15
> view name P1
> show #!209 models
> save /Users/shoichi/Desktop/Composition2.png supersample 2
> transparentBackground true
> hide #!209 models
> hide #!83 models
> hide #!88 models
> hide #!107-140 models
> hide #!175-232 models
> show #!107 models
> show #!108 models
> show #!109 models
> show #!110 models
> show #!111 models
> show #!112 models
> show #!113 models
> show #!114 models
> show #!115 models
> show #!116 models
> show #!117 models
> show #!118 models
> show #!119 models
> show #!120 models
> show #!121 models
> show #!122 models
> hide #!122 models
> show #!122 models
> show #!214 models
> show #!215 models
> show #!216 models
> show #!217 models
> show #!218 models
> show #!219 models
> show #!220 models
> show #!221 models
> show #!222 models
> show #!223 models
> show #!224 models
> show #!225 models
> show #!226 models
> show #!227 models
> show #!228 models
> show #!229 models
> hide #!141-174 models
> show #!230 models
> show #!231 models
> turn x -15
> turn x 20
> turn x 5
> show #!123 models
> view name P2
> show #!175-232 models
> show #!124-174 models
> show #!88 models
> turn x -5
> show #!4 models
> save /Users/shoichi/Desktop/Composition2.png supersample 2
> transparentBackground true
> hide #!88 models
> hide #!89 models
> hide #!4 models
> hide #!3 models
> hide #!209 models
> hide #!175-232 models
> hide #!107-123 models
> hide #!107-140 models
> save /Users/shoichi/Desktop/Composition_medial.png supersample 2
> transparentBackground true
> hide #!141-174 models
> show #!107-140 models
> show #!175-191 models
> show #!214-232 models
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> view P2
> turn x 205
> turn x -205
> turn x -20
> view p2
Expected an objects specifier or a view name or a keyword
> view P2
> view -25
Expected an objects specifier or a view name or a keyword
> turn x 25
> turn x -25
[Repeated 1 time(s)]
> select add #107
2 models selected
> select add #108
4 models selected
> select add #109
6 models selected
> select add #110
8 models selected
> select add #111
10 models selected
> select add #112
12 models selected
> select add #113
14 models selected
> select add #115
16 models selected
> select add #114
18 models selected
> select add #116
20 models selected
> select add #117
22 models selected
> select add #118
24 models selected
> select add #119
26 models selected
> select add #120
28 models selected
> select add #121
30 models selected
> select add #122
32 models selected
> ui mousemode right "crop volume"
> volume #232 region 0,0,26,255,255,255
> volume #231 region 3,0,0,255,255,255
> volume #231 region 0,0,0,255,255,255
> select add #123
34 models selected
> hide #!124-232 models
> volume sel showOutlineBox true
> volume #116 region 0,0,0,199,199,199
> volume #115 region 0,0,0,192,199,199
> volume #116 region 0,0,0,199,199,199
[Repeated 1 time(s)]
> view orient
> turn x 90
[Repeated 2 time(s)]
> volume #120 region 0,0,2,199,199,199
> select clear
> volume #120 region 0,0,61,199,199,199
> volume #121 region 0,0,62,199,199,199
> volume #122 region 0,0,0,199,199,199
[Repeated 1 time(s)]
> volume #119 region 0,0,0,199,199,199
> select clear
> hide #!107 models
> show #!107 models
> hide #!107 models
> hide #!108 models
> hide #!109 models
> hide #!110 models
> hide #!111 models
> hide #!112 models
> hide #!113 models
> hide #!114 models
> hide #!115 models
> hide #!116 models
> hide #!117 models
> hide #!118 models
> hide #!122 models
> show #!122 models
> hide #!123 models
> hide #!122 models
> hide #!119 models
> volume #121 region 0,0,62,199,199,199
> volume #121 region 0,0,62,190,199,199
> volume #121 region 0,0,0,190,199,199
> hide #!120 models
> show #!120 models
> hide #!121 models
> volume #120 region 0,0,0,199,199,199
> show #!121 models
> show #!122 models
> volume #!120-122 showOutlineBox false
> show #!107 models
> show #!108 models
> show #!109 models
> show #!110 models
> show #!111 models
> show #!112 models
> show #!113 models
> show #!114 models
> show #!115 models
> show #!116 models
> show #!118 models
> show #!117 models
> show #!119 models
> show #!123 models
> view P2
> volume #!107-123 showOutlineBox false
> select ~sel & ##selected
Nothing selected
> view P1
> view P2
> show #!89 models
> hide #!89 models
> hide #!108 models
> hide #!109 models
> hide #!110 models
> hide #!111 models
> hide #!112 models
> hide #!107 models
> hide #!113 models
> hide #!114 models
> hide #!115 models
> hide #!123 models
> hide #!122 models
> hide #!121 models
> hide #!120 models
> hide #!119 models
> hide #!118 models
> hide #!117 models
> volume #116 region 0,0,0,199,199,199
> volume #!116 showOutlineBox true
> volume #116 region 0,0,61,199,199,199
> volume #!116 showOutlineBox false
> show #!107 models
> show #!108 models
> show #!109 models
> show #!110 models
> show #!111 models
> show #!112 models
> show #!113 models
> show #!115 models
> show #!114 models
> show #!117 models
> show #!118 models
> show #!119 models
> show #!120 models
> show #!121 models
> show #!122 models
> show #!123 models
> volume #107-123 region 0,0,61,199,199,199
> view P2
> show #!124 models
> show #!125 models
> show #!126 models
> show #!127 models
> show #!128 models
> show #!129 models
> show #!130 models
> show #!131 models
> show #!132 models
> show #!133 models
> show #!134 models
> show #!135 models
> show #!136 models
> show #!137 models
> show #!138 models
> show #!139 models
> show #!140 models
> show #!175-191 models
> show #!214-232 models
> save /Users/shoichi/Desktop/Composition3_medial.png supersample 2
> transparentBackground true
> hide #!214-232 models
> hide #!175-191 models
> hide #!107-140 models
> show #!192-208 models
> show #!4 models
> hide #!4 models
> hide #!192 models
> hide #!193 models
> hide #!194 models
> hide #!195 models
> hide #!196 models
> hide #!197 models
> hide #!198 models
> hide #!199 models
> hide #!200 models
> hide #!201 models
> hide #!202 models
> hide #!203 models
> hide #!204 models
> hide #!205 models
> hide #!206 models
> hide #!207 models
> hide #!208 models
> show #!107 models
> hide #!107 models
> show #!118 models
> hide #!118 models
> show #!115 models
> volume #!115 showOutlineBox true
> volume #115 region 0,0,61,190,199,199
> volume #115 region 0,0,0,190,199,199
> volume #115 region 0,0,0,199,199,199
> volume #115 region 0,0,0,199,199,71
> volume #!115 showOutlineBox false
> view P2
> volume #107-123 region 0,0,0,199,199,71
> show #!107 models
> show #!108 models
> show #!109 models
> show #!110 models
> show #!111 models
> show #!112 models
> show #!113 models
> show #!114 models
> show #!116 models
> show #!117 models
> show #!118 models
> show #!119 models
> show #!120 models
> show #!121 models
> show #!122 models
> show #!123 models
> show #!192-208 models
> show #!4 models
> save /Users/shoichi/Desktop/Composition4_medial.png supersample 2
> transparentBackground true
> save /Users/shoichi/Desktop/For_Composition-
> maps/Cleanup3_Building_Composition.cxs includeMaps true
——— End of log from Tue Sep 9 15:35:44 2025 ———
opened ChimeraX session
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/09092025/For_Composition-maps/Individual-
> MOdels/1xPflCD_Cage.pdb"
Chain information for 1xPflCD_Cage.pdb #2
---
Chain | Description
A D | No description available
B E | No description available
C F | No description available
L X | No description available
c | No description available
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/09092025/For_Composition-maps/Segmented for
> Compositions/Resegment-PflABCD/1unit_PflABCD.mrc"
Opened 1unit_PflABCD.mrc as #5, grid size 200,200,200, pixel 2.14, shown at
level 0.0254, step 1, values float32
> show #!167 models
> select add #5
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,80.692,0,1,0,230.3,0,0,1,221.48
> volume #5 level 0.008421
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.6421,0.50185,-0.57953,470.1,-0.70423,-0.68485,0.1872,606.29,-0.30294,0.52833,0.79316,245.39
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.6421,0.50185,-0.57953,483.03,-0.70423,-0.68485,0.1872,692.04,-0.30294,0.52833,0.79316,292.23
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.61177,0.59906,-0.51658,446.98,-0.77868,-0.57101,0.26,672.85,-0.13922,0.56132,0.81581,247.87
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.61177,0.59906,-0.51658,427.64,-0.77868,-0.57101,0.26,661.19,-0.13922,0.56132,0.81581,225.95
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.95336,0.20464,-0.22189,496.22,-0.26238,-0.92522,0.27407,608.04,-0.14921,0.31951,0.93576,240.2
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.95336,0.20464,-0.22189,525,-0.26238,-0.92522,0.27407,604.74,-0.14921,0.31951,0.93576,250.78
> view matrix models
> #5,-0.95336,0.20464,-0.22189,510.51,-0.26238,-0.92522,0.27407,600.04,-0.14921,0.31951,0.93576,217.04
> volume #5 level 0.004039
> ui tool show "Fit in Map"
> fitmap #2 inMap #167
Fit molecule 1xPflCD_Cage.pdb (#2) to map 1xPflC.mrc gaussian copy (#167)
using 16838 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 16838, contour level = 0.0010738
Position of 1xPflCD_Cage.pdb (#2) relative to 1xPflC.mrc gaussian copy (#167)
coordinates:
Matrix rotation and translation
-0.93089425 -0.36503026 -0.01374048 661.01120682
0.36496286 -0.93099409 0.00721828 514.09260469
-0.01542720 0.00170469 0.99987954 -232.71151912
Axis -0.00755270 0.00231052 0.99996881
Axis point 280.98545554 319.62206504 0.00000000
Rotation angle (degrees) 158.59192822
Shift along axis -236.50885839
> fitmap #2 inMap #167
Fit molecule 1xPflCD_Cage.pdb (#2) to map 1xPflC.mrc gaussian copy (#167)
using 16838 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 16838, contour level = 0.0010738
Position of 1xPflCD_Cage.pdb (#2) relative to 1xPflC.mrc gaussian copy (#167)
coordinates:
Matrix rotation and translation
-0.93089425 -0.36503026 -0.01374048 661.01120682
0.36496286 -0.93099409 0.00721828 514.09260469
-0.01542720 0.00170469 0.99987954 -232.71151912
Axis -0.00755270 0.00231052 0.99996881
Axis point 280.98545554 319.62206504 0.00000000
Rotation angle (degrees) 158.59192822
Shift along axis -236.50885839
> fitmap #2 inMap #167
Fit molecule 1xPflCD_Cage.pdb (#2) to map 1xPflC.mrc gaussian copy (#167)
using 16838 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 16838, contour level = 0.0010738
Position of 1xPflCD_Cage.pdb (#2) relative to 1xPflC.mrc gaussian copy (#167)
coordinates:
Matrix rotation and translation
-0.93089425 -0.36503026 -0.01374048 661.01120682
0.36496286 -0.93099409 0.00721828 514.09260469
-0.01542720 0.00170469 0.99987954 -232.71151912
Axis -0.00755270 0.00231052 0.99996881
Axis point 280.98545554 319.62206504 0.00000000
Rotation angle (degrees) 158.59192822
Shift along axis -236.50885839
> view matrix models
> #5,-0.95336,0.20464,-0.22189,513.13,-0.26238,-0.92522,0.27407,604.03,-0.14921,0.31951,0.93576,224.15
> hide #2 models
> show #2 models
> fitmap #5 inMap #167
Fit map 1unit_PflABCD.mrc in map 1xPflC.mrc gaussian copy using 190573 points
correlation = 0.5216, correlation about mean = 0.3123, overlap = 47.08
steps = 344, shift = 27.3, angle = 21 degrees
Position of 1unit_PflABCD.mrc (#5) relative to 1xPflC.mrc gaussian copy (#167)
coordinates:
Matrix rotation and translation
0.99999427 -0.00337820 -0.00022407 0.72474418
0.00337640 0.99996544 -0.00759714 1.76410533
0.00024973 0.00759634 0.99997112 -1.22720418
Axis 0.91339733 -0.02848334 0.40607144
Axis point 0.00000000 168.49545384 231.86504758
Rotation angle (degrees) 0.47653568
Shift along axis 0.11339922
> fitmap #5 inMap #167
Fit map 1unit_PflABCD.mrc in map 1xPflC.mrc gaussian copy using 190573 points
correlation = 0.5216, correlation about mean = 0.3123, overlap = 47.08
steps = 348, shift = 0.0392, angle = 0.0232 degrees
Position of 1unit_PflABCD.mrc (#5) relative to 1xPflC.mrc gaussian copy (#167)
coordinates:
Matrix rotation and translation
0.99999449 -0.00329623 -0.00039375 0.75967208
0.00329329 0.99996837 -0.00723968 1.66087378
0.00041760 0.00723834 0.99997372 -1.20368478
Axis 0.90898107 -0.05093893 0.41371324
Axis point 0.00000000 173.29551538 229.41493132
Rotation angle (degrees) 0.45630135
Shift along axis 0.10794406
> hide #!167 models
> show #!167 models
> hide #!167 models
> show #!167 models
> hide #!167 models
> hide #!116 models
> show #!116 models
> hide #!5 models
> show #!5 models
> hide #!107-208 models
> hide #!4 models
> select subtract #5
Nothing selected
> hide #2 models
> show #!116 models
> hide #!5 models
> ui mousemode right "crop volume"
> volume #!116 showOutlineBox true
> volume #116 region 0,0,0,199,199,199
> volume #!116 showOutlineBox false
> show #!5 models
> fitmap #5 inMap #116
Fit map 1unit_PflABCD.mrc in map Single_Cage_unit.mrc gaussian copy using
190573 points
correlation = 0.3822, correlation about mean = 0.2659, overlap = 25.07
steps = 152, shift = 5.38, angle = 3.77 degrees
Position of 1unit_PflABCD.mrc (#5) relative to Single_Cage_unit.mrc gaussian
copy (#116) coordinates:
Matrix rotation and translation
0.99999606 0.00065533 0.00272954 -0.53391967
-0.00065318 0.99999948 -0.00078927 0.34391796
-0.00273006 0.00078748 0.99999597 1.00968152
Axis 0.27038883 0.93623691 -0.22438877
Axis point 365.53335285 0.00000000 191.28738668
Rotation angle (degrees) 0.16705855
Shift along axis -0.04893842
> fitmap #5 inMap #116
Fit map 1unit_PflABCD.mrc in map Single_Cage_unit.mrc gaussian copy using
190573 points
correlation = 0.3822, correlation about mean = 0.2659, overlap = 25.07
steps = 88, shift = 0.0155, angle = 0.00166 degrees
Position of 1unit_PflABCD.mrc (#5) relative to Single_Cage_unit.mrc gaussian
copy (#116) coordinates:
Matrix rotation and translation
0.99999613 0.00063824 0.00270904 -0.52681767
-0.00063614 0.99999950 -0.00077787 0.32314980
-0.00270953 0.00077615 0.99999603 1.01356127
Axis 0.26889614 0.93758759 -0.22050937
Axis point 368.73544003 0.00000000 188.82225704
Rotation angle (degrees) 0.16556403
Shift along axis -0.06217775
> show #!169 models
> hide #!169 models
> show #!170 models
> hide #!170 models
> show #!168 models
> hide #!168 models
> show #!167 models
> hide #!167 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #2 models
> hide #!116 models
> select add #2
16838 atoms, 17164 bonds, 2046 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-60.581,0,1,0,237.84,0,0,1,277.4
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.96014,-0.24492,-0.13469,614.58,0.2033,-0.94262,0.26485,691.24,-0.19182,0.22691,0.95484,276.75
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.96014,-0.24492,-0.13469,589.79,0.2033,-0.94262,0.26485,626.99,-0.19182,0.22691,0.95484,242.85
> color #5 #b2b2b284 models
> color #5 #424242ff models
> color #5 #42424259 models
> color #5 #011993ff models
> color #5 #0119937e models
> color #5 #919191ff models
> color #5 #919191a6 models
> view matrix models
> #2,-0.96014,-0.24492,-0.13469,585.55,0.2033,-0.94262,0.26485,622.04,-0.19182,0.22691,0.95484,245.15
> view matrix models
> #2,-0.96014,-0.24492,-0.13469,585.03,0.2033,-0.94262,0.26485,611.84,-0.19182,0.22691,0.95484,242.16
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.95226,-0.27654,-0.12934,590.84,0.26842,-0.96023,0.076866,639.34,-0.14545,0.03848,0.98862,276.56
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.95226,-0.27654,-0.12934,585.15,0.26842,-0.96023,0.076866,637.34,-0.14545,0.03848,0.98862,271.71
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.95679,-0.2842,0.061569,546.71,0.29013,-0.94724,0.13623,614.1,0.019605,0.1482,0.98876,191.12
> fitmap #2 inMap #5
Fit molecule 1xPflCD_Cage.pdb (#2) to map 1unit_PflABCD.mrc (#5) using 16838
atoms
average map value = 0.01933, steps = 168
shifted from previous position = 7.72
rotated from previous position = 18.1 degrees
atoms outside contour = 5997, contour level = 0.0040392
Position of 1xPflCD_Cage.pdb (#2) relative to 1unit_PflABCD.mrc (#5)
coordinates:
Matrix rotation and translation
0.93390400 0.35699461 0.01944616 -83.87195291
-0.35735917 0.93374270 0.02046929 -6.42039720
-0.01085029 -0.02606561 0.99960134 13.41569388
Axis -0.06494673 0.04228343 -0.99699249
Axis point -58.81330121 225.54168847 0.00000000
Rotation angle (degrees) 20.99302791
Shift along axis -8.19961325
> fitmap #2 inMap #5
Fit molecule 1xPflCD_Cage.pdb (#2) to map 1unit_PflABCD.mrc (#5) using 16838
atoms
average map value = 0.01933, steps = 76
shifted from previous position = 0.0902
rotated from previous position = 0.154 degrees
atoms outside contour = 6009, contour level = 0.0040392
Position of 1xPflCD_Cage.pdb (#2) relative to 1unit_PflABCD.mrc (#5)
coordinates:
Matrix rotation and translation
0.93466237 0.35494294 0.02053659 -83.73886216
-0.35535012 0.93448287 0.02163452 -7.57451421
-0.01151208 -0.02751865 0.99955499 14.08003530
Axis -0.06896631 0.04496716 -0.99660504
Axis point -61.93151124 226.19228646 0.00000000
Rotation angle (degrees) 20.87659476
Shift along axis -8.59767797
> fitmap #2 inMap #5
Fit molecule 1xPflCD_Cage.pdb (#2) to map 1unit_PflABCD.mrc (#5) using 16838
atoms
average map value = 0.01933, steps = 48
shifted from previous position = 0.0214
rotated from previous position = 0.0103 degrees
atoms outside contour = 6008, contour level = 0.0040392
Position of 1xPflCD_Cage.pdb (#2) relative to 1unit_PflABCD.mrc (#5)
coordinates:
Matrix rotation and translation
0.93469030 0.35486797 0.02056115 -83.72895675
-0.35527402 0.93451546 0.02147615 -7.55397195
-0.01159352 -0.02737840 0.99955790 14.06270804
Axis -0.06856333 0.04512642 -0.99662564
Axis point -61.86572666 226.22279870 0.00000000
Rotation angle (degrees) 20.87149527
Shift along axis -8.61540333
> fitmap #2 inMap #5
Fit molecule 1xPflCD_Cage.pdb (#2) to map 1unit_PflABCD.mrc (#5) using 16838
atoms
average map value = 0.01933, steps = 56
shifted from previous position = 0.0107
rotated from previous position = 0.0116 degrees
atoms outside contour = 6009, contour level = 0.0040392
Position of 1xPflCD_Cage.pdb (#2) relative to 1unit_PflABCD.mrc (#5)
coordinates:
Matrix rotation and translation
0.93473343 0.35475057 0.02062632 -83.71657322
-0.35516013 0.93455536 0.02162309 -7.63854291
-0.01160564 -0.02753747 0.99955339 14.11922303
Axis -0.06901274 0.04524798 -0.99658911
Axis point -62.09609546 226.24343703 0.00000000
Rotation angle (degrees) 20.86518068
Shift along axis -8.63918276
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/09092025/For_Composition-maps/Individual-
> MOdels/3XPflAB_FlgY.pdb"
Chain information for 3XPflAB_FlgY.pdb #6
---
Chain | Description
BN BO BV BW BX BY | No description available
d j l | No description available
e i k m | No description available
n r s | No description available
> select add #6
63449 atoms, 64516 bonds, 4 pseudobonds, 7818 residues, 3 models selected
> select subtract #2
46611 atoms, 47352 bonds, 4 pseudobonds, 5772 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> view matrix models
> #6,-0.85325,-0.37765,-0.35965,473.03,0.36819,0.052161,-0.92829,359.54,0.36933,-0.92448,0.094543,348.99
> select add #2
63449 atoms, 64516 bonds, 4 pseudobonds, 7818 residues, 3 models selected
> select subtract #2
46611 atoms, 47352 bonds, 4 pseudobonds, 5772 residues, 2 models selected
> select add #2
63449 atoms, 64516 bonds, 4 pseudobonds, 7818 residues, 3 models selected
> show sel surfaces
[Repeated 1 time(s)]
> select subtract #2
46611 atoms, 47352 bonds, 4 pseudobonds, 5772 residues, 27 models selected
> hide sel surfaces
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.85325,-0.37765,-0.35965,683.92,0.36819,0.052161,-0.92829,755.71,0.36933,-0.92448,0.094543,627.45
> hide #!5 models
> select subtract #6
16 models selected
> show #!220 models
> hide #!220 models
> show #!221 models
> show #!220 models
> hide #!221 models
> show #!219 models
> hide #!220 models
> show #!221 models
> hide #!219 models
> show #!222 models
> hide #!221 models
> select add #6
46611 atoms, 47352 bonds, 4 pseudobonds, 5772 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.93213,-0.35311,0.080327,579.82,0.34092,-0.93047,-0.13417,747.47,0.12212,-0.097678,0.9877,280.21
> view matrix models
> #6,-0.99919,0.022167,0.033662,530.26,-0.025248,-0.99525,-0.094066,810.62,0.031416,-0.09484,0.995,292.87
> select subtract #6
16 models selected
> select add #6.16
5071 atoms, 621 residues, 1 model selected
> select subtract #6.16
1 model selected
> select add #6.15
5071 atoms, 621 residues, 1 model selected
> select subtract #6.15
1 model selected
> select add #6.17
5071 atoms, 621 residues, 1 model selected
> select add #6.14
10174 atoms, 1254 residues, 2 models selected
> select add #6.7
11409 atoms, 1409 residues, 3 models selected
> select add #6.6
12644 atoms, 1564 residues, 4 models selected
> select add #6.8
13836 atoms, 1713 residues, 5 models selected
> select subtract #6.8
12644 atoms, 1564 residues, 6 models selected
> select add #6.11
13836 atoms, 1713 residues, 5 models selected
> select subtract #6.11
12644 atoms, 1564 residues, 6 models selected
> select add #6.13
13836 atoms, 1713 residues, 5 models selected
> save /Users/shoichi/Desktop/1xSpoke_CJ_Motor.pdb selectedOnly true
> hide #!6 models
> select add #6
46611 atoms, 47352 bonds, 4 pseudobonds, 5772 residues, 7 models selected
> select subtract #6
16 models selected
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/09092025/For_Composition-maps/Individual-
> MOdels/1xSpoke_CJ_Motor.pdb"
Chain information for 1xSpoke_CJ_Motor.pdb #7
---
Chain | Description
BX BY | No description available
l | No description available
m | No description available
s | No description available
> select add #7
13836 atoms, 14052 bonds, 1 pseudobond, 1713 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,-54.012,0,1,0,-20.553,0,0,1,-29.087
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.99857,-0.053266,-0.0039696,-22.221,0.053222,0.99853,-0.010383,-33.881,0.0045168,0.010157,0.99994,-36.281
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.99857,-0.053266,-0.0039696,-17.363,0.053222,0.99853,-0.010383,-44.843,0.0045168,0.010157,0.99994,-42.768
> fitmap #7 inMap #222
Fit molecule 1xSpoke_CJ_Motor.pdb (#7) to map PflAB_wout_FlgYoverlap.mrc copy
gaussian copy (#222) using 13836 atoms
average map value = 0.02438, steps = 204
shifted from previous position = 6.65
rotated from previous position = 6.75 degrees
atoms outside contour = 4993, contour level = 0.0004499
Position of 1xSpoke_CJ_Motor.pdb (#7) relative to PflAB_wout_FlgYoverlap.mrc
copy gaussian copy (#222) coordinates:
Matrix rotation and translation
-0.99965128 -0.02618670 0.00340238 556.96158410
0.02589175 -0.99730701 -0.06861736 808.84662249
0.00519008 -0.06850534 0.99763725 -240.57212998
Axis 0.00214975 -0.03430677 0.99940904
Axis point 273.52667764 403.92860329 0.00000000
Rotation angle (degrees) 178.50701132
Shift along axis -266.98154610
> fitmap #7 inMap #222
Fit molecule 1xSpoke_CJ_Motor.pdb (#7) to map PflAB_wout_FlgYoverlap.mrc copy
gaussian copy (#222) using 13836 atoms
average map value = 0.02438, steps = 44
shifted from previous position = 0.0144
rotated from previous position = 0.00619 degrees
atoms outside contour = 4992, contour level = 0.0004499
Position of 1xSpoke_CJ_Motor.pdb (#7) relative to PflAB_wout_FlgYoverlap.mrc
copy gaussian copy (#222) coordinates:
Matrix rotation and translation
-0.99965351 -0.02609545 0.00344778 556.88186534
0.02579779 -0.99731191 -0.06858150 808.85550471
0.00522817 -0.06846880 0.99763956 -240.59375219
Axis 0.00217063 -0.03428859 0.99940962
Axis point 273.50781632 403.92144783 0.00000000
Rotation angle (degrees) 178.51232305
Shift along axis -266.97744043
> fitmap #7 inMap #222
Fit molecule 1xSpoke_CJ_Motor.pdb (#7) to map PflAB_wout_FlgYoverlap.mrc copy
gaussian copy (#222) using 13836 atoms
average map value = 0.02438, steps = 48
shifted from previous position = 0.0296
rotated from previous position = 0.0109 degrees
atoms outside contour = 4995, contour level = 0.0004499
Position of 1xSpoke_CJ_Motor.pdb (#7) relative to PflAB_wout_FlgYoverlap.mrc
copy gaussian copy (#222) coordinates:
Matrix rotation and translation
-0.99964881 -0.02627730 0.00342810 556.97440083
0.02598082 -0.99731057 -0.06853194 808.79029165
0.00521972 -0.06841881 0.99764303 -240.62901755
Axis 0.00216360 -0.03426374 0.99941048
Axis point 273.51713513 403.91728791 0.00000000
Rotation angle (degrees) 178.50186152
Shift along axis -266.99427237
> show #!231 models
> hide #!231 models
> show #!231 models
> hide #!231 models
> select clear
> save /Users/shoichi/Desktop/For_Composition-
> maps/Building_Whole_Model_09102025.cxs includeMaps true
——— End of log from Wed Sep 10 09:47:44 2025 ———
opened ChimeraX session
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/09092025/For_Composition-maps/Individual-
> MOdels/CJ_Stator_Complex_with6ykm_Bb_CjFliL.pdb"
Chain information for CJ_Stator_Complex_with6ykm_Bb_CjFliL.pdb
---
Chain | Description
8.2/A 8.2/B 8.2/C 8.2/D 8.2/E | No description available
8.3/A 8.3/B 8.3/C 8.3/D 8.3/E 8.3/F 8.3/G 8.3/H 8.3/I 8.3/J | No description available
8.1/K | No description available
8.1/L | No description available
> show #!5 models
> hide #!222 models
> select add #8
22449 atoms, 22826 bonds, 2863 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> view matrix models #8,1,0,0,-1.3908,0,1,0,28.13,0,0,1,-68.149
> view matrix models #8,1,0,0,-79.74,0,1,0,194.81,0,0,1,-74.266
> view matrix models #8,1,0,0,-53.901,0,1,0,217.25,0,0,1,-20.022
> view matrix models #8,1,0,0,-90.497,0,1,0,182.48,0,0,1,-19.698
> view matrix models #8,1,0,0,-100.46,0,1,0,189.34,0,0,1,-6.9565
> combine #8
Remapping chain ID 'A' in CJ_Stator_Complex_with6ykm_Bb_CjFliL.pdb #8.3 to 'M'
Remapping chain ID 'B' in CJ_Stator_Complex_with6ykm_Bb_CjFliL.pdb #8.3 to 'N'
Remapping chain ID 'C' in CJ_Stator_Complex_with6ykm_Bb_CjFliL.pdb #8.3 to 'O'
Remapping chain ID 'D' in CJ_Stator_Complex_with6ykm_Bb_CjFliL.pdb #8.3 to 'P'
Remapping chain ID 'E' in CJ_Stator_Complex_with6ykm_Bb_CjFliL.pdb #8.3 to 'Q'
> select subtract #8
Nothing selected
> select add #9
22449 atoms, 22826 bonds, 2863 residues, 1 model selected
> ui tool show "Fit in Map"
> fitmap #9 inMap #5
Fit molecule combination (#9) to map 1unit_PflABCD.mrc (#5) using 22449 atoms
average map value = 0.01753, steps = 376
shifted from previous position = 3.05
rotated from previous position = 47.8 degrees
atoms outside contour = 6935, contour level = 0.0040392
Position of combination (#9) relative to 1unit_PflABCD.mrc (#5) coordinates:
Matrix rotation and translation
-0.37231233 -0.92574324 -0.06620400 689.67970535
0.92810605 -0.37123742 -0.02831844 -45.51260744
0.00163820 -0.07198764 0.99740417 -211.57576799
Axis -0.02353369 -0.03656071 0.99905429
Axis point 360.53272668 204.80726333 0.00000000
Rotation angle (degrees) 111.90524931
Shift along axis -225.94241130
> fitmap #9 inMap #5
Fit molecule combination (#9) to map 1unit_PflABCD.mrc (#5) using 22449 atoms
average map value = 0.01753, steps = 44
shifted from previous position = 0.0386
rotated from previous position = 0.201 degrees
atoms outside contour = 6938, contour level = 0.0040392
Position of combination (#9) relative to 1unit_PflABCD.mrc (#5) coordinates:
Matrix rotation and translation
-0.36905755 -0.92703861 -0.06630186 689.01362618
0.92940486 -0.36798102 -0.02822339 -47.00421936
0.00176635 -0.07203732 0.99740037 -211.59378907
Axis -0.02357860 -0.03663111 0.99905066
Axis point 360.77496452 204.70035063 0.00000000
Rotation angle (degrees) 111.70446120
Shift along axis -225.91707373
> hide #!8 models
> select subtract #9
Nothing selected
> show #!3 models
> view orient
> sym #9 C17 copies true center #3
Made 17 copies for combination symmetry C17
> close #10
> show #!8 models
> select add #8.3
8580 atoms, 8710 bonds, 1070 residues, 1 model selected
> select subtract #8.3
Nothing selected
> select add #8.1
4099 atoms, 4171 bonds, 518 residues, 1 model selected
> select subtract #8.1
Nothing selected
> select add #8.2
9770 atoms, 9945 bonds, 1275 residues, 1 model selected
> color #8.2 #a69b32ff models
> color #8.1 #b86006ff models
> color #8.3 #e2cf7bff models
> select clear
> close #9
> combine #8
Remapping chain ID 'A' in CJ_Stator_Complex_with6ykm_Bb_CjFliL.pdb #8.3 to 'M'
Remapping chain ID 'B' in CJ_Stator_Complex_with6ykm_Bb_CjFliL.pdb #8.3 to 'N'
Remapping chain ID 'C' in CJ_Stator_Complex_with6ykm_Bb_CjFliL.pdb #8.3 to 'O'
Remapping chain ID 'D' in CJ_Stator_Complex_with6ykm_Bb_CjFliL.pdb #8.3 to 'P'
Remapping chain ID 'E' in CJ_Stator_Complex_with6ykm_Bb_CjFliL.pdb #8.3 to 'Q'
> hide #!8 models
> fitmap #9 inMap #5
Fit molecule combination (#9) to map 1unit_PflABCD.mrc (#5) using 22449 atoms
average map value = 0.01753, steps = 376
shifted from previous position = 3.05
rotated from previous position = 47.8 degrees
atoms outside contour = 6935, contour level = 0.0040392
Position of combination (#9) relative to 1unit_PflABCD.mrc (#5) coordinates:
Matrix rotation and translation
-0.37231233 -0.92574324 -0.06620400 689.67970535
0.92810605 -0.37123742 -0.02831844 -45.51260744
0.00163820 -0.07198764 0.99740417 -211.57576799
Axis -0.02353369 -0.03656071 0.99905429
Axis point 360.53272668 204.80726333 0.00000000
Rotation angle (degrees) 111.90524931
Shift along axis -225.94241130
> fitmap #9 inMap #5
Fit molecule combination (#9) to map 1unit_PflABCD.mrc (#5) using 22449 atoms
average map value = 0.01753, steps = 44
shifted from previous position = 0.0386
rotated from previous position = 0.201 degrees
atoms outside contour = 6938, contour level = 0.0040392
Position of combination (#9) relative to 1unit_PflABCD.mrc (#5) coordinates:
Matrix rotation and translation
-0.36905755 -0.92703861 -0.06630186 689.01362618
0.92940486 -0.36798102 -0.02822339 -47.00421936
0.00176635 -0.07203732 0.99740037 -211.59378907
Axis -0.02357860 -0.03663111 0.99905066
Axis point 360.77496452 204.70035063 0.00000000
Rotation angle (degrees) 111.70446120
Shift along axis -225.91707373
> hide #!7 models
> show #!7 models
> split #7
Split 1xSpoke_CJ_Motor.pdb (#7) into 5 models
Chain information for 1xSpoke_CJ_Motor.pdb BX #7.1
---
Chain | Description
BX | No description available
Chain information for 1xSpoke_CJ_Motor.pdb BY #7.2
---
Chain | Description
BY | No description available
Chain information for 1xSpoke_CJ_Motor.pdb l #7.3
---
Chain | Description
l | No description available
Chain information for 1xSpoke_CJ_Motor.pdb m #7.4
---
Chain | Description
m | No description available
Chain information for 1xSpoke_CJ_Motor.pdb s #7.5
---
Chain | Description
s | No description available
> color #7.5 #ff0002ff models
> color #7.3 #ff0002ff models
> color #7.4 magenta models
> select add #7.1
1235 atoms, 1241 bonds, 155 residues, 1 model selected
> select subtract #7.1
Nothing selected
> select add #7.2
1235 atoms, 1241 bonds, 155 residues, 1 model selected
> select subtract #7.2
Nothing selected
> color #7.2 snow models
> color #7.1 #dbb3e2ff models
> select clear
> hide #!5 models
> color #2.9 #7b80ffff
> color #2.7 #adffc1ff models
> color #2.8 #adffc1ff models
> color #2.2 #0b6dffff models
> color #2.5 #0b6dffff models
> color #2.2 #0b6dffff models
[Repeated 1 time(s)]
> hide #2.2 models
> show #2.2 models
> hide #2.3 models
> show #2.3 models
> hide #2.6 models
> show #2.6 models
> color #2.3 #20e0ffff models
> color #2.6 #20e0ffff models
> color #2.9 #a7c5d2ff models
> select add #2.4
2637 atoms, 319 residues, 1 model selected
> select add #2.1
5274 atoms, 638 residues, 2 models selected
> color #2.4 #a7c5d2ff models
> color #2.1 #a7c5d2ff models
> color #2.9 #7b80ffff
> select add #2
16838 atoms, 17164 bonds, 2046 residues, 3 models selected
> hide sel surfaces
[Repeated 2 time(s)]
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> select clear
> color #2.9 #7b80ffff models
> select add #2.9
2854 atoms, 356 residues, 1 model selected
> color sel #7b80ffff models
> save /Users/shoichi/Desktop/For_Composition-
> maps/Building_Whole_Model_09102025.cxs includeMaps true
——— End of log from Wed Sep 10 10:14:24 2025 ———
opened ChimeraX session
> open /Users/shoichi/Desktop/For_Composition-maps/Individual-
> MOdels/REDO_PflCD-models_08312025.pdb
Summary of feedback from opening /Users/shoichi/Desktop/For_Composition-
maps/Individual-MOdels/REDO_PflCD-models_08312025.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY V 2 LEU V 49 1 48
Start residue of secondary structure not found: HELIX 2 2 LEU V 50 GLU V 91 1
42
Start residue of secondary structure not found: HELIX 3 3 ASN V 93 GLU V 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE V 105 PHE V 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU V 112 LYS V 114
1 3
112 messages similar to the above omitted
Chain information for REDO_PflCD-models_08312025.pdb
---
Chain | Description
10.4/A 10.7/A | No description available
10.5/B 10.8/B | No description available
10.6/C 10.9/C | No description available
10.3/L 10.1/X | No description available
10.2/c | No description available
> select add #10
19692 atoms, 17164 bonds, 2402 residues, 11 models selected
> close #2
> close #10
> open /Users/shoichi/Desktop/For_Composition-maps/Individual-
> MOdels/REDO_PflCD-models_08312025.pdb
Summary of feedback from opening /Users/shoichi/Desktop/For_Composition-
maps/Individual-MOdels/REDO_PflCD-models_08312025.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY V 2 LEU V 49 1 48
Start residue of secondary structure not found: HELIX 2 2 LEU V 50 GLU V 91 1
42
Start residue of secondary structure not found: HELIX 3 3 ASN V 93 GLU V 100 1
8
Start residue of secondary structure not found: HELIX 4 4 ILE V 105 PHE V 111
1 7
Start residue of secondary structure not found: HELIX 5 5 LEU V 112 LYS V 114
1 3
112 messages similar to the above omitted
Chain information for REDO_PflCD-models_08312025.pdb
---
Chain | Description
2.4/A 2.7/A | No description available
2.5/B 2.8/B | No description available
2.6/C 2.9/C | No description available
2.3/L 2.1/X | No description available
2.2/c | No description available
> comvine #2
Unknown command: comvine #2
> combine #2
Remapping chain ID 'A' in REDO_PflCD-models_08312025.pdb #2.7 to 'D'
Remapping chain ID 'B' in REDO_PflCD-models_08312025.pdb #2.8 to 'E'
Remapping chain ID 'C' in REDO_PflCD-models_08312025.pdb #2.9 to 'F'
> hide #!2 models
> select add #10
16838 atoms, 17164 bonds, 2046 residues, 1 model selected
> show #!5 models
> view matrix models #10,1,0,0,-66.119,0,1,0,297.99,0,0,1,268.4
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.95072,0.31003,-0.0040457,468.78,-0.29554,-0.91006,-0.2906,767.92,-0.093776,-0.27508,0.95684,351.74
> view matrix models
> #10,-0.9545,0.29649,-0.032018,478.35,-0.29182,-0.95074,-0.1046,732.41,-0.061454,-0.090496,0.994,303.19
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.9545,0.29649,-0.032018,452.79,-0.29182,-0.95074,-0.1046,737.3,-0.061454,-0.090496,0.994,298.1
> view matrix models
> #10,-0.9545,0.29649,-0.032018,455.76,-0.29182,-0.95074,-0.1046,720.62,-0.061454,-0.090496,0.994,275.89
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.95587,0.29187,-0.033485,457.26,-0.2895,-0.95519,-0.061727,711.18,-0.05,-0.049309,0.99753,264.84
> view matrix models
> #10,-0.95708,0.28776,-0.034602,458.55,-0.28705,-0.95762,-0.023947,702.49,-0.040026,-0.012987,0.99911,255.47
> view matrix models
> #10,-0.96072,0.27506,-0.036986,462.28,-0.27734,-0.95649,0.090607,674.05,-0.010455,0.097305,0.9952,229.16
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.96072,0.27506,-0.036986,453.38,-0.27734,-0.95649,0.090607,674.4,-0.010455,0.097305,0.9952,223.09
> ui tool show "Fit in Map"
> fitmap #10 inMap #5
Fit molecule combination (#10) to map 1unit_PflABCD.mrc (#5) using 16838 atoms
average map value = 0.01933, steps = 148
shifted from previous position = 0.6
rotated from previous position = 6.51 degrees
atoms outside contour = 6009, contour level = 0.0040392
Position of combination (#10) relative to 1unit_PflABCD.mrc (#5) coordinates:
Matrix rotation and translation
0.99978746 -0.01369900 0.01540661 -1.96965866
0.01385561 0.99985294 -0.01010505 -0.38605904
-0.01526592 0.01031637 0.99983024 3.93373941
Axis 0.44382919 0.66662167 0.59885824
Axis point 207.81185233 0.00000000 165.97832449
Rotation angle (degrees) 1.31826030
Shift along axis 1.22420494
> fitmap #10 inMap #5
Fit molecule combination (#10) to map 1unit_PflABCD.mrc (#5) using 16838 atoms
average map value = 0.01933, steps = 60
shifted from previous position = 0.0104
rotated from previous position = 0.0484 degrees
atoms outside contour = 6008, contour level = 0.0040392
Position of combination (#10) relative to 1unit_PflABCD.mrc (#5) coordinates:
Matrix rotation and translation
0.99977046 -0.01439237 0.01587084 -1.95437557
0.01455160 0.99984447 -0.00996391 -0.62329819
-0.01572497 0.01019256 0.99982440 4.10187121
Axis 0.42566169 0.66723604 0.61123498
Axis point 210.11065821 0.00000000 159.95939567
Rotation angle (degrees) 1.35669785
Shift along axis 1.25941735
> fitmap #10 inMap #5
Fit molecule combination (#10) to map 1unit_PflABCD.mrc (#5) using 16838 atoms
average map value = 0.01933, steps = 48
shifted from previous position = 0.0231
rotated from previous position = 0.023 degrees
atoms outside contour = 6008, contour level = 0.0040392
Position of combination (#10) relative to 1unit_PflABCD.mrc (#5) coordinates:
Matrix rotation and translation
0.99976392 -0.01471991 0.01598165 -1.91902377
0.01487698 0.99984175 -0.00975445 -0.78952502
-0.01583553 0.00998990 0.99982470 4.17352203
Axis 0.41366794 0.66660833 0.62009045
Axis point 212.18158954 0.00000000 156.02708131
Rotation angle (degrees) 1.36749217
Shift along axis 1.26781860
> select clear
> select add #10
16838 atoms, 17164 bonds, 2046 residues, 1 model selected
Alignment identifier is 1
Alignment identifier is 10/c
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
> select #10/C,F:148-189
684 atoms, 694 bonds, 84 residues, 1 model selected
> select #10/C,F
3084 atoms, 3126 bonds, 378 residues, 1 model selected
> color sel #20e0ffff models
> split #10
Split combination (#10) into 9 models
Chain information for combination A #10.1
---
Chain | Description
A | No description available
Chain information for combination B #10.2
---
Chain | Description
B | No description available
Chain information for combination C #10.3
---
Chain | Description
C | No description available
Chain information for combination D #10.4
---
Chain | Description
D | No description available
Chain information for combination E #10.5
---
Chain | Description
E | No description available
Chain information for combination F #10.6
---
Chain | Description
F | No description available
Chain information for combination L #10.7
---
Chain | Description
L | No description available
Chain information for combination X #10.8
---
Chain | Description
X | No description available
Chain information for combination c #10.9
---
Chain | Description
c | No description available
> select add #10.1
2637 atoms, 2686 bonds, 319 residues, 1 model selected
> select add #10.2
4095 atoms, 4174 bonds, 494 residues, 2 models selected
> select subtract #10.2
2637 atoms, 2686 bonds, 319 residues, 1 model selected
> select add #10.4
5274 atoms, 5372 bonds, 638 residues, 2 models selected
> color #10.1 #a7c5d2ff models
> color #10.3 #a7c5d2ff models
> color #10.4 #a7c5d2ff models
> select clear
> select add #10.2
1458 atoms, 1488 bonds, 175 residues, 1 model selected
> select add #10.6
3000 atoms, 3051 bonds, 364 residues, 2 models selected
> select subtract #10.6
1458 atoms, 1488 bonds, 175 residues, 1 model selected
> select add #10.7
2813 atoms, 2876 bonds, 337 residues, 2 models selected
> select subtract #10.7
1458 atoms, 1488 bonds, 175 residues, 1 model selected
> select add #10.5
2916 atoms, 2976 bonds, 350 residues, 2 models selected
> color #10.2 #0b6dffff models
> color #10.5 #0b6dffff models
> select clear
> select add #10.4
2637 atoms, 2686 bonds, 319 residues, 1 model selected
> select subtract #10.4
Nothing selected
> select add #10.3
1542 atoms, 1563 bonds, 189 residues, 1 model selected
> select add #10.6
3084 atoms, 3126 bonds, 378 residues, 2 models selected
> color #10.6 #20e0ffff models
> color #10.3 #20e0ffff models
> select clear
> select add #10.6
1542 atoms, 1563 bonds, 189 residues, 1 model selected
> select subtract #10.6
Nothing selected
> select add #10.7
1355 atoms, 1388 bonds, 162 residues, 1 model selected
> select add #10.8
2710 atoms, 2776 bonds, 324 residues, 2 models selected
> color #10.7 #adffc1ff models
> color #10.8 #adffc1ff models
> color #10.9 #7b80ffff models
> select clear
> combine #10
> hide #!10 models
> show #!10 models
> hide #!10 models
> select add #9
22449 atoms, 22826 bonds, 2863 residues, 1 model selected
> select subtract #9
Nothing selected
> select add #7
13836 atoms, 14052 bonds, 1 pseudobond, 1713 residues, 7 models selected
> select subtract #7
Nothing selected
> combine #7
> hide #!7 models
> hide #!5 models
> view orient
> sym #9 C17 copies true center #3
Made 17 copies for combination symmetry C17
> sym #11 C17 copies true center #3
Made 17 copies for combination symmetry C17
> sym #12 C17 copies true center #3
Made 17 copies for combination symmetry C17
> open /Users/shoichi/Desktop/For_Composition-maps/Individual-
> MOdels/HP_FliF.pdb
Summary of feedback from opening /Users/shoichi/Desktop/For_Composition-
maps/Individual-MOdels/HP_FliF.pdb
---
warnings | Start residue of secondary structure not found: HELIX 270 270 ILEAA 227 VALAA 261 1 35
Start residue of secondary structure not found: HELIX 271 271 LYSAA 264 LYSAA
266 1 3
Start residue of secondary structure not found: HELIX 272 272 ASPAA 392 ILEAA
406 1 15
Start residue of secondary structure not found: HELIX 273 273 SERAA 436 VALAA
489 1 54
Start residue of secondary structure not found: HELIX 274 274 ILEAB 227 VALAB
261 1 35
242 messages similar to the above omitted
Chain information for HP_FliF.pdb #16
---
Chain | Description
0 1 2 3 4 5 6 7 8 9 AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS q r s t u v w x y z | No description available
A B C D E F G H I J K L M N O P Q R S T U | No description available
V W X Y Z a b c d e f g h i j k l m n o p | No description available
> color #16 #348e42ff models
> lighting soft
> lighting simple
> save /Users/shoichi/Desktop/For_Composition-
> maps/Building_Whole_Model_09102025.cxs includeMaps true
[Repeated 1 time(s)]
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #16 models
> lighting soft
> view orient
> turn x 90
[Repeated 2 time(s)]
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!82-232 models
> hide #!82-232 models
> hide #!3 models
> hide #!4 models
> show #!109 models
> volume #!109 showOutlineBox true
> ui mousemode right "crop volume"
> volume #109 region 0,0,0,199,199,62
> volume #109 region 0,0,0,199,199,199
> volume #109 region 32,0,0,199,199,199
> volume #109 region 0,0,0,199,199,199
> volume #109 region 0,0,0,199,199,165
> volume #109 region 0,0,65,199,199,165
> volume #109 region 0,0,0,199,199,165
> volume #!109 showOutlineBox false
> select ~sel & ##selected
Nothing selected
> volume #107-123 region 0,0,0,199,199,165
> show #!82-232 models
> show #!3 models
> show #!4 models
Drag select of 82 Exp_ATP.mrc gaussian
> select subtract #82
Nothing selected
> hide #!82 models
> view orient
> turn x 90
[Repeated 2 time(s)]
> turn z-0.1 90
Expected an axis vector or a keyword
> turn z-0.1
Expected an axis vector or a keyword
> turn z -0.1
[Repeated 1 time(s)]
> view name P1
> save /Users/shoichi/Desktop/Comp_1a.png supersample 2 transparentBackground
> true
> turn x 15
> turn x -15
> turn x 10
> save /Users/shoichi/Desktop/For_Composition-
> maps/Building_Whole_Model_09102025.cxs includeMaps true
> save /Users/shoichi/Desktop/For_Composition-
> maps/Building_Whole_Model_09102025_Backup.cxs includeMaps true
——— End of log from Wed Sep 10 10:46:36 2025 ———
opened ChimeraX session
> view orient
> show #!13 models
> hide #!13 models
> turn x 90
[Repeated 2 time(s)]
> turn y 90
> turn x 25
> turn x -25
> turn x 15
[Repeated 1 time(s)]
> turn x -15
[Repeated 1 time(s)]
> turn x 10
> view name P1
> save /Users/shoichitachiyama/Desktop/Side-10.png supersample 2
> transparentBackground true
> hide #!88 models
> hide #!209 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!124-174 models
> hide #!83 models
> hide #!3 models
> turn x 10
[Repeated 1 time(s)]
> view orient
> turn x 90
[Repeated 2 time(s)]
> turn y 90
> turn x 30
> turn x -30
> turn x 45
> save /Users/shoichitachiyama/Desktop/Side-45.png supersample 2
> transparentBackground true
> turn x 45
> save /Users/shoichitachiyama/Desktop/Side-90.png supersample 2
> transparentBackground true
> save /Users/shoichitachiyama/Desktop/Composition-with-color.cxs includeMaps
> true
——— End of log from Sat Sep 20 19:10:23 2025 ———
opened ChimeraX session
> color #107 #0b6dfffd models
> color #107 #0b6dffff models
> color #107 #5A97FF models
> color #107 #73E0FF models
> color #107 #5A97FF models
> color #107 #20e0ffff models
> color #107 #adffc1ff models
> color #107 #20e0ffff models
> color #107 #1fffffff models
> color #107 #2c90dfff models
> color #107 #5A97FF models
> color #107-123 #5A97FF models
> hide #!87 models
> color #124 #FFBF1D models
> show #!124 models
> color #124-140 #FFBF1D models
> show #!125 models
> show #!126 models
> show #!127 models
> show #!128 models
> show #!129 models
> show #!130 models
> show #!131 models
> show #!132 models
> show #!133 models
> show #!134 models
> show #!135 models
> show #!136 models
> show #!137 models
> show #!138 models
> show #!139 models
> show #!140 models
> show #!140-157 models
> color #141-157 #17198B models
> lighting soft
> show #!140-174 models
> color #158-174 #765FF3 models
> color #175-191 #714B0E models
> color #192-208 #FFFF00 models
> show #!209 models
> show #!3 models
> view P1
> view orient
> show #!88 models
> turn x 90
[Repeated 2 time(s)]
> turn y 90
[Repeated 4 time(s)]
> view orient
> turn x 90
[Repeated 2 time(s)]
> turn y 90
> view P10
Expected an objects specifier or a view name or a keyword
> view name P10
> turn z 0.1
> turn z -0.1
[Repeated 2 time(s)]
> view name P10
> save /Users/shoichi/Desktop/Fig.1a-09072025.png supersample 2
> transparentBackground true
> turn x -90
> turn x 90
[Repeated 1 time(s)]
> hide #!88 models
> hide #!89 models
> hide #!209 models
> hide #!158-174 models
> ui tool show "Side View"
> save /Users/shoichi/Desktop/Fig.1b-09072025.png supersample 2
> transparentBackground true
> hide #!3 models
> hide #!4 models
> hide #!107-157 models
> hide #!175-208 models
> hide #!232 models
> hide #!214 models
> hide #!215 models
> hide #!216 models
> hide #!217 models
> hide #!218 models
> hide #!219 models
> hide #!221 models
> hide #!220 models
> hide #!222 models
> hide #!223 models
> hide #!224 models
> hide #!225 models
> hide #!226 models
> hide #!227 models
> hide #!228 models
> hide #!229 models
> hide #!230 models
> surface dust #231 size 21.4
> save /Users/shoichi/Desktop/Fig.2b-09072025.png supersample 2
> transparentBackground true
> show #!223 models
> hide #!223 models
> show #!224 models
> hide #!224 models
> show #!225 models
> hide #!225 models
> show #!226 models
> show #!227 models
> show #!228 models
> hide #!228 models
> show #!225 models
> show #!224 models
> hide #!231 models
> show #!231 models
> show #!228 models
> show #!229 models
> show #!230 models
> show #!222 models
> show #!223 models
> show #!221 models
> hide #!221 models
> hide #!222 models
> hide #!223 models
> hide #!225 models
> hide #!226 models
> hide #!227 models
> hide #!228 models
> hide #!229 models
> hide #!230 models
> hide #!231 models
> show #!231 models
> show #!230 models
> save /Users/shoichi/Desktop/Composition-before-JMB-color.cxs includeMaps
> true
——— End of log from Sat Sep 27 12:14:37 2025 ———
opened ChimeraX session
> show #!214 models
> show #!214-232 models
> show #!209 models
> hide #!209 models
> show #!175-191 models
> show #!141-157 models
> show #!124-140 models
> show #!107-140 models
> show #!3 models
> ui tool show "Side View"
> color #141 #9d4594ff models
> color #141 #adffc1ff models
> color #141-157 #adffc1ff models
> save /Users/shoichitachiyama/Desktop/Fig1A-top.png supersample 2
> transparentBackground true
> turn x 90
> turn x -90
> show #!158 models
> show #!158-174 models
> show #!192-208 models
> show #!209 models
> show #!88 models
> show #!89 models
> show #!4 models
> save /Users/shoichitachiyama/Desktop/Fig1A-Side.png supersample 2
> transparentBackground true
> hide #!107 models
> hide #!108 models
> hide #!109 models
> hide #!110 models
> save /Users/shoichitachiyama/Desktop/Fig1-Updated_09282025.cxs includeMaps
> true
> close session
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Manuscript/09262025/New Images/Composition-Transparent-Fig2.cxs"
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137,
step 1, values float32
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
level 0.027, step 1, values float32
Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
step 1, values float32
Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at
level 0.0166, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #107, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #108, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #109, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #111, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #112, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #113, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #114, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #115, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #116, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #117, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #118, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #119, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #120, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #121, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #122, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #123, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #124, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #125, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #126, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #127, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #128, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #129, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #130, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #131, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #132, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #133, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #134, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #135, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #136, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #137, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #138, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #139, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #140, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #141, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #142, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #143, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #144, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #145, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #146, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #147, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #148, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #149, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #150, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #151, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #152, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #153, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #154, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #155, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #156, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #157, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #158, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #159, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #160, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #161, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #162, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #163, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #164, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #165, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #166, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #167, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #168, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #169, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #170, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #171, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #172, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #173, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #174, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #175, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #176, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #177, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #178, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #180, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #181, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #182, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #185, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #186, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #187, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #188, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #189, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #190, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #191, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened Single-MotA-ring.mrc gaussian as #192, grid size 200,200,200, pixel
2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #193, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #194, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #195, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #196, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #199, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #200, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #202, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #203, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #204, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #206, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #207, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #208, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #214, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #215, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #219, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #220, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #221, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #222, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #223, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #224, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #225, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14,
shown at level 0.0112, step 1, values float32
Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel
2.14, shown at level 0.00974, step 1, values float32
Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at
level 0.157, step 1, values float32
Opened C-Vrings.mrc as #4, grid size 250,250,250, pixel 4.3, shown at level
0.0283, step 1, values float32
Opened 1unit_PflABCD.mrc as #5, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Opened 3xFlgY.mrc as #22, grid size 256,256,256, pixel 2.14, shown at level
0.0112, step 1, values float32
Opened 1xPflB.mrc as #26, grid size 200,200,200, pixel 2.14, shown at level
0.00045, step 1, values float32
Opened 1xFlgY.mrc as #29, grid size 256,256,256, pixel 2.14, shown at level
0.0112, step 1, values float32
Opened 1xPflB.mrc as #30, grid size 200,200,200, pixel 2.14, shown at level
0.00045, step 1, values float32
opened ChimeraX session
Showing 3xFlgY.seg - 23 regions, 23 surfaces
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Manuscript/09262025/New Images/Composition-Transparent-Fig2.cxs"
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137,
step 1, values float32
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
level 0.027, step 1, values float32
Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
step 1, values float32
Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at
level 0.0166, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #107, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #108, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #109, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #111, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #112, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #113, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #114, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #115, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #116, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #117, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #118, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #119, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #120, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #121, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #122, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #123, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #124, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #125, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #126, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #127, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #128, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #129, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #130, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #131, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #132, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #133, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #134, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #135, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #136, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #137, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #138, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #139, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #140, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #141, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #142, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #143, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #144, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #145, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #146, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #147, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #148, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #149, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #150, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #151, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #152, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #153, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #154, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #155, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #156, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #157, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #158, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #159, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #160, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #161, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #162, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #163, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #164, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #165, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #166, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #167, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #168, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #169, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #170, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #171, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #172, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #173, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #174, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #175, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #176, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #177, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #178, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #180, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #181, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #182, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #185, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #186, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #187, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #188, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #189, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #190, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #191, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened Single-MotA-ring.mrc gaussian as #192, grid size 200,200,200, pixel
2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #193, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #194, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #195, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #196, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #199, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #200, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #202, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #203, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #204, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #206, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #207, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #208, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #214, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #215, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #219, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #220, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #221, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #222, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #223, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #224, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #225, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14,
shown at level 0.0112, step 1, values float32
Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel
2.14, shown at level 0.00974, step 1, values float32
Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at
level 0.157, step 1, values float32
Opened C-Vrings.mrc as #4, grid size 250,250,250, pixel 4.3, shown at level
0.0283, step 1, values float32
Opened 1unit_PflABCD.mrc as #5, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Opened 3xFlgY.mrc as #22, grid size 256,256,256, pixel 2.14, shown at level
0.0112, step 1, values float32
Opened 1xPflB.mrc as #26, grid size 200,200,200, pixel 2.14, shown at level
0.00045, step 1, values float32
Opened 1xFlgY.mrc as #29, grid size 256,256,256, pixel 2.14, shown at level
0.0112, step 1, values float32
Opened 1xPflB.mrc as #30, grid size 200,200,200, pixel 2.14, shown at level
0.00045, step 1, values float32
opened ChimeraX session
Showing 3xFlgY.seg - 23 regions, 23 surfaces
> hide #!21 models
> hide #!25 models
> show #!25 models
> select add #25
78642 atoms, 79390 bonds, 9775 residues, 18 models selected
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
Alignment identifier is 1
Alignment identifier is 2
> select #25.1/BX-BY:155 #25.2/BX-BY:155 #25.3/BX-BY:155 #25.4/BX-BY:155
> #25.5/BX-BY:155 #25.6/BX-BY:155 #25.7/BX-BY:155 #25.8/BX-BY:155 #25.9/BX-
> BY:155 #25.10/BX-BY:155 #25.11/BX-BY:155 #25.12/BX-BY:155 #25.13/BX-BY:155
> #25.14/BX-BY:155 #25.15/BX-BY:155 #25.16/BX-BY:155 #25.17/BX-BY:155
306 atoms, 272 bonds, 34 residues, 17 models selected
> select #25.1/BX-BY #25.2/BX-BY #25.3/BX-BY #25.4/BX-BY #25.5/BX-BY #25.6/BX-
> BY #25.7/BX-BY #25.8/BX-BY #25.9/BX-BY #25.10/BX-BY #25.11/BX-BY #25.12/BX-
> BY #25.13/BX-BY #25.14/BX-BY #25.15/BX-BY #25.16/BX-BY #25.17/BX-BY
41990 atoms, 42194 bonds, 5270 residues, 17 models selected
1 [ID: 1] region 34 chains [1-155] RMSD: 191.985
> select #25.1/s:788 #25.2/s:788 #25.3/s:788 #25.4/s:788 #25.5/s:788
> #25.6/s:788 #25.7/s:788 #25.8/s:788 #25.9/s:788 #25.10/s:788 #25.11/s:788
> #25.12/s:788 #25.13/s:788 #25.14/s:788 #25.15/s:788 #25.16/s:788
> #25.17/s:788
170 atoms, 153 bonds, 17 residues, 17 models selected
> select #25.1/s #25.2/s #25.3/s #25.4/s #25.5/s #25.6/s #25.7/s #25.8/s
> #25.9/s #25.10/s #25.11/s #25.12/s #25.13/s #25.14/s #25.15/s #25.16/s
> #25.17/s
36652 atoms, 37196 bonds, 4505 residues, 17 models selected
2 [ID: 2] region 17 chains [1-265] RMSD: 281.686
> hide sel cartoons
> show #!14 models
> hide #!14 models
> show #!13 models
> hide #!13 models
> show #!15 models
> select add #15
271864 atoms, 276080 bonds, 17 pseudobonds, 33626 residues, 69 models selected
> select add #25
313854 atoms, 318274 bonds, 17 pseudobonds, 38896 residues, 155 models
selected
> select subtract #25
235212 atoms, 238884 bonds, 17 pseudobonds, 29121 residues, 171 models
selected
> hide #!25 models
Drag select of 231 C17-FlgY_New.mrc gaussian
> hide #!231 models
> select subtract #231
Nothing selected
> select add #15
235212 atoms, 238884 bonds, 17 pseudobonds, 29121 residues, 35 models selected
> hide sel surfaces
> show sel cartoons
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
> select #15.1/l:163 #15.2/l:163 #15.3/l:163 #15.4/l:163 #15.5/l:163
> #15.6/l:163 #15.7/l:163 #15.8/l:163 #15.9/l:163 #15.10/l:163 #15.11/l:163
> #15.12/l:163 #15.13/l:163 #15.14/l:163 #15.15/l:163 #15.16/l:163
> #15.17/l:163
119 atoms, 102 bonds, 17 residues, 17 models selected
> select #15.1/l #15.2/l #15.3/l #15.4/l #15.5/l #15.6/l #15.7/l #15.8/l
> #15.9/l #15.10/l #15.11/l #15.12/l #15.13/l #15.14/l #15.15/l #15.16/l
> #15.17/l
20264 atoms, 20706 bonds, 2533 residues, 17 models selected
2 [ID: 2] region 17 chains [1-149] RMSD: 503.595
> select #15.1/BX-BY:155 #15.2/BX-BY:155 #15.3/BX-BY:155 #15.4/BX-BY:155
> #15.5/BX-BY:155 #15.6/BX-BY:155 #15.7/BX-BY:155 #15.8/BX-BY:155 #15.9/BX-
> BY:155 #15.10/BX-BY:155 #15.11/BX-BY:155 #15.12/BX-BY:155 #15.13/BX-BY:155
> #15.14/BX-BY:155 #15.15/BX-BY:155 #15.16/BX-BY:155 #15.17/BX-BY:155
306 atoms, 272 bonds, 34 residues, 17 models selected
> select #15.1/BX-BY #15.2/BX-BY #15.3/BX-BY #15.4/BX-BY #15.5/BX-BY #15.6/BX-
> BY #15.7/BX-BY #15.8/BX-BY #15.9/BX-BY #15.10/BX-BY #15.11/BX-BY #15.12/BX-
> BY #15.13/BX-BY #15.14/BX-BY #15.15/BX-BY #15.16/BX-BY #15.17/BX-BY
41990 atoms, 42194 bonds, 5270 residues, 17 models selected
1 [ID: 1] region 34 chains [1-155] RMSD: 191.261
> hide sel cartoons
> select clear
> show #!25 models
> show #!231 models
> hide #!231 models
Drag select of 29121 residues, 17 pseudobonds
> save /Users/shoichitachiyama/Desktop/Fig4-Final-models/FlgY-
> PflABrings_09282025.pdb selectedOnly true
> close session
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Manuscript/09262025/Comtenue--9252026/Contenue-
> ver2-Fig3_from_09252025.cxs"
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137,
step 1, values float32
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
level 0.027, step 1, values float32
Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
step 1, values float32
Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at
level 0.0166, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #107, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #108, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #109, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #111, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #112, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #113, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #114, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #115, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #116, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #117, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #118, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #119, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #120, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #121, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #122, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #123, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #124, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #125, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #126, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #127, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #128, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #129, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #130, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #131, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #132, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #133, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #134, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #135, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #136, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #137, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #138, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #139, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #140, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #141, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #142, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #143, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #144, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #145, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #146, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #147, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #148, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #149, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #150, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #151, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #152, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #153, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #154, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #155, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #156, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #157, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #158, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #159, grid size 200,200,200, pixel 2.14,
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
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Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel
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Opened PflC-only-Model-area.mrc copy as #36, grid size 200,200,200, pixel
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level 0.00404, step 1, values float32
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level 0.00404, step 1, values float32
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level 0.00404, step 1, values float32
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level 0.00404, step 1, values float32
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level 0.00404, step 1, values float32
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level 0.00404, step 1, values float32
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level 0.00404, step 1, values float32
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level 0.00404, step 1, values float32
Opened Short-cage.mrc copy as #80, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Opened Short-cage.mrc copy as #81, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Opened Long-cage.mrc copy as #84, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Opened Long-cage.mrc as #86, grid size 200,200,200, pixel 2.14, shown at level
0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc as #90, grid size 200,200,200, pixel 2.14,
shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc as #91, grid size 200,200,200, pixel 2.14,
shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #49, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #50, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #51, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #52, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #53, grid size 200,200,200, pixel
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2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #55, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #56, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #57, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #58, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #59, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #60, grid size 200,200,200, pixel
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Opened PflC-region-long-cage.mrc copy as #61, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #62, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #63, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #64, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #93, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #94, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #95, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #96, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #97, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #98, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #99, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #100, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #101, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #102, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #103, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #104, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #105, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #106, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #210, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #211, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #212, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #213, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
opened ChimeraX session
Showing Long-cage.seg - 559 regions, 559 surfaces
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Manuscript/09262025/Comtenue--9252026/Contenue-
> ver2-Fig3_from_09252025.cxs"
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137,
step 1, values float32
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
level 0.027, step 1, values float32
Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
step 1, values float32
Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at
level 0.0166, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #107, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #108, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #109, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #111, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #112, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #113, grid size 200,200,200,
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Opened Single_Cage_unit.mrc gaussian copy as #118, grid size 200,200,200,
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Opened Single_Cage_unit.mrc gaussian copy as #119, grid size 200,200,200,
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Opened Single_Cage_unit.mrc gaussian copy as #120, grid size 200,200,200,
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pixel 2.14, shown at level 0.000793, step 1, values float32
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pixel 2.14, shown at level 0.000793, step 1, values float32
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pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #130, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
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pixel 2.14, shown at level 0.000793, step 1, values float32
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pixel 2.14, shown at level 0.000793, step 1, values float32
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pixel 2.14, shown at level 0.000793, step 1, values float32
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pixel 2.14, shown at level 0.000793, step 1, values float32
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Opened Single-MotA-ring.mrc gaussian copy as #193, grid size 200,200,200,
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Opened Single-MotA-ring.mrc gaussian copy as #194, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #195, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #196, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
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pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200,
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Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200,
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Opened Single-MotA-ring.mrc gaussian copy as #203, grid size 200,200,200,
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Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200,
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Opened Single-MotA-ring.mrc gaussian copy as #206, grid size 200,200,200,
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #219, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #220, grid size
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #221, grid size
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #222, grid size
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #223, grid size
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #224, grid size
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #225, grid size
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size
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Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14,
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Opened PflC-only-Model-area.mrc copy as #20, grid size 200,200,200, pixel
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Opened PflC-only-Model-area.mrc copy as #21, grid size 200,200,200, pixel
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Opened PflC-only-Model-area.mrc copy as #22, grid size 200,200,200, pixel
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Opened PflC-only-Model-area.mrc copy as #23, grid size 200,200,200, pixel
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Opened PflC-only-Model-area.mrc copy as #24, grid size 200,200,200, pixel
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Opened PflC-only-Model-area.mrc copy as #25, grid size 200,200,200, pixel
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Opened PflC-only-Model-area.mrc copy as #27, grid size 200,200,200, pixel
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Opened PflC-only-Model-area.mrc copy as #28, grid size 200,200,200, pixel
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Opened PflC-only-Model-area.mrc copy as #29, grid size 200,200,200, pixel
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Opened PflC-only-Model-area.mrc copy as #30, grid size 200,200,200, pixel
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Opened PflC-only-Model-area.mrc copy as #31, grid size 200,200,200, pixel
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Opened PflC-only-Model-area.mrc copy as #33, grid size 200,200,200, pixel
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Opened PflC-region-long-cage.mrc copy as #50, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #51, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #52, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #53, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #54, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #55, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #56, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #57, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #58, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #59, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #60, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #61, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #62, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #63, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #64, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #93, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #94, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #95, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #96, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #97, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #98, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #99, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #100, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #101, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #102, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #103, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #104, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #105, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #106, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #210, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #211, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #212, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #213, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
opened ChimeraX session
Showing Long-cage.seg - 559 regions, 559 surfaces
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Manuscript/09262025/Comtenue--9252026/Contenue-
> ver2-Fig3_from_09252025.cxs"
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
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Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137,
step 1, values float32
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
level 0.027, step 1, values float32
Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
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Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at
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Opened Single_Cage_unit.mrc gaussian copy as #107, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #108, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #109, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #111, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #112, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #113, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #114, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #115, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #116, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #117, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #118, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #119, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #120, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #121, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #122, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #123, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #124, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #125, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #126, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #127, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #128, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #129, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #130, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #131, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #132, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #133, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #134, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #135, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #136, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #137, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #138, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #139, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #140, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #141, grid size 200,200,200, pixel 2.14,
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Opened 1xPflD.mrc gaussian copy as #142, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #143, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #144, grid size 200,200,200, pixel 2.14,
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Opened 1xPflD.mrc gaussian copy as #145, grid size 200,200,200, pixel 2.14,
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Opened 1xPflD.mrc gaussian copy as #146, grid size 200,200,200, pixel 2.14,
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Opened 1xPflD.mrc gaussian copy as #147, grid size 200,200,200, pixel 2.14,
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Opened 1xPflD.mrc gaussian copy as #148, grid size 200,200,200, pixel 2.14,
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Opened 1xPflD.mrc gaussian copy as #149, grid size 200,200,200, pixel 2.14,
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Opened 1xPflD.mrc gaussian copy as #150, grid size 200,200,200, pixel 2.14,
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Opened 1xPflD.mrc gaussian copy as #151, grid size 200,200,200, pixel 2.14,
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Opened 1xPflD.mrc gaussian copy as #152, grid size 200,200,200, pixel 2.14,
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Opened 1xPflD.mrc gaussian copy as #154, grid size 200,200,200, pixel 2.14,
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Opened 1xPflD.mrc gaussian copy as #155, grid size 200,200,200, pixel 2.14,
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Opened 1xPflD.mrc gaussian copy as #156, grid size 200,200,200, pixel 2.14,
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Opened 1xPflD.mrc gaussian copy as #157, grid size 200,200,200, pixel 2.14,
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Opened 1xPflC.mrc gaussian copy as #158, grid size 200,200,200, pixel 2.14,
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Opened 1xPflC.mrc gaussian copy as #159, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #160, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #161, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #162, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #163, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #164, grid size 200,200,200, pixel 2.14,
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Opened 1xPflC.mrc gaussian copy as #165, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #166, grid size 200,200,200, pixel 2.14,
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Opened 1xPflC.mrc gaussian copy as #167, grid size 200,200,200, pixel 2.14,
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Opened 1xPflC.mrc gaussian copy as #168, grid size 200,200,200, pixel 2.14,
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Opened 1xPflC.mrc gaussian copy as #169, grid size 200,200,200, pixel 2.14,
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Opened 1xPflC.mrc gaussian copy as #170, grid size 200,200,200, pixel 2.14,
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Opened 1xPflC.mrc gaussian copy as #171, grid size 200,200,200, pixel 2.14,
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Opened 1xPflC.mrc gaussian copy as #172, grid size 200,200,200, pixel 2.14,
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Opened 1xPflC.mrc gaussian copy as #173, grid size 200,200,200, pixel 2.14,
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Opened 1xPflC.mrc gaussian copy as #174, grid size 200,200,200, pixel 2.14,
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Opened 1xFliL.mrc gaussian copy as #175, grid size 200,200,200, pixel 2.14,
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Opened 1xFliL.mrc gaussian copy as #177, grid size 200,200,200, pixel 2.14,
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Opened 1xFliL.mrc gaussian copy as #178, grid size 200,200,200, pixel 2.14,
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Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14,
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pixel 2.14, shown at level 0.000997, step 1, values float32
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pixel 2.14, shown at level 0.000997, step 1, values float32
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pixel 2.14, shown at level 0.000997, step 1, values float32
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pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
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pixel 2.14, shown at level 0.000997, step 1, values float32
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pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
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pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
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pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #207, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #208, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #214, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #215, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
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200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
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200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
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200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14,
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Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel
2.14, shown at level 0.00974, step 1, values float32
Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at
level 0.157, step 1, values float32
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Opened PflC-region-long-cage.mrc copy as #49, grid size 200,200,200, pixel
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2.14, shown at level 0.00261, step 1, values float32
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2.14, shown at level 0.00261, step 1, values float32
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2.14, shown at level 0.00261, step 1, values float32
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2.14, shown at level 0.00261, step 1, values float32
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Opened PflD-Longcage-region.mrc copy as #97, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #98, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
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2.14, shown at level 0.00261, step 1, values float32
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2.14, shown at level 0.00261, step 1, values float32
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2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #102, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #103, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
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2.14, shown at level 0.00261, step 1, values float32
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2.14, shown at level 0.00261, step 1, values float32
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2.14, shown at level 0.00261, step 1, values float32
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2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #211, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #212, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #213, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
opened ChimeraX session
Showing Long-cage.seg - 559 regions, 559 surfaces
> hide #!17 models
> select add #47.17
9213 atoms, 9399 bonds, 1 pseudobond, 1123 residues, 2 models selected
> save /Users/shoichitachiyama/Desktop/Fig4-Final-models/Long-cage.pdb
> selectedOnly true
> select subtract #47.17
5 models selected
> show #!48 models
> hide #!47 models
> select add #48.17
6359 atoms, 6486 bonds, 1 pseudobond, 767 residues, 2 models selected
> save /Users/shoichitachiyama/Desktop/Fig4-Final-models/Short-cage.pdb
> selectedOnly true
> close session
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Manuscript/09262025/New Images/Composition-Transparent-Fig2.cxs"
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pixel 2.14, shown at level 0.000793, step 1, values float32
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pixel 2.14, shown at level 0.000793, step 1, values float32
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pixel 2.14, shown at level 0.000793, step 1, values float32
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pixel 2.14, shown at level 0.000793, step 1, values float32
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pixel 2.14, shown at level 0.000793, step 1, values float32
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Opened 1xPflC.mrc gaussian copy as #162, grid size 200,200,200, pixel 2.14,
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Opened 1xFliL.mrc gaussian copy as #180, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #181, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #182, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #185, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #186, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #187, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #188, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #189, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #190, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #191, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened Single-MotA-ring.mrc gaussian as #192, grid size 200,200,200, pixel
2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #193, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #194, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #195, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #196, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #199, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #200, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #202, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #203, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #204, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #206, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #207, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #208, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #214, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #215, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #219, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #220, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #221, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #222, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #223, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #224, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #225, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14,
shown at level 0.0112, step 1, values float32
Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel
2.14, shown at level 0.00974, step 1, values float32
Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at
level 0.157, step 1, values float32
Opened C-Vrings.mrc as #4, grid size 250,250,250, pixel 4.3, shown at level
0.0283, step 1, values float32
Opened 1unit_PflABCD.mrc as #5, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Opened 3xFlgY.mrc as #22, grid size 256,256,256, pixel 2.14, shown at level
0.0112, step 1, values float32
Opened 1xPflB.mrc as #26, grid size 200,200,200, pixel 2.14, shown at level
0.00045, step 1, values float32
Opened 1xFlgY.mrc as #29, grid size 256,256,256, pixel 2.14, shown at level
0.0112, step 1, values float32
Opened 1xPflB.mrc as #30, grid size 200,200,200, pixel 2.14, shown at level
0.00045, step 1, values float32
opened ChimeraX session
Showing 3xFlgY.seg - 23 regions, 23 surfaces
> hide #!21 models
> hide #!25 models
> show #!25 models
> select add #25
78642 atoms, 79390 bonds, 9775 residues, 18 models selected
Alignment identifier is 1
Alignment identifier is 2
> select #25.1/s:788 #25.2/s:788 #25.3/s:788 #25.4/s:788 #25.5/s:788
> #25.6/s:788 #25.7/s:788 #25.8/s:788 #25.9/s:788 #25.10/s:788 #25.11/s:788
> #25.12/s:788 #25.13/s:788 #25.14/s:788 #25.15/s:788 #25.16/s:788
> #25.17/s:788
170 atoms, 153 bonds, 17 residues, 17 models selected
> select #25.1/s #25.2/s #25.3/s #25.4/s #25.5/s #25.6/s #25.7/s #25.8/s
> #25.9/s #25.10/s #25.11/s #25.12/s #25.13/s #25.14/s #25.15/s #25.16/s
> #25.17/s
36652 atoms, 37196 bonds, 4505 residues, 17 models selected
2 [ID: 2] region 17 chains [1-265] RMSD: 281.686
> hide sel cartoons
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!231 models
> show #!107 models
> color #107 #a9a9a94c models
> open /Users/shoichitachiyama/Desktop/Fig4-Final-models/Long-cage.pdb
Chain information for Long-cage.pdb #31
---
Chain | Description
A | No description available
B | No description available
C | No description available
X | No description available
c | No description available
> open /Users/shoichitachiyama/Desktop/Fig4-Final-models/Short-cage.pdb
Chain information for Short-cage.pdb #32
---
Chain | Description
D | No description available
E | No description available
F | No description available
L | No description available
> select add #31
45865 atoms, 46595 bonds, 1 pseudobond, 5628 residues, 36 models selected
> select add #32
52224 atoms, 53081 bonds, 2 pseudobonds, 6395 residues, 38 models selected
> hide sel surfaces
> hide sel atoms
> show sel cartoons
> select clear
> show #!108 models
> show #!117 models
> show #!114 models
> show #!115 models
> color #115 #a9a9a94c models
> hide #!107 models
> hide #!108 models
> hide #!114 models
> hide #!115 models
> hide #!117 models
> select add #31
9213 atoms, 9399 bonds, 1 pseudobond, 1123 residues, 2 models selected
Alignment identifier is 31/A
Alignment identifier is 31/B
Alignment identifier is 31/C
Alignment identifier is 31/X
Alignment identifier is 31/c
> select add #32
15572 atoms, 15885 bonds, 2 pseudobonds, 1890 residues, 4 models selected
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 31/c
> select clear
> select #31/c:311
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #31/c:51-311
2106 atoms, 2150 bonds, 261 residues, 1 model selected
> select clear
> select #31/A:319 #32/D:319
20 atoms, 18 bonds, 2 residues, 2 models selected
> select #31/A #32/D
4288 atoms, 4373 bonds, 2 pseudobonds, 518 residues, 4 models selected
1 [ID: 1] region chains A,D [1-259] RMSD: 42.712
> color sel #a7c5d2ff models
> color sel #5A97FF models
> color sel #73e0ffff models
> color sel #adffc1ff models
> color sel #765FF3 models
> select #31/A:319 #32/D:319
20 atoms, 18 bonds, 2 residues, 2 models selected
> select #31/A #32/D
4288 atoms, 4373 bonds, 2 pseudobonds, 518 residues, 4 models selected
1 [ID: 1] region chains A,D [1-259] RMSD: 42.712
> color (#!31-32 & sel) #a7c5d2ff
> select clear
> select #31/B:175 #32/E:175
24 atoms, 22 bonds, 2 residues, 2 models selected
> select #31/B #32/E
2916 atoms, 2978 bonds, 350 residues, 2 models selected
2 [ID: 2] region chains B,E [1-175] RMSD: 63.267
> color sel #5a97ffff
> select clear
> select #31/C:189 #32/F:189
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #31/C #32/F
2804 atoms, 2844 bonds, 342 residues, 2 models selected
3 [ID: 3] region chains C,F [1-171] RMSD: 63.641
> color sel #73e0ffff
> select clear
> select #31/X:162 #32/L:162
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #31/X #32/L
2710 atoms, 2776 bonds, 324 residues, 2 models selected
4 [ID: 4] region chains L,X [1-162] RMSD: 61.587
> color sel #adffc1ff
> select clear
> select #31/c:311-356
354 atoms, 359 bonds, 46 residues, 1 model selected
> select #31/c
2854 atoms, 2914 bonds, 356 residues, 1 model selected
> color sel #765ff3ff
> select clear
> show #!3 models
> view orient
> sym #31 C17 copies true center #3
Made 17 copies for Long-cage.pdb symmetry C17
> sym #32 C17 copies true center #3
Made 17 copies for Short-cage.pdb symmetry C17
> save /Users/shoichitachiyama/Desktop/Fig4-Final-models/Figure4-Final-
> model_09282025.cxs includeMaps true
> close session
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Lab Slides/Lab
> Meeting/2025/Sep_2025/CJ_Whole_models-Cut.cxs"
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137,
step 1, values float32
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
level 0.027, step 1, values float32
Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
step 1, values float32
Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at
level 0.0166, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #107, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #108, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #109, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #111, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #112, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #113, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #114, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #115, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #116, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #117, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #118, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #119, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #120, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #121, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #122, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #123, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #124, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #125, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #126, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #127, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #128, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #129, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #130, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #131, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #132, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #133, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #134, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #135, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #136, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #137, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #138, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #139, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #140, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #141, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #142, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #143, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #144, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #145, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #146, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #147, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #148, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #149, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #150, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #151, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #152, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #153, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #154, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #155, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #156, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #157, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #158, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #159, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #160, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #161, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #162, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #163, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #164, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #165, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #166, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #167, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #168, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #169, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #170, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #171, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #172, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #173, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #174, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #175, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #176, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #177, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #178, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #180, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #181, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #182, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #185, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #186, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #187, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #188, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #189, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #190, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #191, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened Single-MotA-ring.mrc gaussian as #192, grid size 200,200,200, pixel
2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #193, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #194, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #195, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #196, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #199, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #200, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #202, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #203, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #204, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #206, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #207, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #208, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #214, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #215, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #219, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #220, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #221, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #222, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #223, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #224, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #225, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14,
shown at level 0.0112, step 1, values float32
Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel
2.14, shown at level 0.00974, step 1, values float32
Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at
level 0.157, step 1, values float32
Opened C-Vrings.mrc as #4, grid size 250,250,250, pixel 4.3, shown at level
0.0283, step 1, values float32
Opened 1unit_PflABCD.mrc as #5, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Opened PflAB_wout_FlgYoverlap_imasked as #18, grid size 200,200,200, pixel
2.14, shown at level 0.00045, step 1, values float32
Opened PflC-only-Model-area.mrc as #19, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened PflC-only-Model-area.mrc copy as #20, grid size 200,200,200, pixel
2.14, shown at level 0.00107, step 1, values float32
Opened PflC-only-Model-area.mrc copy as #21, grid size 200,200,200, pixel
2.14, shown at level 0.00107, step 1, values float32
Opened PflC-only-Model-area.mrc copy as #22, grid size 200,200,200, pixel
2.14, shown at level 0.00107, step 1, values float32
Opened PflC-only-Model-area.mrc copy as #23, grid size 200,200,200, pixel
2.14, shown at level 0.00107, step 1, values float32
Opened PflC-only-Model-area.mrc copy as #24, grid size 200,200,200, pixel
2.14, shown at level 0.00107, step 1, values float32
Opened PflC-only-Model-area.mrc copy as #25, grid size 200,200,200, pixel
2.14, shown at level 0.00107, step 1, values float32
Opened PflC-only-Model-area.mrc copy as #26, grid size 200,200,200, pixel
2.14, shown at level 0.00107, step 1, values float32
Opened PflC-only-Model-area.mrc copy as #27, grid size 200,200,200, pixel
2.14, shown at level 0.00107, step 1, values float32
Opened PflC-only-Model-area.mrc copy as #28, grid size 200,200,200, pixel
2.14, shown at level 0.00107, step 1, values float32
Opened PflC-only-Model-area.mrc copy as #29, grid size 200,200,200, pixel
2.14, shown at level 0.00107, step 1, values float32
Opened PflC-only-Model-area.mrc copy as #30, grid size 200,200,200, pixel
2.14, shown at level 0.00107, step 1, values float32
Opened PflC-only-Model-area.mrc copy as #31, grid size 200,200,200, pixel
2.14, shown at level 0.00107, step 1, values float32
Opened PflC-only-Model-area.mrc copy as #32, grid size 200,200,200, pixel
2.14, shown at level 0.00107, step 1, values float32
Opened PflC-only-Model-area.mrc copy as #33, grid size 200,200,200, pixel
2.14, shown at level 0.00107, step 1, values float32
Opened PflC-only-Model-area.mrc copy as #34, grid size 200,200,200, pixel
2.14, shown at level 0.00107, step 1, values float32
Opened PflC-only-Model-area.mrc copy as #35, grid size 200,200,200, pixel
2.14, shown at level 0.00107, step 1, values float32
Opened PflC-only-Model-area.mrc copy as #36, grid size 200,200,200, pixel
2.14, shown at level 0.00107, step 1, values float32
Opened FlgV-ring.mrc as #37, grid size 200,200,120, pixel 4.3,4.3,4.3, shown
at level 0.0486, step 1, values float32
Opened C-ring.mrc as #38, grid size 250,250,250, pixel 4.3, shown at level
0.0283, step 1, values float32
opened ChimeraX session
Showing C-Vrings.seg - 65 regions, 65 surfaces
> select add #43
272320 atoms, 275760 bonds, 34560 residues, 254 models selected
> hide #!17 models
> show #!43.21 models
> show #!43.22 models
> show #!43.23 models
> show #!43.24 models
> show #!43.25 models
> show #!43.26 models
> show #!43.27 models
> show #!43.28 models
> show #!43.29 models
> show #!43.30 models
> show #!43.32 models
> show #!43.31 models
> hide #!43.29 models
> hide #!43.31 models
> hide #!43.32 models
> show #!43.31 models
> show #!43.29 models
> show #!43.32 models
> hide sel surfaces
> show sel cartoons
> save /Users/shoichitachiyama/Desktop/Fig4-Final-models/C40-8uox.pdb
> selectedOnly true
> color #88 #70887a5e models
> color #88 #70887a73 models
> close session
> open /Users/shoichitachiyama/Desktop/Fig4-Final-models/Figure4-Final-
> model_09282025.cxs
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137,
step 1, values float32
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
level 0.027, step 1, values float32
Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
step 1, values float32
Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at
level 0.0166, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #107, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #108, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #109, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #111, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #112, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #113, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #114, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #115, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #116, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #117, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #118, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #119, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #120, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #121, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #122, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #123, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #124, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #125, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #126, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #127, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #128, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #129, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #130, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #131, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #132, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #133, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #134, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #135, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #136, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #137, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #138, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #139, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #140, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #141, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #142, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #143, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #144, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #145, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #146, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #147, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #148, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #149, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #150, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #151, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #152, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #153, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #154, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #155, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #156, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #157, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #158, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #159, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #160, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #161, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #162, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #163, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #164, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #165, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #166, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #167, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #168, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #169, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #170, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #171, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #172, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #173, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #174, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #175, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #176, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #177, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #178, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #180, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #181, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #182, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #185, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #186, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #187, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #188, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #189, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #190, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #191, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened Single-MotA-ring.mrc gaussian as #192, grid size 200,200,200, pixel
2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #193, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #194, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #195, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #196, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #199, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #200, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #202, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #203, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #204, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #206, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #207, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #208, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #214, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #215, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #219, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #220, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #221, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #222, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #223, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #224, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #225, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14,
shown at level 0.0112, step 1, values float32
Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel
2.14, shown at level 0.00974, step 1, values float32
Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at
level 0.157, step 1, values float32
Opened C-Vrings.mrc as #4, grid size 250,250,250, pixel 4.3, shown at level
0.0283, step 1, values float32
Opened 1unit_PflABCD.mrc as #5, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Opened 3xFlgY.mrc as #22, grid size 256,256,256, pixel 2.14, shown at level
0.0112, step 1, values float32
Opened 1xPflB.mrc as #26, grid size 200,200,200, pixel 2.14, shown at level
0.00045, step 1, values float32
Opened 1xFlgY.mrc as #29, grid size 256,256,256, pixel 2.14, shown at level
0.0112, step 1, values float32
Opened 1xPflB.mrc as #30, grid size 200,200,200, pixel 2.14, shown at level
0.00045, step 1, values float32
opened ChimeraX session
Showing 3xFlgY.seg - 23 regions, 23 surfaces
> hide #!21 models
> color #88 #70887a73 models
> show #!88 models
> show #!89 models
> color #89 #70887a73 models
> hide #!88 models
> hide #!89 models
> hide #!3 models
> select add #25
78642 atoms, 79390 bonds, 9775 residues, 18 models selected
> hide sel cartoons
> show sel surfaces
Alignment identifier is 1
Alignment identifier is 2
> select #25.1/s:788 #25.2/s:788 #25.3/s:788 #25.4/s:788 #25.5/s:788
> #25.6/s:788 #25.7/s:788 #25.8/s:788 #25.9/s:788 #25.10/s:788 #25.11/s:788
> #25.12/s:788 #25.13/s:788 #25.14/s:788 #25.15/s:788 #25.16/s:788
> #25.17/s:788
170 atoms, 153 bonds, 17 residues, 17 models selected
> select #25.1/s #25.2/s #25.3/s #25.4/s #25.5/s #25.6/s #25.7/s #25.8/s
> #25.9/s #25.10/s #25.11/s #25.12/s #25.13/s #25.14/s #25.15/s #25.16/s
> #25.17/s
36652 atoms, 37196 bonds, 4505 residues, 17 models selected
2 [ID: 2] region 17 chains [1-265] RMSD: 281.686
> hide sel cartoons
> hide sel surfaces
> select clear
> select add #33
156621 atoms, 159783 bonds, 17 pseudobonds, 19091 residues, 35 models selected
> select add #34
264724 atoms, 270045 bonds, 34 pseudobonds, 32130 residues, 70 models selected
> open /Users/shoichitachiyama/Desktop/Fig4-Final-models/C40-8uox.pdb
Summary of feedback from opening /Users/shoichitachiyama/Desktop/Fig4-Final-
models/C40-8uox.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLUBN 2 GLNBN 97 1 96
Start residue of secondary structure not found: HELIX 2 2 ALABN 101 GLNBN 109
1 9
Start residue of secondary structure not found: HELIX 3 3 ALABN 112 ILEBN 118
1 7
Start residue of secondary structure not found: HELIX 4 4 METBN 119 SERBN 121
1 3
Start residue of secondary structure not found: HELIX 5 5 SERBN 124 VALBN 130
1 7
77395 messages similar to the above omitted
Chain information for C40-8uox.pdb
---
Chain | Description
35.1/B1 35.6/B1 35.11/B1 35.16/B1 35.21/B1 35.26/B1 35.31/B1 35.36/B1 35.41/B1 35.46/B1 35.51/B1 35.56/B1 35.61/B1 35.66/B1 35.71/B1 35.76/B1 35.81/B1 35.86/B1 35.91/B1 35.96/B1 35.101/B1 35.106/B1 35.111/B1 35.116/B1 35.121/B1 35.126/B1 35.131/B1 35.136/B1 35.141/B1 35.146/B1 35.151/B1 35.156/B1 35.161/B1 35.166/B1 35.171/B1 35.176/B1 35.181/B1 35.186/B1 35.191/B1 35.196/B1 | No description available
35.2/C1 35.7/C1 35.12/C1 35.17/C1 35.22/C1 35.27/C1 35.32/C1 35.37/C1 35.42/C1 35.47/C1 35.52/C1 35.57/C1 35.62/C1 35.67/C1 35.72/C1 35.77/C1 35.82/C1 35.87/C1 35.92/C1 35.97/C1 35.102/C1 35.107/C1 35.112/C1 35.117/C1 35.122/C1 35.127/C1 35.132/C1 35.137/C1 35.142/C1 35.147/C1 35.152/C1 35.157/C1 35.162/C1 35.167/C1 35.172/C1 35.177/C1 35.182/C1 35.187/C1 35.192/C1 35.197/C1 | No description available
35.3/D1 35.8/D1 35.13/D1 35.18/D1 35.23/D1 35.28/D1 35.33/D1 35.38/D1 35.43/D1 35.48/D1 35.53/D1 35.58/D1 35.63/D1 35.68/D1 35.73/D1 35.78/D1 35.83/D1 35.88/D1 35.93/D1 35.98/D1 35.103/D1 35.108/D1 35.113/D1 35.118/D1 35.123/D1 35.128/D1 35.133/D1 35.138/D1 35.143/D1 35.148/D1 35.153/D1 35.158/D1 35.163/D1 35.168/D1 35.173/D1 35.178/D1 35.183/D1 35.188/D1 35.193/D1 35.198/D1 35.4/E1 35.9/E1 35.14/E1 35.19/E1 35.24/E1 35.29/E1 35.34/E1 35.39/E1 35.44/E1 35.49/E1 35.54/E1 35.59/E1 35.64/E1 35.69/E1 35.74/E1 35.79/E1 35.84/E1 35.89/E1 35.94/E1 35.99/E1 35.104/E1 35.109/E1 35.114/E1 35.119/E1 35.124/E1 35.129/E1 35.134/E1 35.139/E1 35.144/E1 35.149/E1 35.154/E1 35.159/E1 35.164/E1 35.169/E1 35.174/E1 35.179/E1 35.184/E1 35.189/E1 35.194/E1 35.199/E1 | No description available
35.5/F1 35.10/F1 35.15/F1 35.20/F1 35.25/F1 35.30/F1 35.35/F1 35.40/F1 35.45/F1 35.50/F1 35.55/F1 35.60/F1 35.65/F1 35.70/F1 35.75/F1 35.80/F1 35.85/F1 35.90/F1 35.95/F1 35.100/F1 35.105/F1 35.110/F1 35.115/F1 35.120/F1 35.125/F1 35.130/F1 35.135/F1 35.140/F1 35.145/F1 35.150/F1 35.155/F1 35.160/F1 35.165/F1 35.170/F1 35.175/F1 35.180/F1 35.185/F1 35.190/F1 35.195/F1 35.200/F1 | No description available
> select subtract #33
108103 atoms, 110262 bonds, 17 pseudobonds, 13039 residues, 35 models selected
> select subtract #34
Nothing selected
> color #35 #797979ff models
> select add #35
272320 atoms, 275760 bonds, 34560 residues, 201 models selected
> hide sel cartoons
> show sel surfaces
> select clear
> show #!158 models
> hide #!15 models
> hide #!25 models
> hide #!33 models
> show #!33 models
> hide #!34 models
> hide #!35 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Segmenting 1xPflC.mrc gaussian copy, density threshold 0.001074
Showing 8 region surfaces
65 watershed regions, grouped to 8 regions
Showing 1xPflC gaussian copy.seg - 8 regions, 8 surfaces
> select add #21
9 models selected
> ui mousemode right "translate selected models"
> view matrix models #21,1,0,0,363.59,0,1,0,548.2,0,0,1,107.12
> view matrix models #21,1,0,0,514.38,0,1,0,484.38,0,0,1,91.822
> view matrix models #21,1,0,0,598.19,0,1,0,386.48,0,0,1,234.92
> view matrix models #21,1,0,0,591.9,0,1,0,375.41,0,0,1,236.37
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.97931,-0.20218,0.0091558,634.4,0.20238,0.97862,-0.03661,350.94,-0.0015584,0.037705,0.99929,229.21
> ui mousemode right "translate selected models"
> view matrix models
> #21,0.97931,-0.20218,0.0091558,620.1,0.20238,0.97862,-0.03661,344.01,-0.0015584,0.037705,0.99929,232.02
> hide #!158 models
> select #21.1
1 model selected
> select add #21.2
2 models selected
> select #21.2
1 model selected
Ungrouped to 3 regions
> select #21.1
1 model selected
> select add #21.10
2 models selected
> select add #21.9
3 models selected
> select add #33
156621 atoms, 159783 bonds, 17 pseudobonds, 19091 residues, 38 models selected
> show sel surfaces
Showing 10 region surfaces
> select clear
> select #21.1
1 model selected
> select add #21.10
2 models selected
> select add #21.9
3 models selected
Grouped 3 regions
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Opened 1xPflC_imasked as #36, grid size 200,200,200, pixel 2.14, shown at step
1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/Fig4-Final-models/PflC-model-region.mrc
> models #36
Opened 1xPflC_imasked as #37, grid size 200,200,200, pixel 2.14, shown at step
1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/Fig4-Final-models/PflC-No-model.mrc
> models #37
> hide #!21 models
> hide #!36 models
> show #!3 models
> view orient
> select add #21
9 models selected
> select subtract #21
Nothing selected
> turn z 21.176470588 models #37 center #3
> volume copy #37
Opened PflC-No-model.mrc copy as #38, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> volume #37 show
> turn z 21.176470588 models #37 center #3
> volume copy #37
Opened PflC-No-model.mrc copy as #39, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> volume #37 show
> turn z 21.176470588 models #37 center #3
> volume copy #37
Opened PflC-No-model.mrc copy as #40, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> volume #37 show
> turn z 21.176470588 models #37 center #3
> volume copy #37
Opened PflC-No-model.mrc copy as #41, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> volume #37 show
> turn z 21.176470588 models #37 center #3
> volume copy #37
Opened PflC-No-model.mrc copy as #42, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> volume #37 show
> turn z 21.176470588 models #37 center #3
> volume copy #37
Opened PflC-No-model.mrc copy as #43, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> volume #37 show
> turn z 21.176470588 models #37 center #3
> volume copy #37
Opened PflC-No-model.mrc copy as #44, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> volume #37 show
> turn z 21.176470588 models #37 center #3
> volume copy #37
Opened PflC-No-model.mrc copy as #45, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> volume #37 show
> turn z 21.176470588 models #37 center #3
> volume copy #37
Opened PflC-No-model.mrc copy as #46, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> volume #37 show
> turn z 21.176470588 models #37 center #3
> volume copy #37
Opened PflC-No-model.mrc copy as #47, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> volume #37 show
> turn z 21.176470588 models #37 center #3
> volume copy #37
Opened PflC-No-model.mrc copy as #48, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> volume #37 show
> turn z 21.176470588 models #37 center #3
> volume copy #37
Opened PflC-No-model.mrc copy as #49, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> volume #37 show
> turn z 21.176470588 models #37 center #3
> volume copy #37
Opened PflC-No-model.mrc copy as #50, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> volume #37 show
> turn z 21.176470588 models #37 center #3
> volume copy #37
Opened PflC-No-model.mrc copy as #51, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> volume #37 show
> turn z 21.176470588 models #37 center #3
> volume copy #37
Opened PflC-No-model.mrc copy as #52, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> volume #37 show
> turn z 21.176470588 models #37 center #3
> volume copy #37
Opened PflC-No-model.mrc copy as #53, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> volume #37 show
> turn z 21.176470588 models #37 center #3
> volume copy #37
Opened PflC-No-model.mrc copy as #54, grid size 200,200,200, pixel 2.14, shown
at step 1, values float32
> volume #37 show
> hide #!37 models
> hide #!37-54 models
> show #!108 models
> hide #!33 models
> show #!34 models
Segmenting Single_Cage_unit.mrc gaussian copy, density threshold 0.000576
Showing 10 region surfaces
64 watershed regions, grouped to 10 regions
Showing Single_Cage_unit gaussian copy.seg - 10 regions, 10 surfaces
> select add #21
11 models selected
> view matrix models #21,1,0,0,33.811,0,1,0,514.55,0,0,1,211.9
> view matrix models #21,1,0,0,459.49,0,1,0,744.88,0,0,1,196.8
> view matrix models #21,1,0,0,544.49,0,1,0,645.42,0,0,1,222.34
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.76809,-0.63471,-0.084728,732.84,0.63662,0.77116,-0.0056035,483.03,0.068896,-0.049636,0.99639,209.2
> ui mousemode right "translate selected models"
> view matrix models
> #21,0.76809,-0.63471,-0.084728,747.39,0.63662,0.77116,-0.0056035,359.6,0.068896,-0.049636,0.99639,198.23
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.88003,-0.46559,-0.093623,687.12,0.46828,0.88354,0.00786,392.37,0.07906,-0.050759,0.99558,195.35
> ui mousemode right "translate selected models"
> view matrix models
> #21,0.88003,-0.46559,-0.093623,694.44,0.46828,0.88354,0.00786,386.5,0.07906,-0.050759,0.99558,195.79
> view matrix models
> #21,0.88003,-0.46559,-0.093623,696.98,0.46828,0.88354,0.00786,393.64,0.07906,-0.050759,0.99558,212.91
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.88777,-0.45345,-0.079052,689.87,0.45134,0.89128,-0.04385,407.52,0.090341,0.0032493,0.99591,200.76
> ui mousemode right "translate selected models"
> view matrix models
> #21,0.88777,-0.45345,-0.079052,688.82,0.45134,0.89128,-0.04385,410.81,0.090341,0.0032493,0.99591,200.26
> view matrix models
> #21,0.88777,-0.45345,-0.079052,684.28,0.45134,0.89128,-0.04385,407.72,0.090341,0.0032493,0.99591,201.66
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.87126,-0.48571,-0.070674,693.07,0.48293,0.87403,-0.053338,402.3,0.087678,0.012341,0.99607,201.02
> ui mousemode right "translate selected models"
> view matrix models
> #21,0.87126,-0.48571,-0.070674,689.04,0.48293,0.87403,-0.053338,401.16,0.087678,0.012341,0.99607,201.97
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.81363,-0.57987,-0.041948,716.95,0.57729,0.81434,-0.059926,382.17,0.068909,0.024541,0.99732,205.71
> ui mousemode right "translate selected models"
> view matrix models
> #21,0.81363,-0.57987,-0.041948,714.36,0.57729,0.81434,-0.059926,383.18,0.068909,0.024541,0.99732,205.51
> hide #!108 models
> select #21.6
1 model selected
Ungrouped to 3 regions
Ungrouped to 0 regions
Ungrouped to 7 regions
> select #21.16
1 model selected
> select add #21.17
2 models selected
Grouped 2 regions
> select #21.12
1 model selected
> select add #21.13
2 models selected
Showing 15 region surfaces
> select #21.1
1 model selected
Opened Single_Cage_unit_imasked as #55, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/Fig4-Final-models/Bridge.mrc models #55
> hide #!21 models
> select add #21
16 models selected
> select subtract #21
Nothing selected
> select add #21
16 models selected
> select subtract #21
Nothing selected
> view orient
> turn z 21.176470588 models #55 center #3
> volume copy #55
Opened Single_Cage_unit_imasked copy as #56, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #55 show
> turn z 21.176470588 models #55 center #3
> volume copy #55
Opened Single_Cage_unit_imasked copy as #57, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #55 show
> turn z 21.176470588 models #55 center #3
> volume copy #55
Opened Single_Cage_unit_imasked copy as #58, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #55 show
> turn z 21.176470588 models #55 center #3
> volume copy #55
Opened Single_Cage_unit_imasked copy as #59, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #55 show
> turn z 21.176470588 models #55 center #3
> volume copy #55
Opened Single_Cage_unit_imasked copy as #60, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #55 show
> turn z 21.176470588 models #55 center #3
> volume copy #55
Opened Single_Cage_unit_imasked copy as #61, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #55 show
> turn z 21.176470588 models #55 center #3
> volume copy #55
Opened Single_Cage_unit_imasked copy as #62, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #55 show
> turn z 21.176470588 models #55 center #3
> volume copy #55
Opened Single_Cage_unit_imasked copy as #63, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #55 show
> turn z 21.176470588 models #55 center #3
> volume copy #55
Opened Single_Cage_unit_imasked copy as #64, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #55 show
> turn z 21.176470588 models #55 center #3
> volume copy #55
Opened Single_Cage_unit_imasked copy as #65, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #55 show
> turn z 21.176470588 models #55 center #3
> volume copy #55
Opened Single_Cage_unit_imasked copy as #66, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #55 show
> turn z 21.176470588 models #55 center #3
> volume copy #55
Opened Single_Cage_unit_imasked copy as #67, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #55 show
> turn z 21.176470588 models #55 center #3
> volume copy #55
Opened Single_Cage_unit_imasked copy as #68, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #55 show
> turn z 21.176470588 models #55 center #3
> volume copy #55
Opened Single_Cage_unit_imasked copy as #69, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #55 show
> turn z 21.176470588 models #55 center #3
> volume copy #55
Opened Single_Cage_unit_imasked copy as #70, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #55 show
> turn z 21.176470588 models #55 center #3
> volume copy #55
Opened Single_Cage_unit_imasked copy as #71, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #55 show
> turn z 21.176470588 models #55 center #3
> volume copy #55
Opened Single_Cage_unit_imasked copy as #72, grid size 200,200,200, pixel
2.14, shown at step 1, values float32
> volume #55 show
> save /Users/shoichitachiyama/Desktop/Fig4-Final-models/Figure4-Final-
> model_09282025.cxs includeMaps true
> show #!13 models
> show #13.1 models
> show #13.2 models
> show #13.3 models
> show #13.5 models
> show #13.4 models
> show #13.6 models
> show #13.7 models
> show #13.8 models
> show #13.9 models
> show #13.10 models
> show #13.11 models
> show #13.12 models
> show #13.13 models
> show #13.14 models
> show #13.15 models
> show #13.16 models
> show #13.17 models
> select add #13
381633 atoms, 388042 bonds, 48671 residues, 18 models selected
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
> select #13.1/L:260 #13.2/L:260 #13.3/L:260 #13.4/L:260 #13.5/L:260
> #13.6/L:260 #13.7/L:260 #13.8/L:260 #13.9/L:260 #13.10/L:260 #13.11/L:260
> #13.12/L:260 #13.13/L:260 #13.14/L:260 #13.15/L:260 #13.16/L:260
> #13.17/L:260
153 atoms, 136 bonds, 17 residues, 17 models selected
> select #13.1/L #13.2/L #13.3/L #13.4/L #13.5/L #13.6/L #13.7/L #13.8/L
> #13.9/L #13.10/L #13.11/L #13.12/L #13.13/L #13.14/L #13.15/L #13.16/L
> #13.17/L
34918 atoms, 35547 bonds, 4420 residues, 17 models selected
2 [ID: 2] region 17 chains [1-260] RMSD: 431.797
> color sel #FFBF1D models
> color sel #714B0E models
> color sel #FFFF00 models
> select #13.1/L:258-260 #13.2/L:258-260 #13.3/L:258-260 #13.4/L:258-260
> #13.5/L:258-260 #13.6/L:258-260 #13.7/L:258-260 #13.8/L:258-260
> #13.9/L:258-260 #13.10/L:258-260 #13.11/L:258-260 #13.12/L:258-260
> #13.13/L:258-260 #13.14/L:258-260 #13.15/L:258-260 #13.16/L:258-260
> #13.17/L:258-260
442 atoms, 425 bonds, 51 residues, 17 models selected
> select #13.1/L #13.2/L #13.3/L #13.4/L #13.5/L #13.6/L #13.7/L #13.8/L
> #13.9/L #13.10/L #13.11/L #13.12/L #13.13/L #13.14/L #13.15/L #13.16/L
> #13.17/L
34918 atoms, 35547 bonds, 4420 residues, 17 models selected
2 [ID: 2] region 17 chains [1-260] RMSD: 431.797
> color sel #ffbf1dff
> select #13.1/K:260 #13.2/K:260 #13.3/K:260 #13.4/K:260 #13.5/K:260
> #13.6/K:260 #13.7/K:260 #13.8/K:260 #13.9/K:260 #13.10/K:260 #13.11/K:260
> #13.12/K:260 #13.13/K:260 #13.14/K:260 #13.15/K:260 #13.16/K:260
> #13.17/K:260
153 atoms, 136 bonds, 17 residues, 17 models selected
> select #13.1/K #13.2/K #13.3/K #13.4/K #13.5/K #13.6/K #13.7/K #13.8/K
> #13.9/K #13.10/K #13.11/K #13.12/K #13.13/K #13.14/K #13.15/K #13.16/K
> #13.17/K
34765 atoms, 35360 bonds, 4386 residues, 17 models selected
1 [ID: 1] region 17 chains [1-258] RMSD: 451.995
> color sel #adffc1ff
> color sel #ffbf1dff
> select #13.1/A-E:211-255 #13.2/A-E:211-255 #13.3/A-E:211-255
> #13.4/A-E:211-255 #13.5/A-E:211-255 #13.6/A-E:211-255 #13.7/A-E:211-255
> #13.8/A-E:211-255 #13.9/A-E:211-255 #13.10/A-E:211-255 #13.11/A-E:211-255
> #13.12/A-E:211-255 #13.13/A-E:211-255 #13.14/A-E:211-255 #13.15/A-E:211-255
> #13.16/A-E:211-255 #13.17/A-E:211-255
30005 atoms, 30430 bonds, 3825 residues, 17 models selected
> select #13.1/A-E #13.2/A-E #13.3/A-E #13.4/A-E #13.5/A-E #13.6/A-E #13.7/A-E
> #13.8/A-E #13.9/A-E #13.10/A-E #13.11/A-E #13.12/A-E #13.13/A-E #13.14/A-E
> #13.15/A-E #13.16/A-E #13.17/A-E
166090 atoms, 169065 bonds, 21675 residues, 17 models selected
3 [ID: 3] region 85 chains [1-255] RMSD: 430.751
> select #13.1/M-Q,F-J:178 #13.2/M-Q,F-J:178 #13.3/M-Q,F-J:178
> #13.4/M-Q,F-J:178 #13.5/M-Q,F-J:178 #13.6/M-Q,F-J:178 #13.7/M-Q,F-J:178
> #13.8/M-Q,F-J:178 #13.9/M-Q,F-J:178 #13.10/M-Q,F-J:178 #13.11/M-Q,F-J:178
> #13.12/M-Q,F-J:178 #13.13/M-Q,F-J:178 #13.14/M-Q,F-J:178 #13.15/M-Q,F-J:178
> #13.16/M-Q,F-J:178 #13.17/M-Q,F-J:178
1190 atoms, 1020 bonds, 170 residues, 17 models selected
> select #13.1/M-Q,F-J #13.2/M-Q,F-J #13.3/M-Q,F-J #13.4/M-Q,F-J #13.5/M-Q,F-J
> #13.6/M-Q,F-J #13.7/M-Q,F-J #13.8/M-Q,F-J #13.9/M-Q,F-J #13.10/M-Q,F-J
> #13.11/M-Q,F-J #13.12/M-Q,F-J #13.13/M-Q,F-J #13.14/M-Q,F-J #13.15/M-Q,F-J
> #13.16/M-Q,F-J #13.17/M-Q,F-J
145860 atoms, 148070 bonds, 18190 residues, 17 models selected
4 [ID: 4] region 170 chains [1-107] RMSD: 421.050
> color sel #714b0eff
> select clear
> view P1
> show #!89 models
> view P2
> view P3
Expected an objects specifier or a view name or a keyword
> view orient
> turn x 90
> turn y 90
> turn x 15
> turn x -15
> turn x 10
> select add #34
108103 atoms, 110262 bonds, 17 pseudobonds, 13039 residues, 35 models selected
> hide sel cartoons
> show sel surfaces
> show #!88 models
> show #!209 models
> turn x -10
> turn x 5
> select clear
> show #!12 models
> hide #!12 models
> show #!15 models
> show #!25 models
> show #!33 models
> show #!35 models
> select add #35
272320 atoms, 275760 bonds, 34560 residues, 201 models selected
> select subtract #35
200 models selected
> select add #13
381633 atoms, 388042 bonds, 48671 residues, 18 models selected
> hide sel cartoons
> show sel surfaces
> select subtract #13
289 models selected
> show #!36 models
> hide #!36 models
> show #!37 models
> show #!54 models
> view name P3
> hide #!37 models
> show #!37 models
> hide #!37 models
> show #!36 models
> hide #!36 models
> show #!37 models
> hide #!54 models
> hide #!37 models
> show #!54 models
> close #54
> show #!37 models
> show #!53 models
> view P3
> show #!37-53 models
> save /Users/shoichitachiyama/Desktop/Fig4-Final-models/Figure4-Final-
> model_09282025.cxs includeMaps true
> save /Users/shoichitachiyama/Desktop/Fig4A.png supersample 2
> transparentBackground true
> hide #!88 models
> hide #!89 models
> hide #!209 models
> turnx 40
Unknown command: turnx 40
> turn x 40
> hide #!37 models
> hide #!37-53 models
> hide #!34.17 models
> show #!34.17 models
> hide #!34.17 models
> hide #!34.16 models
> hide #!34.1 models
> hide #!34.2 models
> hide #!34.3 models
> hide #!33.16 models
> hide #!33.17 models
> hide #!3 models
> show #!232 models
> hide #!232 models
> show #16 models
> show #!37 models
> show #!37-53 models
> show #!34.16 models
> show #!34.17 models
> show #!34.1 models
> show #!34.2 models
> show #!34.3 models
> show #!33.16 models
> show #!33.17 models
> show #!3 models
> show #!88 models
> show #!89 models
> show #!209 models
> view P3
> save /Users/shoichitachiyama/Desktop/Fig4A.png supersample 2
> transparentBackground true
> view name P3
> save /Users/shoichitachiyama/Desktop/Fig4A.png supersample 2
> transparentBackground true
> turn x 40
> hide #!209 models
> hide #!88 models
> hide #!89 models
> hide #!37 models
> show #!37 models
> hide #!46 models
> hide #!45 models
> hide #!44 models
> hide #!43 models
> hide #!42 models
> hide #!37-53 models
> hide #!3 models
> hide #!33.16 models
> hide #!33.17 models
> hide #!34.16 models
> hide #!34.17 models
> hide #!34.1 models
> hide #!34.2 models
> hide #!34.3 models
> hide #!33.1 models
> hide #!33.2 models
> hide #!33.3 models
> hide #!33.4 models
> hide #!34.4 models
> hide #!34.5 models
> hide #!57 models
> show #!57 models
> hide #!65 models
> hide #!64 models
> hide #!63 models
> hide #!62 models
> hide #!61 models
> hide #!60 models
> hide #!33.5 models
> show #!33.5 models
> hide #!33.15 models
> show #!33.4 models
> show #!33.15 models
> show #!34.16 models
> hide #!34.16 models
> show #!34.5 models
> show #!34.16 models
> save /Users/shoichitachiyama/Desktop/Fig4B.png supersample 2
> transparentBackground true
> turn x 45
> show #!34.1 models
> show #!34.2 models
> show #!34.3 models
> show #!34.4 models
> show #!33.1 models
> show #!33.2 models
> show #!33.3 models
> show #!33.16 models
> show #!33.17 models
> show #!3 models
> ui tool show "Side View"
> turn x -45
> select add #3
3 models selected
> volume sel showOutlineBox true
> ui mousemode right "tape measure"
> ui mousemode right "crop volume"
> volume #3 region 0,0,0,249,249,135
> turn x 90
> volume sel showOutlineBox false
> turn x -45
> volume sel showOutlineBox true
> volume #59 region 0,0,0,199,190,199
> volume #59 region 0,0,0,199,181,199
> volume #58 region 0,0,0,199,180,199
> hide #!59 models
> show #!59 models
> volume #3 region 0,0,100,249,249,135
> volume #3 region 0,0,-100,249,249,135
> volume #3 region 0,0,0,249,249,100
> view P3
> turn x 40
> turn x 45
> volume #3 region 0,0,0,249,249,120
> volume #3 region 0,0,0,249,249,125
> volume #3 region 0,0,0,249,249,122
> volume sel showOutlineBox false
> select add #3
2 models selected
> select subtract #3
Nothing selected
> save /Users/shoichitachiyama/Desktop/Fig4C.png supersample 2
> transparentBackground true
> save /Users/shoichitachiyama/Desktop/Fig4-Final-models/Figure4-Final-
> model_09282025.cxs includeMaps true
> show #!4 models
> ui tool show "Segment Map"
Segmenting C-Vrings.mrc, density threshold 0.028318
Showing 65 region surfaces
241 watershed regions, grouped to 65 regions
Showing C-Vrings.seg - 65 regions, 65 surfaces
> turn x 90
> select #21.44
1 model selected
> select add #21.41
2 models selected
> select add #21.42
3 models selected
> select add #21.43
4 models selected
> select add #21.60
5 models selected
> select add #21.39
6 models selected
> select add #21.40
7 models selected
> select add #21.55
8 models selected
> select add #21.59
9 models selected
> select add #21.30
10 models selected
> select add #21.51
11 models selected
> select add #21.45
12 models selected
> select add #21.58
13 models selected
> select add #21.50
14 models selected
> select add #21.48
15 models selected
> select add #21.38
16 models selected
> select add #21.56
17 models selected
Opened C-Vrings_imasked as #54, grid size 250,250,250, pixel 4.3, shown at
step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/Fig4-Final-models/V-ring.mrc models #54
> hide #!3 models
> hide #!21 models
> select add #21
66 models selected
> show #!3 models
> hide #!4 models
> select subtract #21
Nothing selected
> turn x 90
> save /Users/shoichitachiyama/Desktop/Fig4C.png supersample 2
> transparentBackground true
> set bgColor white
> turn x 90
> surface dust #3 size 43
> surface dust #55 size 21.4
> surface dust #56 size 21.4
> surface dust #57 size 21.4
> surface dust #58 size 21.4
> surface dust #59 size 21.4
> surface dust #66 size 21.4
> surface dust #67 size 21.4
> surface dust #68 size 21.4
> surface dust #69 size 21.4
> surface dust #70 size 21.4
> surface dust #71 size 21.4
> surface dust #72 size 21.4
> surface dust #54 size 43
> turn x 90
> view P3
> turn x 40
> turn x 45
> turn x -45
> hide #!33.1 models
> hide #!33.2 models
> hide #!33.17 models
> hide #!33.16 models
> hide #!33.15 models
> hide #!34.2 models
> hide #!34.3 models
> hide #!34.1 models
> hide #!34.16 models
> hide #!34.15 models
> hide #!34.14 models
> show #!34.14 models
> show #!34.15 models
> hide #!33.3 models
> show #!33.15 models
> show #!34.16 models
> set bgColor black
> hide #!34.16 models
> show #!34.16 models
> hide #!34.4 models
> surface dust #3 size 43
> surface dust #55 size 21.4
> surface dust #56 size 21.4
> surface dust #57 size 21.4
> surface dust #58 size 21.4
> surface dust #59 size 21.4
> surface dust #66 size 21.4
> surface dust #67 size 21.4
> surface dust #68 size 21.4
> surface dust #69 size 21.4
> surface dust #70 size 21.4
> surface dust #71 size 21.4
> surface dust #72 size 21.4
> surface dust #54 size 43
> save /Users/shoichitachiyama/Desktop/Fig4B.png supersample 2
> transparentBackground true
> turn x 45
> show #!33.1 models
> show #!33.2 models
> show #!33.3 models
> show #!34.1 models
> show #!34.2 models
> show #!34.3 models
> show #!34.4 models
> show #!33.16 models
> show #!33.17 models
> show #!34.17 models
> show #!60 models
> show #!61 models
> show #!62 models
> show #!63 models
> show #!64 models
> show #!65 models
> color #64 #73e0ffff models
> color #64 #5a97ffff models
> surface dust #3 size 43
> surface dust #55 size 21.4
> surface dust #56 size 21.4
> surface dust #57 size 21.4
> surface dust #58 size 21.4
> surface dust #59 size 21.4
> surface dust #60 size 21.4
> surface dust #61 size 21.4
> surface dust #62 size 21.4
> surface dust #63 size 21.4
> surface dust #64 size 21.4
> surface dust #65 size 21.4
> surface dust #66 size 21.4
> surface dust #67 size 21.4
> surface dust #68 size 21.4
> surface dust #69 size 21.4
> surface dust #70 size 21.4
> surface dust #71 size 21.4
> surface dust #72 size 21.4
> surface dust #54 size 43
> save /Users/shoichitachiyama/Desktop/Fig4C.png supersample 2
> transparentBackground true
> view P3
> volume #3 region 0,0,0,249,249,249
> show #!88 models
> show #!89 models
> save /Users/shoichitachiyama/Desktop/Fig4-Final-models/Figure4-Final-
> model_09282025.cxs includeMaps true
> show #!37 models
> show #!37-53 models
> show #!209 models
> surface dust #3 size 43
> surface dust #88 size 43
> surface dust #89 size 43
> surface dust #209 size 43
> surface dust #37 size 21.4
> surface dust #38 size 21.4
> surface dust #39 size 21.4
> surface dust #40 size 21.4
> surface dust #41 size 21.4
> surface dust #42 size 21.4
> surface dust #43 size 21.4
> surface dust #44 size 21.4
> surface dust #45 size 21.4
> surface dust #46 size 21.4
> surface dust #47 size 21.4
> surface dust #48 size 21.4
> surface dust #49 size 21.4
> surface dust #50 size 21.4
> surface dust #51 size 21.4
> surface dust #52 size 21.4
> surface dust #53 size 21.4
> surface dust #55 size 21.4
> surface dust #56 size 21.4
> surface dust #57 size 21.4
> surface dust #58 size 21.4
> surface dust #59 size 21.4
> surface dust #60 size 21.4
> surface dust #61 size 21.4
> surface dust #62 size 21.4
> surface dust #63 size 21.4
> surface dust #64 size 21.4
> surface dust #65 size 21.4
> surface dust #66 size 21.4
> surface dust #67 size 21.4
> surface dust #68 size 21.4
> surface dust #69 size 21.4
> surface dust #70 size 21.4
> surface dust #71 size 21.4
> surface dust #72 size 21.4
> surface dust #54 size 43
> save /Users/shoichitachiyama/Desktop/Fig4A.png supersample 2
> transparentBackground true
> save /Users/shoichitachiyama/Desktop/Fig4-Final-models/Figure4-Final-
> model_09282025.cxs includeMaps true
> close session
> open /Users/shoichitachiyama/Desktop/Fig4-Final-models/Figure4-Final-
> model_09282025.cxs format session
No such file/path: /Users/shoichitachiyama/Desktop/Fig4-Final-
models/Figure4-Final-model_09282025.cxs
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Manuscript/09262025/Comtenue--9252026/Contenue-
> ver2-Fig3_from_09252025.cxs"
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level 0.00404, step 1, values float32
Opened Short-cage.mrc copy as #76, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Opened Short-cage.mrc copy as #77, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Opened Short-cage.mrc copy as #78, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Opened Short-cage.mrc copy as #79, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Opened Short-cage.mrc copy as #80, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Opened Short-cage.mrc copy as #81, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Opened Long-cage.mrc copy as #84, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Opened Long-cage.mrc as #86, grid size 200,200,200, pixel 2.14, shown at level
0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc as #90, grid size 200,200,200, pixel 2.14,
shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc as #91, grid size 200,200,200, pixel 2.14,
shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #49, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #50, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #51, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #52, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #53, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #54, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #55, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #56, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #57, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #58, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #59, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #60, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #61, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #62, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #63, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflC-region-long-cage.mrc copy as #64, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #93, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #94, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #95, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #96, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #97, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #98, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #99, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #100, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #101, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #102, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #103, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #104, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #105, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #106, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #210, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #211, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #212, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
Opened PflD-Longcage-region.mrc copy as #213, grid size 200,200,200, pixel
2.14, shown at level 0.00261, step 1, values float32
opened ChimeraX session
Showing Long-cage.seg - 559 regions, 559 surfaces
> hide #!17 models
> show #!48 models
> view orient
> turn x 90
> turn y 90
> save /Users/shoichitachiyama/Desktop/Ext_18_09282025.png supersample 2
> transparentBackground true
> close session
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Manuscript/09262025/New-Figure4/Fig4-Final-models/FlgY-
> PflABrings_09282025.pdb"
Chain information for FlgY-PflABrings_09282025.pdb
---
Chain | Description
1.18/BX 1.19/BX 1.20/BX 1.21/BX 1.22/BX 1.23/BX 1.24/BX 1.25/BX 1.26/BX 1.27/BX 1.28/BX 1.29/BX 1.30/BX 1.31/BX 1.32/BX 1.33/BX 1.34/BX 1.18/BY 1.19/BY 1.20/BY 1.21/BY 1.22/BY 1.23/BY 1.24/BY 1.25/BY 1.26/BY 1.27/BY 1.28/BY 1.29/BY 1.30/BY 1.31/BY 1.32/BY 1.33/BY 1.34/BY | No description available
1.1/l 1.2/l 1.3/l 1.4/l 1.5/l 1.6/l 1.7/l 1.8/l 1.9/l 1.10/l 1.11/l 1.12/l 1.13/l 1.14/l 1.15/l 1.16/l 1.17/l | No description available
1.1/m 1.2/m 1.3/m 1.4/m 1.5/m 1.6/m 1.7/m 1.8/m 1.9/m 1.10/m 1.11/m 1.12/m 1.13/m 1.14/m 1.15/m 1.16/m 1.17/m | No description available
1.1/s 1.2/s 1.3/s 1.4/s 1.5/s 1.6/s 1.7/s 1.8/s 1.9/s 1.10/s 1.11/s 1.12/s 1.13/s 1.14/s 1.15/s 1.16/s 1.17/s | No description available
> close session
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Manuscript/09262025/New-Figure4/Fig4-Final-models/Figure4-Final-
> model_09282025.cxs"
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137,
step 1, values float32
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
level 0.027, step 1, values float32
Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
step 1, values float32
Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at
level 0.0166, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #107, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #108, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #109, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #111, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #112, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #113, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #114, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #115, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #116, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #117, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #118, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #119, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #120, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #121, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #122, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #123, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #124, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #125, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #126, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #127, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #128, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #129, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #130, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #131, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #132, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #133, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #134, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #135, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #136, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #137, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #138, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #139, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #140, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #141, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #142, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #143, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #144, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #145, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #146, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #147, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #148, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #149, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #150, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #151, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #152, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #153, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #154, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #155, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #156, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #157, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #158, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #159, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #160, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #161, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #162, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #163, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #164, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #165, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #166, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #167, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #168, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #169, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #170, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #171, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #172, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #173, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #174, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #175, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #176, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #177, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #178, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #180, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #181, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #182, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #185, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #186, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #187, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #188, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #189, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #190, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #191, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened Single-MotA-ring.mrc gaussian as #192, grid size 200,200,200, pixel
2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #193, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #194, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #195, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #196, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #199, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #200, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #202, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #203, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #204, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #206, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #207, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #208, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #214, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #215, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #219, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #220, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #221, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #222, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #223, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #224, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #225, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14,
shown at level 0.0112, step 1, values float32
Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel
2.14, shown at level 0.00974, step 1, values float32
Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at
level 0.157, step 1, values float32
Opened C-Vrings.mrc as #4, grid size 250,250,250, pixel 4.3, shown at level
0.0283, step 1, values float32
Opened 1unit_PflABCD.mrc as #5, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Opened 3xFlgY.mrc as #22, grid size 256,256,256, pixel 2.14, shown at level
0.0112, step 1, values float32
Opened 1xPflB.mrc as #26, grid size 200,200,200, pixel 2.14, shown at level
0.00045, step 1, values float32
Opened 1xFlgY.mrc as #29, grid size 256,256,256, pixel 2.14, shown at level
0.0112, step 1, values float32
Opened 1xPflB.mrc as #30, grid size 200,200,200, pixel 2.14, shown at level
0.00045, step 1, values float32
Opened PflC-model-region.mrc as #36, grid size 200,200,200, pixel 2.14, shown
at level 0.00107, step 1, values float32
Opened PflC-No-model.mrc as #37, grid size 200,200,200, pixel 2.14, shown at
level 0.00107, step 1, values float32
Opened PflC-No-model.mrc copy as #38, grid size 200,200,200, pixel 2.14, shown
at level 0.00107, step 1, values float32
Opened PflC-No-model.mrc copy as #39, grid size 200,200,200, pixel 2.14, shown
at level 0.00107, step 1, values float32
Opened PflC-No-model.mrc copy as #40, grid size 200,200,200, pixel 2.14, shown
at level 0.00107, step 1, values float32
Opened PflC-No-model.mrc copy as #41, grid size 200,200,200, pixel 2.14, shown
at level 0.00107, step 1, values float32
Opened PflC-No-model.mrc copy as #42, grid size 200,200,200, pixel 2.14, shown
at level 0.00107, step 1, values float32
Opened PflC-No-model.mrc copy as #43, grid size 200,200,200, pixel 2.14, shown
at level 0.00107, step 1, values float32
Opened PflC-No-model.mrc copy as #44, grid size 200,200,200, pixel 2.14, shown
at level 0.00107, step 1, values float32
Opened PflC-No-model.mrc copy as #45, grid size 200,200,200, pixel 2.14, shown
at level 0.00107, step 1, values float32
Opened PflC-No-model.mrc copy as #46, grid size 200,200,200, pixel 2.14, shown
at level 0.00107, step 1, values float32
Opened PflC-No-model.mrc copy as #47, grid size 200,200,200, pixel 2.14, shown
at level 0.00107, step 1, values float32
Opened PflC-No-model.mrc copy as #48, grid size 200,200,200, pixel 2.14, shown
at level 0.00107, step 1, values float32
Opened PflC-No-model.mrc copy as #49, grid size 200,200,200, pixel 2.14, shown
at level 0.00107, step 1, values float32
Opened PflC-No-model.mrc copy as #50, grid size 200,200,200, pixel 2.14, shown
at level 0.00107, step 1, values float32
Opened PflC-No-model.mrc copy as #51, grid size 200,200,200, pixel 2.14, shown
at level 0.00107, step 1, values float32
Opened PflC-No-model.mrc copy as #52, grid size 200,200,200, pixel 2.14, shown
at level 0.00107, step 1, values float32
Opened PflC-No-model.mrc copy as #53, grid size 200,200,200, pixel 2.14, shown
at level 0.00107, step 1, values float32
Opened Single_Cage_unit_imasked as #55, grid size 200,200,200, pixel 2.14,
shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit_imasked copy as #56, grid size 200,200,200, pixel
2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit_imasked copy as #57, grid size 200,200,200, pixel
2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit_imasked copy as #58, grid size 200,200,200, pixel
2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit_imasked copy as #59, grid size 200,200,200, pixel
2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit_imasked copy as #60, grid size 200,200,200, pixel
2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit_imasked copy as #61, grid size 200,200,200, pixel
2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit_imasked copy as #62, grid size 200,200,200, pixel
2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit_imasked copy as #63, grid size 200,200,200, pixel
2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit_imasked copy as #64, grid size 200,200,200, pixel
2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit_imasked copy as #65, grid size 200,200,200, pixel
2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit_imasked copy as #66, grid size 200,200,200, pixel
2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit_imasked copy as #67, grid size 200,200,200, pixel
2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit_imasked copy as #68, grid size 200,200,200, pixel
2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit_imasked copy as #69, grid size 200,200,200, pixel
2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit_imasked copy as #70, grid size 200,200,200, pixel
2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit_imasked copy as #71, grid size 200,200,200, pixel
2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit_imasked copy as #72, grid size 200,200,200, pixel
2.14, shown at level 0.000576, step 1, values float32
Opened V-ring.mrc as #54, grid size 250,250,250, pixel 4.3, shown at level
0.0283, step 1, values float32
opened ChimeraX session
Showing C-Vrings.seg - 65 regions, 65 surfaces
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!13-300 models
> hide #!3 models
> show #!15 models
> show #!25 models
> hide #!15.1 models
> hide #!15.2 models
> hide #!15.3 models
> hide #!15.4 models
> hide #!15.5 models
> hide #!15.7 models
> hide #!15.8 models
> hide #!15.9 models
> show #!15.9 models
> hide #!15.9 models
> show #!15.7 models
> hide #!15.7 models
> show #!15.5 models
> hide #15.5.6 models
> hide #15.5.3 models
> hide #15.5.2 models
> hide #15.5.1 models
> hide #!15.6 models
> show #!15.6 models
> hide #!15.10 models
> hide #!15.11 models
> hide #!15.12 models
> hide #!15.13 models
> hide #!15.14 models
> hide #!15.15 models
> hide #!15.16 models
> hide #!15.17 models
> hide #!25.1 models
> hide #!25.2 models
> hide #!25.3 models
> hide #!25.4 models
> hide #!25.5 models
> hide #!25.7 models
> hide #!25.8 models
> hide #!25.9 models
> hide #!25.10 models
> hide #!25.11 models
> hide #!25.12 models
> hide #!25.13 models
> hide #!25.14 models
> hide #!25.15 models
> hide #!25.16 models
> hide #!25.17 models
> select add #15.5.4
1192 atoms, 149 residues, 1 model selected
> select add #15.5.5
6295 atoms, 782 residues, 2 models selected
> select add #15.6
20131 atoms, 14052 bonds, 1 pseudobond, 2495 residues, 5 models selected
> hide sel surfaces
> show sel cartoons
> select clear
> select add #15.6.2
1235 atoms, 155 residues, 1 model selected
> select add #15.6.3
2470 atoms, 310 residues, 2 models selected
> hide sel cartoons
> select clear
> select add #25.6
4626 atoms, 4670 bonds, 575 residues, 1 model selected
> hide sel surfaces
> show sel cartoons
> select clear
> view orient
> turn y 90
> turn y -90
> turn x -90
> turn y -90
> turn x -90
> save /Users/shoichitachiyama/Desktop/Ext18-PflAB-1.png supersample 2
> transparentBackground true
> turn x 40
> turn x -40
> save /Users/shoichitachiyama/Desktop/Ext18-PflAB-40.png supersample 2
> transparentBackground true
> graphics silhouettes true
> set bgColor white
> set bgColor #ffffff00
> graphics silhouettes false
> graphics silhouettes true
> save /Users/shoichitachiyama/Desktop/Ext18-PflAB-40.png supersample 2
> transparentBackground true
> turn x 40
> save /Users/shoichitachiyama/Desktop/Ext18-PflAB-1.png supersample 2
> transparentBackground true
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shoichitachiyama/Desktop/Shigella-ipaDnull-bin2-07072025.cxs
Opened IM.mrc as #1, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at level
0.0281, step 1, values float32
Opened MxiA.mrc as #2, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0229, step 1, values float32
Opened MxiGp.mrc as #3, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0192, step 1, values float32
Opened Needle.mrc as #4, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0187, step 1, values float32
Opened OM_complex.mrc as #5, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0194, step 1, values float32
Opened OM.mrc as #6, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at level
0.042, step 1, values float32
Opened PG-layer.mrc as #7, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0181, step 1, values float32
Opened Sortingplatforom.mrc as #8, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0549, step 1, values float32
Opened IM.mrc gaussian as #9, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0143, step 1, values float32
Opened MxiA.mrc gaussian as #10, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.019, step 1, values float32
Opened MxiGp.mrc gaussian as #11, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.012, step 1, values float32
Opened Needle.mrc gaussian as #12, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0123, step 1, values float32
Opened OM.mrc gaussian as #14, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0168, step 1, values float32
Opened PG-layer.mrc gaussian as #15, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0154, step 1, values float32
Opened Sortingplatforom.mrc gaussian as #16, grid size 120,120,200, pixel
4.3,4.3,4.3, shown at level 0.0307, step 1, values float32
Opened IpaD.mrc as #19, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0701, step 1, values float32
Opened Rev-Spa47C24.mrc as #25, grid size 120,120,70, pixel 4.3,4.3,4.3, shown
at level 0.238, step 1, values float32
Opened IMring.mrc as #32, grid size 120,120,70, pixel 4.3,4.3,4.3, shown at
level 0.0343, step 1, values float32
Opened OM-complex.mrc as #28, grid size 120,120,70, pixel 4.3,4.3,4.3, shown
at level 0.0252, step 1, values float32
Opened Pod-bin2.mrc as #13, grid size 50,50,70, pixel 4.3,4.3,4.3, shown at
level 0.0536, step 1, values float32
Opened Exp.mrc as #33, grid size 120,120,70, pixel 4.3,4.3,4.3, shown at level
0.0282, step 1, values float32
Log from Tue Jul 8 20:43:49 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shoichitachiyama/Desktop/Shigella-ipaDnull-bin2-07072025.cxs
Opened IM.mrc as #1, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at level
0.0281, step 1, values float32
Opened MxiA.mrc as #2, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0229, step 1, values float32
Opened MxiGp.mrc as #3, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0192, step 1, values float32
Opened Needle.mrc as #4, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0187, step 1, values float32
Opened OM_complex.mrc as #5, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0194, step 1, values float32
Opened OM.mrc as #6, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at level
0.042, step 1, values float32
Opened PG-layer.mrc as #7, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0181, step 1, values float32
Opened Sortingplatforom.mrc as #8, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0549, step 1, values float32
Opened IM.mrc gaussian as #9, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0143, step 1, values float32
Opened MxiA.mrc gaussian as #10, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.019, step 1, values float32
Opened MxiGp.mrc gaussian as #11, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.012, step 1, values float32
Opened Needle.mrc gaussian as #12, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0123, step 1, values float32
Opened OM.mrc gaussian as #14, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0168, step 1, values float32
Opened PG-layer.mrc gaussian as #15, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0154, step 1, values float32
Opened Sortingplatforom.mrc gaussian as #16, grid size 120,120,200, pixel
4.3,4.3,4.3, shown at level 0.0307, step 1, values float32
Opened IpaD.mrc as #19, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0701, step 1, values float32
Opened Rev-Spa47C24.mrc as #25, grid size 120,120,70, pixel 4.3,4.3,4.3, shown
at level 0.238, step 1, values float32
Opened IMring.mrc as #32, grid size 120,120,70, pixel 4.3,4.3,4.3, shown at
level 0.0343, step 1, values float32
Opened OM-complex.mrc as #28, grid size 120,120,70, pixel 4.3,4.3,4.3, shown
at level 0.0252, step 1, values float32
Opened Pod-bin2.mrc as #13, grid size 50,50,70, pixel 4.3,4.3,4.3, shown at
level 0.0536, step 1, values float32
Opened Exp.mrc as #33, grid size 120,120,70, pixel 4.3,4.3,4.3, shown at level
0.0282, step 1, values float32
Log from Mon Jul 7 21:04:45 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/Project files/Shigella/MxiA-
> project/Data_Images/07072025/Shigella-ipaDnull-bin2-06252025.cxs"
Opened IM.mrc as #1, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at level
0.0281, step 1, values float32
Opened MxiA.mrc as #2, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0229, step 1, values float32
Opened MxiGp.mrc as #3, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0192, step 1, values float32
Opened Needle.mrc as #4, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0187, step 1, values float32
Opened OM_complex.mrc as #5, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0194, step 1, values float32
Opened OM.mrc as #6, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at level
0.042, step 1, values float32
Opened PG-layer.mrc as #7, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0181, step 1, values float32
Opened Sortingplatforom.mrc as #8, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0549, step 1, values float32
Opened IM.mrc gaussian as #9, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0143, step 1, values float32
Opened MxiA.mrc gaussian as #10, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.019, step 1, values float32
Opened MxiGp.mrc gaussian as #11, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.012, step 1, values float32
Opened Needle.mrc gaussian as #12, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0123, step 1, values float32
Opened OM.mrc gaussian as #14, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0168, step 1, values float32
Opened PG-layer.mrc gaussian as #15, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0154, step 1, values float32
Opened Sortingplatforom.mrc gaussian as #16, grid size 120,120,200, pixel
4.3,4.3,4.3, shown at level 0.0307, step 1, values float32
Opened IpaD.mrc as #19, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0701, step 1, values float32
Opened Rev-Spa47C24.mrc as #25, grid size 120,120,70, pixel 4.3,4.3,4.3, shown
at level 0.238, step 1, values float32
Opened IMring.mrc as #32, grid size 120,120,70, pixel 4.3,4.3,4.3, shown at
level 0.0343, step 1, values float32
Opened OM-complex.mrc as #28, grid size 120,120,70, pixel 4.3,4.3,4.3, shown
at level 0.0252, step 1, values float32
Opened Pod-bin2.mrc as #13, grid size 50,50,70, pixel 4.3,4.3,4.3, shown at
level 0.0536, step 1, values float32
Opened Exp.mrc as #33, grid size 120,120,70, pixel 4.3,4.3,4.3, shown at level
0.0282, step 1, values float32
Log from Wed Jun 25 10:52:06 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shoichi/Desktop/Shigella-ipaDnull-bin2-06232025.cxs
Opened IM.mrc as #1, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at level
0.0281, step 1, values float32
Opened MxiA.mrc as #2, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0229, step 1, values float32
Opened MxiGp.mrc as #3, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0192, step 1, values float32
Opened Needle.mrc as #4, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0187, step 1, values float32
Opened OM_complex.mrc as #5, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0194, step 1, values float32
Opened OM.mrc as #6, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at level
0.042, step 1, values float32
Opened PG-layer.mrc as #7, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0181, step 1, values float32
Opened Sortingplatforom.mrc as #8, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0549, step 1, values float32
Opened IM.mrc gaussian as #9, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0143, step 1, values float32
Opened MxiA.mrc gaussian as #10, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.019, step 1, values float32
Opened MxiGp.mrc gaussian as #11, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.012, step 1, values float32
Opened Needle.mrc gaussian as #12, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0123, step 1, values float32
Opened OM.mrc gaussian as #14, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0168, step 1, values float32
Opened PG-layer.mrc gaussian as #15, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0154, step 1, values float32
Opened Sortingplatforom.mrc gaussian as #16, grid size 120,120,200, pixel
4.3,4.3,4.3, shown at level 0.0307, step 1, values float32
Opened IpaD.mrc as #19, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0701, step 1, values float32
Opened Rev-Spa47C24.mrc as #25, grid size 120,120,70, pixel 4.3,4.3,4.3, shown
at level 0.238, step 1, values float32
Opened IMring.mrc as #32, grid size 120,120,70, pixel 4.3,4.3,4.3, shown at
level 0.0343, step 1, values float32
Opened OM-complex.mrc as #28, grid size 120,120,70, pixel 4.3,4.3,4.3, shown
at level 0.0252, step 1, values float32
Opened Pod-bin2.mrc as #13, grid size 50,50,70, pixel 4.3,4.3,4.3, shown at
level 0.0536, step 1, values float32
Log from Mon Jun 23 16:35:51 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shoichi/Desktop/Shigella-ipaDnull-bin2-06232025.cxs
Opened IM.mrc as #1, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at level
0.0281, step 1, values float32
Opened MxiA.mrc as #2, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0229, step 1, values float32
Opened MxiGp.mrc as #3, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0192, step 1, values float32
Opened Needle.mrc as #4, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0187, step 1, values float32
Opened OM_complex.mrc as #5, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0194, step 1, values float32
Opened OM.mrc as #6, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at level
0.042, step 1, values float32
Opened PG-layer.mrc as #7, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0181, step 1, values float32
Opened Sortingplatforom.mrc as #8, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0549, step 1, values float32
Opened IM.mrc gaussian as #9, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0143, step 1, values float32
Opened MxiA.mrc gaussian as #10, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.019, step 1, values float32
Opened MxiGp.mrc gaussian as #11, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.012, step 1, values float32
Opened Needle.mrc gaussian as #12, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0123, step 1, values float32
Opened OM.mrc gaussian as #14, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0168, step 1, values float32
Opened PG-layer.mrc gaussian as #15, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0154, step 1, values float32
Opened Sortingplatforom.mrc gaussian as #16, grid size 120,120,200, pixel
4.3,4.3,4.3, shown at level 0.0307, step 1, values float32
Opened IpaD.mrc as #19, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0701, step 1, values float32
Opened Rev-Spa47C24.mrc as #25, grid size 120,120,70, pixel 4.3,4.3,4.3, shown
at level 0.238, step 1, values float32
Opened IMring.mrc as #32, grid size 120,120,70, pixel 4.3,4.3,4.3, shown at
level 0.0343, step 1, values float32
Opened OM-complex.mrc as #28, grid size 120,120,70, pixel 4.3,4.3,4.3, shown
at level 0.0252, step 1, values float32
Log from Mon Jun 23 14:56:34 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Websites/Shigella-ipaDnull-
> bin2-06202025.cxs
Opened IM.mrc as #1, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at level
0.0281, step 1, values float32
Opened MxiA.mrc as #2, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0229, step 1, values float32
Opened MxiGp.mrc as #3, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0192, step 1, values float32
Opened Needle.mrc as #4, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0187, step 1, values float32
Opened OM_complex.mrc as #5, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0194, step 1, values float32
Opened OM.mrc as #6, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at level
0.042, step 1, values float32
Opened PG-layer.mrc as #7, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0181, step 1, values float32
Opened Sortingplatforom.mrc as #8, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0549, step 1, values float32
Opened IM.mrc gaussian as #9, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0143, step 1, values float32
Opened MxiA.mrc gaussian as #10, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.019, step 1, values float32
Opened MxiGp.mrc gaussian as #11, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.012, step 1, values float32
Opened Needle.mrc gaussian as #12, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0123, step 1, values float32
Opened OM_complex.mrc gaussian as #13, grid size 120,120,200, pixel
4.3,4.3,4.3, shown at level 0.00993, step 1, values float32
Opened OM.mrc gaussian as #14, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0168, step 1, values float32
Opened PG-layer.mrc gaussian as #15, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0154, step 1, values float32
Opened Sortingplatforom.mrc gaussian as #16, grid size 120,120,200, pixel
4.3,4.3,4.3, shown at level 0.0307, step 1, values float32
Opened IpaD.mrc as #19, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0701, step 1, values float32
Opened Rev-Spa47C24.mrc as #25, grid size 120,120,70, pixel 4.3,4.3,4.3, shown
at level 0.238, step 1, values float32
Opened MxiGp.mrc as #28, grid size 120,120,70, pixel 4.3,4.3,4.3, shown at
level 0.0622, step 1, values float32
Log from Fri Jun 20 11:47:25 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Mon Jun 16 14:12:56 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Websites/Shigella-ipaDnull-
> bin2-06142025.cxs
Opened IM.mrc as #1, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at level
0.0281, step 1, values float32
Opened MxiA.mrc as #2, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0229, step 1, values float32
Opened MxiGp.mrc as #3, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0192, step 1, values float32
Opened Needle.mrc as #4, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0187, step 1, values float32
Opened OM_complex.mrc as #5, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0194, step 1, values float32
Opened OM.mrc as #6, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at level
0.042, step 1, values float32
Opened PG-layer.mrc as #7, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0181, step 1, values float32
Opened Sortingplatforom.mrc as #8, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0549, step 1, values float32
Opened IM.mrc gaussian as #9, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0143, step 1, values float32
Opened MxiA.mrc gaussian as #10, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.019, step 1, values float32
Opened MxiGp.mrc gaussian as #11, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.012, step 1, values float32
Opened Needle.mrc gaussian as #12, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0123, step 1, values float32
Opened OM_complex.mrc gaussian as #13, grid size 120,120,200, pixel
4.3,4.3,4.3, shown at level 0.00993, step 1, values float32
Opened OM.mrc gaussian as #14, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0168, step 1, values float32
Opened PG-layer.mrc gaussian as #15, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0154, step 1, values float32
Opened Sortingplatforom.mrc gaussian as #16, grid size 120,120,200, pixel
4.3,4.3,4.3, shown at level 0.0307, step 1, values float32
Opened IpaD.mrc as #19, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0701, step 1, values float32
Log from Mon Jun 16 11:13:56 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Websites/Shigella-ipaDnull-
> bin2-06142025.cxs
Opened IM.mrc as #1, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at level
0.0281, step 1, values float32
Opened MxiA.mrc as #2, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0229, step 1, values float32
Opened MxiGp.mrc as #3, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0192, step 1, values float32
Opened Needle.mrc as #4, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0187, step 1, values float32
Opened OM_complex.mrc as #5, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0194, step 1, values float32
Opened OM.mrc as #6, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at level
0.042, step 1, values float32
Opened PG-layer.mrc as #7, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0181, step 1, values float32
Opened Sortingplatforom.mrc as #8, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0549, step 1, values float32
Opened IM.mrc gaussian as #9, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0143, step 1, values float32
Opened MxiA.mrc gaussian as #10, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.019, step 1, values float32
Opened MxiGp.mrc gaussian as #11, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.012, step 1, values float32
Opened Needle.mrc gaussian as #12, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0123, step 1, values float32
Opened OM_complex.mrc gaussian as #13, grid size 120,120,200, pixel
4.3,4.3,4.3, shown at level 0.00993, step 1, values float32
Opened OM.mrc gaussian as #14, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0168, step 1, values float32
Opened PG-layer.mrc gaussian as #15, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0154, step 1, values float32
Opened Sortingplatforom.mrc gaussian as #16, grid size 120,120,200, pixel
4.3,4.3,4.3, shown at level 0.0307, step 1, values float32
Log from Sat Jun 14 20:42:38 2025 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
> open /Users/shoichitachiyama/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-
> documents/P_aeruginosa_T4pili/PDB/3jvu.pdb1 format pdb
3jvu.pdb1 title:
Crystal structure of unliganded P. Aeruginosa pilt [more info...]
Chain information for 3jvu.pdb1
---
Chain | Description
1.1/A 1.1/B 1.1/C | No description available
1.2/A | No description available
1.2/B | No description available
1.2/C | No description available
> close #1
> open /Users/shoichitachiyama/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/Ownwork/06132025/Segmentation-06132025/IM.mrc
Opened IM.mrc as #1, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at level
0.0612, step 1, values float32
> open /Users/shoichitachiyama/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/Ownwork/06132025/Segmentation-06132025/MxiA.mrc
Opened MxiA.mrc as #2, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0183, step 1, values float32
> open /Users/shoichitachiyama/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/Ownwork/06132025/Segmentation-06132025/MxiGp.mrc
Opened MxiGp.mrc as #3, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0192, step 1, values float32
> open /Users/shoichitachiyama/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/Ownwork/06132025/Segmentation-06132025/Needle.mrc
Opened Needle.mrc as #4, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0187, step 1, values float32
> open /Users/shoichitachiyama/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-
> Bill/Ownwork/06132025/Segmentation-06132025/OM_complex.mrc
Opened OM_complex.mrc as #5, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at level 0.0194, step 1, values float32
> open /Users/shoichitachiyama/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/Ownwork/06132025/Segmentation-06132025/OM.mrc
Opened OM.mrc as #6, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at level
0.0796, step 1, values float32
> open /Users/shoichitachiyama/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/Ownwork/06132025/Segmentation-06132025/PG-
> layer.mrc
Opened PG-layer.mrc as #7, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.0181, step 1, values float32
> open /Users/shoichitachiyama/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-
> Bill/Ownwork/06132025/Segmentation-06132025/Sortingplatforom.mrc
Opened Sortingplatforom.mrc as #8, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at level 0.0549, step 1, values float32
> volume #6 level 0.042
> volume #1 level 0.02813
> volume #2 level 0.02289
> volume gaussian #1 sDev 6
Opened IM.mrc gaussian as #9, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at step 1, values float32
> volume #9 level 0.02861
> close #9
> volume gaussian #1 sDev 8
Opened IM.mrc gaussian as #9, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at step 1, values float32
> volume #9 level 0.01651
> close #9
> volume gaussian #1 sDev 7
Opened IM.mrc gaussian as #9, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at step 1, values float32
> volume #9 level 0.01537
> close #9
> volume gaussian #1 sDev 6
Opened IM.mrc gaussian as #9, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at step 1, values float32
> volume #9 level 0.01427
> volume gaussian #2 sDev 4
Opened MxiA.mrc gaussian as #10, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at step 1, values float32
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> volume #10 level 0.01869
> volume #10 level 0.02009
> close #10
> volume gaussian #2 sDev 5
Opened MxiA.mrc gaussian as #10, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at step 1, values float32
> volume #10 level 0.01905
> hide #!3 models
> show #!9 models
> volume gaussian #3 sDev 3
Opened MxiGp.mrc gaussian as #11, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at step 1, values float32
> volume #11 level 0.01197
> volume gaussian #4 sDev 3
Opened Needle.mrc gaussian as #12, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at step 1, values float32
> close #12
> volume gaussian #4 sDev 4
Opened Needle.mrc gaussian as #12, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at step 1, values float32
> volume gaussian #5 sDev 3
Opened OM_complex.mrc gaussian as #13, grid size 120,120,200, pixel
4.3,4.3,4.3, shown at step 1, values float32
> volume #13 level 0.01105
> volume #13 level 0.009929
> volume gaussian #6 sDev 6
Opened OM.mrc gaussian as #14, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at step 1, values float32
> volume #14 level 0.01435
> hide #!13 models
> hide #!14 models
> show #!14 models
> show #!13 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> close #14
> volume gaussian #6 sDev 4
Opened OM.mrc gaussian as #14, grid size 120,120,200, pixel 4.3,4.3,4.3, shown
at step 1, values float32
> volume #14 level 0.01677
> show #!13 models
> show #!12 models
> show #!11 models
> show #!10 models
> show #!9 models
> volume gaussian #7 sDev 7
Opened PG-layer.mrc gaussian as #15, grid size 120,120,200, pixel 4.3,4.3,4.3,
shown at step 1, values float32
> volume #15 level 0.008469
> volume #15 level 0.007741
> volume gaussian #8 sDev 3
Opened Sortingplatforom.mrc gaussian as #16, grid size 120,120,200, pixel
4.3,4.3,4.3, shown at step 1, values float32
> volume #16 level 0.03071
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> ui tool show "Map Eraser"
> volume erase #9 center 263.81,249.82,417.98 radius 252.84 outside true
> hide #!9 models
> show #!10 models
> show #!11 models
> hide #!10 models
> volume erase #11 center 258.49,255.15,458.12 radius 139.62 outside true
> hide #!11 models
> show #!12 models
> volume erase #12 center 251.54,257.07,627.55 radius 287.83 outside true
> volume erase #12 center 258.68,253.74,636.22 radius 231.55 outside true
> volume erase #12 center 498.26,102.07,654.82 radius 231.55
> volume erase #12 center 111.84,-21.873,673.18 radius 231.55
> volume erase #12 center -38.399,336.09,692.01 radius 231.55
> volume erase #12 center 237.28,549.79,682.51 radius 231.55
> volume erase #12 center 517.18,437.76,663.41 radius 231.55
> hide #!12 models
> show #!13 models
> volume erase #13 center 253.69,256.32,584.2 radius 137.9 outside true
> volume erase #13 center 255.86,257.72,593.03 radius 123.72 outside true
> volume erase #13 center 62.838,165.03,546.6 radius 123.72
> volume erase #13 center 157.44,53.683,556.3 radius 123.72
> volume erase #13 center 371.56,78.194,534.46 radius 123.72
> volume erase #13 center 271.6,33.37,562.14 radius 123.72
> volume erase #13 center 248.79,478.96,556.65 radius 123.72
> volume erase #13 center 391.45,445.69,544.2 radius 123.72
> volume erase #13 center 455.75,362.69,544.33 radius 123.72
> volume erase #13 center 488.44,278.1,567.07 radius 123.72
> volume erase #13 center 415.07,408.18,553.07 radius 123.72
> volume erase #13 center 121,442.2,575.18 radius 123.72
> hide #!13 models
> show #!14 models
> show #!15 models
> hide #!14 models
> volume erase #15 center 250.39,261.22,597.71 radius 187.74 outside true
> volume #15 level 0.01538
> show #!16 models
> hide #!15 models
> show #!15 models
> show #!14 models
> show #!13 models
> show #!11 models
> show #!12 models
> show #!10 models
> show #!9 models
> color #15 #9a9a9aff models
> color #15 #717171ff models
> lighting soft
> set bgColor white
> graphics silhouettes true
> close #17
> color #9 #cfffcaff models
> color #9 #c5ffbfff models
> color #9 #9ac795ff models
> color #14 #8ad5a8ff models
> color #14 #9ad5acff models
> color #14 #9ad5adff models
> color #11 #81daffff models
> color #11 #86d8ffff models
> color #13 #5fabebff models
> color #16 #ffa978ff models
> view orient
> turn x 90
[Repeated 2 time(s)]
> view name P1
> view P1
> wait 10
> turn -x 1 360 center #12
> wait 360
> view P1
> wait 10
> turn -y 1 360 center #12
> wait 360
> view P1
> wait 10
> turn -y 1 360 center #12
> wait 360
> view P1
> wait 1
> turn -y 1 360 center #12
> wait 360
> view P1
> wait 1
> turn -y 1 360 center #12
> wait 720
> save /Users/shoichitachiyama/Desktop/Shigella-ipaDnull-bin2-06142025.cxs
> includeMaps true
——— End of log from Sat Jun 14 20:42:38 2025 ———
opened ChimeraX session
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Websites/Shigella-Model_2025.pdb
Summary of feedback from opening /Users/shoichi/Library/CloudStorage/OneDrive-
YaleUniversity/Jun_Lab_documents/Websites/Shigella-Model_2025.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 11 THR A 23 1 13
Start residue of secondary structure not found: HELIX 2 2 GLN A 24 ASN A 40 1
17
Start residue of secondary structure not found: HELIX 3 3 ASN A 43 ASN A 81 1
39
Start residue of secondary structure not found: HELIX 4 4 THR B 11 THR B 23 1
13
Start residue of secondary structure not found: HELIX 5 5 GLN B 24 ASN B 40 1
17
135 messages similar to the above omitted
End residue of secondary structure not found: HELIX 3 3 ASN A 43 ASN A 81 1 39
Start residue of secondary structure not found: HELIX 4 4 THR B 11 THR B 23 1
13
Start residue of secondary structure not found: HELIX 5 5 GLN B 24 ASN B 40 1
17
Start residue of secondary structure not found: HELIX 6 6 ASN B 43 ASN B 81 1
39
Start residue of secondary structure not found: HELIX 7 7 THR C 11 THR C 23 1
13
Start residue of secondary structure not found: HELIX 8 8 GLN C 24 ASN C 40 1
17
63 messages similar to the above omitted
End residue of secondary structure not found: HELIX 3 3 ASN A 43 ASN A 81 1 39
Start residue of secondary structure not found: HELIX 4 4 THR B 11 THR B 23 1
13
Start residue of secondary structure not found: HELIX 5 5 GLN B 24 ASN B 40 1
17
Start residue of secondary structure not found: HELIX 6 6 ASN B 43 ASN B 81 1
39
Start residue of secondary structure not found: HELIX 7 7 THR C 11 THR C 23 1
13
Start residue of secondary structure not found: HELIX 8 8 GLN C 24 ASN C 40 1
17
63 messages similar to the above omitted
End residue of secondary structure not found: HELIX 3 3 ASN A 43 ASN A 81 1 39
Start residue of secondary structure not found: HELIX 4 4 THR B 11 THR B 23 1
13
Start residue of secondary structure not found: HELIX 5 5 GLN B 24 ASN B 40 1
17
Start residue of secondary structure not found: HELIX 6 6 ASN B 43 ASN B 81 1
39
Start residue of secondary structure not found: HELIX 7 7 THR C 11 THR C 23 1
13
Start residue of secondary structure not found: HELIX 8 8 GLN C 24 ASN C 40 1
17
63 messages similar to the above omitted
End residue of secondary structure not found: HELIX 3 3 ASN A 43 ASN A 81 1 39
Start residue of secondary structure not found: HELIX 4 4 THR B 11 THR B 23 1
13
Start residue of secondary structure not found: HELIX 5 5 GLN B 24 ASN B 40 1
17
Start residue of secondary structure not found: HELIX 6 6 ASN B 43 ASN B 81 1
39
Start residue of secondary structure not found: HELIX 7 7 THR C 11 THR C 23 1
13
Start residue of secondary structure not found: HELIX 8 8 GLN C 24 ASN C 40 1
17
63 messages similar to the above omitted
End residue of secondary structure not found: HELIX 3 3 ASN A 43 ASN A 81 1 39
Start residue of secondary structure not found: HELIX 4 4 THR B 11 THR B 23 1
13
Start residue of secondary structure not found: HELIX 5 5 GLN B 24 ASN B 40 1
17
Start residue of secondary structure not found: HELIX 6 6 ASN B 43 ASN B 81 1
39
Start residue of secondary structure not found: HELIX 7 7 THR C 11 THR C 23 1
13
Start residue of secondary structure not found: HELIX 8 8 GLN C 24 ASN C 40 1
17
63 messages similar to the above omitted
End residue of secondary structure not found: HELIX 3 3 ASN A 43 ASN A 81 1 39
Start residue of secondary structure not found: HELIX 4 4 THR B 11 THR B 23 1
13
Start residue of secondary structure not found: HELIX 5 5 GLN B 24 ASN B 40 1
17
Start residue of secondary structure not found: HELIX 6 6 ASN B 43 ASN B 81 1
39
Start residue of secondary structure not found: HELIX 7 7 THR C 11 THR C 23 1
13
Start residue of secondary structure not found: HELIX 8 8 GLN C 24 ASN C 40 1
17
6340 messages similar to the above omitted
Shigella-Model_2025.pdb title:
Structure of the shigella mxih needle filament attached to the basal body
[more info...]
21 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for Shigella-Model_2025.pdb
---
Chain | Description | UniProt
17.3/0 17.3/1 17.3/2 17.3/3 17.3/4 17.3/5 17.3/6 17.3/7 17.3/8 17.3/9 17.3/Y 17.3/Z 17.3/a0 17.3/b0 17.3/y 17.3/z | No description available |
17.1/A 17.1/B 17.1/C 17.1/D 17.1/E 17.1/F 17.1/G 17.1/H 17.1/I 17.1/J 17.1/K 17.1/L 17.1/M 17.1/N 17.1/O 17.1/P 17.1/Q 17.1/R 17.1/S 17.1/T 17.1/U 17.1/V 17.1/W | protein mxih | MXIH_SHIFL 1-83
17.2/A 17.2/B 17.2/C 17.2/D 17.2/E 17.2/F 17.2/G 17.2/H 17.2/I 17.2/J 17.2/K 17.2/L 17.2/M 17.2/N 17.2/O | protein mxih | MXIH_SHIFL 1-83
17.3/A 17.3/B 17.3/D 17.3/E 17.3/G 17.3/H 17.3/J 17.3/K 17.3/M 17.3/N 17.3/P 17.3/Q 17.3/S 17.3/T 17.3/U 17.3/V | protein mxih | MXIH_SHIFL 1-83
17.4/A 17.5/A 17.6/A 17.7/A 17.8/A 17.9/A | protein mxih | MXIH_SHIFL 1-83
17.76/A 17.77/A 17.78/A 17.79/A 17.80/A 17.81/A 17.76/B 17.77/B 17.78/B 17.79/B 17.80/B 17.81/B | protein mxih | MXIH_SHIFL 1-83
17.82/A 17.84/A 17.86/A 17.88/A 17.90/A 17.92/A 17.83/B 17.85/B 17.87/B 17.89/B 17.91/B 17.93/B | protein mxih | MXIH_SHIFL 1-83
17.94/A 17.94/D 17.94/G | protein mxih | MXIH_SHIFL 1-83
17.10/Aa 17.11/Ab 17.12/Ac 17.13/Ad 17.14/Ae 17.15/Af 17.16/Ag 17.17/Ah 17.18/Ai 17.19/Aj 17.20/Ak 17.21/Al 17.22/Am 17.23/An 17.24/Ao 17.25/Ap 17.26/Aq 17.27/Ar 17.28/As 17.29/At 17.30/Au 17.31/Av 17.32/Aw 17.33/Ax | No description available |
17.34/Ay 17.36/Ba 17.37/Bb 17.38/Bc 17.39/Bd 17.41/Bf 17.42/Bg 17.43/Bh 17.44/Bi 17.46/Bk 17.47/Bl 17.48/Bm 17.49/Bn 17.51/Bp 17.52/Bq 17.53/Br 17.54/Bs 17.56/Bu 17.57/Bv 17.58/Bw 17.59/Bx 17.61/Bz 17.62/Ca 17.63/Cb | No description available |
17.35/Az 17.95/Az 17.40/Be 17.96/Be 17.45/Bj 17.97/Bj 17.50/Bo 17.98/Bo 17.55/Bt 17.99/Bt 17.60/By 17.100/By | No description available |
17.94/B 17.94/E 17.94/H | protein mxih | MXIH_SHIFL 1-83
17.64/Bk 17.65/Bk 17.66/Bk 17.67/Bk 17.68/Bk 17.69/Bk 17.70/Bk 17.71/Bk 17.72/Bk 17.73/Bk 17.74/Bk 17.75/Bk | No description available |
17.3/C 17.3/F 17.3/I 17.3/L 17.3/O 17.3/R 17.3/W | protein mxih | MXIH_SHIFL 1-83
17.76/C 17.77/C 17.78/C 17.79/C 17.80/C 17.81/C | protein mxih | MXIH_SHIFL 1-83
17.94/C 17.94/F 17.94/I | protein mxih | MXIH_SHIFL 1-83
17.3/X | No description available |
17.3/a 17.3/b 17.3/c 17.3/d 17.3/e 17.3/f 17.3/g 17.3/h 17.3/i 17.3/j 17.3/k 17.3/l 17.3/m 17.3/n 17.3/o 17.3/p 17.3/q 17.3/r 17.3/s 17.3/t 17.3/u 17.3/v 17.3/w 17.3/x | No description available |
> combine #17
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.2 to 'X'
Remapping chain ID 'B' in Shigella-Model_2025.pdb #17.2 to 'Y'
Remapping chain ID 'C' in Shigella-Model_2025.pdb #17.2 to 'Z'
Remapping chain ID 'D' in Shigella-Model_2025.pdb #17.2 to 'a'
Remapping chain ID 'E' in Shigella-Model_2025.pdb #17.2 to 'b'
Remapping chain ID 'F' in Shigella-Model_2025.pdb #17.2 to 'c'
Remapping chain ID 'G' in Shigella-Model_2025.pdb #17.2 to 'd'
Remapping chain ID 'H' in Shigella-Model_2025.pdb #17.2 to 'e'
Remapping chain ID 'I' in Shigella-Model_2025.pdb #17.2 to 'f'
Remapping chain ID 'J' in Shigella-Model_2025.pdb #17.2 to 'g'
Remapping chain ID 'K' in Shigella-Model_2025.pdb #17.2 to 'h'
Remapping chain ID 'L' in Shigella-Model_2025.pdb #17.2 to 'i'
Remapping chain ID 'M' in Shigella-Model_2025.pdb #17.2 to 'j'
Remapping chain ID 'N' in Shigella-Model_2025.pdb #17.2 to 'k'
Remapping chain ID 'O' in Shigella-Model_2025.pdb #17.2 to 'l'
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.3 to 'AA'
Remapping chain ID 'B' in Shigella-Model_2025.pdb #17.3 to 'AB'
Remapping chain ID 'C' in Shigella-Model_2025.pdb #17.3 to 'AC'
Remapping chain ID 'D' in Shigella-Model_2025.pdb #17.3 to 'AD'
Remapping chain ID 'E' in Shigella-Model_2025.pdb #17.3 to 'AE'
Remapping chain ID 'F' in Shigella-Model_2025.pdb #17.3 to 'AF'
Remapping chain ID 'G' in Shigella-Model_2025.pdb #17.3 to 'AG'
Remapping chain ID 'H' in Shigella-Model_2025.pdb #17.3 to 'AH'
Remapping chain ID 'I' in Shigella-Model_2025.pdb #17.3 to 'AI'
Remapping chain ID 'J' in Shigella-Model_2025.pdb #17.3 to 'AJ'
Remapping chain ID 'K' in Shigella-Model_2025.pdb #17.3 to 'AK'
Remapping chain ID 'L' in Shigella-Model_2025.pdb #17.3 to 'AL'
Remapping chain ID 'M' in Shigella-Model_2025.pdb #17.3 to 'AM'
Remapping chain ID 'N' in Shigella-Model_2025.pdb #17.3 to 'AN'
Remapping chain ID 'O' in Shigella-Model_2025.pdb #17.3 to 'AO'
Remapping chain ID 'P' in Shigella-Model_2025.pdb #17.3 to 'AP'
Remapping chain ID 'Q' in Shigella-Model_2025.pdb #17.3 to 'AQ'
Remapping chain ID 'R' in Shigella-Model_2025.pdb #17.3 to 'AR'
Remapping chain ID 'S' in Shigella-Model_2025.pdb #17.3 to 'AS'
Remapping chain ID 'T' in Shigella-Model_2025.pdb #17.3 to 'AT'
Remapping chain ID 'U' in Shigella-Model_2025.pdb #17.3 to 'AU'
Remapping chain ID 'V' in Shigella-Model_2025.pdb #17.3 to 'AV'
Remapping chain ID 'W' in Shigella-Model_2025.pdb #17.3 to 'AW'
Remapping chain ID 'X' in Shigella-Model_2025.pdb #17.3 to 'AX'
Remapping chain ID 'Y' in Shigella-Model_2025.pdb #17.3 to 'AY'
Remapping chain ID 'Z' in Shigella-Model_2025.pdb #17.3 to 'AZ'
Remapping chain ID 'a' in Shigella-Model_2025.pdb #17.3 to 'Aa'
Remapping chain ID 'b' in Shigella-Model_2025.pdb #17.3 to 'Ab'
Remapping chain ID 'c' in Shigella-Model_2025.pdb #17.3 to 'Ac'
Remapping chain ID 'd' in Shigella-Model_2025.pdb #17.3 to 'Ad'
Remapping chain ID 'e' in Shigella-Model_2025.pdb #17.3 to 'Ae'
Remapping chain ID 'f' in Shigella-Model_2025.pdb #17.3 to 'Af'
Remapping chain ID 'g' in Shigella-Model_2025.pdb #17.3 to 'Ag'
Remapping chain ID 'h' in Shigella-Model_2025.pdb #17.3 to 'Ah'
Remapping chain ID 'i' in Shigella-Model_2025.pdb #17.3 to 'Ai'
Remapping chain ID 'j' in Shigella-Model_2025.pdb #17.3 to 'Aj'
Remapping chain ID 'k' in Shigella-Model_2025.pdb #17.3 to 'Ak'
Remapping chain ID 'l' in Shigella-Model_2025.pdb #17.3 to 'Al'
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.4 to 'Am'
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.5 to 'An'
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.6 to 'Ao'
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.7 to 'Ap'
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.8 to 'Aq'
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.9 to 'Ar'
Remapping chain ID 'Aa' in Shigella-Model_2025.pdb #17.10 to 'As'
Remapping chain ID 'Ab' in Shigella-Model_2025.pdb #17.11 to 'At'
Remapping chain ID 'Ac' in Shigella-Model_2025.pdb #17.12 to 'Au'
Remapping chain ID 'Ad' in Shigella-Model_2025.pdb #17.13 to 'Av'
Remapping chain ID 'Ae' in Shigella-Model_2025.pdb #17.14 to 'Aw'
Remapping chain ID 'Af' in Shigella-Model_2025.pdb #17.15 to 'Ax'
Remapping chain ID 'Ag' in Shigella-Model_2025.pdb #17.16 to 'Ay'
Remapping chain ID 'Ah' in Shigella-Model_2025.pdb #17.17 to 'Az'
Remapping chain ID 'Ai' in Shigella-Model_2025.pdb #17.18 to 'A1'
Remapping chain ID 'Aj' in Shigella-Model_2025.pdb #17.19 to 'A2'
Remapping chain ID 'Ak' in Shigella-Model_2025.pdb #17.20 to 'A3'
Remapping chain ID 'Al' in Shigella-Model_2025.pdb #17.21 to 'A4'
Remapping chain ID 'Am' in Shigella-Model_2025.pdb #17.22 to 'A5'
Remapping chain ID 'An' in Shigella-Model_2025.pdb #17.23 to 'A6'
Remapping chain ID 'Ao' in Shigella-Model_2025.pdb #17.24 to 'A7'
Remapping chain ID 'Ap' in Shigella-Model_2025.pdb #17.25 to 'A8'
Remapping chain ID 'Aq' in Shigella-Model_2025.pdb #17.26 to 'A9'
Remapping chain ID 'Ar' in Shigella-Model_2025.pdb #17.27 to 'A0'
Remapping chain ID 'As' in Shigella-Model_2025.pdb #17.28 to 'BA'
Remapping chain ID 'At' in Shigella-Model_2025.pdb #17.29 to 'BB'
Remapping chain ID 'Au' in Shigella-Model_2025.pdb #17.30 to 'BC'
Remapping chain ID 'Av' in Shigella-Model_2025.pdb #17.31 to 'BD'
Remapping chain ID 'Aw' in Shigella-Model_2025.pdb #17.32 to 'BE'
Remapping chain ID 'Ax' in Shigella-Model_2025.pdb #17.33 to 'BF'
Remapping chain ID 'Ay' in Shigella-Model_2025.pdb #17.34 to 'BG'
Remapping chain ID 'Az' in Shigella-Model_2025.pdb #17.35 to 'BH'
Remapping chain ID 'Bk' in Shigella-Model_2025.pdb #17.64 to 'B1'
Remapping chain ID 'Bk' in Shigella-Model_2025.pdb #17.65 to 'B2'
Remapping chain ID 'Bk' in Shigella-Model_2025.pdb #17.66 to 'B3'
Remapping chain ID 'Bk' in Shigella-Model_2025.pdb #17.67 to 'B4'
Remapping chain ID 'Bk' in Shigella-Model_2025.pdb #17.68 to 'B5'
Remapping chain ID 'Bk' in Shigella-Model_2025.pdb #17.69 to 'B6'
Remapping chain ID 'Bk' in Shigella-Model_2025.pdb #17.70 to 'B7'
Remapping chain ID 'Bk' in Shigella-Model_2025.pdb #17.71 to 'B8'
Remapping chain ID 'Bk' in Shigella-Model_2025.pdb #17.72 to 'B9'
Remapping chain ID 'Bk' in Shigella-Model_2025.pdb #17.73 to 'B0'
Remapping chain ID 'Bk' in Shigella-Model_2025.pdb #17.74 to 'CA'
Remapping chain ID 'Bk' in Shigella-Model_2025.pdb #17.75 to 'CB'
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.76 to 'BI'
Remapping chain ID 'B' in Shigella-Model_2025.pdb #17.76 to 'BJ'
Remapping chain ID 'C' in Shigella-Model_2025.pdb #17.76 to 'BK'
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.77 to 'BL'
Remapping chain ID 'B' in Shigella-Model_2025.pdb #17.77 to 'BM'
Remapping chain ID 'C' in Shigella-Model_2025.pdb #17.77 to 'BN'
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.78 to 'BO'
Remapping chain ID 'B' in Shigella-Model_2025.pdb #17.78 to 'BP'
Remapping chain ID 'C' in Shigella-Model_2025.pdb #17.78 to 'BQ'
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.79 to 'BR'
Remapping chain ID 'B' in Shigella-Model_2025.pdb #17.79 to 'BS'
Remapping chain ID 'C' in Shigella-Model_2025.pdb #17.79 to 'BT'
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.80 to 'BU'
Remapping chain ID 'B' in Shigella-Model_2025.pdb #17.80 to 'BV'
Remapping chain ID 'C' in Shigella-Model_2025.pdb #17.80 to 'BW'
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.81 to 'BX'
Remapping chain ID 'B' in Shigella-Model_2025.pdb #17.81 to 'BY'
Remapping chain ID 'C' in Shigella-Model_2025.pdb #17.81 to 'BZ'
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.82 to 'CC'
Remapping chain ID 'B' in Shigella-Model_2025.pdb #17.83 to 'CD'
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.84 to 'CE'
Remapping chain ID 'B' in Shigella-Model_2025.pdb #17.85 to 'CF'
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.86 to 'CG'
Remapping chain ID 'B' in Shigella-Model_2025.pdb #17.87 to 'CH'
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.88 to 'CI'
Remapping chain ID 'B' in Shigella-Model_2025.pdb #17.89 to 'CJ'
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.90 to 'CK'
Remapping chain ID 'B' in Shigella-Model_2025.pdb #17.91 to 'CL'
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.92 to 'CM'
Remapping chain ID 'B' in Shigella-Model_2025.pdb #17.93 to 'CN'
Remapping chain ID 'A' in Shigella-Model_2025.pdb #17.94 to 'CO'
Remapping chain ID 'B' in Shigella-Model_2025.pdb #17.94 to 'CP'
Remapping chain ID 'C' in Shigella-Model_2025.pdb #17.94 to 'CQ'
Remapping chain ID 'D' in Shigella-Model_2025.pdb #17.94 to 'CR'
Remapping chain ID 'E' in Shigella-Model_2025.pdb #17.94 to 'CS'
Remapping chain ID 'F' in Shigella-Model_2025.pdb #17.94 to 'CT'
Remapping chain ID 'G' in Shigella-Model_2025.pdb #17.94 to 'CU'
Remapping chain ID 'H' in Shigella-Model_2025.pdb #17.94 to 'CV'
Remapping chain ID 'I' in Shigella-Model_2025.pdb #17.94 to 'CW'
Remapping chain ID 'Az' in Shigella-Model_2025.pdb #17.95 to 'CX'
Remapping chain ID 'Be' in Shigella-Model_2025.pdb #17.96 to 'CY'
Remapping chain ID 'Bj' in Shigella-Model_2025.pdb #17.97 to 'CZ'
Remapping chain ID 'Bo' in Shigella-Model_2025.pdb #17.98 to 'Cc'
Remapping chain ID 'Bt' in Shigella-Model_2025.pdb #17.99 to 'Cd'
Remapping chain ID 'By' in Shigella-Model_2025.pdb #17.100 to 'Ce'
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!14 models
> hide #!13 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Websites/Segmentation-06132025/IpaD.mrc
Opened IpaD.mrc as #19, grid size 120,120,200, pixel 4.3,4.3,4.3, shown at
level 0.149, step 1, values float32
> volume #19 level 0.1278
> volume #19 level 0.07007
> view orient
[Repeated 1 time(s)]
> turn x 90
[Repeated 2 time(s)]
> color #19 #ffffb287 models
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #18 inMap #19
Fit molecule combination (#18) to map IpaD.mrc (#19) using 363622 atoms
average map value = 0.09591, steps = 84
shifted from previous position = 30.8
rotated from previous position = 6.12 degrees
atoms outside contour = 135688, contour level = 0.070071
Position of combination (#18) relative to IpaD.mrc (#19) coordinates:
Matrix rotation and translation
0.99429345 0.10667947 0.00013920 -27.11517103
-0.10667941 0.99429339 -0.00038562 28.02764504
-0.00017954 0.00036857 0.99999992 30.71854997
Axis 0.00353480 0.00149387 -0.99999264
Axis point 248.90446458 266.46909967 0.00000000
Rotation angle (degrees) 6.12398011
Shift along axis -30.77230074
> fitmap #18 inMap #19
Fit molecule combination (#18) to map IpaD.mrc (#19) using 363622 atoms
average map value = 0.09591, steps = 40
shifted from previous position = 0.0695
rotated from previous position = 0.00781 degrees
atoms outside contour = 135720, contour level = 0.070071
Position of combination (#18) relative to IpaD.mrc (#19) coordinates:
Matrix rotation and translation
0.99427927 0.10681157 0.00016802 -27.15550370
-0.10681150 0.99427921 -0.00039638 28.06244942
-0.00020940 0.00037616 0.99999991 30.65515722
Axis 0.00361633 0.00176676 -0.99999190
Axis point 248.96121509 266.53207465 0.00000000
Rotation angle (degrees) 6.13159687
Shift along axis -30.70353274
> fitmap #18 inMap #19
Fit molecule combination (#18) to map IpaD.mrc (#19) using 363622 atoms
average map value = 0.09591, steps = 40
shifted from previous position = 0.0695
rotated from previous position = 0.00308 degrees
atoms outside contour = 135689, contour level = 0.070071
Position of combination (#18) relative to IpaD.mrc (#19) coordinates:
Matrix rotation and translation
0.99428218 0.10678451 0.00012182 -27.13217386
-0.10678446 0.99428211 -0.00040053 28.06581289
-0.00016389 0.00038523 0.99999991 30.70995083
Axis 0.00367918 0.00133778 -0.99999234
Axis point 248.95009227 266.35332200 0.00000000
Rotation angle (degrees) 6.13003534
Shift along axis -30.77199392
> hide #!19 models
> select add #18
363622 atoms, 369397 bonds, 93 pseudobonds, 45309 residues, 2 models selected
> hide sel cartoons
> hide sel surfaces
> hide sel atoms
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> select subtract #18
219 models selected
> select add #18.1
93 pseudobonds, 1 model selected
> select subtract #18.1
Nothing selected
> select add #18.1
93 pseudobonds, 1 model selected
> select subtract #18.1
Nothing selected
> hide #18.1 models
> show #18.1 models
> hide #18.1 models
> show #18.1 models
> hide #18.1 models
> show #18.1 models
> hide #18.1 models
> hide #18.2 models
> show #18.2 models
> select add #18.2
1102 atoms, 138 residues, 1 model selected
> select subtract #18.2
1 model selected
> select add #18.2
1102 atoms, 138 residues, 1 model selected
> select add #18.3
2204 atoms, 276 residues, 2 models selected
> select add #18.4
3306 atoms, 414 residues, 3 models selected
> select add #18.5
4408 atoms, 552 residues, 4 models selected
> select add #18.6
5510 atoms, 690 residues, 5 models selected
> select add #18.7
6612 atoms, 828 residues, 6 models selected
> select add #18.8
7714 atoms, 966 residues, 7 models selected
> select add #18.9
8816 atoms, 1104 residues, 8 models selected
> select add #18.10
9918 atoms, 1242 residues, 9 models selected
> select add #18.11
11020 atoms, 1380 residues, 10 models selected
> select add #18.48
12122 atoms, 1518 residues, 11 models selected
> select add #18.47
13224 atoms, 1656 residues, 12 models selected
> select add #18.46
14958 atoms, 1867 residues, 13 models selected
> select subtract #18.46
13224 atoms, 1656 residues, 14 models selected
> select add #18.46
14958 atoms, 1867 residues, 13 models selected
> select add #18.45
16692 atoms, 2078 residues, 14 models selected
> select add #18.220
17794 atoms, 2216 residues, 15 models selected
> select add #18.219
18896 atoms, 2354 residues, 16 models selected
> hide sel cartoons
> select add #18.131
20309 atoms, 2529 residues, 17 models selected
> select subtract #18.131
18896 atoms, 2354 residues, 18 models selected
> select add #18.25
20630 atoms, 2565 residues, 17 models selected
> select subtract #18.25
18896 atoms, 2354 residues, 18 models selected
> show sel cartoons
> select clear
Drag select of 345 residues
> select subtract #18.2
2575 atoms, 323 residues, 17 models selected
> select add #18.2
3677 atoms, 461 residues, 16 models selected
> select subtract #18.3
3500 atoms, 439 residues, 17 models selected
> select add #18.3
4602 atoms, 577 residues, 16 models selected
> select subtract #18.4
4441 atoms, 557 residues, 17 models selected
> select add #18.4
5543 atoms, 695 residues, 16 models selected
> select subtract #18.5
5360 atoms, 672 residues, 17 models selected
> select add #18.5
6462 atoms, 810 residues, 16 models selected
> select subtract #18.6
6287 atoms, 788 residues, 17 models selected
> select add #18.6
7389 atoms, 926 residues, 16 models selected
> select subtract #18.7
7211 atoms, 904 residues, 17 models selected
> select add #18.7
8313 atoms, 1042 residues, 16 models selected
> select subtract #18.8
8153 atoms, 1022 residues, 17 models selected
> select add #18.8
9255 atoms, 1160 residues, 16 models selected
> select subtract #18.9
9100 atoms, 1140 residues, 17 models selected
> select add #18.9
10202 atoms, 1278 residues, 16 models selected
> select subtract #18.10
10063 atoms, 1260 residues, 17 models selected
> select add #18.10
11165 atoms, 1398 residues, 16 models selected
> select subtract #18.11
11003 atoms, 1377 residues, 17 models selected
> select add #18.11
12105 atoms, 1515 residues, 16 models selected
> select subtract #18.47
11942 atoms, 1495 residues, 17 models selected
> select add #18.47
13044 atoms, 1633 residues, 16 models selected
> select subtract #18.48
12843 atoms, 1608 residues, 17 models selected
> select add #18.48
13945 atoms, 1746 residues, 16 models selected
> select subtract #18.194
13779 atoms, 1725 residues, 17 models selected
> select add #18.194
14881 atoms, 1863 residues, 16 models selected
> select subtract #18.196
14703 atoms, 1841 residues, 17 models selected
> select add #18.196
15805 atoms, 1979 residues, 16 models selected
> select subtract #18.219
15615 atoms, 1955 residues, 17 models selected
> select add #18.219
16717 atoms, 2093 residues, 16 models selected
> select subtract #18.220
16530 atoms, 2070 residues, 17 models selected
> select add #18.220
17632 atoms, 2208 residues, 16 models selected
> hide sel cartoons
> show sel cartoons
> color (#!18 & sel) #acffddff
> color (#!18 & sel) #afffdbff
> color (#!18 & sel) #b0ffc9ff
> color (#!18 & sel) #a8ffbeff
> color (#!18 & sel) #a8ffbfff
> color (#!18 & sel) #a9ffc4ff
> color (#!18 & sel) #abffc7ff
> color (#!18 & sel) #b0ffcbff
> color (#!18 & sel) #b9ffcfff
> color (#!18 & sel) #bbffd0ff
> color (#!18 & sel) #bcffcfff
> color (#!18 & sel) #bdffcfff
> color (#!18 & sel) #c1ffcfff
> color (#!18 & sel) #c2ffcfff
> color (#!18 & sel) #c3ffcfff
> color (#!18 & sel) #c3ffceff
> color (#!18 & sel) #c4ffccff
[Repeated 1 time(s)]
> color (#!18 & sel) #c8ffcdff
> save /Users/shoichi/Desktop/Shigella-ipaDnull-bin2-06142025.cxs includeMaps
> true
——— End of log from Mon Jun 16 11:13:56 2025 ———
opened ChimeraX session
> show #!19 models
> hide #!19 models
> show #!19 models
> color #19 #919191ff models
> color #19 #929292ff models
> color #19 #9292926f models
> color #19 #92929249 models
> select clear
[Repeated 1 time(s)]
> color #19 #212121ff models
> color #19 #21212106 models
> color #19 #2121211a models
> select add #18
363622 atoms, 369397 bonds, 93 pseudobonds, 45309 residues, 2 models selected
> show sel surfaces
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Websites/Models/MxiGModel_Jian.pdb
Summary of feedback from opening /Users/shoichi/Library/CloudStorage/OneDrive-
YaleUniversity/Jun_Lab_documents/Websites/Models/MxiGModel_Jian.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 11 THR A 23 1 13
Start residue of secondary structure not found: HELIX 2 2 GLN A 24 ASN A 40 1
17
Start residue of secondary structure not found: HELIX 3 3 ASN A 43 ASN A 81 1
39
Start residue of secondary structure not found: HELIX 4 4 THR B 11 THR B 23 1
13
Start residue of secondary structure not found: HELIX 5 5 GLN B 24 ASN B 40 1
17
4549 messages similar to the above omitted
Chain information for MxiGModel_Jian.pdb
---
Chain | Description
20.1/Aa 20.2/Ab 20.3/Ac 20.4/Ad 20.5/Ae 20.6/Af 20.7/Ag 20.8/Ah 20.9/Ai 20.10/Aj 20.11/Ak 20.12/Al 20.13/Am 20.14/An 20.15/Ao 20.16/Ap 20.17/Aq 20.18/Ar 20.19/As 20.20/At 20.21/Au 20.22/Av 20.23/Aw 20.24/Ax | No description available
20.25/Ay 20.27/Ba 20.28/Bb 20.29/Bc 20.30/Bd 20.32/Bf 20.33/Bg 20.34/Bh 20.35/Bi 20.37/Bk 20.38/Bl 20.39/Bm 20.40/Bn 20.42/Bp 20.43/Bq 20.44/Br 20.45/Bs 20.47/Bu 20.48/Bv 20.49/Bw 20.50/Bx 20.52/Bz 20.53/Ca 20.54/Cb | No description available
20.26/Az 20.31/Be 20.36/Bj 20.41/Bo 20.46/Bt 20.51/By | No description available
20.55/Bk 20.56/Bk 20.57/Bk 20.58/Bk 20.59/Bk 20.60/Bk 20.61/Bk 20.62/Bk 20.63/Bk 20.64/Bk 20.65/Bk 20.66/Bk | No description available
> select subtract #18
219 models selected
> select add #18
363622 atoms, 369397 bonds, 93 pseudobonds, 45309 residues, 2 models selected
> hide sel surfaces
[Repeated 1 time(s)]
> select subtract #18
219 models selected
> hide #!18 models
> select add #20
119262 atoms, 121296 bonds, 14790 residues, 67 models selected
> comvine #20
Unknown command: comvine #20
> combine #20
Remapping chain ID 'Bk' in MxiGModel_Jian.pdb #20.55 to 'B1'
Remapping chain ID 'Bk' in MxiGModel_Jian.pdb #20.56 to 'B2'
Remapping chain ID 'Bk' in MxiGModel_Jian.pdb #20.57 to 'B3'
Remapping chain ID 'Bk' in MxiGModel_Jian.pdb #20.58 to 'B4'
Remapping chain ID 'Bk' in MxiGModel_Jian.pdb #20.59 to 'B5'
Remapping chain ID 'Bk' in MxiGModel_Jian.pdb #20.60 to 'B6'
Remapping chain ID 'Bk' in MxiGModel_Jian.pdb #20.61 to 'B7'
Remapping chain ID 'Bk' in MxiGModel_Jian.pdb #20.62 to 'B8'
Remapping chain ID 'Bk' in MxiGModel_Jian.pdb #20.63 to 'B9'
Remapping chain ID 'Bk' in MxiGModel_Jian.pdb #20.64 to 'B0'
Remapping chain ID 'Bk' in MxiGModel_Jian.pdb #20.65 to 'CA'
Remapping chain ID 'Bk' in MxiGModel_Jian.pdb #20.66 to 'CB'
> ui tool show "Fit in Map"
> hide #!20 models
> hide #!19 models
> show #!20 models
> select subtract #20
Nothing selected
> hide #!20 models
> show #!3 models
> hide #!3 models
> show #!11 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #21 inMap #11
Fit molecule combination (#21) to map MxiGp.mrc gaussian (#11) using 119262
atoms
average map value = 0.05915, steps = 96
shifted from previous position = 30.2
rotated from previous position = 2.02 degrees
atoms outside contour = 56989, contour level = 0.01197
Position of combination (#21) relative to MxiGp.mrc gaussian (#11)
coordinates:
Matrix rotation and translation
0.99938175 0.03472784 0.00548504 -11.91171122
-0.03472387 0.99939661 -0.00081815 8.31950899
-0.00551015 0.00062718 0.99998462 31.40504216
Axis 0.02055027 0.15633375 -0.98749048
Axis point 368.69366412 331.83876355 0.00000000
Rotation angle (degrees) 2.01526509
Shift along axis -29.95634895
> fitmap #21 inMap #11
Fit molecule combination (#21) to map MxiGp.mrc gaussian (#11) using 119262
atoms
average map value = 0.05915, steps = 48
shifted from previous position = 0.0285
rotated from previous position = 0.00735 degrees
atoms outside contour = 56986, contour level = 0.01197
Position of combination (#21) relative to MxiGp.mrc gaussian (#11)
coordinates:
Matrix rotation and translation
0.99937794 0.03482402 0.00556970 -11.95976855
-0.03482000 0.99939327 -0.00081565 8.34371750
-0.00559473 0.00062120 0.99998416 31.40152622
Axis 0.02036700 0.15825326 -0.98718848
Axis point 369.82390082 332.54039666 0.00000000
Rotation angle (degrees) 2.02146626
Shift along axis -29.92238891
> show #!16 models
> color #11 #86d8ffa7 models
> color #11 #86d8ff8b models
> hide #!16 models
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Websites/Models/8axn.cif
8axn.cif title:
Inner membrane ring and secretin N0 N1 domains of the type 3 secretion system
of Shigella flexneri [more info...]
Chain information for 8axn.cif #22
---
Chain | Description | UniProt
0 1 2 3 4 5 6 7 8 9 Y Z a0 b0 y z | Outer membrane protein MxiD | MXID_SHIFL 1-566
A B C D E F G H I J K L M N O P Q R S T U V W X | Protein MxiG | MXIG_SHIFL 1-371
a b c d e f g h i j k l m n o p q r s t u v w x | Lipoprotein MxiJ | MXIJ_SHIFL 1-241
> hide #21 models
> hide #!11 models
> show #!5 models
> show #!11 models
> select add #22
94656 atoms, 96264 bonds, 11704 residues, 1 model selected
> view matrix models #22,1,0,0,-28.809,0,1,0,-50.357,0,0,1,233.87
> view matrix models #22,1,0,0,-77.277,0,1,0,-74.727,0,0,1,227.69
> fitmap #22 inMap #11
Fit molecule 8axn.cif (#22) to map MxiGp.mrc gaussian (#11) using 94656 atoms
average map value = 0.07461, steps = 68
shifted from previous position = 7.73
rotated from previous position = 5.13 degrees
atoms outside contour = 31505, contour level = 0.01197
Position of 8axn.cif (#22) relative to MxiGp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
0.99600057 0.08934650 0.00026261 -103.84271910
-0.08934643 0.99600058 -0.00026076 -44.30658929
-0.00028486 0.00023626 0.99999993 220.22555197
Axis 0.00278139 0.00306372 -0.99999144
Axis point -538.96887063 1131.25244200 0.00000000
Rotation angle (degrees) 5.12605469
Shift along axis -220.64823617
> fitmap #22 inMap #11
Fit molecule 8axn.cif (#22) to map MxiGp.mrc gaussian (#11) using 94656 atoms
average map value = 0.07461, steps = 48
shifted from previous position = 0.0672
rotated from previous position = 0.0185 degrees
atoms outside contour = 31526, contour level = 0.01197
Position of 8axn.cif (#22) relative to MxiGp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
0.99597967 0.08957852 0.00042034 -103.95311438
-0.08957849 0.99597976 -0.00010411 -44.25815981
-0.00042797 0.00006604 0.99999991 220.26264183
Axis 0.00094970 0.00473494 -0.99998834
Axis point -533.31462059 1134.19530041 0.00000000
Rotation angle (degrees) 5.13941943
Shift along axis -220.56835786
> fitmap #22 inMap #11
Fit molecule 8axn.cif (#22) to map MxiGp.mrc gaussian (#11) using 94656 atoms
average map value = 0.07461, steps = 48
shifted from previous position = 0.0247
rotated from previous position = 0.042 degrees
atoms outside contour = 31516, contour level = 0.01197
Position of 8axn.cif (#22) relative to MxiGp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
0.99597464 0.08963540 0.00011929 -103.89411205
-0.08963528 0.99597436 -0.00077024 -44.07256008
-0.00018785 0.00075645 0.99999970 219.97557348
Axis 0.00851578 0.00171317 -0.99996227
Axis point -537.49400828 1113.94753412 0.00000000
Rotation angle (degrees) 5.14282355
Shift along axis -220.92751708
> hide #!5 models
> show #21 models
> hide #22 models
> show #22 models
> matchmaker #22 to #21
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 combination, chain Ay (#21) with 8axn.cif, chain B (#22), sequence
alignment score = 1474.8
RMSD between 185 pruned atom pairs is 0.185 angstroms; (across all 190 pairs:
0.819)
> hide sel atoms
> show sel cartoons
> show #!5 models
> hide #!5 models
> show #!13 models
> color #13 #5fabeb71 models
> show #!16 models
> view orient
> turn x 90
[Repeated 2 time(s)]
> select add #21
213918 atoms, 217560 bonds, 26494 residues, 2 models selected
> view matrix models
> #21,0.99938,0.034824,0.0055697,-12.453,-0.03482,0.99939,-0.00081565,8.3437,-0.0055947,0.0006212,0.99998,38.219,#22,0.81523,0.57913,0.00099389,-207.19,-0.57913,0.81523,0.00088373,178.46,-0.00029846,-0.001296,1,227.05
> fitmap #21 inMap #11
Fit molecule combination (#21) to map MxiGp.mrc gaussian (#11) using 119262
atoms
average map value = 0.05915, steps = 52
shifted from previous position = 6.74
rotated from previous position = 0.0214 degrees
atoms outside contour = 56992, contour level = 0.01197
Position of combination (#21) relative to MxiGp.mrc gaussian (#11)
coordinates:
Matrix rotation and translation
0.99936622 0.03517741 0.00545039 -12.05592678
-0.03517349 0.99938089 -0.00081378 8.46311441
-0.00547564 0.00062156 0.99998482 31.46624660
Axis 0.02015680 0.15343668 -0.98795288
Axis point 365.77153476 332.09958673 0.00000000
Rotation angle (degrees) 2.04041197
Shift along axis -30.03162571
> matchmaker #21 to #22
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 8axn.cif, chain B (#22) with combination, chain Ay (#21), sequence
alignment score = 1474.8
RMSD between 185 pruned atom pairs is 0.185 angstroms; (across all 190 pairs:
0.819)
> hide #21 models
> select subtract #21
94656 atoms, 96264 bonds, 11704 residues, 1 model selected
> hide #!11 models
> select clear
Drag select of 13 OM_complex.mrc gaussian , 8986 residues
> hide sel cartoons
Alignment identifier is 1
Alignment identifier is 2
> select subtract #13
72635 atoms, 8986 residues, 1 model selected
> hide #!13 models
> select add #22
94656 atoms, 96264 bonds, 11704 residues, 1 model selected
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
> show sel cartoons
> select clear
[Repeated 1 time(s)]
> select #22/a,d,c,b,e,h,k,n,q,t,x,g,j,m,p,s,w,v,u,f,i,l,o,r
34272 atoms, 34776 bonds, 4320 residues, 1 model selected
> select clear
> select #22/C,B,A,S,P,M,J,G,D,U,T,Q,N,K,H,E,V,R,O,L,I,F,W-X
42752 atoms, 43504 bonds, 5176 residues, 1 model selected
> select clear
> select #22/B,A,S,P,M,J,G,D,U,T,Q,N,K,H,E,V:276-368/C,R,O,L,I,F,W-X:276-361
18080 atoms, 18376 bonds, 2176 residues, 1 model selected
> select clear
> select #22/B,A,S,P,M,J,G,D,U,T,Q,N,K,H,E,V:349-368/C,R,O,L,I,F,W-X:349-361
3728 atoms, 3832 bonds, 424 residues, 1 model selected
> select #22/C,B,A,S,P,M,J,G,D,U,T,Q,N,K,H,E,V,R,O,L,I,F,W-X:347
216 atoms, 192 bonds, 24 residues, 1 model selected
> select #22/C,B,A,S,P,M,J,G,D,U,T,Q,N,K,H,E,V,R,O,L,I,F,W-X:151-347
38880 atoms, 39504 bonds, 4728 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> show sel surfaces
> select #22/C,B,A,S,P,M,J,G,D,U,T,Q,N,K,H,E,V,R,O,L,I,F,W-X:347
216 atoms, 192 bonds, 24 residues, 1 model selected
> select #22/C,B,A,S,P,M,J,G,D,U,T,Q,N,K,H,E,V,R,O,L,I,F,W-X:151-347
38880 atoms, 39504 bonds, 4728 residues, 1 model selected
> hide sel cartoons
> hide sel surfaces
> select #22/C,B,A,S,P,M,J,G,D,U,T,Q,N,K,H,E,V,R,O,L,I,F,W-X:349
288 atoms, 288 bonds, 24 residues, 1 model selected
> select #22/B,A,S,P,M,J,G,D,U,T,Q,N,K,H,E,V:349-368/C,R,O,L,I,F,W-X:349-361
3728 atoms, 3832 bonds, 424 residues, 1 model selected
> select #22/C,B,A,S,P,M,J,G,D,U,T,Q,N,K,H,E,V,R,O,L,I,F,W-X:356-357
456 atoms, 456 bonds, 48 residues, 1 model selected
> select #22/B,A,S,P,M,J,G,D,U,T,Q,N,K,H,E,V:356-368/C,R,O,L,I,F,W-X:356-361
2360 atoms, 2440 bonds, 256 residues, 1 model selected
> select #22/C,B,A,S,P,M,J,G,D,U,T,Q,N,K,H,E,V,R,O,L,I,F,W-X:347-348
360 atoms, 336 bonds, 48 residues, 1 model selected
> select #22/B,A,S,P,M,J,G,D,U,T,Q,N,K,H,E,V:347-368/C,R,O,L,I,F,W-X:347-361
4088 atoms, 4192 bonds, 472 residues, 1 model selected
> show sel cartoons
> select add #21
123350 atoms, 125488 bonds, 15262 residues, 26 models selected
Alignment identifier is 4
Alignment identifier is 5
Alignment identifier is 6
Alignment identifier is 7
Alignment identifier is 8
> select clear
> select #22/C,B,A,S,P,M,J,G,D,U,T,Q,N,K,H,E,V,R,O,L,I,F,W-X
42752 atoms, 43504 bonds, 5176 residues, 1 model selected
> hide sel cartoons
> show #21 models
> select clear
> select #22/B,A,S,P,M,J,G,D,U,T,Q,N,K,H,E,V:333-368/C,R,O,L,I,F,W-X:333-361
6800 atoms, 6952 bonds, 808 residues, 1 model selected
> show sel cartoons
> color (#!22 & sel) #89eae671
[Repeated 1 time(s)]
> color (#!22 & sel) #8aeae971
> color (#!22 & sel) #8ae9ea71
> color (#!22 & sel) #8ae3ea71
> color (#!22 & sel) #88daea71
> color (#!22 & sel) #84d0ea71
> color (#!22 & sel) #85dbea71
> color (#!22 & sel) #8ceadd71
> color (#!22 & sel) #93eace71
> color (#!22 & sel) #94eac171
> color (#!22 & sel) #95eac071
> color (#!22 & sel) #96eab571
> color (#!22 & sel) #90eaad71
> color (#!22 & sel) #8feaad71
> color (#!22 & sel) #83eaac71
> color (#!22 & sel) #7feaaa71
> color (#!22 & sel) #76eaa571
> color (#!22 & sel) #6dea9e71
> color (#!22 & sel) #67ea9971
> color (#!22 & sel) #65ea9771
[Repeated 1 time(s)]
> color (#!22 & sel) #71ea9471
> color (#!22 & sel) #7aea9471
> color (#!22 & sel) #7dea9471
> color (#!22 & sel) #7fea9571
> color (#!22 & sel) #80ea9671
> color (#!22 & sel) #84ea9d71
> color (#!22 & sel) #85ea9d71
> select clear
> select #22/a,d,c,b,e,h,k,n,q,t,x,g,j,m,p,s,w,v,u,f,i,l,o,r
34272 atoms, 34776 bonds, 4320 residues, 1 model selected
> color (#!22 & sel) #85ea9d71
> select clear
> select #22/0-1,a0,Y-Z,2,4,6,8,b0,y-z,3,5,7,9
17632 atoms, 17984 bonds, 2208 residues, 1 model selected
> select add #21
136894 atoms, 139280 bonds, 16998 residues, 2 models selected
> select add #22
213918 atoms, 217560 bonds, 26494 residues, 2 models selected
> select subtract #22
119262 atoms, 121296 bonds, 14790 residues, 25 models selected
Alignment identifier is 4
Alignment identifier is 5
Alignment identifier is 6
Alignment identifier is 7
> select #21/Aa-Ax:21
264 atoms, 240 bonds, 24 residues, 1 model selected
> select #21/Aa-Ax
33672 atoms, 34152 bonds, 4248 residues, 1 model selected
> select clear
> select #22/a,d,c,b,e,h,k,n,q,t,x,g,j,m,p,s,w,v,u,f,i,l,o,r
34272 atoms, 34776 bonds, 4320 residues, 1 model selected
> hide sel cartoons
> select #21/Ay,Ba-Bd,Bf-Bi,Bk-Bn,Bp-Bs,Bu-Bx,Bz,Ca-Cb:1
192 atoms, 168 bonds, 24 residues, 1 model selected
> select #21/Ay,Ba-Bd,Bf-Bi,Bk-Bn,Bp-Bs,Bu-Bx,Bz,Ca-Cb
66384 atoms, 67560 bonds, 8160 residues, 1 model selected
> hide #!22 models
> select clear
> select #21/Ay,Ba-Bd,Bf-Bi,Bk-Bn,Bp-Bs,Bu-Bx,Bz,Ca-Cb:1
192 atoms, 168 bonds, 24 residues, 1 model selected
> select #21/Ay,Ba-Bd,Bf-Bi,Bk-Bn,Bp-Bs,Bu-Bx,Bz,Ca-Cb
66384 atoms, 67560 bonds, 8160 residues, 1 model selected
> hide sel cartoons
> hide sel surfaces
> show sel cartoons
> select #21/Az,Be,Bj,Bo,Bt,By:1
48 atoms, 42 bonds, 6 residues, 1 model selected
> select #21/Az,Be,Bj,Bo,Bt,By
8478 atoms, 8664 bonds, 1050 residues, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> hide #!16 models
> select #21/B1-B9,B0,CA-CB:111
96 atoms, 84 bonds, 12 residues, 1 model selected
> select #21/B1-B9,B0,CA-CB
10728 atoms, 10920 bonds, 1332 residues, 1 model selected
> hide sel cartoons
> show #!22 models
> select add #21
119262 atoms, 121296 bonds, 14790 residues, 1 model selected
> select subtract #21
Nothing selected
Drag select of 15424 residues
> save /Users/shoichi/Desktop/MxiGmodel_Jian-8axn.pdb selectedOnly true
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Websites/Models/MxiGmodel_Jian-8axn.pdb
Summary of feedback from opening /Users/shoichi/Library/CloudStorage/OneDrive-
YaleUniversity/Jun_Lab_documents/Websites/Models/MxiGmodel_Jian-8axn.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 11 THR A 23 1 13
Start residue of secondary structure not found: HELIX 2 2 GLN A 24 ASN A 40 1
17
Start residue of secondary structure not found: HELIX 3 3 ASN A 43 ASN A 81 1
39
Start residue of secondary structure not found: HELIX 4 4 THR B 11 THR B 23 1
13
Start residue of secondary structure not found: HELIX 5 5 GLN B 24 ASN B 40 1
17
133 messages similar to the above omitted
Chain information for MxiGmodel_Jian-8axn.pdb
---
Chain | Description
23.2/0 23.2/1 23.2/2 23.2/3 23.2/4 23.2/5 23.2/6 23.2/7 23.2/8 23.2/9 23.2/Y 23.2/Z 23.2/a0 23.2/b0 23.2/y 23.2/z | No description available
23.2/A 23.2/B 23.2/D 23.2/E 23.2/G 23.2/H 23.2/J 23.2/K 23.2/M 23.2/N 23.2/P 23.2/Q 23.2/S 23.2/T 23.2/U 23.2/V | No description available
23.1/Aa 23.1/Ab 23.1/Ac 23.1/Ad 23.1/Ae 23.1/Af 23.1/Ag 23.1/Ah 23.1/Ai 23.1/Aj 23.1/Ak 23.1/Al 23.1/Am 23.1/An 23.1/Ao 23.1/Ap 23.1/Aq 23.1/Ar 23.1/As 23.1/At 23.1/Au 23.1/Av 23.1/Aw 23.1/Ax | No description available
23.1/Ay 23.1/Ba 23.1/Bb 23.1/Bc 23.1/Bd 23.1/Bf 23.1/Bg 23.1/Bh 23.1/Bi 23.1/Bk 23.1/Bl 23.1/Bm 23.1/Bn 23.1/Bp 23.1/Bq 23.1/Br 23.1/Bs 23.1/Bu 23.1/Bv 23.1/Bw 23.1/Bx 23.1/Bz 23.1/Ca 23.1/Cb | No description available
23.2/C 23.2/F 23.2/I 23.2/L 23.2/O 23.2/R 23.2/W 23.2/X | No description available
> close #20
> close #22
> select add #23
224544 atoms, 126648 bonds, 27832 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> close #21
> select clear
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Websites/Models/8axl.cif
8axl.cif title:
Outer membrane secretin pore of the type 3 secretion system of Shigella
flexneri [more info...]
Chain information for 8axl.cif #20
---
Chain | Description | UniProt
A B C D E F G H I J K L M N O | Outer membrane protein MxiD | MXID_SHIFL 1-566
> show #!18 models
> select add #20
37650 atoms, 38160 bonds, 60 pseudobonds, 4800 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> view matrix models #20,1,0,0,-69.565,0,1,0,-86.42,0,0,1,224.19
> matchmaker #20 to #18
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 combination, chain X (#18) with 8axl.cif, chain A (#20), sequence
alignment score = 1560.4
RMSD between 320 pruned atom pairs is 0.001 angstroms; (across all 320 pairs:
0.001)
> hide #!18 models
> select subtract #20
Nothing selected
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Websites/Models/6zni.pdb
6zni.pdb title:
Structure of the shigella mxih needle filament attached to the basal body
[more info...]
Chain information for 6zni.pdb #21
---
Chain | Description | UniProt
A B C D E F G H I J K L M N O P Q R S T U V W | protein mxih | MXIH_SHIFL 1-83
> select add #21
14812 atoms, 15019 bonds, 1886 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.78066,-0.23011,0.58105,-32.728,-0.316,0.6568,0.68466,-11.662,-0.53918,-0.7181,0.44002,382.39
> view matrix models
> #21,0.59856,-0.67653,-0.429,316.77,0.59033,0.0105,0.8071,-92.083,-0.54152,-0.73634,0.40566,394.11
> view matrix models
> #21,-0.064308,0.99788,0.0099181,11.506,0.96056,0.064592,-0.27045,53.548,-0.27052,-0.0078654,-0.96268,483.39
> ui mousemode right "translate selected models"
> view matrix models
> #21,-0.064308,0.99788,0.0099181,60.254,0.96056,0.064592,-0.27045,137.33,-0.27052,-0.0078654,-0.96268,779.91
> hide #!20 models
> hide #!23 models
> show #!12 models
> hide sel atoms
> show sel cartoons
> fitmap #21 inMap #12
Fit molecule 6zni.pdb (#21) to map Needle.mrc gaussian (#12) using 14812 atoms
average map value = 0.06181, steps = 200
shifted from previous position = 38.6
rotated from previous position = 20.6 degrees
atoms outside contour = 2366, contour level = 0.012281
Position of 6zni.pdb (#21) relative to Needle.mrc gaussian (#12) coordinates:
Matrix rotation and translation
-0.29857094 0.95276880 -0.05556094 132.63758028
0.95438742 0.29805122 -0.01761031 0.41295711
-0.00021855 -0.05828459 -0.99829999 726.72353822
Axis -0.59204975 -0.80555695 0.02356055
Axis point 58.40204108 0.00000000 364.39242169
Rotation angle (degrees) 178.03148033
Shift along axis -61.73869688
> fitmap #21 inMap #12
Fit molecule 6zni.pdb (#21) to map Needle.mrc gaussian (#12) using 14812 atoms
average map value = 0.06181, steps = 28
shifted from previous position = 0.104
rotated from previous position = 1.1 degrees
atoms outside contour = 2373, contour level = 0.012281
Position of 6zni.pdb (#21) relative to Needle.mrc gaussian (#12) coordinates:
Matrix rotation and translation
-0.31681368 0.94681893 -0.05624065 137.76386323
0.94848731 0.31631597 -0.01777728 -2.09579099
0.00095795 -0.05897563 -0.99825896 726.51810645
Axis -0.58428457 -0.81120384 0.02366142
Axis point 61.72467869 0.00000000 364.33458089
Rotation angle (degrees) 177.97959679
Shift along axis -61.60273696
> color #12 #b2ffb251 models
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Websites/Models/6zni.pdb
6zni.pdb title:
Structure of the shigella mxih needle filament attached to the basal body
[more info...]
Chain information for 6zni.pdb #22
---
Chain | Description | UniProt
A B C D E F G H I J K L M N O P Q R S T U V W | protein mxih | MXIH_SHIFL 1-83
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Websites/Models/6zni.pdb
6zni.pdb title:
Structure of the shigella mxih needle filament attached to the basal body
[more info...]
Chain information for 6zni.pdb #24
---
Chain | Description | UniProt
A B C D E F G H I J K L M N O P Q R S T U V W | protein mxih | MXIH_SHIFL 1-83
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Websites/Models/6zni.pdb
6zni.pdb title:
Structure of the shigella mxih needle filament attached to the basal body
[more info...]
Chain information for 6zni.pdb #25
---
Chain | Description | UniProt
A B C D E F G H I J K L M N O P Q R S T U V W | protein mxih | MXIH_SHIFL 1-83
> matchmaker #22 to #21
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 6zni.pdb, chain A (#21) with 6zni.pdb, chain A (#22), sequence
alignment score = 488.1
RMSD between 82 pruned atom pairs is 0.000 angstroms; (across all 82 pairs:
0.000)
> matchmaker #24 to #21
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 6zni.pdb, chain A (#21) with 6zni.pdb, chain A (#24), sequence
alignment score = 488.1
RMSD between 82 pruned atom pairs is 0.000 angstroms; (across all 82 pairs:
0.000)
> matchmaker #25 to #21
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 6zni.pdb, chain A (#21) with 6zni.pdb, chain A (#25), sequence
alignment score = 488.1
RMSD between 82 pruned atom pairs is 0.000 angstroms; (across all 82 pairs:
0.000)
> view orient
> turn x 90
[Repeated 2 time(s)]
> select add #22
29624 atoms, 30038 bonds, 3772 residues, 2 models selected
> select add #24
44436 atoms, 45057 bonds, 5658 residues, 3 models selected
> select add #25
59248 atoms, 60076 bonds, 7544 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> select subtract #21
44436 atoms, 45057 bonds, 5658 residues, 3 models selected
> view matrix models
> #22,-0.31681,0.94682,-0.056241,139.82,0.94849,0.31632,-0.017777,-2.0958,0.00095795,-0.058976,-0.99826,822.41,#24,-0.31681,0.94682,-0.056241,139.82,0.94849,0.31632,-0.017777,-2.0958,0.00095795,-0.058976,-0.99826,822.41,#25,-0.31681,0.94682,-0.056241,139.82,0.94849,0.31632,-0.017777,-2.0958,0.00095795,-0.058976,-0.99826,822.41
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #22,-0.31681,0.94682,-0.056241,140.02,0.94849,0.31632,-0.017777,-2.0958,0.00095795,-0.058976,-0.99826,828.95,#24,-0.31681,0.94682,-0.056241,140.02,0.94849,0.31632,-0.017777,-2.0958,0.00095795,-0.058976,-0.99826,828.95,#25,-0.31681,0.94682,-0.056241,140.02,0.94849,0.31632,-0.017777,-2.0958,0.00095795,-0.058976,-0.99826,828.95
> view orient
> turn x 90
[Repeated 2 time(s)]
> select subtract #22
29624 atoms, 30038 bonds, 3772 residues, 2 models selected
> view matrix models
> #24,-0.31681,0.94682,-0.056241,138.54,0.94849,0.31632,-0.017777,-2.0958,0.00095795,-0.058976,-0.99826,940.33,#25,-0.31681,0.94682,-0.056241,138.54,0.94849,0.31632,-0.017777,-2.0958,0.00095795,-0.058976,-0.99826,940.33
> select subtract #24
14812 atoms, 15019 bonds, 1886 residues, 1 model selected
> view matrix models
> #25,-0.31681,0.94682,-0.056241,138.13,0.94849,0.31632,-0.017777,-2.0958,0.00095795,-0.058976,-0.99826,1032.7
> select clear
> combine #21,22,24,25
Remapping chain ID 'A' in 6zni.pdb #22 to 'X'
Remapping chain ID 'B' in 6zni.pdb #22 to 'Y'
Remapping chain ID 'C' in 6zni.pdb #22 to 'Z'
Remapping chain ID 'D' in 6zni.pdb #22 to 'a'
Remapping chain ID 'E' in 6zni.pdb #22 to 'b'
Remapping chain ID 'F' in 6zni.pdb #22 to 'c'
Remapping chain ID 'G' in 6zni.pdb #22 to 'd'
Remapping chain ID 'H' in 6zni.pdb #22 to 'e'
Remapping chain ID 'I' in 6zni.pdb #22 to 'f'
Remapping chain ID 'J' in 6zni.pdb #22 to 'g'
Remapping chain ID 'K' in 6zni.pdb #22 to 'h'
Remapping chain ID 'L' in 6zni.pdb #22 to 'i'
Remapping chain ID 'M' in 6zni.pdb #22 to 'j'
Remapping chain ID 'N' in 6zni.pdb #22 to 'k'
Remapping chain ID 'O' in 6zni.pdb #22 to 'l'
Remapping chain ID 'P' in 6zni.pdb #22 to 'm'
Remapping chain ID 'Q' in 6zni.pdb #22 to 'n'
Remapping chain ID 'R' in 6zni.pdb #22 to 'o'
Remapping chain ID 'S' in 6zni.pdb #22 to 'p'
Remapping chain ID 'T' in 6zni.pdb #22 to 'q'
Remapping chain ID 'U' in 6zni.pdb #22 to 'r'
Remapping chain ID 'V' in 6zni.pdb #22 to 's'
Remapping chain ID 'W' in 6zni.pdb #22 to 't'
Remapping chain ID 'A' in 6zni.pdb #24 to 'u'
Remapping chain ID 'B' in 6zni.pdb #24 to 'v'
Remapping chain ID 'C' in 6zni.pdb #24 to 'w'
Remapping chain ID 'D' in 6zni.pdb #24 to 'x'
Remapping chain ID 'E' in 6zni.pdb #24 to 'y'
Remapping chain ID 'F' in 6zni.pdb #24 to 'z'
Remapping chain ID 'G' in 6zni.pdb #24 to '1'
Remapping chain ID 'H' in 6zni.pdb #24 to '2'
Remapping chain ID 'I' in 6zni.pdb #24 to '3'
Remapping chain ID 'J' in 6zni.pdb #24 to '4'
Remapping chain ID 'K' in 6zni.pdb #24 to '5'
Remapping chain ID 'L' in 6zni.pdb #24 to '6'
Remapping chain ID 'M' in 6zni.pdb #24 to '7'
Remapping chain ID 'N' in 6zni.pdb #24 to '8'
Remapping chain ID 'O' in 6zni.pdb #24 to '9'
Remapping chain ID 'P' in 6zni.pdb #24 to '0'
Remapping chain ID 'Q' in 6zni.pdb #24 to 'AA'
Remapping chain ID 'R' in 6zni.pdb #24 to 'AB'
Remapping chain ID 'S' in 6zni.pdb #24 to 'AC'
Remapping chain ID 'T' in 6zni.pdb #24 to 'AD'
Remapping chain ID 'U' in 6zni.pdb #24 to 'AE'
Remapping chain ID 'V' in 6zni.pdb #24 to 'AF'
Remapping chain ID 'W' in 6zni.pdb #24 to 'AG'
Remapping chain ID 'A' in 6zni.pdb #25 to 'AH'
Remapping chain ID 'B' in 6zni.pdb #25 to 'AI'
Remapping chain ID 'C' in 6zni.pdb #25 to 'AJ'
Remapping chain ID 'D' in 6zni.pdb #25 to 'AK'
Remapping chain ID 'E' in 6zni.pdb #25 to 'AL'
Remapping chain ID 'F' in 6zni.pdb #25 to 'AM'
Remapping chain ID 'G' in 6zni.pdb #25 to 'AN'
Remapping chain ID 'H' in 6zni.pdb #25 to 'AO'
Remapping chain ID 'I' in 6zni.pdb #25 to 'AP'
Remapping chain ID 'J' in 6zni.pdb #25 to 'AQ'
Remapping chain ID 'K' in 6zni.pdb #25 to 'AR'
Remapping chain ID 'L' in 6zni.pdb #25 to 'AS'
Remapping chain ID 'M' in 6zni.pdb #25 to 'AT'
Remapping chain ID 'N' in 6zni.pdb #25 to 'AU'
Remapping chain ID 'O' in 6zni.pdb #25 to 'AV'
Remapping chain ID 'P' in 6zni.pdb #25 to 'AW'
Remapping chain ID 'Q' in 6zni.pdb #25 to 'AX'
Remapping chain ID 'R' in 6zni.pdb #25 to 'AY'
Remapping chain ID 'S' in 6zni.pdb #25 to 'AZ'
Remapping chain ID 'T' in 6zni.pdb #25 to 'Aa'
Remapping chain ID 'U' in 6zni.pdb #25 to 'Ab'
Remapping chain ID 'V' in 6zni.pdb #25 to 'Ac'
Remapping chain ID 'W' in 6zni.pdb #25 to 'Ad'
> hide #21 models
> hide #22 models
> hide #24 models
> hide #25 models
> show #!23 models
> show #!18 models
> hide #!18 models
> show #!20 models
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Websites/Models/4a5p.pdb
4a5p.pdb title:
Structure of the shigella flexneri mxia protein [more info...]
Chain information for 4a5p.pdb #27
---
Chain | Description | UniProt
A B C | protein VIRH | MXIA_SHIFL 318-686
Non-standard residues in 4a5p.pdb #27
---
EDO — 1,2-ethanediol (ethylene glycol)
7 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Websites/Models/4a5p.pdb1
4a5p.pdb1 title:
Structure of the shigella flexneri mxia protein [more info...]
7 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
7 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for 4a5p.pdb1
---
Chain | Description
28.1/A 28.1/B 28.1/C | No description available
28.2/A 28.3/A | No description available
28.2/B 28.3/B | No description available
28.2/C 28.3/C | No description available
7 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close #27
> select add #28
22242 atoms, 22458 bonds, 33 pseudobonds, 2745 residues, 7 models selected
> hide #!20 models
> hide #!23 models
> hide #!12 models
> hide #26 models
> show #!10 models
> view matrix models #28,1,0,0,274.61,0,1,0,310.47,0,0,1,23.308
> view matrix models #28,1,0,0,298.19,0,1,0,239.33,0,0,1,182.08
> ui mousemode right "rotate selected models"
> view matrix models
> #28,0.7761,0.63004,0.026991,292.44,0.62918,-0.77651,0.034219,247.77,0.042518,-0.0095748,-0.99905,293.21
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.7761,0.63004,0.026991,261.93,0.62918,-0.77651,0.034219,258.81,0.042518,-0.0095748,-0.99905,382.2
> view matrix models
> #28,0.7761,0.63004,0.026991,257.17,0.62918,-0.77651,0.034219,256.4,0.042518,-0.0095748,-0.99905,381.79
> combine #28
Remapping chain ID 'A' in 4a5p.pdb1 #28.2 to 'D'
Remapping chain ID 'B' in 4a5p.pdb1 #28.2 to 'E'
Remapping chain ID 'C' in 4a5p.pdb1 #28.2 to 'F'
Remapping chain ID 'A' in 4a5p.pdb1 #28.3 to 'G'
Remapping chain ID 'B' in 4a5p.pdb1 #28.3 to 'H'
Remapping chain ID 'C' in 4a5p.pdb1 #28.3 to 'I'
> close #28
> fitmap #27 inMap #10
Fit molecule combination (#27) to map MxiA.mrc gaussian (#10) using 22242
atoms
average map value = 0.05827, steps = 56
shifted from previous position = 9.4
rotated from previous position = 3.42 degrees
atoms outside contour = 2863, contour level = 0.019047
Position of combination (#27) relative to MxiA.mrc gaussian (#10) coordinates:
Matrix rotation and translation
0.80161758 0.59783594 0.00119784 256.79406485
0.59783710 -0.80161669 -0.00121864 256.80090367
0.00023166 0.00169299 -0.99999854 390.87730243
Axis 0.94910936 0.31494648 0.00037653
Axis point 0.00000000 85.63611045 195.45014568
Rotation angle (degrees) 179.91211531
Shift along axis 324.75136672
> fitmap #27 inMap #10
Fit molecule combination (#27) to map MxiA.mrc gaussian (#10) using 22242
atoms
average map value = 0.05827, steps = 44
shifted from previous position = 0.00845
rotated from previous position = 0.00998 degrees
atoms outside contour = 2864, contour level = 0.019047
Position of combination (#27) relative to MxiA.mrc gaussian (#10) coordinates:
Matrix rotation and translation
0.80161460 0.59783962 0.00134779 256.78414266
0.59784100 -0.80161391 -0.00113018 256.79761361
0.00040474 0.00171173 -0.99999845 390.86914264
Axis 0.94910857 0.31494874 0.00046162
Axis point 0.00000000 85.63956603 195.43305746
Rotation angle (degrees) 179.91421985
Shift along axis 324.77454690
> fitmap #27 inMap #10
Fit molecule combination (#27) to map MxiA.mrc gaussian (#10) using 22242
atoms
average map value = 0.05827, steps = 44
shifted from previous position = 0.0089
rotated from previous position = 0.0587 degrees
atoms outside contour = 2868, contour level = 0.019047
Position of combination (#27) relative to MxiA.mrc gaussian (#10) coordinates:
Matrix rotation and translation
0.80160920 0.59784750 0.00102281 256.80554474
0.59784794 -0.80160952 -0.00015900 256.73242545
0.00072484 0.00073894 -0.99999946 390.86381964
Axis 0.94910698 0.31495352 0.00046032
Axis point 0.00000000 85.70810059 195.38887860
Rotation angle (degrees) 179.97289645
Shift along axis 324.77463920
> show #!16 models
> color #16 #ffa97874 models
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Websites/Models/AlphaFold-
> Spa33model-C6_2024-08_27.pdb
Chain information for AlphaFold-Spa33model-C6_2024-08_27.pdb
---
Chain | Description
28.1/A 28.2/A 28.3/A 28.4/A 28.5/A 28.6/A 28.1/B 28.2/B 28.3/B 28.4/B 28.5/B 28.6/B | No description available
28.1/C 28.2/C 28.3/C 28.4/C 28.5/C 28.6/C | No description available
> select add #28
23868 atoms, 24252 bonds, 2982 residues, 7 models selected
> view orient
> turn x 90
[Repeated 1 time(s)]
> ui tool show "Side View"
> ui mousemode right "rotate selected models"
> view matrix models
> #28,0.99355,0.11343,2.5187e-17,-27.575,-0.11343,0.99355,-1.4331e-18,30.902,-2.5187e-17,-1.4331e-18,1,3.1371e-16
> turn x 90
[Repeated 2 time(s)]
> select subtract #28.1
19890 atoms, 20210 bonds, 2485 residues, 6 models selected
> select add #28
23868 atoms, 24252 bonds, 2982 residues, 7 models selected
> select subtract #28.2
19890 atoms, 20210 bonds, 2485 residues, 6 models selected
> select subtract #28.3
15912 atoms, 16168 bonds, 1988 residues, 5 models selected
> select subtract #28.4
11934 atoms, 12126 bonds, 1491 residues, 4 models selected
> select subtract #28.5
7956 atoms, 8084 bonds, 994 residues, 3 models selected
> select subtract #28.6
3978 atoms, 4042 bonds, 497 residues, 2 models selected
Alignment identifier is 1
Alignment identifier is 28.1/C
> select #28.1/C:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #28.1/C:1-2
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #28.1/A-B:28-29
38 atoms, 38 bonds, 4 residues, 1 model selected
> select #28.1/A-B:1-29
444 atoms, 446 bonds, 58 residues, 1 model selected
> hide sel cartoons
> select #28.1/C:292-293
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #28.1/C
2350 atoms, 2390 bonds, 293 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #28.1
3978 atoms, 4042 bonds, 497 residues, 1 model selected
> select #28.1/A-B:1-2
30 atoms, 28 bonds, 4 residues, 1 model selected
> select #28.1/A-B:1
14 atoms, 12 bonds, 2 residues, 1 model selected
> hide #!16 models
Drag select of 439 residues
> save /Users/shoichi/Desktop/Spa33model-mono.pdb selectedOnly true
> select add #28
23868 atoms, 24252 bonds, 2982 residues, 7 models selected
> close #28
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Websites/Models/Spa33model-mono.pdb
Summary of feedback from opening /Users/shoichi/Library/CloudStorage/OneDrive-
YaleUniversity/Jun_Lab_documents/Websites/Models/Spa33model-mono.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 11 THR A 23 1 13
Start residue of secondary structure not found: HELIX 2 2 GLN A 24 ASN A 40 1
17
Start residue of secondary structure not found: HELIX 3 3 ASN A 43 ASN A 81 1
39
Start residue of secondary structure not found: HELIX 4 4 THR B 11 THR B 23 1
13
Start residue of secondary structure not found: HELIX 5 5 GLN B 24 ASN B 40 1
17
64 messages similar to the above omitted
Chain information for Spa33model-mono.pdb #28
---
Chain | Description
A B | No description available
C | No description available
> show #!16 models
> select add #28
3534 atoms, 3594 bonds, 439 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #28,1,0,0,3.3589,0,1,0,0.82161,0,0,1,29.811
> ui mousemode right "rotate selected models"
> view matrix models
> #28,0.99428,0.10602,-0.013231,-7.1066,-0.1061,0.99434,-0.0053161,31.3,0.012592,0.0066894,0.9999,25.508
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.99428,0.10602,-0.013231,-9.1113,-0.1061,0.99434,-0.0053161,32.259,0.012592,0.0066894,0.9999,25.674
> ui mousemode right "rotate selected models"
> view matrix models
> #28,0.99682,0.078395,-0.014205,-5.7599,-0.078466,0.99691,-0.0045742,24.301,0.013802,0.0056743,0.99989,25.491
> view matrix models
> #28,0.98842,0.073651,0.13264,-32.999,-0.06973,0.99699,-0.033978,27.974,-0.13474,0.024336,0.99058,64.85
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.98842,0.073651,0.13264,-31.781,-0.06973,0.99699,-0.033978,27.558,-0.13474,0.024336,0.99058,68.423
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Websites/Models/MxiNmodelC6.pdb
Chain information for MxiNmodelC6.pdb
---
Chain | Description
29.1/A 29.3/A 29.5/A 29.7/A 29.9/A 29.11/A 29.2/B 29.4/B 29.6/B 29.8/B 29.10/B 29.12/B | No description available
> view orient
> turn x 90
[Repeated 1 time(s)]
> select add #29
26118 atoms, 26478 bonds, 3211 residues, 14 models selected
> select subtract #28
22584 atoms, 22884 bonds, 2772 residues, 13 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.99286,0.11925,2.648e-17,-28.899,-0.11925,0.99286,-1.5846e-18,32.578,-2.648e-17,-1.5846e-18,1,3.6932e-16
> view orient
> turn x 90
[Repeated 2 time(s)]
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.99286,0.11925,2.648e-17,-29.955,-0.11925,0.99286,-1.5846e-18,32.578,-2.648e-17,-1.5846e-18,1,23.679
> view matrix models
> #29,0.99286,0.11925,2.648e-17,-30.072,-0.11925,0.99286,-1.5846e-18,32.347,-2.648e-17,-1.5846e-18,1,25.236
> view orient
> sym #28 C6 copies true center #12
Made 6 copies for Spa33model-mono.pdb symmetry C6
> view orient
> turn x 90
[Repeated 2 time(s)]
> view matrix models
> #29,0.99286,0.11925,2.648e-17,-30.05,-0.11925,0.99286,-1.5846e-18,32.347,-2.648e-17,-1.5846e-18,1,29.438
> turn y 10
[Repeated 3 time(s)]
> select subtract #29
Nothing selected
> select add #30
21204 atoms, 21564 bonds, 2634 residues, 7 models selected
> view matrix models #30,1,0,0,0.1321,0,1,0,-0.11085,0,0,1,2.1183
> select #16
2 models selected
> select clear
> color #16 #424242ff models
> color #16 #4242424d models
> color #16 #42424233 models
> color #10 #42424233 models
> show #!11 models
> show #!12 models
> show #26 models
> color #12 #b2ffb252 models
> hide #!27 models
> show #!27 models
> close #28
> show #!18 models
> hide #!18 models
> show #!23 models
> show #!20 models
> show #21 models
> hide #21 models
> show #22 models
> hide #22 models
> show #24 models
> hide #24 models
> close #22
> close #24-25
> show #!14 models
> show #!9 models
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Websites/Models/fold_2025_06_16_13_31mxik/fold_2025_06_16_13_31mxik_model_0.cif
Chain information for fold_2025_06_16_13_31mxik_model_0.cif #22
---
Chain | Description
A | .
> hide #!9 models
> select add #22
1414 atoms, 1445 bonds, 175 residues, 1 model selected
> view matrix models #22,1,0,0,91.432,0,1,0,335.13,0,0,1,388.61
> view matrix models #22,1,0,0,128.29,0,1,0,329.95,0,0,1,306.4
> ui mousemode right "rotate selected models"
> view matrix models
> #22,-0.11878,-0.65273,-0.74822,124.94,0.81954,-0.48989,0.29727,330.92,-0.56058,-0.57788,0.59313,304.54
> view matrix models
> #22,0.16567,-0.62276,0.76467,131.39,-0.67292,0.49544,0.54929,332.16,-0.72093,-0.60556,-0.33699,300.57
> view matrix models
> #22,0.21314,-0.86239,0.45919,130.04,-0.63741,0.23345,0.73431,332.9,-0.74046,-0.4492,-0.49994,299.91
> view matrix models
> #22,-0.71739,-0.38059,-0.58352,125.69,0.67925,-0.56824,-0.46446,327.66,-0.15481,-0.72956,0.66617,304.82
> view matrix models
> #22,-0.90279,-0.32322,-0.28371,126.97,0.42619,-0.58384,-0.69101,326.68,0.057709,-0.74476,0.66484,304.82
> ui mousemode right "translate selected models"
> view matrix models
> #22,-0.90279,-0.32322,-0.28371,134.79,0.42619,-0.58384,-0.69101,287.94,0.057709,-0.74476,0.66484,313.78
> show #!9 models
> ui mousemode right "rotate selected models"
> view matrix models
> #22,-0.95361,0.27808,-0.11531,135.64,0.29232,0.76378,-0.57549,288.72,-0.071963,-0.5825,-0.80964,307.54
> view matrix models
> #22,-0.93015,0.29609,0.21713,137.06,0.32764,0.93625,0.12683,291.74,-0.16573,0.18911,-0.96787,307.04
> show #!17 models
> hide #!17 models
> hide #!16 models
> view matrix models
> #22,-0.90664,0.35768,0.22374,137.1,0.37455,0.92648,0.036651,291.36,-0.19418,0.11703,-0.97396,306.99
> show #!16 models
> view orient
> turn x 90
[Repeated 1 time(s)]
> sym #22 C6 copies true center #12
Made 6 copies for fold_2025_06_16_13_31mxik_model_0.cif symmetry C6
> color #9 #bddbb4ff models
> color #9 #bddbb49a models
> color #9 #bddbb480 models
> color #9 #bddbb474 models
> color #9 #bddbb466 models
> color #14 #9ad5ad86 models
> color #14 #9ad5ad44 models
> color #14 #9ad5ad37 models
> color #14 #9ad5ad38 models
> show #!13 models
> select subtract #22
Nothing selected
> close #22
> hide #!30 models
> hide #!29 models
> hide #!27 models
> hide #26 models
> hide #!24 models
> hide #!23 models
> show #!27 models
> hide #!27 models
> show #26 models
> select add #26
59248 atoms, 60076 bonds, 7544 residues, 1 model selected
> color #26 #929292ff
> color #26 #919191ff
> hide sel cartoons
> show sel surfaces
> lighting simple
> select subtract #26
92 models selected
> select add #20
37650 atoms, 38160 bonds, 60 pseudobonds, 4800 residues, 2 models selected
> color #20 #8e9157ff
> color #20 #8f9155ff
> color #20 #e0e385ff
> color #20 #e2e586ff
> color #20 #e1e586ff
> color #20 #cebce5ff
> color #20 #e5e0d2ff
> color #20 #e5c2a6ff
> color #20 #e5b497ff
> color #20 #e5bf89ff
> color #20 #e5d286ff
> hide sel cartoons
> show sel surfaces
> select subtract #20
15 models selected
> show #!23 models
> color #23 #3d7fbfff models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!13 models
> select add #23
124488 atoms, 126648 bonds, 15424 residues, 3 models selected
> hide sel cartoons
> show sel surfaces
[Repeated 1 time(s)]
> select clear
> hide #!20 models
> show #!20 models
> color #23 #6db8c6ff models
> color #23 #6cc6acff models
> color #23 #60c6bfff models
> color #23 #6cc6bcff models
> color #23 #67c6bdff models
> color #20 #4f9fdfff
> color #20 #25acdfff
> lighting soft
> hide #!23.2 models
> show #!23.2 models
> color #23.2 #25acdfff
> select clear
> show #!30 models
> hide #!30 models
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Websites/Models/fold_2025_06_16_13_42spa47c6/fold_2025_06_16_13_42spa47c6_model_0.cif
Chain information for fold_2025_06_16_13_42spa47c6_model_0.cif #22
---
Chain | Description
A B C D E F | .
> select add #22
20088 atoms, 20418 bonds, 2580 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> ui mousemode right "translate selected models"
> view matrix models #22,1,0,0,97.105,0,1,0,390.87,0,0,1,222.34
> view matrix models #22,1,0,0,119.46,0,1,0,491.99,0,0,1,208.01
> ui mousemode right "rotate selected models"
> view matrix models
> #22,-0.03505,0.70595,-0.7074,122.86,-0.0025248,-0.70789,-0.70632,489.51,-0.99938,-0.02297,0.026594,210.27
> view matrix models
> #22,0.97443,-0.015899,-0.22415,120.34,-0.17774,-0.66484,-0.72553,489.4,-0.13749,0.74682,-0.65066,217.41
> view matrix models
> #22,1,-0.00039656,-0.0014594,119.46,-0.0013606,-0.65725,-0.75367,489.89,-0.00066034,0.75367,-0.65725,217.73
> ui mousemode right "translate selected models"
> view matrix models
> #22,1,-0.00039656,-0.0014594,260,-0.0013606,-0.65725,-0.75367,235.71,-0.00066034,0.75367,-0.65725,215.95
> view matrix models
> #22,1,-0.00039656,-0.0014594,257.06,-0.0013606,-0.65725,-0.75367,246.56,-0.00066034,0.75367,-0.65725,217.12
> view matrix models
> #22,1,-0.00039656,-0.0014594,262.5,-0.0013606,-0.65725,-0.75367,258.86,-0.00066034,0.75367,-0.65725,196.6
> fitmap #22 inMap #16
Fit molecule fold_2025_06_16_13_42spa47c6_model_0.cif (#22) to map
Sortingplatforom.mrc gaussian (#16) using 20088 atoms
average map value = 0.07671, steps = 64
shifted from previous position = 12.3
rotated from previous position = 19.2 degrees
atoms outside contour = 2571, contour level = 0.030714
Position of fold_2025_06_16_13_42spa47c6_model_0.cif (#22) relative to
Sortingplatforom.mrc gaussian (#16) coordinates:
Matrix rotation and translation
0.95240268 0.04462846 0.30155834 257.45389313
0.23440527 -0.73964801 -0.63085257 256.91227185
0.19489305 0.67151254 -0.71490390 185.77478880
Axis 0.98631548 0.08078044 0.14372298
Axis point 0.00000000 90.68459302 118.58085556
Rotation angle (degrees) 138.68355108
Shift along axis 301.38435330
> fitmap #22 inMap #16
Fit molecule fold_2025_06_16_13_42spa47c6_model_0.cif (#22) to map
Sortingplatforom.mrc gaussian (#16) using 20088 atoms
average map value = 0.07671, steps = 28
shifted from previous position = 0.0746
rotated from previous position = 0.0488 degrees
atoms outside contour = 2559, contour level = 0.030714
Position of fold_2025_06_16_13_42spa47c6_model_0.cif (#22) relative to
Sortingplatforom.mrc gaussian (#16) coordinates:
Matrix rotation and translation
0.95256240 0.04505665 0.30098964 257.48938038
0.23441501 -0.73935592 -0.63119126 256.97795217
0.19409911 0.67180555 -0.71484461 185.77454038
Axis 0.98635971 0.08091540 0.14334299
Axis point 0.00000000 90.66267550 118.65718632
Rotation angle (degrees) 138.66137819
Shift along axis 301.40010415
> select subtract #22
Nothing selected
> show #!24 models
> show #!27 models
> show #!29 models
> show #!30 models
> color #27 #a48fb5ff
> color #27 #aa83b5ff
> color #27 #b57f83ff
> color #27 #ba8387ff
> color #27 #c68b90ff
> hide #!26 models
> show #!26 models
> hide #!24 models
> show #!24 models
> color #24 #665abfff models
> color #24 #2667bfff models
> select add #24
8484 atoms, 8670 bonds, 1050 residues, 7 models selected
> hide sel cartoons
> show sel surfaces
> select add #27
30726 atoms, 31128 bonds, 33 pseudobonds, 3795 residues, 15 models selected
> hide sel cartoons
> show sel surfaces
> select subtract #24
22242 atoms, 22458 bonds, 33 pseudobonds, 2745 residues, 17 models selected
> select subtract #27
9 models selected
> select add #26
59248 atoms, 60076 bonds, 7544 residues, 1 model selected
> select subtract #26
92 models selected
> select add #30
21204 atoms, 21564 bonds, 2634 residues, 7 models selected
> hide sel cartoons
> show sel surfaces
> color #30 #bfbdb3ff models
> color #30 #bfa48aff models
> color #30 #7fbf76ff models
> color #30 #26bfadff models
> color #30 #24bfa8ff models
> color #30 #87b8bfff models
> color #30 #92b9bfff models
> color #30 #8bbbbfff models
> select subtract #30
18 models selected
> select add #29
22584 atoms, 22884 bonds, 2772 residues, 13 models selected
> hide sel cartoons
> show sel surfaces
> color #29 #bc99bfff models
> color #29 #b2a6bfff models
> color #29 #b3bfbaff models
> color #29 #b5bfbdff models
> color #29 #bcbfbfff models
> color #29 #c5c8c9ff models
> select subtract #29
12 models selected
> color #22 #ae82f2ff
> select add #22
20088 atoms, 20418 bonds, 2580 residues, 1 model selected
> hide sel cartoons
> show sel surfaces
> select subtract #22
6 models selected
> select add #22
20088 atoms, 20418 bonds, 2580 residues, 1 model selected
> color #22 #68566dff
> color #22 #564f6dff
> color #22 #9185b7ff
> color #22 #9489bcff
> select clear
> color #22 #bcb59eff
> color #22 #bcb69fff
> color #22 #9c7abcff
> color #22 #b487bcff
> color #22 #b587bcff
> select clear
> hide #!9 models
> show #!9 models
> color #9 #e0cdcd66 models
> color #9 #e0c4cf66 models
> color #9 #e0c3cf66 models
> color #9 #e0bc9e66 models
> color #9 #e0caac66 models
> color #9 #e0c6ac66 models
> color #14 #daae8638 models
> color #14 #daac8738 models
> save /Users/shoichi/Desktop/Shigella-ipaDnull-bin2-06142025.cxs includeMaps
> true
> show #!10 models
> show #!13 models
> show #!12 models
> show #!11 models
> color #10 #4242424d models
> color #10 #42424214 models
> color #10 #42424233 models
> color #10-#13 #42424233 models
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #10-13 #42424233 models
> save /Users/shoichi/Desktop/Shigella-ipaDnull-bin2-06142025.cxs includeMaps
> true
——— End of log from Mon Jun 16 14:12:56 2025 ———
opened ChimeraX session
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/MxiA-project/Data_Images/06202025/Segment-
> Spa47C24_06202025/Rev-Spa47C24.mrc
Opened Rev-Spa47C24.mrc as #25, grid size 120,120,70, pixel 4.3,4.3,4.3, shown
at level 0.238, step 1, values float32
> select add #25
2 models selected
> hide #!22 models
> hide #!23 models
> hide #!24 models
> hide #!27 models
> hide #!29 models
> hide #!30 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #21 models
> hide #21 models
> hide #!20 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!14 models
> hide #!9 models
> hide #!12 models
> hide #!13 models
> ui mousemode right "translate selected models"
> view matrix models #25,1,0,0,-4.6731,0,1,0,4.2243,0,0,1,287.52
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #25 inMap #11
Fit map Rev-Spa47C24.mrc in map MxiGp.mrc gaussian using 10080 points
correlation = 0.2019, correlation about mean = 0.2782, overlap = 40.17
steps = 104, shift = 15.6, angle = 3.9 degrees
Position of Rev-Spa47C24.mrc (#25) relative to MxiGp.mrc gaussian (#11)
coordinates:
Matrix rotation and translation
0.99768124 -0.06805937 -0.00026768 17.28983287
0.06805929 0.99768124 -0.00028383 -17.48536765
0.00028638 0.00026495 0.99999992 301.72510016
Axis 0.00403152 -0.00407037 0.99998359
Axis point 246.62020234 227.75734102 0.00000000
Rotation angle (degrees) 3.90259322
Shift along axis 301.86102490
> fitmap #25 inMap #11
Fit map Rev-Spa47C24.mrc in map MxiGp.mrc gaussian using 10080 points
correlation = 0.2024, correlation about mean = 0.2764, overlap = 40.27
steps = 48, shift = 0.0996, angle = 0.027 degrees
Position of Rev-Spa47C24.mrc (#25) relative to MxiGp.mrc gaussian (#11)
coordinates:
Matrix rotation and translation
0.99769230 -0.06789737 0.00017026 17.18938433
0.06789741 0.99769228 -0.00021958 -17.44859855
-0.00015496 0.00023064 0.99999996 301.74930757
Axis 0.00331540 0.00239493 0.99999164
Axis point 275.41448060 229.07143673 0.00000000
Rotation angle (degrees) 3.89326164
Shift along axis 301.76198530
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/MxiA-project/Data_Images/06202025/Segment-
> Spa47C24_06202025/MxiGp.mrc
Opened MxiGp.mrc as #28, grid size 120,120,70, pixel 4.3,4.3,4.3, shown at
level 0.145, step 1, values float32
> select add #28
4 models selected
> select subtract #25
2 models selected
> view matrix models #28,1,0,0,-31.641,0,1,0,35.188,0,0,1,360.65
> view matrix models #28,1,0,0,-3.7843,0,1,0,1.6165,0,0,1,357.03
> fitmap #28 inMap #25
Fit map MxiGp.mrc in map Rev-Spa47C24.mrc using 10077 points
correlation = 0.3919, correlation about mean = -0.08546, overlap = 147.3
steps = 60, shift = 15.2, angle = 7.99 degrees
Position of MxiGp.mrc (#28) relative to Rev-Spa47C24.mrc (#25) coordinates:
Matrix rotation and translation
0.99744614 -0.07142013 -0.00059740 19.30484239
0.07142000 0.99744630 -0.00023263 -17.63417404
0.00061249 0.00018937 0.99999979 40.33165687
Axis 0.00295428 -0.00846985 0.99995977
Axis point 251.38422815 259.63389258 0.00000000
Rotation angle (degrees) 4.09572037
Shift along axis 40.53642499
> fitmap #28 inMap #11
Fit map MxiGp.mrc in map MxiGp.mrc gaussian using 10077 points
correlation = 0.961, correlation about mean = 0.5563, overlap = 346.8
steps = 88, shift = 24.8, angle = 5.3 degrees
Position of MxiGp.mrc (#28) relative to MxiGp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
0.99889978 -0.04689439 0.00038279 11.42802080
0.04689465 0.99889959 -0.00070142 -12.54874811
-0.00034948 0.00071860 0.99999968 367.04767981
Axis 0.01513843 0.00780652 0.99985493
Axis point 331.45563020 117.42326478 0.00000000
Rotation angle (degrees) 2.68823404
Shift along axis 367.06947341
> fitmap #28 inMap #11
Fit map MxiGp.mrc in map MxiGp.mrc gaussian using 10077 points
correlation = 0.961, correlation about mean = 0.5565, overlap = 346.8
steps = 64, shift = 0.00771, angle = 0.0204 degrees
Position of MxiGp.mrc (#28) relative to MxiGp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
0.99890206 -0.04684726 0.00004850 11.44812764
0.04684729 0.99890173 -0.00081266 -12.52510195
-0.00001038 0.00081404 0.99999967 366.94284178
Axis 0.01735917 0.00062837 0.99984912
Axis point 274.67317031 101.91367915 0.00000000
Rotation angle (degrees) 2.68553947
Shift along axis 367.07833730
> fitmap #28 inMap #11
Fit map MxiGp.mrc in map MxiGp.mrc gaussian using 10077 points
correlation = 0.961, correlation about mean = 0.5563, overlap = 346.8
steps = 60, shift = 0.00906, angle = 0.0405 degrees
Position of MxiGp.mrc (#28) relative to MxiGp.mrc gaussian (#11) coordinates:
Matrix rotation and translation
0.99891218 -0.04663001 0.00030481 11.36292385
0.04663007 0.99891221 -0.00019038 -12.53428729
-0.00029560 0.00020438 0.99999994 367.16537813
Axis 0.00423274 0.00643786 0.99997032
Axis point 324.21917652 202.79431181 0.00000000
Rotation angle (degrees) 2.67275316
Shift along axis 367.12188246
> fitmap #25 inMap #28
Fit map Rev-Spa47C24.mrc in map MxiGp.mrc using 10080 points
correlation = 0.2327, correlation about mean = 0.3131, overlap = 80.91
steps = 80, shift = 1.11, angle = 7.76 degrees
Position of Rev-Spa47C24.mrc (#25) relative to MxiGp.mrc (#28) coordinates:
Matrix rotation and translation
0.98774375 -0.15605271 0.00313506 42.63040832
0.15604726 0.98774773 0.00191419 -37.04143982
-0.00339536 -0.00140151 0.99999325 -63.06514846
Axis -0.01062093 0.02091837 0.99972477
Axis point 248.33122396 249.30124290 0.00000000
Rotation angle (degrees) 8.98018920
Shift along axis -64.27541228
> fitmap #25 inMap #28
Fit map Rev-Spa47C24.mrc in map MxiGp.mrc using 10080 points
correlation = 0.2327, correlation about mean = 0.3132, overlap = 80.88
steps = 44, shift = 0.0241, angle = 0.0148 degrees
Position of Rev-Spa47C24.mrc (#25) relative to MxiGp.mrc (#28) coordinates:
Matrix rotation and translation
0.98777062 -0.15587864 0.00332499 42.52923039
0.15587294 0.98777527 0.00191003 -37.01180036
-0.00358207 -0.00136839 0.99999265 -63.01424518
Axis -0.01051296 0.02214900 0.99969940
Axis point 247.84999171 249.05653442 0.00000000
Rotation angle (degrees) 8.97031126
Shift along axis -64.26218570
> fitmap #25 inMap #28
Fit map Rev-Spa47C24.mrc in map MxiGp.mrc using 10080 points
correlation = 0.2327, correlation about mean = 0.3133, overlap = 80.87
steps = 48, shift = 0.0138, angle = 0.00547 degrees
Position of Rev-Spa47C24.mrc (#25) relative to MxiGp.mrc (#28) coordinates:
Matrix rotation and translation
0.98778295 -0.15579942 0.00337388 42.50062019
0.15579372 0.98778780 0.00189267 -36.99721913
-0.00362755 -0.00134392 0.99999252 -62.99637684
Axis -0.01038406 0.02246289 0.99969375
Axis point 247.73674760 249.08203577 0.00000000
Rotation angle (degrees) 8.96576627
Shift along axis -64.24947729
> hide #!11 models
> color #28 #42424233 models
> show #!23 models
> hide #!25 models
> hide #!23 models
> select subtract #28
Nothing selected
> show #!23 models
> select add #23
124488 atoms, 126648 bonds, 15424 residues, 3 models selected
> hide sel surfaces
> show sel cartoons
> combine #23 MxiG_Jian
Expected a keyword
> combine #23
> select subtract #23
88 models selected
> hide #!23 models
> fitmap #31 inMap #28
Fit molecule combination (#31) to map MxiGp.mrc (#28) using 124488 atoms
average map value = 0.09267, steps = 68
shifted from previous position = 6.94
rotated from previous position = 1.74 degrees
atoms outside contour = 90696, contour level = 0.14517
Position of combination (#31) relative to MxiGp.mrc (#28) coordinates:
Matrix rotation and translation
0.99703404 0.07696189 -0.00001485 -17.56932868
-0.07696189 0.99703401 -0.00023570 21.43211382
-0.00000333 0.00023614 0.99999997 -374.12177169
Axis 0.00306541 -0.00007483 -0.99999530
Axis point 269.06903722 253.55455848 0.00000000
Rotation angle (degrees) 4.41397719
Shift along axis 374.06455202
> fitmap #31 inMap #28
Fit molecule combination (#31) to map MxiGp.mrc (#28) using 124488 atoms
average map value = 0.09268, steps = 40
shifted from previous position = 0.0955
rotated from previous position = 0.0122 degrees
atoms outside contour = 90750, contour level = 0.14517
Position of combination (#31) relative to MxiGp.mrc (#28) coordinates:
Matrix rotation and translation
0.99704976 0.07675789 0.00003767 -17.54393107
-0.07675788 0.99704973 -0.00026863 21.39308617
-0.00005818 0.00026495 0.99999996 -374.21058938
Axis 0.00347571 0.00062439 -0.99999376
Axis point 265.83608478 255.72205291 0.00000000
Rotation angle (degrees) 4.40226055
Shift along axis 374.16063601
> show #!13 models
> show #!16 models
> select add #31
124488 atoms, 126648 bonds, 15424 residues, 1 model selected
> show sel surfaces
> select subtract #31
88 models selected
> volume #28 level 0.03927
> volume #28 level 0.06221
> show #!14 models
> show #!9 models
> show #!22 models
> show #!23 models
> show #!24 models
> hide #!23 models
> show #!25 models
> hide #!25 models
> show #!26 models
> show #!27 models
> show #!29 models
> show #!30 models
> show #!20 models
> save /Users/shoichi/Desktop/Shigella-ipaDnull-bin2-06202025.cxs includeMaps
> true
——— End of log from Fri Jun 20 11:47:25 2025 ———
opened ChimeraX session
> hide #!31 models
> hide #!30 models
> hide #!29 models
> hide #!28 models
> hide #!27 models
> hide #!26 models
> hide #!24 models
> hide #!22 models
> show #!28 models
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/MxiA-project/Data_Images/06232025/Chimera-
> figure-2025/MxiGc24-segment_06232025/IMring.mrc
Opened IMring.mrc as #32, grid size 120,120,70, pixel 4.3,4.3,4.3, shown at
level 0.124, step 1, values float32
> select add #32
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #32,1,0,0,-1.8511,0,1,0,-6.501,0,0,1,360.99
> view orient
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #32 inMap #28
Fit map IMring.mrc in map MxiGp.mrc using 10080 points
correlation = 0.9706, correlation about mean = 0.7263, overlap = 490.4
steps = 52, shift = 8.78, angle = 2.83 degrees
Position of IMring.mrc (#32) relative to MxiGp.mrc (#28) coordinates:
Matrix rotation and translation
0.99999640 -0.00268401 -0.00004259 0.54801834
0.00268401 0.99999640 0.00005687 -0.85830238
0.00004244 -0.00005698 1.00000000 0.63881912
Axis -0.02120181 -0.01583502 0.99964981
Axis point 316.28453482 208.81446260 0.00000000
Rotation angle (degrees) 0.15383654
Shift along axis 0.64056766
> fitmap #32 inMap #28
Fit map IMring.mrc in map MxiGp.mrc using 10080 points
correlation = 0.9704, correlation about mean = 0.724, overlap = 490.8
steps = 28, shift = 0.0629, angle = 0.00238 degrees
Position of IMring.mrc (#32) relative to MxiGp.mrc (#28) coordinates:
Matrix rotation and translation
0.99999628 -0.00272547 -0.00004487 0.55445650
0.00272547 0.99999628 0.00005953 -0.87213119
0.00004471 -0.00005965 1.00000000 0.57627958
Axis -0.02185674 -0.01642789 0.99962613
Axis point 316.79019210 207.64080376 0.00000000
Rotation angle (degrees) 0.15621659
Shift along axis 0.57827279
> ui mousemode right "rotate selected models"
> view matrix models
> #32,0.99922,-0.03945,0.00025588,9.2918,0.03945,0.99922,-0.00013554,-10.94,-0.00025033,0.00014553,1,367.74
> fitmap #32 inMap #28
Fit map IMring.mrc in map MxiGp.mrc using 10080 points
correlation = 0.9705, correlation about mean = 0.7254, overlap = 491.1
steps = 44, shift = 0.0116, angle = 0.535 degrees
Position of IMring.mrc (#32) relative to MxiGp.mrc (#28) coordinates:
Matrix rotation and translation
0.99999767 -0.00215842 -0.00003994 0.41231729
0.00215842 0.99999767 0.00006305 -0.72372918
0.00003981 -0.00006314 1.00000000 0.58850747
Axis -0.02921407 -0.01846376 0.99940264
Axis point 330.47722820 198.64937036 0.00000000
Rotation angle (degrees) 0.12374226
Shift along axis 0.58947321
> fitmap #32 inMap #28
Fit map IMring.mrc in map MxiGp.mrc using 10080 points
correlation = 0.9705, correlation about mean = 0.7251, overlap = 491.1
steps = 28, shift = 0.00495, angle = 0.00528 degrees
Position of IMring.mrc (#32) relative to MxiGp.mrc (#28) coordinates:
Matrix rotation and translation
0.99999747 -0.00225054 -0.00004034 0.43599311
0.00225054 0.99999747 0.00005959 -0.74702901
0.00004021 -0.00005968 1.00000000 0.58256698
Axis -0.02648643 -0.01788754 0.99948912
Axis point 327.51602251 200.23361527 0.00000000
Rotation angle (degrees) 0.12901252
Shift along axis 0.58408397
> fitmap #32 inMap #28
Fit map IMring.mrc in map MxiGp.mrc using 10080 points
correlation = 0.9705, correlation about mean = 0.7251, overlap = 491.2
steps = 28, shift = 0.00374, angle = 0.00721 degrees
Position of IMring.mrc (#32) relative to MxiGp.mrc (#28) coordinates:
Matrix rotation and translation
0.99999774 -0.00212470 -0.00004020 0.40333930
0.00212470 0.99999774 0.00006423 -0.71525376
0.00004006 -0.00006432 1.00000000 0.58006643
Axis -0.03023282 -0.01887383 0.99936468
Axis point 331.68615986 197.74816940 0.00000000
Rotation angle (degrees) 0.12181396
Shift along axis 0.58100339
> hide #!28 models
> close #28
> color #32 #42424233 models
> select clear
> volume #32 level 0.03435
> show #!31 models
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/MxiA-project/Data_Images/06232025/Chimera-
> figure-2025/MxiGc24-segment_06232025/OM-complex.mrc
Opened OM-complex.mrc as #28, grid size 120,120,70, pixel 4.3,4.3,4.3, shown
at level 0.115, step 1, values float32
> select add #32
3 models selected
> hide #!31 models
> select subtract #32
Nothing selected
> select add #28
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #28,1,0,0,0.85224,0,1,0,22.54,0,0,1,366.23
> volume #28 level 0.02522
> fitmap #28 inMap #13
Fit map OM-complex.mrc in map OM_complex.mrc gaussian using 25812 points
correlation = 0.9502, correlation about mean = 0.8712, overlap = 422
steps = 80, shift = 23.7, angle = 0.0286 degrees
Position of OM-complex.mrc (#28) relative to OM_complex.mrc gaussian (#13)
coordinates:
Matrix rotation and translation
0.99999991 0.00001030 -0.00042764 -1.00891484
-0.00001019 0.99999997 0.00025633 -1.11759534
0.00042764 -0.00025633 0.99999988 366.65051617
Axis -0.51400804 -0.85753937 -0.02054159
Axis point -857085.69830933 0.00000000 -9453.29814582
Rotation angle (degrees) 0.02857257
Shift along axis -6.05461342
> fitmap #28 inMap #13
Fit map OM-complex.mrc in map OM_complex.mrc gaussian using 25812 points
correlation = 0.9502, correlation about mean = 0.8712, overlap = 422
steps = 24, shift = 0.000998, angle = 0.000692 degrees
Position of OM-complex.mrc (#28) relative to OM_complex.mrc gaussian (#13)
coordinates:
Matrix rotation and translation
0.99999991 0.00000125 -0.00043553 -1.00538701
-0.00000114 0.99999997 0.00025764 -1.12011375
0.00043554 -0.00025764 0.99999987 366.64961680
Axis -0.50913519 -0.86068331 -0.00236848
Axis point -841840.58360902 0.00000000 -1414.86161399
Rotation angle (degrees) 0.02899362
Shift along axis 0.60754009
> fitmap #28 inMap #13
Fit map OM-complex.mrc in map OM_complex.mrc gaussian using 25812 points
correlation = 0.9502, correlation about mean = 0.8712, overlap = 422
steps = 24, shift = 0.000617, angle = 0.000813 degrees
Position of OM-complex.mrc (#28) relative to OM_complex.mrc gaussian (#13)
coordinates:
Matrix rotation and translation
0.99999991 -0.00000783 -0.00042467 -1.00503696
0.00000794 0.99999997 0.00025674 -1.12225863
0.00042467 -0.00025674 0.99999988 366.65178330
Axis -0.51729333 -0.85566059 0.01589222
Axis point -863100.32359779 0.00000000 6717.43764727
Rotation angle (degrees) 0.02843650
Shift along axis 7.30708177
> select subtract #28
Nothing selected
> color #28 skyblue models
> color #28 #42424233 models
> select clear
> close #13
> show #!31 models
> save /Users/shoichi/Desktop/Shigella-ipaDnull-bin2-06232025.cxs includeMaps
> true
> show #!29 models
> show #!30 models
> show #!27 models
> show #!26 models
> hide #!26 models
> show #!26 models
> show #!25 models
> show #!24 models
> hide #!25 models
> view orient
> turn x 90
[Repeated 2 time(s)]
> hide #!31 models
> show #!31 models
> save /Users/shoichi/Desktop/Shigella-ipaDnull-bin2-06232025.cxs includeMaps
> true
——— End of log from Mon Jun 23 14:56:34 2025 ———
opened ChimeraX session
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/MxiA-project/Data_Images/06232025/Chimera/Pod-
> bin2.mrc
Opened Pod-bin2.mrc as #13, grid size 50,50,70, pixel 1, shown at level 0.181,
step 1, values float32
> close #13
> open /Users/shoichi/Desktop/Chimera/Pod-bin2.mrc
Opened Pod-bin2.mrc as #13, grid size 50,50,70, pixel 1, shown at level 0.181,
step 1, values float32
> close #13
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/MxiA-project/Data_Images/06232025/Chimera/Pod-
> bin2.mrc
Opened Pod-bin2.mrc as #13, grid size 50,50,70, pixel 4.3,4.3,4.3, shown at
level 0.181, step 1, values float32
> select add #13
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.62851,-0.25056,0.73634,133.49,-0.35934,0.93315,0.01081,47.376,-0.68982,-0.2578,-0.67652,291.48
> hide #!31 models
> hide #!30 models
> hide #!29 models
> hide #!28 models
> hide #!27 models
> hide #!26 models
> hide #!24 models
> view matrix models
> #13,-0.56339,0.70615,-0.42888,160.05,-0.80773,-0.5799,0.10626,238.96,-0.17367,0.40628,0.89709,-8.5629
> volume #13 level 0.05361
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.56339,0.70615,-0.42888,180.18,-0.80773,-0.5799,0.10626,320.53,-0.17367,0.40628,0.89709,-23.592
> view matrix models
> #13,-0.56339,0.70615,-0.42888,198.51,-0.80773,-0.5799,0.10626,353.08,-0.17367,0.40628,0.89709,104.86
> view matrix models
> #13,-0.56339,0.70615,-0.42888,200.93,-0.80773,-0.5799,0.10626,348.39,-0.17367,0.40628,0.89709,110.48
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.56577,0.75796,-0.32467,184.87,-0.78983,-0.61123,-0.050592,366.07,-0.23679,0.22781,0.94447,131.35
> view matrix models
> #13,-0.56994,0.77677,-0.26797,177.44,-0.77686,-0.61563,-0.13225,373.61,-0.26769,0.1328,0.95431,143.76
> view matrix models
> #13,-0.59158,0.7929,-0.14611,165.41,-0.79569,-0.6034,-0.052845,366.09,-0.13006,0.084995,0.98786,130.76
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.59158,0.7929,-0.14611,181.42,-0.79569,-0.6034,-0.052845,360.3,-0.13006,0.084995,0.98786,131.39
> view matrix models
> #13,-0.59158,0.7929,-0.14611,183.9,-0.79569,-0.6034,-0.052845,353.78,-0.13006,0.084995,0.98786,132.36
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #13 inMap #16
Fit map Pod-bin2.mrc in map Sortingplatforom.mrc gaussian using 3880 points
correlation = 0.9089, correlation about mean = 0.6155, overlap = 73.9
steps = 64, shift = 8.12, angle = 10.4 degrees
Position of Pod-bin2.mrc (#13) relative to Sortingplatforom.mrc gaussian (#16)
coordinates:
Matrix rotation and translation
-0.49998850 0.86591937 -0.01396970 146.49877400
-0.86568359 -0.50017984 -0.02029886 345.53810317
-0.02456454 0.00194414 0.99969635 131.60389066
Axis 0.01284403 0.00611790 -0.99989880
Axis point 174.04689439 130.41714716 0.00000000
Rotation angle (degrees) 120.01561447
Shift along axis -127.59497143
> fitmap #13 inMap #16
Fit map Pod-bin2.mrc in map Sortingplatforom.mrc gaussian using 3880 points
correlation = 0.9088, correlation about mean = 0.6148, overlap = 73.9
steps = 28, shift = 0.0927, angle = 0.054 degrees
Position of Pod-bin2.mrc (#13) relative to Sortingplatforom.mrc gaussian (#16)
coordinates:
Matrix rotation and translation
-0.49966043 0.86610757 -0.01404011 146.53723891
-0.86585038 -0.49985515 -0.02116456 345.59394112
-0.02534881 0.00158154 0.99967741 131.74934474
Axis 0.01313176 0.00652873 -0.99989246
Axis point 174.16008568 130.43268391 0.00000000
Rotation angle (degrees) 119.99464694
Shift along axis -127.55459674
> fitmap #13 inMap #16
Fit map Pod-bin2.mrc in map Sortingplatforom.mrc gaussian using 3880 points
correlation = 0.9088, correlation about mean = 0.6151, overlap = 73.9
steps = 40, shift = 0.0297, angle = 0.0238 degrees
Position of Pod-bin2.mrc (#13) relative to Sortingplatforom.mrc gaussian (#16)
coordinates:
Matrix rotation and translation
-0.49987809 0.86598362 -0.01393777 146.53795431
-0.86573423 -0.50006965 -0.02084657 345.56114042
-0.02502265 0.00164565 0.99968553 131.69801715
Axis 0.01298703 0.00640042 -0.99989518
Axis point 174.10786181 130.42494455 0.00000000
Rotation angle (degrees) 120.00867435
Shift along axis -127.56938498
> view matrix models
> #13,-0.49988,0.86598,-0.013938,147.32,-0.86573,-0.50007,-0.020847,345.12,-0.025023,0.0016457,0.99969,131.68
> fitmap #13 inMap #16
Fit map Pod-bin2.mrc in map Sortingplatforom.mrc gaussian using 3880 points
correlation = 0.9089, correlation about mean = 0.6152, overlap = 73.9
steps = 36, shift = 0.918, angle = 0.013 degrees
Position of Pod-bin2.mrc (#13) relative to Sortingplatforom.mrc gaussian (#16)
coordinates:
Matrix rotation and translation
-0.50004472 0.86588748 -0.01393389 146.55140000
-0.86564108 -0.50023594 -0.02072486 345.56008108
-0.02491563 0.00169838 0.99968811 131.68108155
Axis 0.01294863 0.00634156 -0.99989605
Axis point 174.08737958 130.42744448 0.00000000
Rotation angle (degrees) 120.01960324
Shift along axis -127.57836293
> fitmap #13 inMap #16
Fit map Pod-bin2.mrc in map Sortingplatforom.mrc gaussian using 3880 points
correlation = 0.9089, correlation about mean = 0.6152, overlap = 73.9
steps = 40, shift = 0.00476, angle = 0.00411 degrees
Position of Pod-bin2.mrc (#13) relative to Sortingplatforom.mrc gaussian (#16)
coordinates:
Matrix rotation and translation
-0.49998717 0.86592045 -0.01395047 146.54718424
-0.86567461 -0.50017877 -0.02070403 345.55457196
-0.02490577 0.00172481 0.99968831 131.67705964
Axis 0.01295136 0.00632605 -0.99989612
Axis point 174.09092137 130.42149269 0.00000000
Rotation angle (degrees) 120.01580111
Shift along axis -127.57939777
> fitmap #13 inMap #16
Fit map Pod-bin2.mrc in map Sortingplatforom.mrc gaussian using 3880 points
correlation = 0.9089, correlation about mean = 0.6156, overlap = 73.9
steps = 40, shift = 0.064, angle = 0.0268 degrees
Position of Pod-bin2.mrc (#13) relative to Sortingplatforom.mrc gaussian (#16)
coordinates:
Matrix rotation and translation
-0.50009398 0.86585883 -0.01394651 146.50725354
-0.86562416 -0.50028463 -0.02025095 345.53797281
-0.02451169 0.00194505 0.99969765 131.59682942
Axis 0.01281778 0.00610120 -0.99989923
Axis point 174.03474038 130.42044838 0.00000000
Rotation angle (degrees) 120.02252842
Shift along axis -127.59747599
> hide #!13 models
> show #!17 models
> hide #!17 models
> show #!30 models
> show #!29 models
> show #!28 models
> hide #!28 models
> show #!27 models
> hide #!27 models
> show #!24 models
> select subtract #13
Nothing selected
> show #!13 models
> color #13 #42424233 models
> hide #!16 models
> save /Users/shoichi/Desktop/Shigella-ipaDnull-bin2-06232025.cxs includeMaps
> true
——— End of log from Mon Jun 23 16:35:51 2025 ———
opened ChimeraX session
> hide #!32 models
> show #!32 models
> hide #!30 models
> hide #!29 models
> hide #!24.6 models
> show #!24.6 models
> hide #!24 models
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/MxiA-project/Data_Images/06232025/Chimera-
> figure-2025/MxiGc24-segment_06232025/Exp.mrc
Opened Exp.mrc as #33, grid size 120,120,70, pixel 4.3,4.3,4.3, shown at level
0.0223, step 1, values float32
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/MxiA-project/Data_Images/06232025/Chimera-
> figure-2025/Rev-Sfc24.mrc
Opened Rev-Sfc24.mrc as #34, grid size 120,120,70, pixel 4.3,4.3,4.3, shown at
level 0.18, step 1, values float32
> select add #34
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #34,1,0,0,11.288,0,1,0,-42.246,0,0,1,376.35
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #34 inMap #32
Fit map Rev-Sfc24.mrc in map IMring.mrc using 10080 points
correlation = 0.04856, correlation about mean = 0.1798, overlap = 12.51
steps = 172, shift = 18.7, angle = 3.26 degrees
Position of Rev-Sfc24.mrc (#34) relative to IMring.mrc (#32) coordinates:
Matrix rotation and translation
0.99999192 -0.00211181 -0.00342002 6.05102135
0.00202545 0.99968387 -0.02506126 -51.18900847
0.00347187 0.02505413 0.99968007 -11.47223564
Axis 0.98737942 -0.13578481 0.08151294
Axis point 0.00000000 471.57862028 -1983.53947835
Rotation angle (degrees) 1.45420739
Shift along axis 11.99020796
> fitmap #34 inMap #32
Fit map Rev-Sfc24.mrc in map IMring.mrc using 10080 points
correlation = 0.04808, correlation about mean = 0.1795, overlap = 12.41
steps = 64, shift = 1.29, angle = 0.0595 degrees
Position of Rev-Sfc24.mrc (#34) relative to IMring.mrc (#32) coordinates:
Matrix rotation and translation
0.99998810 -0.00206758 -0.00441924 4.90446280
0.00195746 0.99969100 -0.02478033 -51.38519993
0.00446911 0.02477139 0.99968315 -11.60966081
Axis 0.98115932 -0.17599578 0.07969864
Axis point 0.00000000 484.84770651 -1987.83944704
Rotation angle (degrees) 1.44696503
Shift along axis 12.93036354
> volume #34 level 0.03602
> volume #34 level 0.09177
> view orient
> ui tool show "Side View"
> select add #34
3 models selected
> view matrix models
> #34,0.9987,-0.050796,-0.0029443,9.6384,0.050706,0.9984,-0.025094,-36.178,0.0042143,0.024913,0.99968,356.13
> volume #34 level 0.1289
> ui mousemode right "rotate selected models"
> view matrix models
> #34,0.98582,-0.16779,2.5626e-05,42.68,0.16774,0.98551,-0.025266,-62.996,0.0042143,0.024913,0.99968,356.13
> view matrix models
> #34,0.97905,-0.20362,0.00094705,53.525,0.20358,0.97873,-0.025249,-70.491,0.0042143,0.024913,0.99968,356.13
> fitmap #34 inMap #32
Fit map Rev-Sfc24.mrc in map IMring.mrc using 24548 points
correlation = 0.7283, correlation about mean = 0.6591, overlap = 525.3
steps = 96, shift = 26.3, angle = 9.07 degrees
Position of Rev-Sfc24.mrc (#34) relative to IMring.mrc (#32) coordinates:
Matrix rotation and translation
1.00000000 -0.00005124 0.00003157 0.01118532
0.00005124 1.00000000 0.00002780 -0.01372703
-0.00003157 -0.00002779 1.00000000 0.09007187
Axis -0.41924703 0.47624459 0.77293144
Axis point 810.60604599 695.98979865 0.00000000
Rotation angle (degrees) 0.00379852
Shift along axis 0.05839255
> fitmap #34 inMap #32
Fit map Rev-Sfc24.mrc in map IMring.mrc using 24548 points
correlation = 0.7283, correlation about mean = 0.6589, overlap = 525.3
steps = 24, shift = 0.0936, angle = 0.0234 degrees
Position of Rev-Sfc24.mrc (#34) relative to IMring.mrc (#32) coordinates:
Matrix rotation and translation
0.99999993 0.00035249 0.00008781 -0.07085793
-0.00035250 0.99999994 0.00003190 0.11012226
-0.00008780 -0.00003193 1.00000000 0.01904066
Axis -0.08751818 0.24077135 -0.96662802
Axis point 302.59590163 197.52194537 0.00000000
Rotation angle (degrees) 0.02089382
Shift along axis 0.01431041
> fitmap #34 inMap #32
Fit map Rev-Sfc24.mrc in map IMring.mrc using 24548 points
correlation = 0.7283, correlation about mean = 0.6591, overlap = 525.6
steps = 44, shift = 0.0424, angle = 0.0144 degrees
Position of Rev-Sfc24.mrc (#34) relative to IMring.mrc (#32) coordinates:
Matrix rotation and translation
0.99999999 0.00010817 0.00003312 -0.03041882
-0.00010817 0.99999999 0.00004000 0.02113275
-0.00003311 -0.00004001 1.00000000 -0.01031539
Axis -0.33339844 0.27598716 -0.90148576
Axis point 130.87338983 203.33061577 0.00000000
Rotation angle (degrees) 0.00687481
Shift along axis 0.02527314
> volume #34 level 0.06461
> fitmap #34 inMap #32
Fit map Rev-Sfc24.mrc in map IMring.mrc using 73104 points
correlation = 0.656, correlation about mean = 0.6574, overlap = 599.6
steps = 28, shift = 0.134, angle = 0.013 degrees
Position of Rev-Sfc24.mrc (#34) relative to IMring.mrc (#32) coordinates:
Matrix rotation and translation
0.99999999 -0.00011364 0.00000035 0.02707610
0.00011364 0.99999999 0.00000271 -0.03152306
-0.00000035 -0.00000271 1.00000000 0.10540233
Axis -0.02383402 0.00310652 0.99971110
Axis point 280.27565978 260.19631750 0.00000000
Rotation angle (degrees) 0.00651282
Shift along axis 0.10462863
> fitmap #34 inMap #32
Fit map Rev-Sfc24.mrc in map IMring.mrc using 73104 points
correlation = 0.656, correlation about mean = 0.6572, overlap = 599.3
steps = 28, shift = 0.0685, angle = 0.0202 degrees
Position of Rev-Sfc24.mrc (#34) relative to IMring.mrc (#32) coordinates:
Matrix rotation and translation
0.99999997 0.00021169 0.00009331 -0.11794174
-0.00021170 0.99999997 0.00010461 0.02003968
-0.00009329 -0.00010463 0.99999999 0.11709633
Axis -0.41204757 0.36747303 -0.83377478
Axis point 166.90748032 638.26875088 0.00000000
Rotation angle (degrees) 0.01454750
Shift along axis -0.04167032
> fitmap #34 inMap #32
Fit map Rev-Sfc24.mrc in map IMring.mrc using 73104 points
correlation = 0.656, correlation about mean = 0.6573, overlap = 599.7
steps = 48, shift = 0.0318, angle = 0.0262 degrees
Position of Rev-Sfc24.mrc (#34) relative to IMring.mrc (#32) coordinates:
Matrix rotation and translation
0.99999996 -0.00024012 0.00015471 0.00104880
0.00024011 0.99999997 0.00007400 -0.06837207
-0.00015472 -0.00007396 0.99999999 0.10748545
Axis -0.25071948 0.52433369 0.81376528
Axis point 396.90456660 57.92191754 0.00000000
Rotation angle (degrees) 0.01690620
Shift along axis 0.05135519
> fitmap #34 inMap #32
Fit map Rev-Sfc24.mrc in map IMring.mrc using 73104 points
correlation = 0.656, correlation about mean = 0.6574, overlap = 599.9
steps = 44, shift = 0.0174, angle = 0.0244 degrees
Position of Rev-Sfc24.mrc (#34) relative to IMring.mrc (#32) coordinates:
Matrix rotation and translation
0.99999997 0.00018407 0.00013268 -0.10497284
-0.00018408 0.99999998 0.00005271 0.04530194
-0.00013267 -0.00005273 0.99999999 0.07911296
Axis -0.22632514 0.56953920 -0.79019114
Axis point 286.12831174 586.25659376 -0.00000000
Rotation angle (degrees) 0.01334694
Shift along axis -0.01295514
> fitmap #34 inMap #32
Fit map Rev-Sfc24.mrc in map IMring.mrc using 73104 points
correlation = 0.656, correlation about mean = 0.6575, overlap = 600.4
steps = 40, shift = 0.0481, angle = 0.0195 degrees
Position of Rev-Sfc24.mrc (#34) relative to IMring.mrc (#32) coordinates:
Matrix rotation and translation
0.99999999 -0.00012348 -0.00000077 0.03414568
0.00012348 0.99999999 -0.00000200 -0.03116819
0.00000077 0.00000200 1.00000000 0.01984330
Axis 0.01621715 -0.00624124 0.99984901
Axis point 251.39042668 273.80768471 0.00000000
Rotation angle (degrees) 0.00707597
Shift along axis 0.02058858
> select subtract #34
Nothing selected
> hide #!32 models
> select add #33
3 models selected
> view matrix models
> #33,0.98106,0.19355,-0.0078346,-43.471,0.063676,-0.28404,0.9567,170.14,0.18294,-0.93908,-0.29098,384.62
> undo
> ui mousemode right "translate selected models"
> view matrix models #33,1,0,0,-0.75143,0,1,0,18.436,0,0,1,379.44
> fitmap #33 inMap #34
Fit map Exp.mrc in map Rev-Sfc24.mrc using 10071 points
correlation = 0.9623, correlation about mean = 0.9032, overlap = 34.69
steps = 188, shift = 23.9, angle = 2.4 degrees
Position of Exp.mrc (#33) relative to Rev-Sfc24.mrc (#34) coordinates:
Matrix rotation and translation
0.99588889 0.09058030 -0.00072100 -22.17556000
-0.09058090 0.99588874 -0.00084381 24.54560282
0.00064160 0.00090564 0.99999938 -2.67284634
Axis 0.00965615 -0.00752091 -0.99992509
Axis point 259.51145442 256.83725865 0.00000000
Rotation angle (degrees) 5.19739984
Shift along axis 2.27391049
> fitmap #33 inMap #34
Fit map Exp.mrc in map Rev-Sfc24.mrc using 10071 points
correlation = 0.962, correlation about mean = 0.9024, overlap = 34.68
steps = 40, shift = 0.0652, angle = 0.0818 degrees
Position of Exp.mrc (#33) relative to Rev-Sfc24.mrc (#34) coordinates:
Matrix rotation and translation
0.99575869 0.09200098 -0.00066475 -22.57071480
-0.09200152 0.99575852 -0.00082777 24.91166536
0.00058577 0.00088542 0.99999944 -2.65375957
Axis 0.00931010 -0.00679576 -0.99993357
Axis point 259.07093181 257.50470889 0.00000000
Rotation angle (degrees) 5.27909982
Shift along axis 2.27415413
> hide #!34 models
> volume #33 level 0.0282
> color #33 #42424233 models
> select clear
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/MxiA-project/Model-PDB-AlphaFolds/6rwy.pdb1
6rwy.pdb1 title:
Export apparatus core and inner rod of the shigella type 3 secretion system
[more info...]
Chain information for 6rwy.pdb1 #35
---
Chain | Description
A G H I J K | No description available
B C D E F | No description available
L M N O P Q R S T U V | No description available
a b c d e | No description available
f | No description available
g h i j k | No description available
> select add #35
22743 atoms, 23078 bonds, 3 pseudobonds, 3160 residues, 2 models selected
> view matrix models #35,1,0,0,-4.6654,0,1,0,-2.1689,0,0,1,2.2084
> view matrix models #35,1,0,0,-91.196,0,1,0,-40.005,0,0,1,205.21
> view matrix models #35,1,0,0,-75.528,0,1,0,-74.953,0,0,1,205.52
> fitmap #35 inMap #33
Fit molecule 6rwy.pdb1 (#35) to map Exp.mrc (#33) using 22743 atoms
average map value = 0.03909, steps = 60
shifted from previous position = 10.9
rotated from previous position = 3.76 degrees
atoms outside contour = 11081, contour level = 0.0282
Position of 6rwy.pdb1 (#35) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.99741760 -0.03266759 -0.06396064 -43.37423719
0.03327497 0.99941048 0.00845379 -87.59819848
0.06364677 -0.01056025 0.99791661 -187.77700704
Axis -0.13122930 -0.88070887 0.45511620
Axis point 2905.35176727 0.00000000 -800.81795837
Rotation angle (degrees) 4.15448090
Shift along axis -2.61987781
> fitmap #35 inMap #33
Fit molecule 6rwy.pdb1 (#35) to map Exp.mrc (#33) using 22743 atoms
average map value = 0.03909, steps = 24
shifted from previous position = 0.00687
rotated from previous position = 0.126 degrees
atoms outside contour = 11085, contour level = 0.0282
Position of 6rwy.pdb1 (#35) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.99749474 -0.03046883 -0.06384280 -44.16910568
0.03108711 0.99947870 0.00871326 -86.97208983
0.06354403 -0.01067612 0.99792193 -187.70382242
Axis -0.13577780 -0.89205051 0.43105716
Axis point 2945.80706779 0.00000000 -801.76090259
Rotation angle (degrees) 4.09446743
Shift along axis 2.66960472
> hide sel atoms
> show sel cartoons
> view orient
> turn x 90
[Repeated 2 time(s)]
> view matrix models
> #35,0.99788,0.012764,-0.063768,-59.237,-0.01212,0.99987,0.010477,-74.276,0.063894,-0.0096822,0.99791,195.83
> fitmap #35 inMap #33
Fit molecule 6rwy.pdb1 (#35) to map Exp.mrc (#33) using 22743 atoms
average map value = 0.03909, steps = 60
shifted from previous position = 18.5
rotated from previous position = 0.279 degrees
atoms outside contour = 11083, contour level = 0.0282
Position of 6rwy.pdb1 (#35) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.99763100 -0.02561100 -0.06384716 -45.85770181
0.02625088 0.99961302 0.00920332 -85.57822793
0.06358675 -0.01085756 0.99791725 -187.65065701
Axis -0.14428373 -0.91654180 0.37300580
Axis point 3013.35399803 0.00000000 -796.02195102
Rotation angle (degrees) 3.98635331
Shift along axis 15.05776032
> split #35
Split 6rwy.pdb1 (#35) into 33 models
Chain information for 6rwy.pdb1 A #35.1
---
Chain | Description
A | No description available
Chain information for 6rwy.pdb1 B #35.2
---
Chain | Description
B | No description available
Chain information for 6rwy.pdb1 C #35.3
---
Chain | Description
C | No description available
Chain information for 6rwy.pdb1 D #35.4
---
Chain | Description
D | No description available
Chain information for 6rwy.pdb1 E #35.5
---
Chain | Description
E | No description available
Chain information for 6rwy.pdb1 F #35.6
---
Chain | Description
F | No description available
Chain information for 6rwy.pdb1 G #35.7
---
Chain | Description
G | No description available
Chain information for 6rwy.pdb1 H #35.8
---
Chain | Description
H | No description available
Chain information for 6rwy.pdb1 I #35.9
---
Chain | Description
I | No description available
Chain information for 6rwy.pdb1 J #35.10
---
Chain | Description
J | No description available
Chain information for 6rwy.pdb1 K #35.11
---
Chain | Description
K | No description available
Chain information for 6rwy.pdb1 L #35.12
---
Chain | Description
L | No description available
Chain information for 6rwy.pdb1 M #35.13
---
Chain | Description
M | No description available
Chain information for 6rwy.pdb1 N #35.14
---
Chain | Description
N | No description available
Chain information for 6rwy.pdb1 O #35.15
---
Chain | Description
O | No description available
Chain information for 6rwy.pdb1 P #35.16
---
Chain | Description
P | No description available
Chain information for 6rwy.pdb1 Q #35.17
---
Chain | Description
Q | No description available
Chain information for 6rwy.pdb1 R #35.18
---
Chain | Description
R | No description available
Chain information for 6rwy.pdb1 S #35.19
---
Chain | Description
S | No description available
Chain information for 6rwy.pdb1 T #35.20
---
Chain | Description
T | No description available
Chain information for 6rwy.pdb1 U #35.21
---
Chain | Description
U | No description available
Chain information for 6rwy.pdb1 V #35.22
---
Chain | Description
V | No description available
Chain information for 6rwy.pdb1 a #35.23
---
Chain | Description
a | No description available
Chain information for 6rwy.pdb1 b #35.24
---
Chain | Description
b | No description available
Chain information for 6rwy.pdb1 c #35.25
---
Chain | Description
c | No description available
Chain information for 6rwy.pdb1 d #35.26
---
Chain | Description
d | No description available
Chain information for 6rwy.pdb1 e #35.27
---
Chain | Description
e | No description available
Chain information for 6rwy.pdb1 f #35.28
---
Chain | Description
f | No description available
Chain information for 6rwy.pdb1 g #35.29
---
Chain | Description
g | No description available
Chain information for 6rwy.pdb1 h #35.30
---
Chain | Description
h | No description available
Chain information for 6rwy.pdb1 i #35.31
---
Chain | Description
i | No description available
Chain information for 6rwy.pdb1 j #35.32
---
Chain | Description
j | No description available
Chain information for 6rwy.pdb1 k #35.33
---
Chain | Description
k | No description available
> hide #!20 models
> hide #35.12 models
> hide #35.13 models
> hide #35.14 models
> hide #35.15 models
> hide #35.16 models
> hide #35.17 models
> hide #35.18 models
> hide #35.19 models
> hide #35.20 models
> hide #35.21 models
> hide #35.22 models
> hide #35.7 models
> hide #35.8 models
> hide #35.9 models
> hide #35.10 models
> hide #35.11 models
> hide #35.2 models
> hide #35.3 models
> hide #35.4 models
> hide #35.6 models
> hide #35.5 models
> hide #35.1 models
> select add #35.23
1643 atoms, 1678 bonds, 208 residues, 1 model selected
> select add #35.24
3286 atoms, 3356 bonds, 416 residues, 2 models selected
> select add #35.25
4929 atoms, 5034 bonds, 624 residues, 3 models selected
> select add #35.26
6572 atoms, 6712 bonds, 832 residues, 4 models selected
> select add #35.28
8453 atoms, 8641 bonds, 1072 residues, 5 models selected
> select add #35.27
10096 atoms, 10319 bonds, 1280 residues, 6 models selected
> select add #35.30
10759 atoms, 10995 bonds, 1366 residues, 7 models selected
> select add #35.29
11422 atoms, 11671 bonds, 1452 residues, 8 models selected
> select add #35.31
11996 atoms, 12257 bonds, 1 pseudobond, 1527 residues, 10 models selected
> select add #35.32
12524 atoms, 12797 bonds, 2 pseudobonds, 1595 residues, 12 models selected
> select add #35.33
12867 atoms, 13147 bonds, 3 pseudobonds, 1638 residues, 14 models selected
> save /Users/shoichi/Desktop/Exp_6rwy.pdb selectedOnly true
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/MxiA-project/Model-PDB-AlphaFolds/Exp_6rwy.pdb
Summary of feedback from opening /Users/shoichi/Library/CloudStorage/OneDrive-
YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-Projects/Project-
with-Bill/MxiA-project/Model-PDB-AlphaFolds/Exp_6rwy.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 11 THR A 23 1 13
Start residue of secondary structure not found: HELIX 2 2 GLN A 24 ASN A 40 1
17
Start residue of secondary structure not found: HELIX 3 3 ASN A 43 ASN A 81 1
39
Start residue of secondary structure not found: HELIX 4 4 THR B 11 THR B 23 1
13
Start residue of secondary structure not found: HELIX 5 5 GLN B 24 ASN B 40 1
17
754 messages similar to the above omitted
Chain information for Exp_6rwy.pdb
---
Chain | Description
36.1/a 36.2/b 36.3/c 36.4/d 36.5/e | No description available
36.6/f | No description available
36.7/g 36.8/h | No description available
36.9/i | No description available
36.10/j | No description available
36.11/k | No description available
> select add #35
22743 atoms, 23078 bonds, 3 pseudobonds, 3160 residues, 37 models selected
> select subtract #35
Nothing selected
> hide #!35 models
> select add #36
12867 atoms, 13147 bonds, 3 pseudobonds, 1638 residues, 15 models selected
> view orient
> turn x 90
[Repeated 2 time(s)]
> view matrix models #36,1,0,0,1.8402,0,1,0,-7.3614e-15,0,0,1,22.102
> combine #36
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 316
shifted from previous position = 14.7
rotated from previous position = 20.6 degrees
atoms outside contour = 2517, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.97215783 0.23225297 -0.03110797 -36.48471750
-0.21917028 0.94819832 0.22996594 -39.18940239
0.08290680 -0.21674525 0.97270137 -310.80580561
Axis -0.69231910 -0.17670165 -0.69962190
Axis point 156.75641938 -568.23716310 0.00000000
Rotation angle (degrees) 18.82141158
Shift along axis 249.63044579
> select subtract #36
Nothing selected
> hide #!36 models
> show #!35 models
> hide #!35 models
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 44
shifted from previous position = 0.0237
rotated from previous position = 0.537 degrees
atoms outside contour = 2518, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.97005550 0.24114627 -0.02899658 -39.23648975
-0.22826290 0.94593773 0.23042975 -36.50652393
0.08299623 -0.21691080 0.97265684 -310.77604186
Axis -0.67981987 -0.17019457 -0.71335738
Axis point 156.72094753 -535.52573200 0.00000000
Rotation angle (degrees) 19.20894193
Shift along axis 254.58134139
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 44
shifted from previous position = 0.0162
rotated from previous position = 0.248 degrees
atoms outside contour = 2519, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.96904395 0.24527257 -0.02819900 -40.42088046
-0.23247603 0.94495711 0.23024108 -35.07248352
0.08311866 -0.21655813 0.97272497 -310.93483988
Axis -0.67337250 -0.16776719 -0.72001642
Axis point 157.89194862 -520.78803134 0.00000000
Rotation angle (degrees) 19.37577446
Shift along axis 256.98051248
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 28
shifted from previous position = 0.0648
rotated from previous position = 0.0971 degrees
atoms outside contour = 2509, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.96863326 0.24682847 -0.02872841 -40.40134866
-0.23388087 0.94461726 0.23021288 -34.59326791
0.08396044 -0.21627282 0.97271615 -311.22221523
Axis -0.67072132 -0.16928384 -0.72213288
Axis point 160.83362397 -516.13702243 0.00000000
Rotation angle (degrees) 19.44123990
Shift along axis 257.69792107
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06746, steps = 40
shifted from previous position = 0.0997
rotated from previous position = 1.18 degrees
atoms outside contour = 2519, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.96366431 0.26609641 -0.02331951 -46.71349923
-0.25378087 0.93929856 0.23089713 -28.45567455
0.08334488 -0.21658928 0.97269868 -310.98516898
Axis -0.64462062 -0.15365398 -0.74890234
Axis point 157.55723427 -450.67017193 0.00000000
Rotation angle (degrees) 20.30960300
Shift along axis 267.38233255
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06746, steps = 28
shifted from previous position = 0.0588
rotated from previous position = 0.0884 degrees
atoms outside contour = 2507, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.96394851 0.26497357 -0.02433681 -45.95977070
-0.25246266 0.93964523 0.23093169 -28.89301795
0.08405877 -0.21646213 0.97266555 -311.18545152
Axis -0.64599219 -0.15651244 -0.74712646
Axis point 159.68219339 -455.04109604 0.00000000
Rotation angle (degrees) 20.26021000
Shift along axis 266.70665549
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06746, steps = 36
shifted from previous position = 0.059
rotated from previous position = 0.834 degrees
atoms outside contour = 2517, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.96020555 0.27853448 -0.02058754 -50.30086275
-0.26646024 0.93567851 0.23131074 -24.47016918
0.08369134 -0.21662010 0.97266206 -311.05082031
Axis -0.62813123 -0.14622976 -0.76424343
Axis point 157.45642500 -412.32042966 0.00000000
Rotation angle (degrees) 20.88898113
Shift along axis 272.89235505
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06746, steps = 28
shifted from previous position = 0.0572
rotated from previous position = 0.201 degrees
atoms outside contour = 2501, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.96102174 0.27557271 -0.02229133 -48.89154354
-0.26321841 0.93663567 0.23114862 -25.45689706
0.08457710 -0.21627137 0.97266305 -311.36854755
Axis -0.63154775 -0.15084823 -0.76052104
Axis point 160.51258554 -422.13786937 -0.00000000
Rotation angle (degrees) 20.74595341
Shift along axis 271.51980439
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06746, steps = 40
shifted from previous position = 0.114
rotated from previous position = 0.934 degrees
atoms outside contour = 2516, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.95677138 0.29034963 -0.01690027 -54.24303291
-0.27874957 0.93202561 0.23157490 -20.51184159
0.08298917 -0.21685329 0.97267027 -310.81188942
Axis -0.61311299 -0.13657373 -0.77810030
Axis point 154.50693313 -377.00324123 0.00000000
Rotation angle (degrees) 21.45053528
Shift along axis 277.90131068
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06746, steps = 28
shifted from previous position = 0.0915
rotated from previous position = 0.405 degrees
atoms outside contour = 2500, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.95862930 0.28399751 -0.01937193 -51.83607203
-0.27204105 0.93405344 0.23138247 -22.64444243
0.08380646 -0.21654005 0.97266998 -311.10230759
Axis -0.62088266 -0.14301955 -0.77074647
Axis point 157.48594051 -396.19307279 0.00000000
Rotation angle (degrees) 21.14407053
Shift along axis 275.20372299
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 40
shifted from previous position = 0.0325
rotated from previous position = 0.935 degrees
atoms outside contour = 2497, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.95402487 0.29929815 -0.01603642 -56.17567245
-0.28767749 0.92937671 0.23130194 -17.37440552
0.08413212 -0.21605449 0.97274984 -311.34959895
Axis -0.60065328 -0.13449356 -0.78811619
Axis point 157.82962251 -352.91585473 0.00000000
Rotation angle (degrees) 21.86318717
Shift along axis 281.45850608
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 40
shifted from previous position = 0.0938
rotated from previous position = 0.597 degrees
atoms outside contour = 2503, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.95112319 0.30856628 -0.01230992 -59.65431835
-0.29745493 0.92612763 0.23196590 -14.37103207
0.08297741 -0.21696650 0.97264602 -310.76314943
Axis -0.59055654 -0.12534750 -0.79720197
Axis point 153.01157515 -327.45218791 0.00000000
Rotation angle (degrees) 22.33942125
Shift along axis 284.77161490
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 28
shifted from previous position = 0.0668
rotated from previous position = 0.454 degrees
atoms outside contour = 2498, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.95337543 0.30141874 -0.01490093 -57.11152235
-0.28994531 0.92854514 0.23180951 -16.84120644
0.08370792 -0.21668104 0.97264706 -311.02884295
Axis -0.59901117 -0.13170356 -0.78983530
Axis point 155.58109502 -347.05758758 0.00000000
Rotation angle (degrees) 21.98470642
Shift along axis 282.09004500
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06748, steps = 40
shifted from previous position = 0.0247
rotated from previous position = 1.12 degrees
atoms outside contour = 2497, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.94755539 0.31943266 -0.01007796 -62.53011616
-0.30846488 0.92235933 0.23259983 -10.88040410
0.08359549 -0.21729252 0.97252031 -310.77431451
Axis -0.57819656 -0.12038806 -0.80696682
Axis point 152.95845016 -300.88561926 0.00000000
Rotation angle (degrees) 22.89527177
Shift along axis 288.24912922
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06748, steps = 196
shifted from previous position = 0.275
rotated from previous position = 6.03 degrees
atoms outside contour = 2516, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.91061366 0.41271950 0.02110411 -91.92267912
-0.40571723 0.88311805 0.23557598 22.71238621
0.07858938 -0.22308101 0.97162677 -307.49389271
Axis -0.48795796 -0.06115768 -0.87072198
Axis point 136.22711377 -115.71161571 0.00000000
Rotation angle (degrees) 28.03273362
Shift along axis 311.20705701
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 40
shifted from previous position = 0.0948
rotated from previous position = 0.898 degrees
atoms outside contour = 2512, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.90430007 0.42608641 0.02630122 -96.27299907
-0.41984476 0.87651820 0.23547022 28.07916406
0.07727716 -0.22397816 0.97152562 -306.86169323
Axis -0.47660751 -0.05287975 -0.87752436
Axis point 134.26059045 -94.76874164 0.00000000
Rotation angle (degrees) 28.81602027
Shift along axis 313.67822778
> select add #37
12867 atoms, 13147 bonds, 3 pseudobonds, 1638 residues, 2 models selected
> view orient
> turn x 90
[Repeated 2 time(s)]
> view matrix models
> #37,0.88528,0.46366,0.036102,-106.56,-0.45862,0.8575,0.23315,43.037,0.077144,-0.22296,0.97177,79.067
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 72
shifted from previous position = 20.8
rotated from previous position = 0.481 degrees
atoms outside contour = 2511, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.90079049 0.43330196 0.02873850 -98.32308247
-0.42743077 0.87300777 0.23486244 31.19999943
0.07667743 -0.22384557 0.97160369 -306.76491610
Axis -0.46974220 -0.04909210 -0.88143759
Axis point 134.11253872 -83.92177367 0.00000000
Rotation angle (degrees) 29.22595638
Shift along axis 315.04895705
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 28
shifted from previous position = 0.0881
rotated from previous position = 0.69 degrees
atoms outside contour = 2506, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89556547 0.44382392 0.03134996 -100.99634174
-0.43819349 0.86759990 0.23506782 35.26655153
0.07712950 -0.22425597 0.97147326 -306.70958011
Axis -0.46139810 -0.04598628 -0.88600060
Axis point 134.86180551 -69.97063128 0.00000000
Rotation angle (degrees) 29.85139496
Shift along axis 316.72261334
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 28
shifted from previous position = 0.113
rotated from previous position = 0.92 degrees
atoms outside contour = 2514, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.90246639 0.42989237 0.02733078 -97.18986602
-0.42378755 0.87469951 0.23516987 29.70709181
0.07719151 -0.22381535 0.97156995 -306.89335347
Axis -0.47292364 -0.05137489 -0.87960437
Axis point 134.59471718 -89.23458408 0.00000000
Rotation angle (degrees) 29.02974247
Shift along axis 314.38192225
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 40
shifted from previous position = 0.0358
rotated from previous position = 0.539 degrees
atoms outside contour = 2508, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89842276 0.43815904 0.02920975 -99.19110537
-0.43221066 0.87054189 0.23526742 32.88583296
0.07765624 -0.22399437 0.97149165 -306.92433299
Axis -0.46611467 -0.04916939 -0.88335694
Axis point 135.40426879 -78.11433990 0.00000000
Rotation angle (degrees) 29.51483713
Shift along axis 315.74119313
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 40
shifted from previous position = 0.105
rotated from previous position = 0.62 degrees
atoms outside contour = 2504, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89393780 0.44692368 0.03368125 -102.50135810
-0.44172928 0.86584329 0.23492687 36.69464322
0.07583170 -0.22488801 0.97142933 -306.18633286
Axis -0.45914720 -0.04208924 -0.88736258
Axis point 133.02904390 -64.97443284 0.00000000
Rotation angle (degrees) 30.04811532
Shift along axis 317.21705560
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 28
shifted from previous position = 0.115
rotated from previous position = 0.804 degrees
atoms outside contour = 2510, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89992272 0.43507607 0.02911888 -98.73409564
-0.42922052 0.87207973 0.23504615 31.83387789
0.07686897 -0.22402179 0.97154794 -306.74154948
Axis -0.46852644 -0.04873392 -0.88210429
Axis point 134.31242573 -81.69650868 0.00000000
Rotation angle (degrees) 29.33441145
Shift along axis 315.28618152
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 36
shifted from previous position = 0.0953
rotated from previous position = 0.448 degrees
atoms outside contour = 2504, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89659216 0.44173645 0.03148658 -100.79748505
-0.43619417 0.86858072 0.23516415 34.45417341
0.07653194 -0.22458060 0.97144553 -306.45943993
Axis -0.46343059 -0.04540649 -0.88496912
Axis point 133.73323211 -72.40106826 0.00000000
Rotation angle (degrees) 29.73725103
Shift along axis 316.35533473
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 28
shifted from previous position = 0.11
rotated from previous position = 0.771 degrees
atoms outside contour = 2513, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.90230337 0.43022137 0.02753538 -97.33949968
-0.42415013 0.87451703 0.23519489 29.83327906
0.07710571 -0.22389628 0.97155811 -306.84469626
Axis -0.47271932 -0.05104183 -0.87973358
Axis point 134.42082336 -88.71395964 0.00000000
Rotation angle (degrees) 29.05083100
Shift along axis 314.43310092
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 40
shifted from previous position = 0.0181
rotated from previous position = 0.511 degrees
atoms outside contour = 2507, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89844147 0.43814279 0.02887597 -99.02578382
-0.43210877 0.87055337 0.23541205 32.78427291
0.07800602 -0.22398151 0.97146659 -307.00647837
Axis -0.46625270 -0.04986361 -0.88324517
Axis point 135.80530966 -78.46119855 0.00000000
Rotation angle (degrees) 29.51453840
Shift along axis 315.69828774
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 36
shifted from previous position = 0.101
rotated from previous position = 0.522 degrees
atoms outside contour = 2506, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89466699 0.44554139 0.03261660 -101.81955415
-0.44014180 0.86661685 0.23505410 36.02578634
0.07646023 -0.22465108 0.97143488 -306.41395689
Axis -0.46023802 -0.04389445 -0.88670979
Axis point 133.84591683 -67.26281795 0.00000000
Rotation angle (degrees) 29.96170923
Shift along axis 316.98015163
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 28
shifted from previous position = 0.101
rotated from previous position = 0.826 degrees
atoms outside contour = 2512, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.90086803 0.43314603 0.02865865 -98.26801868
-0.42723813 0.87302139 0.23516215 31.02573130
0.07683994 -0.22409412 0.97153355 -306.71089778
Axis -0.47032174 -0.04934219 -0.88111453
Axis point 134.07806725 -84.40785637 0.00000000
Rotation angle (degrees) 29.22472317
Shift along axis 314.93413586
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 36
shifted from previous position = 0.0873
rotated from previous position = 0.516 degrees
atoms outside contour = 2507, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89702346 0.44087858 0.03122484 -100.56014533
-0.43530634 0.86903240 0.23514055 34.12334041
0.07653303 -0.22451896 0.97145969 -306.48305045
Axis -0.46408011 -0.04574392 -0.88461130
Axis point 133.74442886 -73.53778176 0.00000000
Rotation angle (degrees) 29.68539583
Shift along axis 316.22539615
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 28
shifted from previous position = 0.115
rotated from previous position = 0.831 degrees
atoms outside contour = 2513, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.90315769 0.42846252 0.02694538 -96.81966205
-0.42230950 0.87539339 0.23524690 29.11132680
0.07720667 -0.22384433 0.97156206 -306.88791911
Axis -0.47424756 -0.05192061 -0.87885921
Axis point 134.49541167 -91.31340629 0.00000000
Rotation angle (degrees) 28.94832832
Shift along axis 314.11628340
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 40
shifted from previous position = 0.0364
rotated from previous position = 0.588 degrees
atoms outside contour = 2509, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89875096 0.43749997 0.02899116 -99.00445363
-0.43152127 0.87087727 0.23529168 32.61101453
0.07769236 -0.22397892 0.97149233 -306.93891595
Axis -0.46667981 -0.04948688 -0.88304077
Axis point 135.42086570 -79.04471548 0.00000000
Rotation angle (degrees) 29.47618687
Shift along axis 315.62913969
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 40
shifted from previous position = 0.0995
rotated from previous position = 0.601 degrees
atoms outside contour = 2507, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89441850 0.44598789 0.03332197 -102.20916020
-0.44078288 0.86646626 0.23440704 36.55563001
0.07567034 -0.22434575 0.97156728 -306.34974761
Axis -0.45907197 -0.04237783 -0.88738776
Axis point 133.36087951 -65.78360653 0.00000000
Rotation angle (degrees) 29.97700279
Shift along axis 317.22322991
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 28
shifted from previous position = 0.0922
rotated from previous position = 0.746 degrees
atoms outside contour = 2514, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89997567 0.43495953 0.02922328 -98.78534713
-0.42911600 0.87208028 0.23523485 31.71397404
0.07683259 -0.22424582 0.97149913 -306.65274386
Axis -0.46895168 -0.04859065 -0.88188620
Axis point 134.01873267 -81.91850950 0.00000000
Rotation angle (degrees) 29.33413674
Shift along axis 315.21737538
> close #35-36
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/MxiA-project/Model-PDB-AlphaFolds/6rwy.pdb1
6rwy.pdb1 title:
Export apparatus core and inner rod of the shigella type 3 secretion system
[more info...]
Chain information for 6rwy.pdb1 #35
---
Chain | Description
A G H I J K | No description available
B C D E F | No description available
L M N O P Q R S T U V | No description available
a b c d e | No description available
f | No description available
g h i j k | No description available
> matchmaker #37 to #35
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 6rwy.pdb1, chain f (#35) with combination, chain f (#37), sequence
alignment score = 1227.8
RMSD between 240 pruned atom pairs is 0.001 angstroms; (across all 240 pairs:
0.001)
> matchmaker #35 to #37
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 combination, chain f (#37) with 6rwy.pdb1, chain f (#35), sequence
alignment score = 1227.8
RMSD between 240 pruned atom pairs is 0.001 angstroms; (across all 240 pairs:
0.001)
> show #!7 models
> hide #!7 models
> show #!12 models
> hide #!37 models
> hide #!35 models
> hide #!33 models
> show #!35 models
> fitmap #35 inMap #12
Fit molecule 6rwy.pdb1 (#35) to map Needle.mrc gaussian (#12) using 22743
atoms
average map value = 0.05154, steps = 76
shifted from previous position = 11.5
rotated from previous position = 15 degrees
atoms outside contour = 4533, contour level = 0.012281
Position of 6rwy.pdb1 (#35) relative to Needle.mrc gaussian (#12) coordinates:
Matrix rotation and translation
0.87803641 0.47858703 -0.00255505 -192.64047971
-0.47852090 0.87798327 0.01277250 119.46473498
0.00835605 -0.00999207 0.99991516 209.09071995
Axis -0.02377648 -0.01139611 -0.99965234
Axis point 130.99637747 446.12669410 0.00000000
Rotation angle (degrees) 28.60186207
Shift along axis -205.79914853
> fitmap #35 inMap #12
Fit molecule 6rwy.pdb1 (#35) to map Needle.mrc gaussian (#12) using 22743
atoms
average map value = 0.05154, steps = 24
shifted from previous position = 0.027
rotated from previous position = 0.102 degrees
atoms outside contour = 4531, contour level = 0.012281
Position of 6rwy.pdb1 (#35) relative to Needle.mrc gaussian (#12) coordinates:
Matrix rotation and translation
0.87884036 0.47710585 -0.00310138 -192.24835410
-0.47703354 0.87879083 0.01287176 118.65116797
0.00886666 -0.00983277 0.99991235 208.88473927
Axis -0.02378722 -0.01253874 -0.99963841
Axis point 129.94428451 446.20277398 0.00000000
Rotation angle (degrees) 28.50544415
Shift along axis -205.72389102
> fitmap #35 inMap #12
Fit molecule 6rwy.pdb1 (#35) to map Needle.mrc gaussian (#12) using 22743
atoms
average map value = 0.05154, steps = 24
shifted from previous position = 0.00171
rotated from previous position = 0.102 degrees
atoms outside contour = 4529, contour level = 0.012281
Position of 6rwy.pdb1 (#35) relative to Needle.mrc gaussian (#12) coordinates:
Matrix rotation and translation
0.87967555 0.47556249 -0.00335195 -191.93472314
-0.47548863 0.87962901 0.01278152 117.88941222
0.00902689 -0.00964978 0.99991269 208.77241920
Axis -0.02357725 -0.01301123 -0.99963734
Axis point 129.27153288 446.50117910 0.00000000
Rotation angle (degrees) 28.40481137
Shift along axis -205.70530071
> matchmaker #37 to #35
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 6rwy.pdb1, chain f (#35) with combination, chain f (#37), sequence
alignment score = 1227.8
RMSD between 240 pruned atom pairs is 0.001 angstroms; (across all 240 pairs:
0.001)
> hide #!35 models
> show #!35 models
> select subtract #37
Nothing selected
> select add #35
22743 atoms, 23078 bonds, 3 pseudobonds, 3160 residues, 2 models selected
> hide sel atoms
> show sel cartoons
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 35/f
Alignment identifier is 5
> select #35/A,G-K:59
30 atoms, 24 bonds, 6 residues, 1 model selected
> select #35/A,G-K:25-59
1050 atoms, 1044 bonds, 210 residues, 1 model selected
> select #35/f:210-256
387 atoms, 397 bonds, 47 residues, 1 model selected
> select #35/f
1881 atoms, 1929 bonds, 240 residues, 1 model selected
> select clear
> select #35/a-e
8215 atoms, 8390 bonds, 1040 residues, 1 model selected
> select clear
> select #35/a-e
8215 atoms, 8390 bonds, 1040 residues, 1 model selected
> color sel #e34affff
> color sel #e34bffff
> color sel #e44dffff
> color sel #e34effff
> color sel #e24effff
> color sel #e04fffff
> color sel #de56ffff
> color sel #df61ffff
> color sel #e46fffff
> color sel #e572ffff
> color sel #e473ffff
> color sel #ce73ffff
> color sel #cd73ffff
> color sel #ca72ffff
> color sel #c773ffff
> color sel #bd73ffff
> color sel #b472ffff
> color sel #ab6effff
> color sel #9d6affff
> color sel #7c5effff
> color sel #6c5affff
> color sel #6960ffff
> color sel #6b65ffff
> color sel #7771ffff
> color sel #7c77ffff
> color sel #8079ffff
> color sel #9081ffff
> color sel #9686ffff
> color sel #ab96ffff
> color sel #bb9effff
> color sel #c4a6ffff
> color sel #cdb0ffff
> color sel #ccb0ffff
> color sel #c4adffff
> color sel #b6a7ffff
> color sel #b2a5ffff
> color sel #aba0ffff
> color sel #a69cffff
> color sel #a199ffff
> color sel #9d96ffff
> color sel #9c95ffff
> color sel #9c94ffff
> color sel #9994ffff
> color sel #9093ffff
> color sel #8e93ffff
> color sel #8e94ffff
> color sel #9097ffff
> color sel #979dffff
> color sel #999effff
> color sel #9ca0ffff
> color sel #e5c7ffff
> color sel #ffc5e7ff
> color sel #ff9da2ff
> color sel #ff9596ff
> color sel #ff9494ff
> color sel #ff9790ff
> color sel #ff998dff
> color sel #ffa184ff
> color sel #ffa27cff
> color sel #ff9e75ff
> color sel #ff9667ff
> color sel #ff8e5cff
> color sel #ff8c59ff
> color sel #ff7d54ff
> color sel #ff7255ff
> color sel #ff5e50ff
> color sel #ff364cff
[Repeated 1 time(s)]
> color sel #ff3950ff
> color sel #ff3d53ff
> color sel #ff475cff
> color sel #ff5364ff
> color sel #ff5b68ff
> color sel #ff616bff
> color sel #ff646aff
> color sel #ff6469ff
> color sel #ff6966ff
> color sel #ff7167ff
> color sel #ff7767ff
> color sel #ff7e66ff
> color sel #ff7e65ff
> color sel #ff7d64ff
> color sel #ff7a61ff
> color sel #ff7a60ff
> color sel #ff624cff
> color sel #ff5c49ff
> color sel #ff5747ff
> color sel #ff5647ff
> select #35/f:256
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #35/f
1881 atoms, 1929 bonds, 240 residues, 1 model selected
> color sel #ff5647ff
> select #35/g-k:86
35 atoms, 30 bonds, 5 residues, 1 model selected
> select #35/g-k
2771 atoms, 2828 bonds, 3 pseudobonds, 358 residues, 2 models selected
> color sel #ff5647ff
> select clear
> show #!20 models
> hide #!20 models
> show #!37 models
> close #37
> show #!27 models
> hide #!27 models
> show #!26 models
> hide #!26 models
> show #21 models
> hide #21 models
> show #21 models
> matchmaker #21 to #35
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 6rwy.pdb1, chain M (#35) with 6zni.pdb, chain A (#21), sequence
alignment score = 471.3
RMSD between 68 pruned atom pairs is 0.800 angstroms; (across all 73 pairs:
1.078)
> select add #21
14812 atoms, 15019 bonds, 1886 residues, 1 model selected
> view matrix models
> #21,-0.3511,-0.93587,-0.029745,518.01,-0.93631,0.35116,0.003362,377.64,0.007299,0.029031,-0.99955,873.02
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/MxiG_Linker/Manuscript-
> start-2023/Newest_ver/Figures-maps/PDB/6zni.pdb
6zni.pdb title:
Structure of the shigella mxih needle filament attached to the basal body
[more info...]
Chain information for 6zni.pdb #36
---
Chain | Description | UniProt
A B C D E F G H I J K L M N O P Q R S T U V W | protein mxih | MXIH_SHIFL 1-83
> matchmaker #36 to #21
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 6zni.pdb, chain A (#21) with 6zni.pdb, chain A (#36), sequence
alignment score = 488.1
RMSD between 82 pruned atom pairs is 0.000 angstroms; (across all 82 pairs:
0.000)
> select add #36
29624 atoms, 30038 bonds, 3772 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> view matrix models
> #21,-0.3511,-0.93587,-0.029745,513.47,-0.93631,0.35116,0.003362,379.08,0.007299,0.029031,-0.99955,909.24,#36,-0.3511,-0.93587,-0.029745,513.47,-0.93631,0.35116,0.0033619,379.08,0.007299,0.029031,-0.99955,909.24
> undo
> select subtract #21
14812 atoms, 15019 bonds, 1886 residues, 1 model selected
> view matrix models
> #36,-0.3511,-0.93587,-0.029745,503.75,-0.93631,0.35116,0.0033619,377.16,0.007299,0.029031,-0.99955,987.31
> select add #21
29624 atoms, 30038 bonds, 3772 residues, 2 models selected
> combine #21,36
Remapping chain ID 'A' in 6zni.pdb #36 to 'X'
Remapping chain ID 'B' in 6zni.pdb #36 to 'Y'
Remapping chain ID 'C' in 6zni.pdb #36 to 'Z'
Remapping chain ID 'D' in 6zni.pdb #36 to 'a'
Remapping chain ID 'E' in 6zni.pdb #36 to 'b'
Remapping chain ID 'F' in 6zni.pdb #36 to 'c'
Remapping chain ID 'G' in 6zni.pdb #36 to 'd'
Remapping chain ID 'H' in 6zni.pdb #36 to 'e'
Remapping chain ID 'I' in 6zni.pdb #36 to 'f'
Remapping chain ID 'J' in 6zni.pdb #36 to 'g'
Remapping chain ID 'K' in 6zni.pdb #36 to 'h'
Remapping chain ID 'L' in 6zni.pdb #36 to 'i'
Remapping chain ID 'M' in 6zni.pdb #36 to 'j'
Remapping chain ID 'N' in 6zni.pdb #36 to 'k'
Remapping chain ID 'O' in 6zni.pdb #36 to 'l'
Remapping chain ID 'P' in 6zni.pdb #36 to 'm'
Remapping chain ID 'Q' in 6zni.pdb #36 to 'n'
Remapping chain ID 'R' in 6zni.pdb #36 to 'o'
Remapping chain ID 'S' in 6zni.pdb #36 to 'p'
Remapping chain ID 'T' in 6zni.pdb #36 to 'q'
Remapping chain ID 'U' in 6zni.pdb #36 to 'r'
Remapping chain ID 'V' in 6zni.pdb #36 to 's'
Remapping chain ID 'W' in 6zni.pdb #36 to 't'
> select subtract #36
14812 atoms, 15019 bonds, 1886 residues, 1 model selected
> hide #36 models
> hide #21 models
> select subtract #21
Nothing selected
> color #37 #ffcdc1ff
> color #37 #fff0b9ff
> color #37 #fffab8ff
> color #37 #cdca94ff
> select add #37
29624 atoms, 30038 bonds, 3772 residues, 1 model selected
> color sel #ff5647ff
> color #37 #cdca94ff
> select #35/B-F:33-73
1025 atoms, 1020 bonds, 205 residues, 1 model selected
> select #35/B-F:11-73
1575 atoms, 1570 bonds, 315 residues, 1 model selected
> color sel #cdca94ff
> select #35/A,G-K:59
30 atoms, 24 bonds, 6 residues, 1 model selected
> select #35/A,G-K:25-59
1050 atoms, 1044 bonds, 210 residues, 1 model selected
> color sel #cdca94ff
> select #35/L-V:39-83
4004 atoms, 4059 bonds, 495 residues, 1 model selected
> select #35/L-V
6281 atoms, 6347 bonds, 803 residues, 1 model selected
> color sel #cdca94ff
> select clear
> select #35/g-k:86
35 atoms, 30 bonds, 5 residues, 1 model selected
> select #35/g-k
2771 atoms, 2828 bonds, 3 pseudobonds, 358 residues, 2 models selected
> select #35/B-F:73
25 atoms, 20 bonds, 5 residues, 1 model selected
> select #35/B-F:11-73
1575 atoms, 1570 bonds, 315 residues, 1 model selected
> select #35/A,G-K:25-59
1050 atoms, 1044 bonds, 210 residues, 1 model selected
> select #35/A,G-K:25-59
1050 atoms, 1044 bonds, 210 residues, 1 model selected
> select #35/L-V:83
121 atoms, 110 bonds, 11 residues, 1 model selected
> select #35/L-V
6281 atoms, 6347 bonds, 803 residues, 1 model selected
> select clear
> select #35/a-e
8215 atoms, 8390 bonds, 1040 residues, 1 model selected
> select #35/f:214-256
355 atoms, 364 bonds, 43 residues, 1 model selected
> select #35/f
1881 atoms, 1929 bonds, 240 residues, 1 model selected
> select #35/g-k:86
35 atoms, 30 bonds, 5 residues, 1 model selected
> select #35/g-k
2771 atoms, 2828 bonds, 3 pseudobonds, 358 residues, 2 models selected
> select add #35
22743 atoms, 23078 bonds, 3 pseudobonds, 3160 residues, 2 models selected
> select subtract #35
Nothing selected
> hide #!35 models
> show #!35 models
> fitmap #37 inMap #12
Fit molecule combination (#37) to map Needle.mrc gaussian (#12) using 29624
atoms
average map value = 0.06417, steps = 548
shifted from previous position = 70.3
rotated from previous position = 11.1 degrees
atoms outside contour = 8428, contour level = 0.012281
Position of combination (#37) relative to Needle.mrc gaussian (#12)
coordinates:
Matrix rotation and translation
-0.49153012 -0.85972065 -0.13884720 566.36821533
-0.86955619 0.49323881 0.02423863 329.40732755
0.04764637 0.13264946 -0.99001714 908.59071574
Axis 0.50204458 -0.86364149 -0.04554785
Axis point 350.50708701 0.00000000 464.01580445
Rotation angle (degrees) 173.80173096
Shift along axis -41.53209647
> fitmap #37 inMap #12
Fit molecule combination (#37) to map Needle.mrc gaussian (#12) using 29624
atoms
average map value = 0.06423, steps = 48
shifted from previous position = 0.0821
rotated from previous position = 1.4 degrees
atoms outside contour = 8424, contour level = 0.012281
Position of combination (#37) relative to Needle.mrc gaussian (#12)
coordinates:
Matrix rotation and translation
-0.51261344 -0.84748446 -0.13783161 568.00591214
-0.85732198 0.51402279 0.02792129 321.77742772
0.04718573 0.13247890 -0.99006204 908.81302700
Axis 0.49146888 -0.86966667 -0.04624087
Axis point 347.11623201 0.00000000 463.91377007
Rotation angle (degrees) 173.89374851
Shift along axis -42.70617861
> view orient
> turn x 90
[Repeated 2 time(s)]
> select add #37
29624 atoms, 30038 bonds, 3772 residues, 1 model selected
> view matrix models
> #37,-0.51261,-0.84748,-0.13783,569.7,-0.85732,0.51402,0.027921,321.78,0.047186,0.13248,-0.99006,856.35
> close #37
> show #36 models
> show #21 models
> fitmap #36 inMap #12
Fit molecule 6zni.pdb (#36) to map Needle.mrc gaussian (#12) using 14812 atoms
average map value = 0.0782, steps = 132
shifted from previous position = 32.5
rotated from previous position = 1.92 degrees
atoms outside contour = 571, contour level = 0.012281
Position of 6zni.pdb (#36) relative to Needle.mrc gaussian (#12) coordinates:
Matrix rotation and translation
-0.33643885 -0.94170519 -0.00049053 521.74293397
-0.94170368 0.33643919 -0.00169149 382.53410278
0.00175792 -0.00010715 -0.99999845 975.28376338
Axis 0.57600370 -0.81744690 0.00055009
Axis point 395.23518164 0.00000000 487.99286048
Rotation angle (degrees) 179.92120163
Shift along axis -11.63896146
> view orient
> turn x 90
[Repeated 2 time(s)]
> select add #36
14812 atoms, 15019 bonds, 1886 residues, 1 model selected
> view matrix models
> #36,-0.33644,-0.94171,-0.00049053,521.99,-0.9417,0.33644,-0.0016915,382.53,0.0017579,-0.00010715,-1,1003.3
> select subtract #36
Nothing selected
> select add #21
14812 atoms, 15019 bonds, 1886 residues, 1 model selected
> view matrix models
> #21,-0.3511,-0.93587,-0.029745,531.02,-0.93631,0.35116,0.003362,377.64,0.007299,0.029031,-0.99955,883.73
> turn y 10
[Repeated 47 time(s)]
> select add #36
29624 atoms, 30038 bonds, 3772 residues, 2 models selected
> view matrix models
> #21,-0.3511,-0.93587,-0.029745,530.99,-0.93631,0.35116,0.003362,377.58,0.007299,0.029031,-0.99955,877.32,#36,-0.33644,-0.94171,-0.00049053,521.96,-0.9417,0.33644,-0.0016915,382.48,0.0017579,-0.00010715,-1,996.86
> turn y 10
[Repeated 40 time(s)]
> select clear
> select add #35
22743 atoms, 23078 bonds, 3 pseudobonds, 3160 residues, 2 models selected
> hide #!35 models
> show #!35 models
> select #35/A,G-K:58-59
60 atoms, 54 bonds, 12 residues, 1 model selected
> select #35/A,G-K:25-59
1050 atoms, 1044 bonds, 210 residues, 1 model selected
> hide sel cartoons
> select #35/B-F:73
25 atoms, 20 bonds, 5 residues, 1 model selected
> select #35/B-F:11-73
1575 atoms, 1570 bonds, 315 residues, 1 model selected
> hide sel cartoons
> select #35/L-V:40-83
3905 atoms, 3960 bonds, 484 residues, 1 model selected
> select #35/L-V
6281 atoms, 6347 bonds, 803 residues, 1 model selected
> hide sel cartoons
> select clear
> select #35/a-e
8215 atoms, 8390 bonds, 1040 residues, 1 model selected
> hide sel cartoons
> select #35/f:209-256
396 atoms, 406 bonds, 48 residues, 1 model selected
> select #35/f
1881 atoms, 1929 bonds, 240 residues, 1 model selected
> hide sel cartoons
> select #35/g-k:86
35 atoms, 30 bonds, 5 residues, 1 model selected
> select #35/g-k
2771 atoms, 2828 bonds, 3 pseudobonds, 358 residues, 2 models selected
> hide sel cartoons
> select clear
> hide #21 models
> hide #!12 models
Drag select of 194 residues
> color sel #cdca94ff
> select clear
> select add #35
22743 atoms, 23078 bonds, 3 pseudobonds, 3160 residues, 2 models selected
> show sel cartoons
> select subtract #35
Nothing selected
> select add #36
14812 atoms, 15019 bonds, 1886 residues, 1 model selected
> show #21 models
> show sel surfaces
> select add #21
29624 atoms, 30038 bonds, 3772 residues, 25 models selected
> show sel surfaces
> show sel cartoons
> combine #21,36
Remapping chain ID 'A' in 6zni.pdb #36 to 'X'
Remapping chain ID 'B' in 6zni.pdb #36 to 'Y'
Remapping chain ID 'C' in 6zni.pdb #36 to 'Z'
Remapping chain ID 'D' in 6zni.pdb #36 to 'a'
Remapping chain ID 'E' in 6zni.pdb #36 to 'b'
Remapping chain ID 'F' in 6zni.pdb #36 to 'c'
Remapping chain ID 'G' in 6zni.pdb #36 to 'd'
Remapping chain ID 'H' in 6zni.pdb #36 to 'e'
Remapping chain ID 'I' in 6zni.pdb #36 to 'f'
Remapping chain ID 'J' in 6zni.pdb #36 to 'g'
Remapping chain ID 'K' in 6zni.pdb #36 to 'h'
Remapping chain ID 'L' in 6zni.pdb #36 to 'i'
Remapping chain ID 'M' in 6zni.pdb #36 to 'j'
Remapping chain ID 'N' in 6zni.pdb #36 to 'k'
Remapping chain ID 'O' in 6zni.pdb #36 to 'l'
Remapping chain ID 'P' in 6zni.pdb #36 to 'm'
Remapping chain ID 'Q' in 6zni.pdb #36 to 'n'
Remapping chain ID 'R' in 6zni.pdb #36 to 'o'
Remapping chain ID 'S' in 6zni.pdb #36 to 'p'
Remapping chain ID 'T' in 6zni.pdb #36 to 'q'
Remapping chain ID 'U' in 6zni.pdb #36 to 'r'
Remapping chain ID 'V' in 6zni.pdb #36 to 's'
Remapping chain ID 'W' in 6zni.pdb #36 to 't'
> select subtract #36
14812 atoms, 15019 bonds, 1886 residues, 47 models selected
> select subtract #21
23 models selected
> hide #!21 models
> hide #!36 models
> select add #37
29624 atoms, 30038 bonds, 3772 residues, 1 model selected
> color sel #cdca94ff
> show sel surfaces
> select add #35
52367 atoms, 53116 bonds, 3 pseudobonds, 6932 residues, 49 models selected
> show sel surfaces
> select clear
> show #!36 models
> hide #!36 models
> close #36
> close #34
> show #!33 models
> hide #!33 models
> show #!33 models
> show #!32 models
> show #!31 models
> hide #!31 models
> hide #!32 models
> hide #!33 models
> hide #!35 models
> show #!35 models
> show #!26 models
> hide #!26 models
> close #26
> show #!27 models
> save /Users/shoichi/Desktop/Shigella-ipaDnull-bin2-06252025.cxs includeMaps
> true
——— End of log from Wed Jun 25 10:52:06 2025 ———
opened ChimeraX session
> hide #!37 models
> show #!37 models
> show #!33 models
> hide #!33 models
> show #!33 models
> show #!32 models
> show #!28 models
> hide #!13 models
> show #!15 models
> hide #!15 models
> show #!16 models
> show #!15 models
> color #16 #42424208 models
> color #16 #4242421e models
> color #16 #42424240 models
> hide #!15 models
> color #14 #5e5e5eff models
> color #14 #5e5e5e81 models
> set bgColor black
> color #14 #5e5e5e80 models
> color #14 #5e5e5e67 models
> color #14 darkgrey models
> color #14 #a9a9a95b models
> color #14 #a9a9a967 models
> color #9 #a9a9a967 models
> show #!20 models
> show #!23 models
> select add #23
124488 atoms, 126648 bonds, 15424 residues, 3 models selected
> show sel surfaces
> select clear
> hide #!27 models
> hide #!23 models
> show #!23 models
> hide #!37 models
> hide #!35 models
> show #!7 models
> hide #!7 models
> show #!12 models
> view orient
> turn x 90
[Repeated 2 time(s)]
> view name P1
> save /Users/shoichitachiyama/Desktop/IMring.png supersample 2
> transparentBackground true
> color #9 darkgrey models
> color #9 #a9a9a980 models
> color #10 #a9a9a980 models
> color #12 #a9a9a980 models
> color #16 #a9a9a980 models
> color #28 #a9a9a980 models
> color #32 #a9a9a980 models
> color #33 #a9a9a980 models
> save /Users/shoichitachiyama/Desktop/IMring.png supersample 2
> transparentBackground true
> turn x 90
> ui tool show "Side View"
> hide #!9 models
> save /Users/shoichitachiyama/Desktop/IMring-2.png supersample 2
> transparentBackground true
> view P1
> show #!9 models
> show #!22 models
> show #!24 models
> show #!21 models
> hide #!21 models
> color #22 #009193ff
> color #22 #005493ff
> color #22 #009193ff
> color #22 #005759ff
> color #22 #005051ff
> color #24 #bfa292ff models
> color #24 #bf6943ff models
> color #24 #bf726cff models
> color #24 #bf746eff models
> color #24 #bf7570ff models
> color #24 #bf713aff models
> color #24 #bf5e32ff models
> show #!29 models
> color #29 #b6bfb4ff models
> color #29 #afbfbaff models
> color #29 #abaebfff models
> color #29 #92a0bfff models
> color #29 #99a9bfff models
> color #29 #94a0bfff models
> show #!30 models
> color #30 #bcbfa6ff models
> color #30 #bfb590ff models
> save /Users/shoichitachiyama/Desktop/Sorting_platform.png supersample 2
> transparentBackground true
> save /Users/shoichitachiyama/Desktop/Shigella-ipaDnull-bin2-07072025.cxs
> includeMaps true
> turn x 90
[Repeated 2 time(s)]
> save /Users/shoichitachiyama/Desktop/Sorting3_platform.png supersample 2
> transparentBackground true
> hide #!9 models
> save /Users/shoichitachiyama/Desktop/Sorting3_platform.png supersample 2
> transparentBackground true
> hide #!14 models
> save /Users/shoichitachiyama/Desktop/Sorting3_platform.png supersample 2
> transparentBackground true
> save /Users/shoichitachiyama/Desktop/Sorting2_platform.png supersample 2
> transparentBackground true
> turn x 90
> show #!21 models
> hide #!21 models
> show #!37 models
> show #!35 models
> show #!31 models
> hide #!31 models
> show #!27 models
> color #27 #d27473ff
> color #27 #d26969ff
> color #27 #d26968ff
> show #!9 models
> show #!14 models
> volume #312 region 60,0,0,120,120,200
No volumes specified
> volume #9 region 60,0,0,120,120,200
> volume #9 region 0,60,0,120,120,200
> volume #14 region 0,60,0,120,120,200
> volume #14 region 0,0,0,120,120,200
> volume #9 region 0,0,0,120,120,200
> save /Users/shoichitachiyama/Desktop/Overall.png supersample 2
> transparentBackground true
> volume #14 region 0,60,0,120,120,200
> volume #9 region 0,60,0,120,120,200
> hide #!24.6 models
> show #!24.6 models
> hide #!24.5 models
> show #!24.5 models
> hide #!24 models
> show #!24 models
> hide #!24.1 models
> show #!24.1 models
> hide #!24.2 models
> hide #!24.3 models
> hide #!29.2 models
> show #!29.2 models
> hide #!29.5 models
> hide #!29.6 models
> hide #!29.4 models
> hide #!29.3 models
> hide #!30.2 models
> show #!30.2 models
> hide #!30 models
> show #!30 models
> hide #!30.5 models
> show #!30.5 models
> hide #!30.6 models
> hide #!30.1 models
> hide #!10 models
> hide #!12 models
> hide #!16 models
> show #!24.3 models
> hide #!24.3 models
> show #!24.2 models
> show #!29.3 models
> show #!29.4 models
> show #!30.6 models
> show #!21 models
> hide #!21 models
> hide #!28 models
> hide #!32 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #!29.6 models
> show #!29.5 models
> show #!30.1 models
> show #!24.3 models
> save /Users/shoichitachiyama/Desktop/Overall2.png supersample 2
> transparentBackground true
> hide #!24.3 models
> hide #!29.5 models
> hide #!29.6 models
> hide #!30.1 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #23.1.1 models
> show #23.1.1 models
> hide #23.1.13 models
> show #23.1.13 models
> hide #23.1.20 models
> show #23.1.20 models
> hide #23.1.48 models
> show #23.1.48 models
> hide #23.1.44 models
> show #23.1.44 models
> hide #23.1.36 models
> hide #23.1.35 models
> show #23.1.35 models
> show #23.1.36 models
> hide #23.1.34 models
> hide #23.1.33 models
> hide #23.1.32 models
> hide #23.1.31 models
> hide #23.1.30 models
> hide #23.1.29 models
> hide #23.1.28 models
> show #23.1.28 models
> select add #23.1.29
2766 atoms, 340 residues, 1 model selected
> select add #23.1.30
5532 atoms, 680 residues, 2 models selected
> select add #23.1.31
8298 atoms, 1020 residues, 3 models selected
> select add #23.1.32
11064 atoms, 1360 residues, 4 models selected
> select add #23.1.33
13830 atoms, 1700 residues, 5 models selected
> select add #23.1.34
16596 atoms, 2040 residues, 6 models selected
> hide sel cartoons
> select subtract #23.1.29
13830 atoms, 1700 residues, 7 models selected
> select subtract #23.1.30
11064 atoms, 1360 residues, 6 models selected
> select subtract #23.1.31
8298 atoms, 1020 residues, 5 models selected
> select subtract #23.1.32
5532 atoms, 680 residues, 4 models selected
> select subtract #23.1.33
2766 atoms, 340 residues, 3 models selected
> select subtract #23.1.34
1 model selected
> hide #23.1.7 models
> show #23.1.7 models
> hide #23.1.4 models
> hide #23.1.3 models
> hide #23.1.5 models
> hide #23.1.2 models
> hide #23.1.1 models
> hide #!23.1 models
> show #!23.1 models
> hide #23.1.48 models
> show #23.1.48 models
> hide #23.1.6 models
> hide #23.1.18 models
> show #23.1.18 models
> hide #23.1.17 models
> show #23.1.17 models
> hide #23.1.15 models
> show #23.1.15 models
> hide #23.1.12 models
> show #23.1.12 models
> hide #23.1.13 models
> show #23.1.13 models
> hide #23.1.8 models
> show #23.1.8 models
> hide #23.1.7 models
> show #23.1.7 models
> hide #23.1.24 models
> show #23.1.24 models
> hide #23.1.22 models
> show #23.1.22 models
> hide #23.1.21 models
> hide #23.1.22 models
> hide #23.1.20 models
> hide #23.1.23 models
> show #23.1.22 models
> hide #23.1.22 models
> select add #23.1.23
1403 atoms, 177 residues, 1 model selected
> select add #23.1.22
2806 atoms, 354 residues, 2 models selected
> select add #23.1.21
4209 atoms, 531 residues, 3 models selected
> select add #23.1.20
5612 atoms, 708 residues, 4 models selected
> hide sel cartoons
> select add #23.1.6
7015 atoms, 885 residues, 5 models selected
> select add #23.1.5
8418 atoms, 1062 residues, 6 models selected
> select add #23.1.4
9821 atoms, 1239 residues, 7 models selected
> select add #23.1.3
11224 atoms, 1416 residues, 8 models selected
> select add #23.1.2
12627 atoms, 1593 residues, 9 models selected
> select add #23.1.1
14030 atoms, 1770 residues, 10 models selected
> hide sel cartoons
[Repeated 1 time(s)]
> hide #!23 models
> show #!23 models
> select clear
> hide #!33 models
> save /Users/shoichitachiyama/Desktop/Overall3.png supersample 2
> transparentBackground true
> save /Users/shoichitachiyama/Desktop/Shigella-ipaDnull-bin2-07072025.cxs
> includeMaps true
——— End of log from Mon Jul 7 21:04:45 2025 ———
opened ChimeraX session
> hide #!37 models
> hide #!30 models
> hide #!29 models
> hide #!35 models
> hide #!24 models
> hide #!23 models
> hide #!22 models
> hide #!20 models
> hide #!14 models
> hide #!9 models
> select add #27
22242 atoms, 22458 bonds, 33 pseudobonds, 2745 residues, 2 models selected
> hide sel surfaces
> show sel cartoons
> select clear
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project files/Shigella/MxiA-
> project/Data_Images/07072025/fold_2025_05_14_18_58mxia1/fold_2025_05_14_18_58mxia1_model_0.cif"
Chain information for fold_2025_05_14_18_58mxia1_model_0.cif #26
---
Chain | Description
A | .
> hide #26 models
> show #26 models
> ui tool show "Side View"
> select add #26
5358 atoms, 5438 bonds, 686 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #26,1,0,0,135.58,0,1,0,-2.256e-13,0,0,1,290.29
> view P1
> view matrix models #26,1,0,0,224.75,0,1,0,201.52,0,0,1,332.43
> view matrix models #26,1,0,0,227.1,0,1,0,185.42,0,0,1,351.22
> hide #27.1 models
> hide #27.2 models
> hide #27.3 models
> hide #27.4 models
> hide #27.5 models
> hide #27.9 models
> hide #27.8 models
> hide #27.7 models
> hide #27.6 models
> hide #27.10 models
> hide #!27 models
> show #!27 models
> show #27.1 models
> hide #27.1 models
> show #27.2 models
> hide #!27 models
> show #!27 models
> matchmaker #26 to #27
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 combination, chain A (#27) with
fold_2025_05_14_18_58mxia1_model_0.cif, chain A (#26), sequence alignment
score = 1659.8
RMSD between 262 pruned atom pairs is 0.900 angstroms; (across all 295 pairs:
1.890)
> close #26
> select add #27
22242 atoms, 22458 bonds, 33 pseudobonds, 2745 residues, 2 models selected
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
> select #27/A-C:363
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #27/A-C:363-365
72 atoms, 69 bonds, 9 residues, 1 model selected
> select #27/F,I:686
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #27/F,I:675-686
196 atoms, 196 bonds, 24 residues, 1 model selected
> select #27/F,I:356
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #27/F,I:356-358
40 atoms, 38 bonds, 6 residues, 1 model selected
> select #27/F,I:356
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #27/F,I:356-366
164 atoms, 164 bonds, 22 residues, 1 model selected
> select #27/E,H:357
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #27/E,H:357-363
100 atoms, 100 bonds, 14 residues, 1 model selected
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project files/Shigella/MxiA-
> project/Data_Images/07072025/fold_2025_06_25_11_12mxian9/fold_2025_06_25_11_12mxian9_model_0.cif"
Chain information for fold_2025_06_25_11_12mxian9_model_0.cif #26
---
Chain | Description
A B C D E F G H I | .
> select clear
> select add #26
23454 atoms, 23841 bonds, 3096 residues, 1 model selected
> view matrix models #26,1,0,0,146.86,0,1,0,151.64,0,0,1,307.37
> hide sel atoms
> show sel cartoons
> view matrix models #26,1,0,0,251.22,0,1,0,311.07,0,0,1,372.74
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.88671,-0.1247,0.4452,254.1,0.36009,0.79023,-0.49585,304.06,-0.28998,0.59999,0.7456,376.86
> matchmaker #26 to #27
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 combination, chain A (#27) with
fold_2025_06_25_11_12mxian9_model_0.cif, chain A (#26), sequence alignment
score = 81.9
Fewer than 3 residues aligned; cannot match combination, chain A with
fold_2025_06_25_11_12mxian9_model_0.cif, chain A
> view matrix models
> #26,0.60949,-0.15384,0.77772,257.26,0.74455,0.44806,-0.49486,300.01,-0.27233,0.88067,0.38763,376.41
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.60949,-0.15384,0.77772,285.96,0.74455,0.44806,-0.49486,246.82,-0.27233,0.88067,0.38763,406.33
> view matrix models
> #26,0.60949,-0.15384,0.77772,274.92,0.74455,0.44806,-0.49486,246.93,-0.27233,0.88067,0.38763,406.52
> view matrix models
> #26,0.60949,-0.15384,0.77772,273.03,0.74455,0.44806,-0.49486,246.95,-0.27233,0.88067,0.38763,406.94
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.62253,-0.2226,0.75027,272.12,0.73187,0.50512,-0.4574,247.84,-0.27716,0.83385,0.47737,407.28
> view matrix models
> #26,0.9126,0.08348,0.40023,271.4,0.25148,0.65721,-0.71051,248.11,-0.32235,0.74907,0.57878,407.44
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.9126,0.08348,0.40023,271.28,0.25148,0.65721,-0.71051,250.69,-0.32235,0.74907,0.57878,407.22
> view matrix models
> #26,0.9126,0.08348,0.40023,265.43,0.25148,0.65721,-0.71051,250.09,-0.32235,0.74907,0.57878,407.91
> view matrix models
> #26,0.9126,0.08348,0.40023,260.97,0.25148,0.65721,-0.71051,250.94,-0.32235,0.74907,0.57878,408.4
> mlp sel
Map values for surface "fold_2025_06_25_11_12mxian9_model_0.cif_A SES
surface": minimum -27.73, mean -0.7528, maximum 23.91
Map values for surface "fold_2025_06_25_11_12mxian9_model_0.cif_B SES
surface": minimum -27.06, mean -0.7287, maximum 23.08
Map values for surface "fold_2025_06_25_11_12mxian9_model_0.cif_C SES
surface": minimum -27.17, mean -0.7259, maximum 23.76
Map values for surface "fold_2025_06_25_11_12mxian9_model_0.cif_D SES
surface": minimum -27.79, mean -0.6774, maximum 23.47
Map values for surface "fold_2025_06_25_11_12mxian9_model_0.cif_E SES
surface": minimum -27.83, mean -0.6658, maximum 23.42
Map values for surface "fold_2025_06_25_11_12mxian9_model_0.cif_F SES
surface": minimum -27.05, mean -0.7118, maximum 23.14
Map values for surface "fold_2025_06_25_11_12mxian9_model_0.cif_G SES
surface": minimum -28.03, mean -0.7055, maximum 23.34
Map values for surface "fold_2025_06_25_11_12mxian9_model_0.cif_H SES
surface": minimum -28.28, mean -0.728, maximum 23.46
Map values for surface "fold_2025_06_25_11_12mxian9_model_0.cif_I SES
surface": minimum -27.24, mean -0.7021, maximum 23.39
To also show corresponding color key, enter the above mlp command and add key
true
> show #!9 models
> view P1
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.93635,0.02058,0.35046,259.9,0.25148,0.65721,-0.71051,250.94,-0.24495,0.75342,0.61021,408.47
> view matrix models
> #26,0.93421,0.014723,0.35641,259.9,0.24097,0.71067,-0.66097,251.88,-0.26303,0.70337,0.66037,408.47
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.93421,0.014723,0.35641,258.25,0.24097,0.71067,-0.66097,251.88,-0.26303,0.70337,0.66037,412.5
> turn x 90
> view matrix models
> #26,0.93421,0.014723,0.35641,256.64,0.24097,0.71067,-0.66097,262.97,-0.26303,0.70337,0.66037,412.5
> volume #312 region 0,0,0,120,120,200
No volumes specified
> volume #9 region 0,0,0,120,120,200
> view matrix models
> #26,0.93421,0.014723,0.35641,255.67,0.24097,0.71067,-0.66097,257.12,-0.26303,0.70337,0.66037,412.5
> show #!35 models
> view orient
> view matrix models
> #26,0.93421,0.014723,0.35641,255.72,0.24097,0.71067,-0.66097,257.87,-0.26303,0.70337,0.66037,412.5
> volume #9 region 0,60,0,120,120,200
> view P1
> color #26 #d26968ff
> select add #27
45696 atoms, 46299 bonds, 33 pseudobonds, 5841 residues, 12 models selected
> show sel surfaces
> save /Users/shoichitachiyama/Desktop/Shigella-ipaDnull-bin2-07072025.cxs
> includeMaps true
——— End of log from Tue Jul 8 20:43:49 2025 ———
opened ChimeraX session
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: 2 days, 6 hours
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
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