Opened 4 weeks ago

Closed 3 weeks ago

#18858 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by pett) 

The following bug report has been submitted:
Platform:        macOS-15.6-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 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, chimerax.pdb_lib._load_libs, 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.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, psutil._psutil_osx, psutil._psutil_posix, chimerax.segment._segment, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 65)


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{
  "uptime" : 3800000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac13,1",
  "coalitionID" : 13198,
  "osVersion" : {
    "train" : "macOS 15.6",
    "build" : "24G84",
    "releaseType" : "User"
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  "captureTime" : "2025-09-23 00:04:16.7850 -0400",
  "codeSigningMonitor" : 1,
  "incident" : "2964511B-2823-47A3-A045-1E4FB0BB82EA",
  "pid" : 9277,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-09-21 19:53:13.0853 -0400",
  "procStartAbsTime" : 90325475494919,
  "procExitAbsTime" : 92760600499917,
  "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" : 3860081,
  "sleepWakeUUID" : "33DCD15E-AB4C-4937-83CB-3B0726637761",
  "sip" : "enabled",
  "vmRegionInfo" : "0x51bab6661768 is not in any region.  Bytes after previous region: 89366431405929  Bytes before following region: 15690750355608\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      MALLOC_MEDIUM              73702a0000-7378000000   [125.4M] rw-\/rwx SM=SHM  \n--->  GAP OF 0x5f8c88000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  ",
  "exception" : {"codes":"0x0000000000000001, 0x000051bab6661768","rawCodes":[1,89862365910888],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000051bab6661768"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":9277},
  "ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
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fault"},"pc":{"value":6914642892},"far":{"value":0}}},{"id":37547440,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":161},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":162},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":162},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":162}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13259960008},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8777078032},{"value":0},{"value":4381795216,"symbolLocation":912,"symbol":"thread_status"},{"value":4381795280,"symbolLocation":976,"symbol":"thread_status"},{"value":13259960544},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4381708288,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6914900192},"cpsr":{"value":1610616832},"fp":{"value":13259960128},"sp":{"value":13259959984},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6914642892},"far":{"value":0}}},{"id":37547441,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":161},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":162},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":162},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":162}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13272329928},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8777078032},{"value":0},{"value":4381795344,"symbolLocation":1040,"symbol":"thread_status"},{"value":4381795408,"symbolLocation":1104,"symbol":"thread_status"},{"value":13272330464},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4381708288,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6914900192},"cpsr":{"value":1610616832},"fp":{"value":13272330048},"sp":{"value":13272329904},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6914642892},"far":{"value":0}}},{"id":38359256,"name":"QFileInfoGatherer","threadState":{"x":[{"value":260},{"value":0},{"value":4096},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":27956407688},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8777078032},{"value":0},{"value":105555146931072},{"value":105555146931136},{"value":27956408544},{"value":0},{"value":0},{"value":4096},{"value":4097},{"value":4352},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6914900192},"cpsr":{"value":1610616832},"fp":{"value":27956407808},"sp":{"value":27956407664},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6914642892},"far":{"value":0}},"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":161},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":162},{"imageOffset":2091016,"imageIndex":45},{"imageOffset":2090828,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":108,"imageIndex":45},{"imageOffset":4204344,"symbol":"QFileInfoGatherer::run()","symbolLocation":136,"imageIndex":49},{"imageOffset":2051468,"imageIndex":45},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":162},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":162}]},{"id":38416476,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":162}],"threadState":{"x":[{"value":13843591168},{"value":73755},{"value":13843054592},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13843591168},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6914878316},"far":{"value":0}}},{"id":38443416,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":162}],"threadState":{"x":[{"value":13813444608},{"value":179831},{"value":13812908032},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13813444608},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6914878316},"far":{"value":0}}},{"id":38496842,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":162}],"threadState":{"x":[{"value":13844164608},{"value":114939},{"value":13843628032},{"value":13844163456},{"value":7094276},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13844162928},"esr":{"value":0,"description":" Address size fault"},"pc":{"value":6914878316},"far":{"value":0}}}],
  "usedImages" : [
[deleted to fit within ticket limits]

],
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},
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    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
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},
  "logWritingSignature" : "21fd85c95149e325a0547644f6eb7c1d938de282",
  "trialInfo" : {
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      "factorPackIds" : {
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}
}
===== Log before crash start =====
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/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  
opened ChimeraX session  

> select clear

> hide #!26 models

> hide #!27 models

> hide #!35 models

> show #!10 models

> show #!11 models

> hide #!11 models

> show #!11 models

> show #!12 models

> lighting soft

> graphics silhouettes false

> set bgColor white

> graphics silhouettes true

> show #!13 models

> hide #!13 models

> show #!7 models

> hide #!7 models

> show #!14 models

> show #!15 models

> show #!16 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!18 models

> hide #!18 models

> show #!19 models

> hide #!19 models

> show #!19 models

> hide #!19 models

> show #!20 models

> hide #!20 models

> show #!21 models

> hide #!21 models

> show #!23 models

> hide #!23 models

> show #!22 models

> hide #!22 models

> show #!24 models

> hide #!24 models

> show #!28 models

> color #9 #9cb8a380 models

> color #9 #98b89e80 models

> color #9 #98b89eff models

> color #9 #a2b8a4ff models

> color #14 #a9a9a966 models

> color #14 #a2b8a4ff models

> color #10 darkgrey models

> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project files/Shigella/MxiA-
> project/Data_Images/07082025/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  
opened ChimeraX session  

> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Lab Slides/Lab
> Meeting/2025/July_2025/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  
opened ChimeraX session  

> show #!25 models

> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/Shigella/Sean_Spa33_mutants/08032025/Building_model_08042025.cxs"

Opened 1unit-map_SP.mrc as #1, grid size 120,120,100, pixel 4.3,4.3,4.3, shown
at level 0.0195, step 1, values float32  
Opened Global-map_SP.mrc as #2, grid size 120,120,100, pixel 4.3,4.3,4.3,
shown at level 0.125, step 1, values float32  
opened ChimeraX session  

> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project files/Shigella/MxiA-
> project/Data_Images/07082025/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  
opened ChimeraX session  

> hide #!9 models

> hide #!26 models

> hide #!27 models

> select add #26

45696 atoms, 46299 bonds, 33 pseudobonds, 5841 residues, 3 models selected  

> select subtract #26

22242 atoms, 22458 bonds, 33 pseudobonds, 2745 residues, 2 models selected  

> select add #27

22242 atoms, 22458 bonds, 33 pseudobonds, 2745 residues, 2 models selected  

> hide #!35 models

> show #!29 models

> hide #!29 models

> show #!28 models

> hide #!28 models

> show #!28 models

> select subtract #27

Nothing selected  

> show #!25 models

> volume #25 level 0.08402

> volume #25 level 0.07453

> hide #!25 models

> show #!24 models

> hide #!24 models

> show #!23 models

> hide #!23 models

> show #!22 models

> hide #!22 models

> show #!21 models

> hide #!21 models

> show #!19 models

> hide #!19 models

> show #!19 models

> set bgColor white

> hide #!19 models

> show #!18 models

> hide #!18 models

> show #!17 models

> hide #!17 models

> show #!16 models

> show #!15 models

> hide #!15 models

> show #!15 models

> show #!14 models

> hide #!14 models

> show #!14 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!12 models

> show #!11 models

> hide #!11 models

> show #!11 models

> show #!10 models

> hide #!10 models

> show #!10 models

> show #!9 models

> hide #!9 models

> show #!9 models

> open /Users/shoichitachiyama/Desktop/For-chimera-Shigella-C24/Sf-
> IMcomplexC24.mrc

Opened Sf-IMcomplexC24.mrc as #34, grid size 120,120,70, pixel 4.3,4.3,4.3,
shown at level 0.222, step 1, values float32  
Drag select of 34 Sf-IMcomplexC24.mrc  

> ui mousemode right "translate selected models"

> view matrix models #34,1,0,0,-8.4944,0,1,0,-53.933,0,0,1,366.97

> view matrix models #34,1,0,0,-3.3349,0,1,0,0.60543,0,0,1,369.18

> view matrix models #34,1,0,0,-0.83934,0,1,0,0.28041,0,0,1,373.89

> volume #34 level 0.08834

> volume #34 level 0.04977

> volume #34 level 0.04817

> 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.  

> hide #!12 models

> show #!12 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> fitmap #28 inMap #11

Fit map OM-complex.mrc in map MxiGp.mrc gaussian using 25812 points  
correlation = -0.1916, correlation about mean = 0.2251, overlap = -6.093  
steps = 104, shift = 0.658, angle = 0.127 degrees  
  
Position of OM-complex.mrc (#28) relative to MxiGp.mrc gaussian (#11)
coordinates:  
Matrix rotation and translation  
0.99999874 0.00106982 0.00117312 -1.50145698  
-0.00106884 0.99999908 -0.00083633 -0.65859833  
-0.00117401 0.00083508 0.99999896 367.42166235  
Axis 0.46578366 0.65409169 -0.59599467  
Axis point 201296.94409133 0.00000000 -85898.36893268  
Rotation angle (degrees) 0.10279983  
Shift along axis -220.11148877  
  

> fitmap #28 inMap #11

Fit map OM-complex.mrc in map MxiGp.mrc gaussian using 25812 points  
correlation = -0.1917, correlation about mean = 0.2251, overlap = -6.099  
steps = 84, shift = 0.0672, angle = 0.0492 degrees  
  
Position of OM-complex.mrc (#28) relative to MxiGp.mrc gaussian (#11)
coordinates:  
Matrix rotation and translation  
0.99999919 0.00122595 0.00034097 -1.42041107  
-0.00122562 0.99999877 -0.00097472 -0.58887632  
-0.00034216 0.00097430 0.99999947 367.17065250  
Axis 0.60801407 0.21310822 -0.76479002  
Axis point 48656.47738105 -138567.26800027 0.00000000  
Rotation angle (degrees) 0.09183237  
Shift along axis -281.79757598  
  

> fitmap #28 inMap #11

Fit map OM-complex.mrc in map MxiGp.mrc gaussian using 25812 points  
correlation = -0.1915, correlation about mean = 0.2248, overlap = -6.086  
steps = 64, shift = 0.119, angle = 0.092 degrees  
  
Position of OM-complex.mrc (#28) relative to MxiGp.mrc gaussian (#11)
coordinates:  
Matrix rotation and translation  
0.99999818 0.00159710 0.00104295 -1.62806282  
-0.00159754 0.99999864 0.00042000 -0.70090794  
-0.00104228 -0.00042167 0.99999937 367.72949474  
Axis -0.21544361 0.53375835 -0.81773228  
Axis point 100002.79709672 41700.54813854 0.00000000  
Rotation angle (degrees) 0.11191875  
Shift along axis -300.72763630  
  

> fitmap #28 inMap #11

Fit map OM-complex.mrc in map MxiGp.mrc gaussian using 25812 points  
correlation = -0.1918, correlation about mean = 0.225, overlap = -6.105  
steps = 148, shift = 0.168, angle = 0.138 degrees  
  
Position of OM-complex.mrc (#28) relative to MxiGp.mrc gaussian (#11)
coordinates:  
Matrix rotation and translation  
0.99999716 0.00232855 -0.00051663 -1.56660305  
-0.00232919 0.99999650 -0.00125192 -0.26552621  
0.00051371 0.00125311 0.99999908 366.88952209  
Axis 0.46492119 -0.19122499 -0.86445433  
Axis point -26113.84909317 -62818.82807987 -0.00000000  
Rotation angle (degrees) 0.15435714  
Shift along axis -317.83680694  
  

> view matrix models #34,1,0,0,-0.28144,0,1,0,1.1331,0,0,1,361.8

> fitmap #28 inMap #11

Fit map OM-complex.mrc in map MxiGp.mrc gaussian using 25812 points  
correlation = -0.192, correlation about mean = 0.2249, overlap = -6.112  
steps = 80, shift = 0.039, angle = 0.0582 degrees  
  
Position of OM-complex.mrc (#28) relative to MxiGp.mrc gaussian (#11)
coordinates:  
Matrix rotation and translation  
0.99999606 0.00278206 0.00036589 -1.84443175  
-0.00278168 0.99999560 -0.00103384 -0.19388248  
-0.00036876 0.00103282 0.99999940 367.17354175  
Axis 0.34556944 0.12284064 -0.93031819  
Axis point 15110.45054894 -41827.65557422 0.00000000  
Rotation angle (degrees) 0.17132808  
Shift along axis -342.24942084  
  

> fitmap #28 inMap #11

Fit map OM-complex.mrc in map MxiGp.mrc gaussian using 25812 points  
correlation = -0.1918, correlation about mean = 0.2252, overlap = -6.098  
steps = 140, shift = 0.0736, angle = 0.0586 degrees  
  
Position of OM-complex.mrc (#28) relative to MxiGp.mrc gaussian (#11)
coordinates:  
Matrix rotation and translation  
0.99999375 0.00353482 -0.00006432 -1.97047055  
-0.00353485 0.99999363 -0.00049280 -0.05839698  
0.00006258 0.00049302 0.99999988 367.17940662  
Axis 0.13808601 -0.01777476 -0.99026073  
Axis point -1821.62568629 -13660.35424483 0.00000000  
Rotation angle (degrees) 0.20452345  
Shift along axis -363.87440317  
  

> fitmap #28 inMap #11

Fit map OM-complex.mrc in map MxiGp.mrc gaussian using 25812 points  
correlation = -0.1917, correlation about mean = 0.2251, overlap = -6.097  
steps = 120, shift = 0.0358, angle = 0.06 degrees  
  
Position of OM-complex.mrc (#28) relative to MxiGp.mrc gaussian (#11)
coordinates:  
Matrix rotation and translation  
0.99999009 0.00444426 0.00025259 -2.24184270  
-0.00444424 0.99999012 -0.00008297 0.09125946  
-0.00025295 0.00008185 0.99999996 367.37566220  
Axis 0.01850935 0.05677463 -0.99821543  
Axis point 4708.05107654 -1012.52632072 0.00000000  
Rotation angle (degrees) 0.25509299  
Shift along axis -366.75636860  
  

> fitmap #28 inMap #11

Fit map OM-complex.mrc in map MxiGp.mrc gaussian using 25812 points  
correlation = -0.1918, correlation about mean = 0.2248, overlap = -6.105  
steps = 80, shift = 0.0637, angle = 0.0515 degrees  
  
Position of OM-complex.mrc (#28) relative to MxiGp.mrc gaussian (#11)
coordinates:  
Matrix rotation and translation  
0.99998801 0.00489043 -0.00027068 -2.28701360  
-0.00489061 0.99998782 -0.00066125 0.30497070  
0.00026744 0.00066257 0.99999974 367.11509851  
Axis 0.13392385 -0.05443923 -0.98949521  
Axis point -3961.15338732 -9498.69875486 0.00000000  
Rotation angle (degrees) 0.28318210  
Shift along axis -363.58152002  
  

> fitmap #28 inMap #9

Fit map OM-complex.mrc in map IM.mrc gaussian using 25812 points  
correlation = -0.3221, correlation about mean = 0.1923, overlap = -14.43  
steps = 84, shift = 2.54, angle = 0.399 degrees  
  
Position of OM-complex.mrc (#28) relative to IM.mrc gaussian (#9) coordinates:  
Matrix rotation and translation  
0.99999966 -0.00059382 0.00057511 -1.02461266  
0.00059178 0.99999354 0.00354475 -4.11867611  
-0.00057721 -0.00354441 0.99999355 369.91433125  
Axis -0.97386574 0.15829867 0.16287128  
Axis point -0.00000000 101573.73028102 4052.92186273  
Rotation angle (degrees) 0.20854011  
Shift along axis 60.59427476  
  

> fitmap #28 inMap #9

Fit map OM-complex.mrc in map IM.mrc gaussian using 25812 points  
correlation = -0.3225, correlation about mean = 0.1925, overlap = -14.45  
steps = 48, shift = 0.0505, angle = 0.0619 degrees  
  
Position of OM-complex.mrc (#28) relative to IM.mrc gaussian (#9) coordinates:  
Matrix rotation and translation  
0.99999889 -0.00141539 0.00046032 -0.81773082  
0.00141343 0.99999002 0.00423709 -4.44675909  
-0.00046631 -0.00423643 0.99999092 370.06122072  
Axis -0.94347649 0.10317436 0.31497169  
Axis point 0.00000000 78654.11038813 4080.51591718  
Rotation angle (degrees) 0.25729244  
Shift along axis 116.87152627  
  

> hide #!28 models

> show #!28 models

> hide #!28 models

> show #!28 models

> fitmap #34 inMap #9

Fit map Sf-IMcomplexC24.mrc in map IM.mrc gaussian using 96273 points  
correlation = 0.2367, correlation about mean = -0.168, overlap = 105.5  
steps = 88, shift = 9.53, angle = 1.09 degrees  
  
Position of Sf-IMcomplexC24.mrc (#34) relative to IM.mrc gaussian (#9)
coordinates:  
Matrix rotation and translation  
0.99998040 0.00621853 0.00072790 -2.60899045  
-0.00623061 0.99981909 0.01797103 -5.62248612  
-0.00061601 -0.01797522 0.99983824 373.37469423  
Axis -0.94434657 0.03530587 -0.32705207  
Axis point 0.00000000 18588.67642201 264.53433309  
Rotation angle (degrees) 1.09053857  
Shift along axis -119.84768241  
  

> fitmap #34 inMap #9

Fit map Sf-IMcomplexC24.mrc in map IM.mrc gaussian using 96273 points  
correlation = 0.2368, correlation about mean = -0.1679, overlap = 105.5  
steps = 44, shift = 0.0728, angle = 0.128 degrees  
  
Position of Sf-IMcomplexC24.mrc (#34) relative to IM.mrc gaussian (#9)
coordinates:  
Matrix rotation and translation  
0.99996405 0.00844568 0.00074901 -3.19640196  
-0.00845781 0.99980183 0.01802106 -5.01829887  
-0.00059666 -0.01802675 0.99983733 373.44712604  
Axis -0.90488361 0.03377925 -0.42431665  
Axis point 0.00000000 17048.94079030 174.02665897  
Rotation angle (degrees) 1.14132046  
Shift along axis -155.73697672  
  

> volume #34 level 0.03049

> hide #!9 models

> hide #!10 models

> hide #!11 models

> hide #!12 models

> hide #!14 models

> hide #!15 models

> hide #!16 models

> hide #!28 models

> 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 Sf-IMcomplexC24.mrc, density threshold 0.030491  
Showing 75 region surfaces  
1195 watershed regions, grouped to 75 regions  
Showing Sf-IMcomplexC24.seg - 75 regions, 75 surfaces  

> select #36.16

1 model selected  

> select add #36.60

2 models selected  

> select add #36.24

3 models selected  

> select add #36.26

4 models selected  

> select add #36.20

5 models selected  

> select add #36.13

6 models selected  

> select add #36.40

7 models selected  

> select add #36.55

8 models selected  

> select add #36.23

9 models selected  

> select add #36.31

10 models selected  

> select subtract #36.31

9 models selected  

> select add #36.45

10 models selected  

> select add #36.31

11 models selected  

> select add #36.42

12 models selected  

> select add #36.19

13 models selected  

> select add #36.43

14 models selected  

> select add #36.15

15 models selected  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select #36.15

1 model selected  
Ungrouped to 5 regions  
Ungrouped to 11 regions  
Ungrouped to 4 regions  
Ungrouped to 0 regions  
Drag select of 1643, 4484 of 11296 triangles, 1637, 2671 of 9176 triangles,
1638, 2473 of 8828 triangles, 1644, 3388 of 8108 triangles, 1641, 2579 of 7400
triangles, 1653, 2498 of 7588 triangles, 1649, 2072 of 6632 triangles, 1595,
2075 of 5820 triangles, 1603, 2290 of 4704 triangles, 1623, 1802 of 4932
triangles, 1614, 92 of 4452 triangles, 1598, 119 of 4256 triangles, 1452, 44
of 2156 triangles, 1635, 1142 of 2144 triangles, 769, 818, 881 of 1680
triangles, 787, 808, 1050 of 1792 triangles, 789, 1296 of 2112 triangles, 748,
803, 1117 of 1932 triangles  
Grouped 21 regions  

> select #36.89

1 model selected  

> select add #36.90

2 models selected  

> select add #36.13

3 models selected  
Grouped 3 regions  

> select #36.78

1 model selected  

> select add #36.79

2 models selected  

> select add #36.13

3 models selected  
Grouped 3 regions  

> select clear

> select #36.13

1 model selected  
Showing 64 region surfaces  
Opened Sf-IMcomplexC24_imasked as #38, grid size 120,120,70, pixel
4.3,4.3,4.3, 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/Shigella-Segment-Meeting/MxiGc24P.mrc
> models #38

Opened Sf-IMcomplexC24_imasked as #39, grid size 120,120,70, pixel
4.3,4.3,4.3, shown at step 1, values float32  
Segmenting Sf-IMcomplexC24_imasked, density threshold 0.030491  
Showing 60 region surfaces  
1078 watershed regions, grouped to 60 regions  
Showing Sf-IMcomplexC24_imasked.seg - 60 regions, 60 surfaces  

> select #36.32

1 model selected  

> select add #36.45

2 models selected  

> select add #36.36

3 models selected  

> select add #36.44

4 models selected  

> select add #36.54

5 models selected  

> select add #36.31

6 models selected  

> select add #36.26

7 models selected  

> select add #36.49

8 models selected  

> select add #36.30

9 models selected  

> select add #36.38

10 models selected  

> select add #36.34

11 models selected  

> select add #36.48

12 models selected  

> select add #36.27

13 models selected  

> select add #36.18

14 models selected  

> select add #36.23

15 models selected  

> select add #36.14

16 models selected  
Grouped 16 regions  

> select add #36.29

2 models selected  

> select add #36.25

3 models selected  

> select add #36.22

4 models selected  

> select add #36.33

5 models selected  

> select add #36.19

6 models selected  

> select add #36.35

7 models selected  

> select add #36.15

8 models selected  
Grouped 8 regions  

> select add #36.16

2 models selected  

> select add #36.28

3 models selected  

> select add #36.37

4 models selected  
Grouped 4 regions  

> select clear

> select #36.14

1 model selected  
Opened Sf-IMcomplexC24_imasked_imasked as #40, grid size 120,120,70, pixel
4.3,4.3,4.3, shown at step 1, values float32  
Segmenting Sf-IMcomplexC24_imasked_imasked, density threshold 0.030491  
Showing 26 region surfaces  
129 watershed regions, grouped to 26 regions  
Showing Sf-IMcomplexC24_imasked_imasked.seg - 26 regions, 26 surfaces  

> select #36.5

1 model selected  

> select add #36.3

2 models selected  

> select #36.3

1 model selected  

> select add #36.5

2 models selected  

> select add #36.1

3 models selected  

> select #36.3

1 model selected  

> select add #36.5

2 models selected  

> select add #36.1

3 models selected  
Ungrouped to 11 regions  
Ungrouped to 24 regions  
Ungrouped to 6 regions  
Ungrouped to 0 regions  

> select #36.57

1 model selected  

> select add #36.32

2 models selected  

> select add #36.41

3 models selected  

> select add #36.38

4 models selected  

> select add #36.58

5 models selected  

> select add #36.2

6 models selected  

> select add #36.31

7 models selected  

> select add #36.7

8 models selected  

> select add #36.40

9 models selected  

> select add #36.8

10 models selected  
Ungrouped to 7 regions  
Ungrouped to 13 regions  
Ungrouped to 8 regions  
Ungrouped to 2 regions  

> select #36.7

1 model selected  

> select add #36.58

2 models selected  

> select add #36.71

3 models selected  

> select add #36.31

4 models selected  

> select add #36.68

5 models selected  

> select add #36.40

6 models selected  
Showing 71 region surfaces  

> select add #36.41

7 models selected  

> select add #36.32

8 models selected  

> select add #36.57

9 models selected  

> select add #36.38

10 models selected  
Grouped 10 regions  

> select clear

> select #36.4

1 model selected  

> select add #36.51

2 models selected  

> select add #36.34

3 models selected  

> select add #36.6

4 models selected  

> select add #36.12

5 models selected  
Ungrouped to 6 regions  
Ungrouped to 14 regions  
Ungrouped to 4 regions  
Ungrouped to 0 regions  

> select #36.34

1 model selected  

> select add #36.51

2 models selected  

> select add #36.58

3 models selected  

> select add #36.4

4 models selected  

> select add #36.12

5 models selected  

> select add #36.57

6 models selected  
Showing 75 region surfaces  

> select add #36.7

7 models selected  
Grouped 7 regions  
Opened Sf-IMcomplexC24_imasked_imasked_imasked as #41, grid size 120,120,70,
pixel 4.3,4.3,4.3, 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/Shigella-Segment-Meeting/OM-
> complexC24.mrc models #41

> close #39-40

> close #38,41

> close #36

> hide #!34 models

> open /Users/shoichitachiyama/Desktop/Shigella-Segment-Meeting/MxiGc24P.mrc

Opened MxiGc24P.mrc as #36, grid size 120,120,70, pixel 4.3,4.3,4.3, shown at
level 0.146, step 1, values float32  

> open /Users/shoichitachiyama/Desktop/Shigella-Segment-Meeting/OM-
> complexC24.mrc

Opened OM-complexC24.mrc as #38, grid size 120,120,70, pixel 4.3,4.3,4.3,
shown at level 0.132, step 1, values float32  

> hide #!36 models

> show #!36 models

> show #!28 models

> show #!29 models

> hide #!29 models

> open /Users/shoichitachiyama/Desktop/For-chimera-Shigella-C24/Sf-
> IMcomplexC24.mrc

Opened Sf-IMcomplexC24.mrc as #39, grid size 120,120,70, pixel 4.3,4.3,4.3,
shown at level 0.222, step 1, values float32  

> hide #!38 models

> hide #!36 models

> show #!9 models

> volume #39 level 0.06263

> select add #39

2 models selected  

> view matrix models #39,1,0,0,-18.535,0,1,0,-6.2875,0,0,1,354.52

> fitmap #39 inMap #9

Fit map Sf-IMcomplexC24.mrc in map IM.mrc gaussian using 69029 points  
correlation = 0.2138, correlation about mean = -0.1899, overlap = 83.92  
steps = 72, shift = 22.4, angle = 0.99 degrees  
  
Position of Sf-IMcomplexC24.mrc (#39) relative to IM.mrc gaussian (#9)
coordinates:  
Matrix rotation and translation  
0.99994351 0.01061992 0.00043167 -3.69011956  
-0.01062482 0.99985087 0.01361462 -3.47124881  
-0.00028702 -0.01361844 0.99990722 371.91096778  
Axis -0.78829019 0.02080320 -0.61495187  
Axis point 0.00000000 17109.33285333 97.24755556  
Rotation angle (degrees) 0.98974762  
Shift along axis -225.87067345  
  

> fitmap #39 inMap #9

Fit map Sf-IMcomplexC24.mrc in map IM.mrc gaussian using 69029 points  
correlation = 0.2136, correlation about mean = -0.1897, overlap = 83.81  
steps = 40, shift = 0.0112, angle = 0.0593 degrees  
  
Position of Sf-IMcomplexC24.mrc (#39) relative to IM.mrc gaussian (#9)
coordinates:  
Matrix rotation and translation  
0.99995396 0.00958788 0.00038961 -3.41289672  
-0.00959227 0.99986226 0.01354412 -3.72862091  
-0.00025970 -0.01354724 0.99990820 371.88084771  
Axis -0.81600428 0.01955750 -0.57771491  
Axis point -0.00000000 18403.48310234 156.13759674  
Rotation angle (degrees) 0.95115436  
Shift along axis -212.12909536  
  

> hide #!28 models

> hide #!9 models

> show #!37 models

> hide #!37 models

> show #!36 models

> show #!38 models

> select add #36

4 models selected  

> select add #38

6 models selected  

> select clear

> select add #36

2 models selected  

> select add #38

4 models selected  

> view matrix models
> #36,1,0,0,-38.579,0,1,0,-51.145,0,0,1,329.8,#38,1,0,0,-38.579,0,1,0,-51.145,0,0,1,329.8

> view matrix models
> #36,1,0,0,9.4599,0,1,0,-19.514,0,0,1,350.03,#38,1,0,0,9.4599,0,1,0,-19.514,0,0,1,350.03

> view matrix models
> #36,1,0,0,-7.0146,0,1,0,-16.39,0,0,1,353.93,#38,1,0,0,-7.0146,0,1,0,-16.39,0,0,1,353.93

> fitmap #36 inMap #39

Fit map MxiGc24P.mrc in map Sf-IMcomplexC24.mrc using 10076 points  
correlation = 1, correlation about mean = 1, overlap = 761.1  
steps = 68, shift = 19.4, angle = 0.939 degrees  
  
Position of MxiGc24P.mrc (#36) relative to Sf-IMcomplexC24.mrc (#39)
coordinates:  
Matrix rotation and translation  
0.99999997 -0.00020808 0.00013044 0.03645608  
0.00020810 0.99999997 -0.00011597 -0.03913831  
-0.00013042 0.00011600 0.99999998 -0.02442950  
Axis 0.42704434 0.48023569 0.76616370  
Axis point 137.46463051 220.21541538 0.00000000  
Rotation angle (degrees) 0.01556158  
Shift along axis -0.02194425  
  

> fitmap #36 inMap #39

Fit map MxiGc24P.mrc in map Sf-IMcomplexC24.mrc using 10076 points  
correlation = 1, correlation about mean = 0.9997, overlap = 759.2  
steps = 28, shift = 0.13, angle = 0.0464 degrees  
  
Position of MxiGc24P.mrc (#36) relative to Sf-IMcomplexC24.mrc (#39)
coordinates:  
Matrix rotation and translation  
0.99999981 0.00060200 0.00012213 -0.17133368  
-0.00060199 0.99999981 -0.00011435 0.16749047  
-0.00012219 0.00011428 0.99999999 0.10359201  
Axis 0.18295611 0.19551364 -0.96348403  
Axis point 310.10963932 254.79497484 0.00000000  
Rotation angle (degrees) 0.03579914  
Shift along axis -0.09840912  
  

> fitmap #38 inMap #39

Fit map OM-complexC24.mrc in map Sf-IMcomplexC24.mrc using 10079 points  
correlation = 1, correlation about mean = 0.9997, overlap = 551.5  
steps = 80, shift = 20.3, angle = 0.823 degrees  
  
Position of OM-complexC24.mrc (#38) relative to Sf-IMcomplexC24.mrc (#39)
coordinates:  
Matrix rotation and translation  
0.99998993 -0.00447141 -0.00039222 1.19452793  
0.00447136 0.99998999 -0.00013230 -1.14283343  
0.00039281 0.00013054 0.99999991 -0.00426787  
Axis 0.02926645 -0.08740979 0.99574244  
Axis point 253.63111382 265.72160668 0.00000000  
Rotation angle (degrees) 0.25728780  
Shift along axis 0.13060473  
  

> fitmap #38 inMap #39

Fit map OM-complexC24.mrc in map Sf-IMcomplexC24.mrc using 10079 points  
correlation = 1, correlation about mean = 0.9997, overlap = 551.8  
steps = 28, shift = 0.0781, angle = 0.0587 degrees  
  
Position of OM-complexC24.mrc (#38) relative to Sf-IMcomplexC24.mrc (#39)
coordinates:  
Matrix rotation and translation  
0.99999400 -0.00345334 -0.00027321 0.98385519  
0.00345331 0.99999403 -0.00011235 -0.86969305  
0.00027360 0.00011140 0.99999996 0.03150905  
Axis 0.03227822 -0.07888250 0.99636121  
Axis point 249.32304748 283.23460551 0.00000000  
Rotation angle (degrees) 0.19858414  
Shift along axis 0.13175505  
  

> close #39

> volume #38 level 0.03594

> volume #36 level 0.03333

> surface dust #36 size 43

> surface dust #38 size 43

> color #36 #b3faffff models

> color #36 #6cd3ffff models

> color #36 #56bfffff models

> color #36 #a9a9a980 models

> color #38 #a9a9a980 models

> select clear

> show #!33 models

> show #!32 models

> hide #!32 models

> show #!32 models

> hide #!32 models

> close #32

> show #!29 models

> hide #!29 models

> show #!28 models

> hide #!28 models

> close #28

> show #!15 models

> show #!16 models

> show #!14 models

> show #!12 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> open /Users/shoichitachiyama/Desktop/Shigella-Segment-Meeting/6RWY.cif

6RWY.cif title:  
Export apparatus core and inner rod of the Shigella type 3 secretion system
[more info...]  
  
Chain information for 6RWY.cif #28  
---  
Chain | Description | UniProt  
A G H I J K | Inner rod protein |   
B C D E F | Inner rod protein |   
L M N O P Q R S T U V | Protein MxiH | MXIH_SHIFL 1-83  
a b c d e | Surface presentation of antigens protein SpaP | SPAP_SHIFL 1-216  
f | Surface presentation of antigens protein SpaR | SPAR_SHIFL 1-256  
g h i j k | Surface presentation of antigens protein SpaQ | SPAQ_SHIFL 1-86  
  
Drag select of 249 atoms  

> hide sel atoms

> show sel cartoons

> select add #28

22743 atoms, 23078 bonds, 3 pseudobonds, 3160 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> view matrix models #28,1,0,0,-84.841,0,1,0,-61.648,0,0,1,234.96

> hide #!33 models

> show #!33 models

> show #!35 models

> hide #!35 models

> hide #!36 models

> hide #!38 models

> view matrix models #28,1,0,0,-74.078,0,1,0,-74.547,0,0,1,192.36

> view matrix models #28,1,0,0,-76.374,0,1,0,-77.794,0,0,1,191.61

> hide #!12 models

> show #!12 models

> hide #!12 models

> fitmap #28 inMap #33

Fit molecule 6RWY.cif (#28) to map Exp.mrc (#33) using 22743 atoms  
average map value = 0.0391, steps = 68  
shifted from previous position = 4.1  
rotated from previous position = 3.92 degrees  
atoms outside contour = 11080, contour level = 0.0282  
  
Position of 6RWY.cif (#28) relative to Exp.mrc (#33) coordinates:  
Matrix rotation and translation  
0.99780869 -0.01928560 -0.06329204 -48.13904166  
0.01995100 0.99975196 0.00989808 -83.72762481  
0.06308545 -0.01113913 0.99794596 -187.38600859  
Axis -0.15700576 -0.94318531 0.29283213  
Axis point 3091.60223959 0.00000000 -789.09616374  
Rotation angle (degrees) 3.84141051  
Shift along axis 31.65612874  
  

> fitmap #28 inMap #33

Fit molecule 6RWY.cif (#28) to map Exp.mrc (#33) using 22743 atoms  
average map value = 0.03909, steps = 28  
shifted from previous position = 0.0257  
rotated from previous position = 0.0552 degrees  
atoms outside contour = 11075, contour level = 0.0282  
  
Position of 6RWY.cif (#28) relative to Exp.mrc (#33) coordinates:  
Matrix rotation and translation  
0.99783300 -0.01839336 -0.06317424 -48.47541036  
0.01908075 0.99976494 0.01029472 -83.54330313  
0.06297004 -0.01147782 0.99794941 -187.23463937  
Axis -0.16323456 -0.94573762 0.28095345  
Axis point 3100.94830589 0.00000000 -785.02188705  
Rotation angle (degrees) 3.82394828  
Shift along axis 34.31868914  
  

> open /Users/shoichitachiyama/Desktop/Shigella-Segment-Meeting/6RWX.cif

6RWX.cif title:  
Periplasmic inner membrane ring of the Shigella type 3 secretion system [more
info...]  
  
Chain information for 6RWX.cif #32  
---  
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 | 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  
  

> select subtract #28

Nothing selected  

> select add #32

70968 atoms, 72048 bonds, 8784 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> show #!36 models

> view matrix models #32,1,0,0,-109.42,0,1,0,40.678,0,0,1,149.59

> view matrix models #32,1,0,0,-64.432,0,1,0,-74.769,0,0,1,218.9

> view matrix models #32,1,0,0,-70.025,0,1,0,-73.26,0,0,1,217.84

> fitmap #32 inMap #36

Fit molecule 6RWX.cif (#32) to map MxiGc24P.mrc (#36) using 70968 atoms  
average map value = 0.1504, steps = 48  
shifted from previous position = 8.26  
rotated from previous position = 3.88 degrees  
atoms outside contour = 11644, contour level = 0.033329  
  
Position of 6RWX.cif (#32) relative to MxiGc24P.mrc (#36) coordinates:  
Matrix rotation and translation  
0.99706755 -0.07652596 0.00029486 -48.22871685  
0.07652603 0.99706755 -0.00025339 -98.77828868  
-0.00027460 0.00027521 0.99999992 -148.87930341  
Axis 0.00345369 0.00372065 0.99998711  
Axis point 1257.77732012 -671.68149737 0.00000000  
Rotation angle (degrees) 4.38896410  
Shift along axis -149.41147196  
  

> fitmap #32 inMap #36

Fit molecule 6RWX.cif (#32) to map MxiGc24P.mrc (#36) using 70968 atoms  
average map value = 0.1504, steps = 28  
shifted from previous position = 0.0368  
rotated from previous position = 0.0424 degrees  
atoms outside contour = 11656, contour level = 0.033329  
  
Position of 6RWX.cif (#32) relative to MxiGc24P.mrc (#36) coordinates:  
Matrix rotation and translation  
0.99712394 -0.07578766 0.00029311 -48.49175141  
0.07578773 0.99712394 -0.00025701 -98.55098676  
-0.00027279 0.00027849 0.99999992 -148.91782442  
Axis 0.00353285 0.00373346 0.99998679  
Axis point 1267.15134273 -680.95727133 0.00000000  
Rotation angle (degrees) 4.34654031  
Shift along axis -149.45510718  
  

> fitmap #32 inMap #36

Fit molecule 6RWX.cif (#32) to map MxiGc24P.mrc (#36) using 70968 atoms  
average map value = 0.1504, steps = 40  
shifted from previous position = 0.0394  
rotated from previous position = 0.0481 degrees  
atoms outside contour = 11640, contour level = 0.033329  
  
Position of 6RWX.cif (#32) relative to MxiGc24P.mrc (#36) coordinates:  
Matrix rotation and translation  
0.99705998 -0.07662454 0.00028081 -48.18992315  
0.07662460 0.99705999 -0.00023406 -98.81337058  
-0.00026205 0.00025489 0.99999993 -148.87416859  
Axis 0.00319054 0.00354231 0.99998864  
Axis point 1256.92956314 -670.91736570 0.00000000  
Rotation angle (degrees) 4.39462191  
Shift along axis -149.37625644  
  

> fitmap #32 inMap #36

Fit molecule 6RWX.cif (#32) to map MxiGc24P.mrc (#36) using 70968 atoms  
average map value = 0.1504, steps = 28  
shifted from previous position = 0.0754  
rotated from previous position = 0.0334 degrees  
atoms outside contour = 11663, contour level = 0.033329  
  
Position of 6RWX.cif (#32) relative to MxiGc24P.mrc (#36) coordinates:  
Matrix rotation and translation  
0.99710444 -0.07604381 0.00029133 -48.39892530  
0.07604388 0.99710444 -0.00025157 -98.63144582  
-0.00027136 0.00027299 0.99999993 -148.80171698  
Axis 0.00344904 0.00369969 0.99998721  
Axis point 1263.95844827 -677.81651911 0.00000000  
Rotation angle (degrees) 4.36125738  
Shift along axis -149.33164917  
  

> open /Users/shoichitachiyama/Desktop/Shigella-Segment-Meeting/6RWK.cif

6RWK.cif title:  
MxiD N0 N1 and MxiG C-terminal domains of the Shigella type 3 secretion system
[more info...]  
  
Chain information for 6RWK.cif #39  
---  
Chain | Description | UniProt  
0 1 2 3 4 5 6 7 8 9 X Y Z x y z | Outer membrane protein MxiD | MXID_SHIFL 1-566  
A B D E G H J K M N P Q S T U V | Protein MxiG | MXIG_SHIFL 1-371  
  

> select subtract #32

Nothing selected  

> select add #32

70968 atoms, 72048 bonds, 8784 residues, 1 model selected  

> select add #33

70968 atoms, 72048 bonds, 8784 residues, 3 models selected  

> select subtract #32

2 models selected  

> select subtract #33

Nothing selected  

> select add #36

2 models selected  

> select subtract #36

Nothing selected  

> select add #39

21760 atoms, 22224 bonds, 2688 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> view matrix models #39,1,0,0,-95.841,0,1,0,-68.315,0,0,1,230.08

> view matrix models #39,1,0,0,-73.018,0,1,0,-81.271,0,0,1,225.4

> open /Users/shoichitachiyama/Desktop/Shigella-Segment-Meeting/7AH9.cif

Summary of feedback from opening /Users/shoichitachiyama/Desktop/Shigella-
Segment-Meeting/7AH9.cif  
---  
warnings | Atom H1 is not in the residue template for MET /1A:1  
Atom H1 is not in the residue template for MET /1B:1  
Atom H1 is not in the residue template for MET /1C:1  
Atom H1 is not in the residue template for MET /1D:1  
Atom H1 is not in the residue template for MET /1E:1  
4 messages similar to the above omitted  
Too many hydrogens missing from residue template(s) to warn about  
  
7AH9.cif title:  
Substrate-engaged type 3 secretion system needle complex from Salmonella
enterica typhimurium - SpaR state 1 [more info...]  
  
Chain information for 7AH9.cif #40  
---  
Chain | Description | UniProt  
1A 1B 1C 1D 1E | Surface presentation of antigens protein SpaP | SPAP_SALTY 1-224  
1F | Surface presentation of antigens protein SpaR | SPAR_SALTY 1-263  
1G 1H 1I 1J | Surface presentation of antigens protein SpaQ | SPAQ_SALTY 1-86  
1K 1L 1M 1N 1O 1P | Protein PrgJ | PRGJ_SALTY 1-101  
1Z | SptP3x-GFP-FLAG |   
2A 2B 2C 2D 2E 2F 2G 2H 2I 2J 2K 2L 2M 2N 2O 2P 2Q 2R 2S 2T 2U 2V 2W 2X 2Y 2Z 3A 3B 3C 3D 3E 3F 3G 3H 3I 3J 3K 3L 3M 3N 3O 3P 3Q 3R 3S 3T 3U 3V 3W 3X 3Y 3Z 4A 4B 4C 4D 4E 4F 4G 4H 4I 4J 4K 4L 4M 4N 4O 4P 4Q 4R 4S 4T | Protein PrgI | PRGI_SALTY 1-80  
5A 5B 5C 5D 5E 5F 5G 5H 5I 5J 5K 5L 5M 5N 5O 5P | Type 3 secretion system secretin | SCTC_SALTY 1-562  
6A 6B 6C 6D 6E 6F 6G 6H 6I 6J 6K 6L 6M 6N 6O 6P 6Q 6R 6S 6T 6U 6V 6W 6X | Lipoprotein PrgK | PRGK_SALTY 1-252  
7A 7B 7C 7D 7E 7F 7G 7H 7I 7J 7K 7L 7M 7N 7O 7P 7Q 7R 7S 7T 7U 7V 7W 7X | Protein PrgH | PRGH_SALTY 1-392  
  
Non-standard residues in 7AH9.cif #40  
---  
3PH — 1,2-diacyl-glycerol-3-Sn-phosphate (phosphatidic acid)  
LDA — lauryl dimethylamine-N-oxide  
  

> select subtract #39

Nothing selected  

> select add #40

399559 atoms, 403366 bonds, 17 pseudobonds, 25314 residues, 2 models selected  

> close #28

> close #32

> close #39

> hide sel atoms

> show sel cartoons

> view matrix models #40,1,0,0,-56.724,0,1,0,12.127,0,0,1,345.02

> view matrix models #40,1,0,0,-23.286,0,1,0,-45.952,0,0,1,347.77

> view matrix models #40,1,0,0,-61.607,0,1,0,-82.159,0,0,1,347.61

> show #!34 models

> fitmap #40 inMap #34

Fit molecule 7AH9.cif (#40) to map Sf-IMcomplexC24.mrc (#34) using 399559
atoms  
average map value = 0.1233, steps = 152  
shifted from previous position = 14.1  
rotated from previous position = 5.47 degrees  
atoms outside contour = 137015, contour level = 0.030491  
  
Position of 7AH9.cif (#40) relative to Sf-IMcomplexC24.mrc (#34) coordinates:  
Matrix rotation and translation  
0.99622693 0.08648507 0.00722691 -101.67677425  
-0.08637372 0.99615709 -0.01451336 -40.15255410  
-0.00845433 0.01383438 0.99986856 -17.82819131  
Axis 0.16118733 0.08916465 -0.98288774  
Axis point -513.45239613 1148.69775677 0.00000000  
Rotation angle (degrees) 5.04477128  
Shift along axis -2.44608565  
  

> fitmap #40 inMap #34

Fit molecule 7AH9.cif (#40) to map Sf-IMcomplexC24.mrc (#34) using 399559
atoms  
average map value = 0.1233, steps = 60  
shifted from previous position = 0.0409  
rotated from previous position = 0.00974 degrees  
atoms outside contour = 137026, contour level = 0.030491  
  
Position of 7AH9.cif (#40) relative to Sf-IMcomplexC24.mrc (#34) coordinates:  
Matrix rotation and translation  
0.99622710 0.08648654 0.00718584 -101.67698589  
-0.08637437 0.99615461 -0.01467829 -40.15349907  
-0.00842768 0.01400223 0.99986645 -17.87698811  
Axis 0.16303319 0.08875437 -0.98262040  
Axis point -513.35872591 1148.39208209 0.00000000  
Rotation angle (degrees) 5.04620909  
Shift along axis -2.57422826  
  

> fitmap #40 inMap #34

Fit molecule 7AH9.cif (#40) to map Sf-IMcomplexC24.mrc (#34) using 399559
atoms  
average map value = 0.1233, steps = 84  
shifted from previous position = 0.0222  
rotated from previous position = 0.0141 degrees  
atoms outside contour = 137034, contour level = 0.030491  
  
Position of 7AH9.cif (#40) relative to Sf-IMcomplexC24.mrc (#34) coordinates:  
Matrix rotation and translation  
0.99622716 0.08649800 0.00703916 -101.66105644  
-0.08638952 0.99615619 -0.01448088 -40.17347304  
-0.00826467 0.01381813 0.99987037 -17.86380104  
Axis 0.16092202 0.08702510 -0.98312295  
Axis point -513.82368273 1148.62122728 0.00000000  
Rotation angle (degrees) 5.04440150  
Shift along axis -2.29329031  
  

> hide #!33 models

> show #!33 models

> hide #!34 models

> 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 #28  
---  
Chain | Description  
A B C D E F G H I | .  
  

[deleted to fit within ticket limits]


> 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  

> hide #!88 models

> hide #!89 models

> close #87

> hide #!209 models

> hide #!214-231 models

> hide #!107-123 models

> hide #!107-140 models

> hide #!175-208 models

> hide #!4 models

> color #3 #a9a9a973 models

> color #83 #a9a9a973 models

> color #232 #a9a9a973 models

> save /Users/shoichi/Desktop/TEST-A.png supersample 2 transparentBackground
> true

> hide #!141-174 models

> show231 #!141-174 models

Unknown command: show231 #!141-174 models  

> show #!231 models

> show #!214-230 models

> turn x -10

> view P1

> turn x 15

> view P1

> turn x 20

> hide #!83 models

> save /Users/shoichi/Desktop/TEST-B.png supersample 2 transparentBackground
> true

> hide #!3 models

> hide #!232 models

> show #!232 models

> hide #!214-231 models

> hide #!232 models

> show #!141-174 models

> show #!3 models

> show #!83 models

> show #!209 models

> hide #!209 models

> show #!209 models

> color #209 #a9a9a973 models

> save /Users/shoichi/Desktop/TEST-A.png supersample 2 transparentBackground
> true

> hide #!209 models

> hide #!3 models

> hide #!83 models

> show #!232 models

> hide #!141-174 models

> show #!231 models

> show #!214-231 models

> save /Users/shoichi/Desktop/TEST-B.png supersample 2 transparentBackground
> true

> hide #!214-233 models

> show #!107-123 models

> show #!89 models

> color #89 #a9a9a973 models

> show #!192-208 models

> hide #!192-208 models

> show #!175-191 models

> show #!124-140 models

> show #!192-208 models

> save /Users/shoichi/Desktop/TEST-C.png supersample 2 transparentBackground
> true

> show #!4 models

> color #4 #a9a9a973 models

> save /Users/shoichi/Desktop/TEST-C2.png supersample 2 transparentBackground
> true

> save /Users/shoichi/Desktop/For_Composition-maps/Part-
> Transparent_Building_Whole_Model_09102025.cxs includeMaps true

> hide #!89-140 models

> hide #!175-208 models

> hide #!4 models

> show #!15 models

> hide #!15 models

> show #!14 models

> hide #!14 models

> show #!5 models

> hide #!5 models

> show #!2 models

> show #!5 models

> hide #!5 models

> show #!13 models

> show #!14 models

> show #!15 models

> hide #!13 models

> hide #!15 models

> show #!5 models

> hide #!14 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!8 models

> hide #!8 models

> show #9 models

> hide #9 models

> show #!10 models

> hide #!5 models

> hide #!2 models

> view orient

> turn x 90

[Repeated 2 time(s)]

> turn y 90

[Repeated 4 time(s)]

> turn x 20

> show #!158 models

> hide #!158 models

> show #!159 models

> hide #!159 models

> show #!172 models

> hide #!172 models

> show #!171 models

> hide #!171 models

> show #!170 models

> hide #!170 models

> show #!169 models

> hide #!169 models

> show #!168 models

> hide #!168 models

> show #!167 models

> show #!149 models

> hide #!149 models

> show #!148 models

> hide #!148 models

> show #!151 models

> hide #!151 models

> show #!150 models

> save /Users/shoichi/Desktop/For_Composition-
> maps/Partial2-Transparent_Building_Whole_Model_09102025.cxs includeMaps true

> ui tool show "Segment Map"

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 #17

9 models selected  

> ui mousemode right "translate selected models"

> view matrix models #17,1,0,0,125.26,0,1,0,317.78,0,0,1,37.199

> view matrix models #17,1,0,0,123.09,0,1,0,270.75,0,0,1,292.64

> ui mousemode right "rotate selected models"

> view matrix models
> #17,-0.37095,0.38013,-0.84729,630.27,-0.35944,-0.90004,-0.24643,803.39,-0.85627,0.21313,0.47051,614.27

> view matrix models
> #17,-0.50136,0.13628,-0.85444,710.5,-0.27954,-0.96007,0.010897,711.83,-0.81884,0.24431,0.51943,584.14

> view matrix models
> #17,-0.67457,0.23019,-0.7014,675.99,-0.42281,-0.89933,0.11149,695.47,-0.60513,0.37177,0.70399,451.48

> ui mousemode right "translate selected models"

> view matrix models
> #17,-0.67457,0.23019,-0.7014,631.58,-0.42281,-0.89933,0.11149,665,-0.60513,0.37177,0.70399,416.37

> view matrix models
> #17,-0.67457,0.23019,-0.7014,626.36,-0.42281,-0.89933,0.11149,699.72,-0.60513,0.37177,0.70399,399.73

> ui mousemode right "rotate selected models"

> view matrix models
> #17,-0.80535,0.5354,-0.25447,441.51,-0.58932,-0.76951,0.24607,662.96,-0.064066,0.34814,0.93525,213.58

> view matrix models
> #17,-0.88684,0.38717,-0.25223,487.85,-0.4549,-0.82739,0.32937,617.77,-0.081167,0.40684,0.90989,214.02

> view matrix models
> #17,-0.89264,0.3758,-0.24893,490.24,-0.44339,-0.83148,0.33473,614.37,-0.081185,0.40917,0.90884,213.91

> view matrix models
> #17,-0.91325,0.40473,-0.046462,419.72,-0.40738,-0.90829,0.095147,703.88,-0.0036916,0.10582,0.99438,230.05

> ui mousemode right "translate selected models"

> view matrix models
> #17,-0.91325,0.40473,-0.046462,426.65,-0.40738,-0.90829,0.095147,695.32,-0.0036916,0.10582,0.99438,226.23

> view matrix models
> #17,-0.91325,0.40473,-0.046462,425.29,-0.40738,-0.90829,0.095147,694.38,-0.0036916,0.10582,0.99438,221.82

> hide #!167 models

> hide #!150 models

> select #17.1

1 model selected  

> select #17.2

1 model selected  
Ungrouped to 3 regions  
[Repeated 1 time(s)]Ungrouped to 4 regions  
Ungrouped to 0 regions  

> select #17.1

1 model selected  

> select add #17.13

2 models selected  

> select add #17.15

3 models selected  

> select add #17.9

4 models selected  

> select add #17.16

5 models selected  

> select add #17.14

6 models selected  
Grouped 6 regions  

> select #17.12

1 model selected  
Ungrouped to 0 regions  
Ungrouped to 7 regions  

> select #17.12

1 model selected  

> select add #17.1

2 models selected  
Grouped 2 regions  
Opened 1xPflC_imasked as #18, grid size 200,200,200, pixel 2.14, shown at step
1, values float32  

> save /Users/shoichi/Desktop/For_Composition-maps/For-
> Zoom_in/PflC_Fit_region.mrc models #18

Opened 1xPflC_imasked as #19, grid size 200,200,200, pixel 2.14, shown at step
1, values float32  

> save /Users/shoichi/Desktop/For_Composition-maps/For-
> Zoom_in/PflC_Unfit_region.mrc models #19

> hide #!17 models

> color #18 #a9a9a973 models

> color #19 #a9a9a973 models

> select add #10.7

1355 atoms, 1388 bonds, 162 residues, 2 models selected  

> select subtract #10.7

1 model selected  

> select add #10.8

1355 atoms, 1388 bonds, 162 residues, 2 models selected  

> hide #10.7 models

> hide #10.6 models

> hide #10.5 models

> hide #10.4 models

> hide #10.3 models

> hide #10.2 models

> hide #10.1 models

> select clear

> show #!150 models

> color #150 #a9a9a973 models

> select clear

Drag select of 150 1xPflD.mrc gaussian copy , 88 residues  

> select #150

2 models selected  

> hide #!150 models

> hide #10.8-9 cartoons

> show #10.8-9 cartoons

Drag select of 1 residues  

> select clear

> select add #10.8

1355 atoms, 1388 bonds, 162 residues, 1 model selected  

> select add #10.9

4209 atoms, 4302 bonds, 518 residues, 2 models selected  

> show sel surfaces

> hide sel cartoons

> select #10.8/X:88@CG

1 atom, 1 residue, 1 model selected  

> select add #10.8/X:88@CE

2 atoms, 1 residue, 2 models selected  

> select add #10.8/X:89@N

3 atoms, 2 residues, 2 models selected  

> select add #10.8/X:89@CG

4 atoms, 2 residues, 2 models selected  

> select clear

Drag select of combination X_X SES surface, 4767 of 231216 triangles  
Drag select of combination X_X SES surface, 6261 of 231216 triangles  

> select clear

Drag select of combination X_X SES surface, 6560 of 231216 triangles  

> select clear

Drag select of combination X_X SES surface, 78531 of 231216 triangles  

> select clear

> hide #10.8.1 models

> hide #10.9.1 models

> select add #10.8

1355 atoms, 1388 bonds, 162 residues, 1 model selected  

> show sel surfaces

> show sel cartoons

> hide sel surfaces

> select clear

Drag select of 7 residues  

> hide sel cartoons

Drag select of 82 residues  

> hide sel cartoons

Drag select of 73 residues, 18 PflC_Fit_region.mrc  

> show sel surfaces

> select clear

> select add #10.9.1

2854 atoms, 356 residues, 1 model selected  

> show #10.9.1 models

> select clear

> show #10.2 models

> show #10.3 models

> show #10.5 models

> show #10.6 models

> show #11 models

> show #10.1 models

> view orient

> turn x 90

[Repeated 2 time(s)]

> turn y 90

> turn x 20

> hide #10.1 models

> hide #10.2 models

> hide #10.3 models

> hide #10.5 models

> hide #10.6 models

> hide #!10.8 models

> hide #!10 models

> show #!10 models

> hide #11 models

> show #11 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> split #11

Split combination (#11) into 9 models  
Chain information for combination A #11.1  
---  
Chain | Description  
A | No description available  
  
Chain information for combination B #11.2  
---  
Chain | Description  
B | No description available  
  
Chain information for combination C #11.3  
---  
Chain | Description  
C | No description available  
  
Chain information for combination D #11.4  
---  
Chain | Description  
D | No description available  
  
Chain information for combination E #11.5  
---  
Chain | Description  
E | No description available  
  
Chain information for combination F #11.6  
---  
Chain | Description  
F | No description available  
  
Chain information for combination L #11.7  
---  
Chain | Description  
L | No description available  
  
Chain information for combination X #11.8  
---  
Chain | Description  
X | No description available  
  
Chain information for combination c #11.9  
---  
Chain | Description  
c | No description available  
  

> select add #11

16838 atoms, 17164 bonds, 2046 residues, 10 models selected  

> show #!10 models

> select add #10

33676 atoms, 34328 bonds, 4092 residues, 20 models selected  

> hide sel & #11.1-9#!10.9 surfaces

> show sel & #11.1-9#!10.9 cartoons

[Repeated 1 time(s)]

> hide #!10 models

> select subtract #10

16838 atoms, 17164 bonds, 2046 residues, 12 models selected  

> select subtract #11

Nothing selected  

> show #!10 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> hide #!10 models

> show #!10 models

> hide #10.8.1 models

> show #10.8.1 models

> select add #10.9

2854 atoms, 2914 bonds, 356 residues, 1 model selected  

> show sel surfaces

> select clear

> show #10.2 models

> show #10.3 models

> show #10.4 models

> show #10.1 models

> show #10.5 models

> show #10.6 models

> view orient

> turn x 90

> turn y 90

> view orient

> turn x 90

[Repeated 2 time(s)]

> turn y 90

> hide #10.1 models

> hide #10.2 models

> hide #10.3 models

> hide #10.4 models

> hide #10.5 models

> hide #10.6 models

> show #!150 models

> hide #!10 models

> show #!10 models

> show #10.1 models

> show #10.2 models

> show #10.3 models

> show #10.4 models

> show #10.5 models

> show #10.6 models

> show #10.7 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!150 models

> hide #!5 models

> hide #!10 models

> show #!5 models

> ui tool show "Fit in Map"

> fitmap #18 inMap #5

Fit map PflC_Fit_region.mrc in map 1unit_PflABCD.mrc using 20064 points  
correlation = 0.9767, correlation about mean = 0.9448, overlap = 10.42  
steps = 92, shift = 8.06, angle = 4.83 degrees  
  
Position of PflC_Fit_region.mrc (#18) relative to 1unit_PflABCD.mrc (#5)
coordinates:  
Matrix rotation and translation  
0.99979786 0.00678042 -0.01892788 4.86873431  
-0.00668887 0.99996564 0.00489578 -0.18364103  
0.01896043 -0.00476819 0.99980886 -5.09352376  
Axis -0.23367625 -0.91614500 -0.32568964  
Axis point 259.44782603 0.00000000 262.96633639  
Rotation angle (degrees) 1.18485335  
Shift along axis 0.68944216  
  

> fitmap #19 inMap #5

Fit map PflC_Unfit_region.mrc in map 1unit_PflABCD.mrc using 44750 points  
correlation = 0.9854, correlation about mean = 0.9615, overlap = 36.8  
steps = 80, shift = 9.57, angle = 4.04 degrees  
  
Position of PflC_Unfit_region.mrc (#19) relative to 1unit_PflABCD.mrc (#5)
coordinates:  
Matrix rotation and translation  
0.99999273 0.00352508 -0.00145224 -0.05974640  
-0.00352326 0.99999300 0.00125756 0.30260890  
0.00145666 -0.00125243 0.99999815 -0.03827778  
Axis -0.31267369 -0.36236747 -0.87802334  
Axis point 79.94482881 22.20208884 0.00000000  
Rotation angle (degrees) 0.22997170  
Shift along axis -0.05736571  
  

> fitmap #19 inMap #5

Fit map PflC_Unfit_region.mrc in map 1unit_PflABCD.mrc using 44750 points  
correlation = 0.9854, correlation about mean = 0.9616, overlap = 36.79  
steps = 40, shift = 0.00936, angle = 0.0275 degrees  
  
Position of PflC_Unfit_region.mrc (#19) relative to 1unit_PflABCD.mrc (#5)
coordinates:  
Matrix rotation and translation  
0.99999222 0.00368845 -0.00139495 -0.10472804  
-0.00368732 0.99999287 0.00081069 0.47075706  
0.00139793 -0.00080554 0.99999869 -0.10140290  
Axis -0.20075541 -0.34690927 -0.91616114  
Axis point 122.96258281 31.34062787 0.00000000  
Rotation angle (degrees) 0.23063692  
Shift along axis -0.04938387  
  

> volume copy #150

Opened 1xPflD.mrc gaussian copy as #20, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32  

> volume #150 show

> hide #!150 models

> hide #!5 models

> show #!5 models

> fitmap #20 inMap #5

Fit map 1xPflD.mrc gaussian copy in map 1unit_PflABCD.mrc using 5340 points  
correlation = 0.9504, correlation about mean = 0.8625, overlap = 5.601  
steps = 76, shift = 5.13, angle = 8.15 degrees  
  
Position of 1xPflD.mrc gaussian copy (#20) relative to 1unit_PflABCD.mrc (#5)
coordinates:  
Matrix rotation and translation  
0.98998624 -0.13034555 0.05419657 12.60454504  
0.13454456 0.98743998 -0.08282533 -9.92485490  
-0.04271995 0.08928779 0.99508929 -4.06524796  
Axis 0.52087972 0.29330622 0.80165815  
Axis point 82.91353995 88.75075241 0.00000000  
Rotation angle (degrees) 9.50965963  
Shift along axis 0.39549103  
  

> undo

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> close #20

> volume copy #150

Opened 1xPflD.mrc gaussian copy as #20, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32  

> volume #150 show

> select add #5

2 models selected  

> select subtract #5

Nothing selected  

> color #20 #8efa00ff models

> select add #20

2 models selected  

> view matrix models
> #20,-0.9167,0.39938,-0.012396,412.81,-0.39956,-0.91652,0.018567,722.08,-0.0039455,0.021974,0.99975,232.2

> view matrix models
> #20,-0.9167,0.39938,-0.012396,412.7,-0.39956,-0.91652,0.018567,722.25,-0.0039455,0.021974,0.99975,232.38

> view matrix models
> #20,-0.9167,0.39938,-0.012396,412.58,-0.39956,-0.91652,0.018567,722.2,-0.0039455,0.021974,0.99975,232.05

> view matrix models
> #20,-0.9167,0.39938,-0.012396,413.41,-0.39956,-0.91652,0.018567,723.21,-0.0039455,0.021974,0.99975,231.37

> view matrix models
> #20,-0.9167,0.39938,-0.012396,412.47,-0.39956,-0.91652,0.018567,722.43,-0.0039455,0.021974,0.99975,232.32

> view matrix models
> #20,-0.9167,0.39938,-0.012396,412.6,-0.39956,-0.91652,0.018567,722.79,-0.0039455,0.021974,0.99975,232.27

> close #20

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!150 models

> show #!150 models

> hide #!150 models

> show #!150 models

> hide #!150 models

> show #!150 models

> volume copy #150

Opened 1xPflD.mrc gaussian copy as #20, grid size 200,200,200, pixel 2.14,
shown at step 1, values float32  

> volume #150 show

> hide #!20 models

> show #!20 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!20 models

> show #!20 models

> hide #!5 models

> show #!10 models

> hide #!10 models

> show #!5 models

> show #!10 models

> hide #!18 models

> hide #!19 models

> hide #!20 models

> hide #!10 models

> show #!20 models

> select add #20

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #20,-0.85108,0.52492,0.011381,358.84,-0.52471,-0.84957,-0.053895,765.69,-0.018621,-0.051841,0.99848,253.11

> ui mousemode right "translate selected models"

> view matrix models
> #20,-0.85108,0.52492,0.011381,361.9,-0.52471,-0.84957,-0.053895,769.17,-0.018621,-0.051841,0.99848,251.08

> ui mousemode right "rotate selected models"

> view matrix models
> #20,-0.90124,0.43309,-0.014197,404.23,-0.43319,-0.9013,0.0040126,736.1,-0.011058,0.0097663,0.99989,235.08

> ui mousemode right "translate selected models"

> view matrix models
> #20,-0.90124,0.43309,-0.014197,402.06,-0.43319,-0.9013,0.0040126,733.65,-0.011058,0.0097663,0.99989,236.47

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!19 models

> show #!18 models

> color #20 #929000ff models

> view matrix models
> #20,-0.90124,0.43309,-0.014197,401.12,-0.43319,-0.9013,0.0040126,733.24,-0.011058,0.0097663,0.99989,236.76

> color #20 #a9a9a973 models

> select clear

> select add #10.8

1355 atoms, 1388 bonds, 162 residues, 1 model selected  

> show #!10 models

> select subtract #10.8

1 model selected  

> hide #10.1 models

> hide #10.3 models

> hide #10.2 models

> hide #10.5 models

> hide #10.4 models

> hide #10.6 models

> hide #10.7 models

> show #10.7 models

> hide #10.7 models

> select add #10.8

1355 atoms, 1388 bonds, 162 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select add #10.9.1

4209 atoms, 1388 bonds, 518 residues, 3 models selected  

> view matrix models
> #10.8,-0.92782,0.373,0.0047033,420.93,-0.372,-0.92612,0.062557,700.31,0.027689,0.056292,0.99803,218.26,#10.9,-0.92782,0.373,0.0047033,420.93,-0.372,-0.92612,0.062557,700.31,0.027689,0.056292,0.99803,218.26

> view matrix models
> #10.8,-0.92782,0.373,0.0047033,418.42,-0.372,-0.92612,0.062557,698.57,0.027689,0.056292,0.99803,218.36,#10.9,-0.92782,0.373,0.0047033,418.42,-0.372,-0.92612,0.062557,698.57,0.027689,0.056292,0.99803,218.36

> select clear

> view orient

> turn x 90

[Repeated 2 time(s)]

> turn y 90

> show #!167 models

> hide #!167 models

> show #!168 models

> show #!169 models

> hide #!169 models

> show #!166 models

> view orient

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> turn x 90

[Repeated 2 time(s)]

> turn y 90

> show #!149 models

> show #!151 models

> color #149 #a9a9a973 models

> color #150 #a9a9a973 models

> color #151 #a9a9a973 models

> color #166 #a9a9a973 models

> color #168 #a9a9a973 models

> turn y 10

> turn y -10

[Repeated 3 time(s)]

> turn x 20

> turn x -20

[Repeated 1 time(s)]

> turn x 20

[Repeated 1 time(s)]

> show #!165 models

> show #!169 models

> turn x -20

> turn z -0.1

> turn z 0.1

[Repeated 5 time(s)]

> turn x 20

> color #165-169 #a9a9a973 models

> show #!148 models

> show #!152 models

> color #148-152 #a9a9a973 models

> turn x -20

> turn z 0.1

[Repeated 1 time(s)]

> turn x 20

> turn z 0.1

[Repeated 43 time(s)]

> show #!147 models

> hide #!147 models

> show #!164 models

> show #!163 models

> show #!162 models

> show #!161 models

> show #!160 models

> show #!159 models

> show #!158 models

> show #!174 models

> show #!173 models

> show #!172 models

> show #!171 models

> show #!170 models

> view orient

> turn x 90

[Repeated 2 time(s)]

> turn y 90

> turn y -10

[Repeated 1 time(s)]

> turn x 20

> turn x -20

> turn y -1

[Repeated 8 time(s)]

> turn x 20

> turn x -20

> turn x -1

> turn x 1

> turn y 1

[Repeated 15 time(s)]

> turn x 20

> view orient

> turn x 90

[Repeated 2 time(s)]

> turn y 90

> turn y -10

[Repeated 1 time(s)]

> turn x 20

> color #158-174 #a9a9a973 models

> turn z 0.1

> turn z -0.1

[Repeated 12 time(s)]

> hide #!158 models

> hide #!159 models

> hide #!160 models

> show #!160 models

> hide #!160 models

> hide #!161 models

> hide #!162 models

> hide #!164 models

> hide #!165 models

> hide #!174 models

> hide #!173 models

> hide #!172 models

> show #!172 models

> hide #!172 models

> hide #!171 models

> hide #!163 models

> show #!171 models

> save /Users/shoichi/Desktop/Zoom-PflDC.png supersample 2
> transparentBackground true

> show #!165 models

> hide #!165 models

> show #!165 models

> show #!172 models

> save /Users/shoichi/Desktop/Zoom-PflDC.png supersample 2
> transparentBackground true

> save /Users/shoichi/Desktop/For_Composition-maps/For-Zoom_in/ZoomPflCD-
> Transparent_Building_Whole_Model_09102025.cxs includeMaps true

> view P1

> hide #!165 models

> hide #!166 models

> hide #!168 models

> hide #!169 models

> hide #!170 models

> hide #!171 models

> hide #!172 models

> show #10.7 models

> select add #10.8

1355 atoms, 1388 bonds, 162 residues, 1 model selected  

> show sel cartoons

> show #10.1 models

> show #10.2 models

> show #10.3 models

> show #10.4 models

> show #10.5 models

> show #10.6 models

> hide #!10.9 models

> hide #10.9.1 models

> hide #!18 models

> hide #!19 models

> hide #!20 models

> select add #10.1

3992 atoms, 4074 bonds, 481 residues, 3 models selected  

> select add #10.2

5450 atoms, 5562 bonds, 656 residues, 4 models selected  

> select add #10.3

6992 atoms, 7125 bonds, 845 residues, 5 models selected  

> select add #10.4

9629 atoms, 9811 bonds, 1164 residues, 6 models selected  

> select add #10.5

11087 atoms, 11299 bonds, 1339 residues, 7 models selected  

> select add #10.6

12629 atoms, 12862 bonds, 1528 residues, 8 models selected  

> select subtract #10.8

11274 atoms, 11474 bonds, 1366 residues, 7 models selected  

> select add #10.8

12629 atoms, 12862 bonds, 1528 residues, 7 models selected  

> select add #10.7

13984 atoms, 14250 bonds, 1690 residues, 9 models selected  

> show sel surfaces

> select clear

> hide #!148 models

> hide #!149 models

> hide #!150 models

> hide #!151 models

> hide #!152 models

> show #!115 models

> show #!116 models

> hide #!115 models

> color #116 #a9a9a973 models

> select add #10

16838 atoms, 17164 bonds, 2046 residues, 10 models selected  

> hide sel & #!10.1-8 cartoons

> select clear

Drag select of combination X_X SES surface, 87575 of 231216 triangles, 116
Single_Cage_unit.mrc gaussian copy  

> select subtract #116

1 model selected  

> hide #!10.1-8 surfaces

> show #!10.1-8 surfaces

> select add #10

16838 atoms, 17164 bonds, 2046 residues, 11 models selected  

> show sel & #!10.1-8 cartoons

> hide sel & #!10.1-8 surfaces

> hide #!116 models

> select clear

Drag select of 77 residues  

> hide sel cartoons

Drag select of 2 residues  

> hide sel cartoons

> select add #10.6

1556 atoms, 1563 bonds, 191 residues, 3 models selected  

> select add #10.3

3098 atoms, 3126 bonds, 380 residues, 5 models selected  
Alignment identifier is 1  
Alignment identifier is 10.8/X  

> select clear

[Repeated 1 time(s)]

> select add #10.3

1542 atoms, 1563 bonds, 189 residues, 1 model selected  

> select add #10.6

3084 atoms, 3126 bonds, 378 residues, 3 models selected  
Alignment identifier is 1  

> select #10.3/C:17 #10.6/F:17

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select #10.3/C:1-17 #10.6/F:1-17

264 atoms, 264 bonds, 34 residues, 2 models selected  
1 [ID: 1] region chains C,F [1-17] RMSD: 45.494  
  

> hide sel cartoons

> select clear

> select add #10.1

2637 atoms, 2686 bonds, 319 residues, 1 model selected  

> select add #10.4

5274 atoms, 5372 bonds, 638 residues, 3 models selected  
Alignment identifier is 1  

> select clear

Drag select of 77 residues  

> select #10.1/A:177-178 #10.4/D:177-178

38 atoms, 38 bonds, 4 residues, 2 models selected  

> select #10.1/A:178-237 #10.4/D:178-237

986 atoms, 994 bonds, 120 residues, 2 models selected  
1 [ID: 1] region chains A,D [178-237] RMSD: 39.161  
  

> hide sel cartoons

> select clear

Drag select of 1457 residues  

> show sel surfaces

> hide sel cartoons

> select clear

> show #!152 models

> hide #!152 models

> show #!116 models

> select add #8.1

4099 atoms, 4171 bonds, 518 residues, 1 model selected  

> select subtract #8.1

Nothing selected  

> show #!8 models

> select add #8

22449 atoms, 22826 bonds, 2863 residues, 4 models selected  

> show sel surfaces

> select clear

> show #!200 models

> hide #!200 models

> show #!199 models

> hide #!199 models

> show #!202 models

> color #202 #a9a9a973 models

> show #!185 models

> hide #!185 models

> show #!186 models

> hide #!186 models

> show #!184 models

> color #184 #a9a9a973 models

> show #!136 models

> hide #!136 models

> show #!134 models

> hide #!134 models

> show #!133 models

> color #133 #a9a9a973 models

> select add #8.1

4099 atoms, 4171 bonds, 518 residues, 1 model selected  

> select add #8.2

13869 atoms, 14116 bonds, 1793 residues, 4 models selected  

> select subtract #8.2

4099 atoms, 4171 bonds, 518 residues, 8 models selected  

> select add #8.3

12679 atoms, 12881 bonds, 1588 residues, 4 models selected  

> select add #8

22449 atoms, 22826 bonds, 2863 residues, 16 models selected  

> view matrix models #8,1,0,0,-95.76,0,1,0,192.15,0,0,1,-6.5072

> select subtract #8.2

12679 atoms, 12881 bonds, 1588 residues, 20 models selected  

> select subtract #8.1

8580 atoms, 8710 bonds, 1070 residues, 14 models selected  

> view matrix models #8,1,0,0,-96.239,0,1,0,193.45,0,0,1,-4.8087

> undo

> select clear

> select add #8.3

8580 atoms, 8710 bonds, 1070 residues, 1 model selected  

> view matrix models #8.3,1,0,0,-2.4497,0,1,0,7.9784,0,0,1,6.3413

> view matrix models #8.3,1,0,0,-3.38,0,1,0,10.118,0,0,1,7.1685

> ui tool show "Fit in Map"

> fitmap #8.3 inMap #184

Fit molecule CJ_Stator_Complex_with6ykm_Bb_CjFliL.pdb (#8.3) to map 1xFliL.mrc
gaussian copy (#184) using 8580 atoms  
average map value = 0.02163, steps = 76  
shifted from previous position = 2.96  
rotated from previous position = 16.6 degrees  
atoms outside contour = 1215, contour level = 0.00084765  
  
Position of CJ_Stator_Complex_with6ykm_Bb_CjFliL.pdb (#8.3) relative to
1xFliL.mrc gaussian copy (#184) coordinates:  
Matrix rotation and translation  
-0.87255369 -0.41653843 0.25523673 534.15291720  
0.41245645 -0.90812686 -0.07200899 517.45618732  
0.26178184 0.04244232 0.96419340 -314.69395252  
Axis 0.13675891 -0.00782081 0.99057349  
Axis point 231.73585257 320.28207722 0.00000000  
Rotation angle (degrees) 155.26374376  
Shift along axis -242.72424226  
  

> fitmap #8.3 inMap #184

Fit molecule CJ_Stator_Complex_with6ykm_Bb_CjFliL.pdb (#8.3) to map 1xFliL.mrc
gaussian copy (#184) using 8580 atoms  
average map value = 0.02163, steps = 28  
shifted from previous position = 0.0107  
rotated from previous position = 0.0306 degrees  
atoms outside contour = 1216, contour level = 0.00084765  
  
Position of CJ_Stator_Complex_with6ykm_Bb_CjFliL.pdb (#8.3) relative to
1xFliL.mrc gaussian copy (#184) coordinates:  
Matrix rotation and translation  
-0.87276813 -0.41627268 0.25493694 534.27262322  
0.41226046 -0.90824335 -0.07166124 517.40467975  
0.26137540 0.04255678 0.96429862 -314.63530716  
Axis 0.13656011 -0.00769788 0.99060188  
Axis point 231.80026547 320.24138031 0.00000000  
Rotation angle (degrees) 155.27920149  
Shift along axis -242.70091206  
  

> select clear

> select add #8.1

4099 atoms, 4171 bonds, 518 residues, 1 model selected  

> view matrix models #8.1,1,0,0,-12.122,0,1,0,5.2828,0,0,1,0.77398

> ui mousemode right "rotate selected models"

> view matrix models
> #8.1,1,0.0005564,-0.0015096,-11.603,-0.00055666,1,-0.0001725,5.5506,0.0015095,0.00017334,1,0.20886

> view matrix models
> #8.1,0.99544,0.03254,-0.08968,20.347,-0.03346,0.9994,-0.0087731,20.826,0.089341,0.011734,0.99593,-31.298

> view matrix models
> #8.1,0.99529,0.030543,-0.092006,22.055,-0.029482,0.99948,0.012864,9.632,0.092352,-0.010091,0.99568,-25.636

> view matrix models
> #8.1,0.99477,0.028635,-0.098074,25.559,-0.017431,0.99341,0.11325,-38.205,0.10067,-0.11094,0.98871,5.0525

> view matrix models
> #8.1,0.99805,0.019029,-0.059396,9.7646,-0.012739,0.99444,0.10454,-36.157,0.061055,-0.10358,0.99274,14.48

> ui mousemode right "translate selected models"

> view matrix models
> #8.1,0.99805,0.019029,-0.059396,11.791,-0.012739,0.99444,0.10454,-44.857,0.061055,-0.10358,0.99274,15.747

> select clear

> show #!115 models

> show #!117 models

> color #115-117 #a9a9a973 models

> show #!132 models

> show #!134 models

> color #132-134 #a9a9a973 models

> show #!183 models

> show #!185 models

> color #183-185 #a9a9a973 models

> show #!89 models

> view orient

> ui mousemode right "crop volume"

> volume #89 region 0,0,0,249,249,153

> volume #89 region 0,0,0,249,249,249

> hide #!115 models

> hide #!116 models

> hide #!117 models

> hide #!132 models

> hide #!133 models

> hide #!134 models

> hide #!183 models

> hide #!184 models

> hide #!185 models

> hide #!8 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> volume #!89,202 showOutlineBox true

> hide #!89 models

> hide #!202 models

> show #!8 models

> hide #!8 models

> show #!89 models

> volume #!89 showOutlineBox false

> volume #!89 showOutlineBox true

> view orient

> show #9 models

> show #!8 models

> hide #9 models

> show #9 models

> hide #9 models

> volume #89 region 0,0,0,82,249,249

> volume #89 region 0,0,0,82,236,249

> show #!10 models

> turn x 90

[Repeated 2 time(s)]

> turn y 90

> volume #89 region 40,0,0,82,236,249

> volume #89 region 40,0,0,67,236,249

> view orient

> turn x 90

[Repeated 2 time(s)]

> turn y 90

[Repeated 4 time(s)]

> show #!115 models

> show #!116 models

> show #!117 models

> show #!132 models

> show #!133 models

> show #!134 models

> show #!183 models

> show #!184 models

> show #!185 models

> show #!202 models

> show #!201 models

> show #!203 models

> select add #201

2 models selected  

> select add #202

4 models selected  

> select add #203

6 models selected  

> volume sel showOutlineBox false

> select clear

> color #201-203 #a9a9a973 models

> turn z -0.1

[Repeated 1 time(s)]

> turn x 20

> view name S1

> select add #8.1

4099 atoms, 4171 bonds, 518 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #8.1,0.99805,0.019029,-0.059396,12.138,-0.012739,0.99444,0.10454,-45.724,0.061055,-0.10358,0.99274,21.36

> select clear

> volume #!89,115-117,132-134,183-185,201-203 showOutlineBox false

> view S1

[Repeated 1 time(s)]

> select add #8.1

4099 atoms, 4171 bonds, 518 residues, 1 model selected  

> view matrix models
> #8.1,0.99805,0.019029,-0.059396,13.235,-0.012739,0.99444,0.10454,-45.765,0.061055,-0.10358,0.99274,19.717

> view matrix models
> #8.1,0.99805,0.019029,-0.059396,13.235,-0.012739,0.99444,0.10454,-45.925,0.061055,-0.10358,0.99274,19.718

> select clear

> view S1

> turn x -20

> save /Users/shoichi/Desktop/Zoom-Cage.png supersample 2
> transparentBackground true

> view S1

> save /Users/shoichi/Desktop/Zoom-Cage-20.png supersample 2
> transparentBackground true

> save /Users/shoichi/Desktop/For_Composition-maps/For-Zoom_in/ZoomCage-
> Stator-Transparent_Building_Whole_Model_09102025.cxs includeMaps true

> hide #!8 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> show #9 models

> hide #9 models

> show #!8 models

> hide #!8 models

> show #9 models

> hide #9 models

> hide #!10 models

> show #!11 models

> hide #!11 models

> show #!12 models

> hide #!132 models

> hide #!133 models

> hide #!134 models

> hide #!89 models

> hide #!115 models

> hide #!116 models

> hide #!117 models

> hide #!183 models

> hide #!184 models

> hide #!185 models

> hide #!201 models

> hide #!202 models

> hide #!203 models

> show #!215 models

> hide #!215 models

> show #!223 models

> hide #!223 models

> show #!222 models

> show #!231 models

> hide #!222 models

> view orient

> volume #!231 showOutlineBox true

> ui mousemode right "crop volume"

> volume #231 region 0,0,0,255,255,206

> volume #231 region 0,0,0,98,255,206

> volume #231 region 0,9,0,98,255,206

> volume #231 region 0,9,0,255,255,206

> volume #!231 showOutlineBox false

> ui tool show "Segment Map"

Segmenting C17-FlgY_New.mrc gaussian, density threshold 0.011237  
Showing 51 region surfaces  
1094 watershed regions, grouped to 51 regions  
Showing C17-FlgY_New gaussian.seg - 51 regions, 51 surfaces  
Segmenting C17-FlgY_New.mrc gaussian, density threshold 0.011237  
Showing 51 region surfaces  
1094 watershed regions, grouped to 51 regions  
Showing C17-FlgY_New gaussian.seg - 51 regions, 51 surfaces  

> select #17.22

1 model selected  

> select add #17.6

2 models selected  

> select #17.33

1 model selected  

> select add #17.7

2 models selected  

> select add #17.41

3 models selected  

> select add #17.39

4 models selected  

> select add #17.46

5 models selected  
Opened C17-FlgY_New_imasked as #21, grid size 256,256,256, pixel 2.14, shown
at step 1, values float32  

> save /Users/shoichi/Desktop/For_Composition-maps/For-
> Zoom_in/1xFlgY_fit_region.mrc models #21

> hide #!17 models

> select add #17

52 models selected  

> select subtract #17

Nothing selected  

> hide #!21 models

> show #!21 models

> open /Users/shoichi/Desktop/For_Composition-maps/For-
> Zoom_in/1xFlgY_fit_region.mrc

Opened 1xFlgY_fit_region.mrc as #22, grid size 256,247,207, pixel
2.14,2.14,2.14, shown at level 0.000562, step 1, values float32  

> volume #22 level 0.01163

> volume #22 level 0.0112

> close #22

> hide #!231 models

> volume #21 level 0.01201

> color #21 #a9a9a973 models

> ui tool show "Segment Map"

Segmenting C17-FlgY_New_imasked, density threshold 0.012014  
Showing 4 region surfaces  
88 watershed regions, grouped to 4 regions  
Showing C17-FlgY_New_imasked.seg - 4 regions, 4 surfaces  

> select #17.3

1 model selected  

> select add #17.4

2 models selected  

> select add #17.1

3 models selected  

> select add #17.2

4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #17.1,1,0,0,186.1,0,1,0,205.48,0,0,1,-59.564,#17.2,1,0,0,186.1,0,1,0,205.48,0,0,1,-59.564,#17.3,1,0,0,186.1,0,1,0,205.48,0,0,1,-59.564,#17.4,1,0,0,186.1,0,1,0,205.48,0,0,1,-59.564

> view matrix models
> #17.1,1,0,0,286.07,0,1,0,279.84,0,0,1,86.445,#17.2,1,0,0,286.07,0,1,0,279.84,0,0,1,86.445,#17.3,1,0,0,286.07,0,1,0,279.84,0,0,1,86.445,#17.4,1,0,0,286.07,0,1,0,279.84,0,0,1,86.445

> view matrix models
> #17.1,1,0,0,264.55,0,1,0,322.24,0,0,1,160.56,#17.2,1,0,0,264.55,0,1,0,322.24,0,0,1,160.56,#17.3,1,0,0,264.55,0,1,0,322.24,0,0,1,160.56,#17.4,1,0,0,264.55,0,1,0,322.24,0,0,1,160.56

> view matrix models
> #17.1,1,0,0,264.56,0,1,0,303.14,0,0,1,161.57,#17.2,1,0,0,264.56,0,1,0,303.14,0,0,1,161.57,#17.3,1,0,0,264.56,0,1,0,303.14,0,0,1,161.57,#17.4,1,0,0,264.56,0,1,0,303.14,0,0,1,161.57

> ui mousemode right "rotate selected models"

> view matrix models
> #17.1,0.99094,0.13408,-0.0071964,230.88,-0.13408,0.99097,-0.00064751,322.54,0.0070446,0.0016066,0.99997,160.26,#17.2,0.99094,0.13408,-0.0071964,230.88,-0.13408,0.99097,-0.00064751,322.54,0.0070446,0.0016066,0.99997,160.26,#17.3,0.99094,0.13408,-0.0071964,230.88,-0.13408,0.99097,-0.00064751,322.54,0.0070446,0.0016066,0.99997,160.26,#17.4,0.99094,0.13408,-0.0071964,230.88,-0.13408,0.99097,-0.00064751,322.54,0.0070446,0.0016066,0.99997,160.26

> view matrix models
> #17.1,0.98624,0.16507,-0.0088821,223.59,-0.16509,0.98628,-0.00065899,327.71,0.0086515,0.0021162,0.99996,159.93,#17.2,0.98624,0.16507,-0.0088821,223.59,-0.16509,0.98628,-0.00065899,327.71,0.0086515,0.0021162,0.99996,159.93,#17.3,0.98624,0.16507,-0.0088821,223.59,-0.16509,0.98628,-0.00065899,327.71,0.0086515,0.0021162,0.99996,159.93,#17.4,0.98624,0.16507,-0.0088821,223.59,-0.16509,0.98628,-0.00065899,327.71,0.0086515,0.0021162,0.99996,159.93

> ui mousemode right "translate selected models"

> view matrix models
> #17.1,0.98624,0.16507,-0.0088821,226.44,-0.16509,0.98628,-0.00065899,311.03,0.0086515,0.0021162,0.99996,160.84,#17.2,0.98624,0.16507,-0.0088821,226.44,-0.16509,0.98628,-0.00065899,311.03,0.0086515,0.0021162,0.99996,160.84,#17.3,0.98624,0.16507,-0.0088821,226.44,-0.16509,0.98628,-0.00065899,311.03,0.0086515,0.0021162,0.99996,160.84,#17.4,0.98624,0.16507,-0.0088821,226.44,-0.16509,0.98628,-0.00065899,311.03,0.0086515,0.0021162,0.99996,160.84

> hide #!21 models

> select clear

> select #17.3

1 model selected  
Ungrouped to 3 regions  
Showing 6 region surfaces  
[Repeated 1 time(s)]

> select add #17.1

4 models selected  

> select add #17.2

5 models selected  

> select add #17.4

6 models selected  

> hide #17.6 models

> show #17.6 models

Segmenting C17-FlgY_New_imasked, density threshold 0.012014  
Showing 4 region surfaces  
88 watershed regions, grouped to 4 regions  
Showing C17-FlgY_New_imasked.seg - 4 regions, 4 surfaces  

> select #17.3

1 model selected  

> select add #17.4

2 models selected  
Ungrouped to 5 regions  
Ungrouped to 19 regions  

> select clear

Drag select of 126, 128, 89, 108, 12, 29, 18, 110, 28, 9, 26, 120, 118, 93,
20, 13, 21, 5, 105, 19, 112  

> view matrix models
> #17.1,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11,#17.2,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11,#17.3,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11,#17.4,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11,#17.10,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11,#17.11,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11,#17.12,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11,#17.13,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11,#17.14,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11,#17.15,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11,#17.16,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11,#17.17,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11,#17.18,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11,#17.19,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11,#17.20,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11,#17.21,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11,#17.22,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11,#17.23,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11,#17.24,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11,#17.25,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11,#17.26,1,0,0,253.27,0,1,0,230.46,0,0,1,-10.11

> view matrix models
> #17.1,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84,#17.2,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84,#17.3,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84,#17.4,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84,#17.10,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84,#17.11,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84,#17.12,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84,#17.13,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84,#17.14,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84,#17.15,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84,#17.16,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84,#17.17,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84,#17.18,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84,#17.19,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84,#17.20,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84,#17.21,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84,#17.22,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84,#17.23,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84,#17.24,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84,#17.25,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84,#17.26,1,0,0,251.5,0,1,0,223.76,0,0,1,167.84

> view matrix models
> #17.1,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98,#17.2,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98,#17.3,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98,#17.4,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98,#17.10,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98,#17.11,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98,#17.12,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98,#17.13,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98,#17.14,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98,#17.15,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98,#17.16,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98,#17.17,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98,#17.18,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98,#17.19,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98,#17.20,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98,#17.21,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98,#17.22,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98,#17.23,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98,#17.24,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98,#17.25,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98,#17.26,1,0,0,253.36,0,1,0,281.19,0,0,1,154.98

> ui mousemode right "rotate selected models"

> view matrix models
> #17.1,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6,#17.2,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6,#17.3,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6,#17.4,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6,#17.10,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6,#17.11,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6,#17.12,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6,#17.13,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6,#17.14,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6,#17.15,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6,#17.16,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6,#17.17,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6,#17.18,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6,#17.19,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6,#17.20,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6,#17.21,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6,#17.22,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6,#17.23,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6,#17.24,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6,#17.25,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6,#17.26,0.9843,0.17271,-0.036362,219.56,-0.17199,0.98485,0.022059,299.58,0.039621,-0.015459,0.9991,154.6

> view matrix models
> #17.1,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62,#17.2,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62,#17.3,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62,#17.4,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62,#17.10,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62,#17.11,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62,#17.12,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62,#17.13,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62,#17.14,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62,#17.15,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62,#17.16,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62,#17.17,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62,#17.18,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62,#17.19,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62,#17.20,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62,#17.21,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62,#17.22,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62,#17.23,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62,#17.24,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62,#17.25,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62,#17.26,0.97816,0.20375,-0.041178,213.69,-0.18965,0.95583,0.22455,244.29,0.085112,-0.21183,0.97359,209.62

> ui mousemode right "translate selected models"

> view matrix models
> #17.1,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222,#17.2,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222,#17.3,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222,#17.4,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222,#17.10,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222,#17.11,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222,#17.12,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222,#17.13,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222,#17.14,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222,#17.15,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222,#17.16,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222,#17.17,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222,#17.18,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222,#17.19,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222,#17.20,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222,#17.21,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222,#17.22,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222,#17.23,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222,#17.24,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222,#17.25,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222,#17.26,0.97816,0.20375,-0.041178,226.25,-0.18965,0.95583,0.22455,257.64,0.085112,-0.21183,0.97359,222

> view matrix models
> #17.1,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95,#17.2,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95,#17.3,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95,#17.4,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95,#17.10,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95,#17.11,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95,#17.12,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95,#17.13,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95,#17.14,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95,#17.15,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95,#17.16,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95,#17.17,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95,#17.18,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95,#17.19,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95,#17.20,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95,#17.21,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95,#17.22,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95,#17.23,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95,#17.24,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95,#17.25,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95,#17.26,0.97816,0.20375,-0.041178,225.05,-0.18965,0.95583,0.22455,248.26,0.085112,-0.21183,0.97359,223.95

> select clear

> select #17.11

1 model selected  

> select add #17.24

2 models selected  

> select subtract #17.24

1 model selected  

> select add #17.25

2 models selected  

> select add #17.26

3 models selected  

> select add #17.24

4 models selected  

> select add #17.12

5 models selected  

> select add #17.13

6 models selected  

> select add #17.14

7 models selected  

> select subtract #17.14

6 models selected  

> select subtract #17.13

5 models selected  

> select add #17.22

6 models selected  

> select add #17.20

7 models selected  

> select add #17.19

8 models selected  

> select add #17.3

9 models selected  

> select add #17.10

10 models selected  

> select add #17.21

11 models selected  

> select add #17.23

12 models selected  

> select add #17.4

13 models selected  

> select subtract #17.4

12 models selected  
Opened C17-FlgY_New_imasked_imasked as #22, grid size 256,256,256, pixel 2.14,
shown at step 1, values float32  

> save /Users/shoichi/Desktop/For_Composition-maps/For-
> Zoom_in/1xFlgY_fit2_region.mrc models #22

Cell requested for row 16 is out of bounds for table with 169 rows! Resizing
table model.  

> hide #!17 models

> select add #17

22 models selected  

> select subtract #17

Nothing selected  

> ui tool show "Fit in Map"

> show #!231 models

> fitmap #22 inMap #231

Fit map C17-FlgY_New_imasked_imasked in map C17-FlgY_New.mrc gaussian using
13864 points  
correlation = 0.9999, correlation about mean = 0.9993, overlap = 15.92  
steps = 44, shift = 0.0627, angle = 0.373 degrees  
  
Position of C17-FlgY_New_imasked_imasked (#22) relative to C17-FlgY_New.mrc
gaussian (#231) coordinates:  
Matrix rotation and translation  
0.99999757 -0.00198440 -0.00095976 0.89824196  
0.00199025 0.99997921 0.00613379 -2.18049367  
0.00094756 -0.00613568 0.99998073 1.52348524  
Axis -0.94109287 -0.14629535 0.30486371  
Axis point 0.00000000 250.24989437 357.81317137  
Rotation angle (degrees) 0.37349856  
Shift along axis -0.06187765  
  

> hide #!231 models

> select add #12

13836 atoms, 14052 bonds, 1 pseudobond, 1713 residues, 2 models selected  

> show sel surfaces

> select clear

> show #!21 models

> hide #!22 models

> show #!220 models

> hide #!220 models

> show #!223 models

> hide #!223 models

> show #!222 models

> color #222 #a9a9a973 models

> show #!221 models

> show #!223 models

> show #!231 models

> hide #!231 models

> hide #!221 models

> hide #!222 models

> hide #!223 models

> show #!231 models

> ui tool show "Segment Map"

Segmenting C17-FlgY_New.mrc gaussian, density threshold 0.011237  
Showing 51 region surfaces  
1094 watershed regions, grouped to 51 regions  
Showing C17-FlgY_New gaussian.seg - 51 regions, 51 surfaces  

> select #17.46

1 model selected  

> select add #17.41

2 models selected  

> select add #17.39

3 models selected  

> select subtract #17.39

2 models selected  

> select add #17.10

3 models selected  

> select subtract #17.10

2 models selected  

> select add #17.29

3 models selected  

> select add #17.10

4 models selected  

> select add #17.33

5 models selected  

> select add #17.7

6 models selected  

> select add #17.22

7 models selected  

> select add #17.6

8 models selected  

> select add #17.39

9 models selected  
Opened C17-FlgY_New_imasked as #23, grid size 256,256,256, pixel 2.14, shown
at step 1, values float32  

> hide #!17 models

> select add #17

52 models selected  

> select subtract #17

Nothing selected  

> hide #!23 models

> show #!23 models

> save /Users/shoichi/Desktop/For_Composition-maps/For-Zoom_in/3XFlgY-Fit.mrc
> models #23

> hide #!231 models

> color #2e #a9a9a973 models

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #23 #a9a9a973 models

> show #!222 models

> show #!223 models

> show #!221 models

> color #221-223 #a9a9a973 models

> view orient

> turn x 90

[Repeated 2 time(s)]

> turn y 90

[Repeated 1 time(s)]

> turn x 20

> hide #!223 models

> show #!223 models

> hide #!221 models

> show #!221 models

> view orient

> turn x 90

[Repeated 2 time(s)]

> turn y 90

> turn x 20

[Repeated 1 time(s)]

> turn x -20

[Repeated 1 time(s)]

> turn z -0.1

> turn z 0.1

[Repeated 4 time(s)]

> turn x 40

> view orient

> turn x 90

[Repeated 2 time(s)]

> turn y 90

[Repeated 1 time(s)]

> turn x 40

> save /Users/shoichi/Desktop/Zoom-PflAB-40.png supersample 2
> transparentBackground true

> save /Users/shoichi/Desktop/For_Composition-maps/For-Zoom_in/ZoomPflAB-
> Transparent_Building_Whole_Model_09102025.cxs includeMaps true

——— End of log from Wed Sep 10 13:06:53 2025 ———

opened ChimeraX session  
Showing C17-FlgY_New gaussian.seg - 51 regions, 51 surfaces  




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: 45 days, 23 hours, 43 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 24
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Q24i-10:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        ASUS PA279:
          Resolution: 6016 x 3384
          UI Looks like: 3008 x 1692 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (2)

comment:1 by pett, 3 weeks ago

Component: Unassigned → Window Toolkit
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on Mac waking from sleep

comment:2 by pett, 3 weeks ago

Resolution: → duplicate
Status: assigned → closed
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