id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16239	Crash moving window between displays	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-14.1.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00000003a0037000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Current thread 0x00000001e110dec0 (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.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, psutil._psutil_osx, psutil._psutil_posix (total: 61)


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fault""},""pc"":{""value"":6626068660},""far"":{""value"":0}},""frames"":[{""imageOffset"":6324,""symbol"":""mach_msg2_trap"",""symbolLocation"":8,""imageIndex"":155},{""imageOffset"":81200,""symbol"":""mach_msg2_internal"",""symbolLocation"":80,""imageIndex"":155},{""imageOffset"":42224,""symbol"":""mach_msg_overwrite"",""symbolLocation"":476,""imageIndex"":155},{""imageOffset"":7224,""symbol"":""mach_msg"",""symbolLocation"":24,""imageIndex"":155},{""imageOffset"":66741424,""imageIndex"":93},{""imageOffset"":66197236,""imageIndex"":93},{""imageOffset"":66429892,""imageIndex"":93},{""imageOffset"":66432404,""imageIndex"":93},{""imageOffset"":66431884,""imageIndex"":93},{""imageOffset"":66431792,""imageIndex"":93},{""imageOffset"":66589352,""imageIndex"":93},{""imageOffset"":28724,""symbol"":""_pthread_start"",""symbolLocation"":136,""imageIndex"":156},{""imageOffset"":7740,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":156}]},{""id"":5090347,""name"":""ThreadPoolForegroundWorker"",""threadState"":{""x"":[{""value"":268451845},{""value"":17179869442},{""value"":0},{""value"":792881027612672},{""value"":0},{""value"":792881027612672},{""value"":32},{""value"":33000},{""value"":18446744073709550527},{""value"":184607},{""value"":0},{""value"":1},{""value"":184607},{""value"":2045},{""value"":2557007984},{""value"":112},{""value"":18446744073709551569},{""value"":579584},{""value"":0},{""value"":33000},{""value"":32},{""value"":792881027612672},{""value"":0},{""value"":792881027612672},{""value"":16439979280},{""value"":0},{""value"":17179870466},{""value"":17179869442},{""value"":1282}],""flavor"":""ARM_THREAD_STATE64"",""lr"":{""value"":6626143536},""cpsr"":{""value"":4096},""fp"":{""value"":16439978624},""sp"":{""value"":16439978544},""esr"":{""value"":1442840704,""description"":"" Address size fault""},""pc"":{""value"":6626068660},""far"":{""value"":0}},""frames"":[{""imageOffset"":6324,""symbol"":""mach_msg2_trap"",""symbolLocation"":8,""imageIndex"":155},{""imageOffset"":81200,""symbol"":""mach_msg2_internal"",""symbolLocation"":80,""imageIndex"":155},{""imageOffset"":42224,""symbol"":""mach_msg_overwrite"",""symbolLocation"":476,""imageIndex"":155},{""imageOffset"":7224,""symbol"":""mach_msg"",""symbolLocation"":24,""imageIndex"":155},{""imageOffset"":66741424,""imageIndex"":93},{""imageOffset"":66197236,""imageIndex"":93},{""imageOffset"":66429892,""imageIndex"":93},{""imageOffset"":66432404,""imageIndex"":93},{""imageOffset"":66432016,""imageIndex"":93},{""imageOffset"":66431744,""imageIndex"":93},{""imageOffset"":66589352,""imageIndex"":93},{""imageOffset"":28724,""symbol"":""_pthread_start"",""symbolLocation"":136,""imageIndex"":156},{""imageOffset"":7740,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":156}]},{""id"":5090401,""frames"":[{""imageOffset"":7720,""symbol"":""start_wqthread"",""symbolLocation"":0,""imageIndex"":156}],""threadState"":{""x"":[{""value"":6169538560},{""value"":0},{""value"":6169001984},{""value"":0},{""value"":278532},{""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"":6169538560},""esr"":{""value"":0,""description"":"" Address size fault""},""pc"":{""value"":6626311720},""far"":{""value"":0}}}],
  ""usedImages"" : [
[deleted to fit within ticket limits]
],
  ""sharedCache"" : {
  ""base"" : 6621904896,
  ""size"" : 4018896896,
  ""uuid"" : ""80dd42b3-8a52-3caf-9848-54a1c2732864""
},
  ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.8G resident=0K(0%) swapped_out_or_unallocated=1.8G(100%)\nWritable regions: Total=142.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=142.7G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               512K        4 \nActivity Tracing                   256K        1 \nCG image                          1776K       78 \nColorSync                          800K       39 \nCoreAnimation                     5152K      299 \nCoreGraphics                       128K        8 \nCoreImage                           32K        2 \nCoreServices                       624K        2 \nCoreUI image data                 5728K       48 \nFoundation                          48K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                           139.0G      903 \nMALLOC guard page                  384K       24 \nMach message                        64K        4 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        848K       53 \nStack                            201.3M       54 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                        3.3G     3061 \nVM_ALLOCATE (reserved)           128.0M        2         reserved VM address space (unallocated)\n__AUTH                            2177K      398 \n__AUTH_CONST                      31.8M      623 \n__CTF                               824        1 \n__DATA                            22.6M      777 \n__DATA_CONST                      41.9M      784 \n__DATA_DIRTY                      2022K      235 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       916.5M      156 \n__OBJC_RO                         70.8M        1 \n__OBJC_RW                         2156K        1 \n__TEXT                           938.4M      801 \ndyld private memory                592K        6 \nmapped file                      545.2M       87 \nshared memory                     3760K       31 \n===========                     =======  ======= \nTOTAL                            145.2G     8494 \nTOTAL, minus reserved VM space   145.1G     8494 \n"",
  ""legacyInfo"" : {
  ""threadTriggered"" : {
    ""name"" : ""CrBrowserMain"",
    ""queue"" : ""com.apple.main-thread""
  }
},
  ""logWritingSignature"" : ""c3b4f3ffe3eb693eca765b5fc8f83ed3b1882cc1"",
  ""trialInfo"" : {
  ""rollouts"" : [
    {
      ""rolloutId"" : ""645c2d2f9e69a025b0a37e29"",
      ""factorPackIds"" : {

      },
      ""deploymentId"" : 240000003
    },
    {
      ""rolloutId"" : ""64b21a7351cbb02ce3442e4e"",
      ""factorPackIds"" : {
        ""REMINDERS_GROCERY"" : ""65542c604a6560536bdb1d22""
      },
      ""deploymentId"" : 240000042
    }
  ],
  ""experiments"" : [
    {
      ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"",
      ""experimentId"" : ""6643969b3099cf28e049862f"",
      ""deploymentId"" : 400000007
    }
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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 /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Final-ver5_-10032024.cxs

Opened 0838-bottom.mrc as #16, grid size 240,240,240, pixel 4.3, shown at
level 0.0144, step 1, values float32  
Opened Hpwt-L0.08-Global-Rod-no-MS.mrc as #113, grid size 240,240,240, pixel
4.3, shown at level 0.0151, step 1, values float32  
Opened Disk.mrc gaussian as #312, grid size 250,250,250, pixel 4.3, shown at
level 0.0186, step 1, values float32  
Opened IM-old-maps.mrc gaussian as #313, grid size 120,120,120, pixel 8.8,
shown at level 0.0702, step 1, values float32  
Opened OM.mrc copy gaussian as #316, grid size 240,240,240, pixel 4.3, shown
at level 0.0323, step 1, values float32  
Opened New_FliF.mrc gaussian as #479, grid size 256,256,256, pixel 2.1, shown
at level 0.0115, step 1, values float32  
Opened New_FlhA.mrc gaussian as #481, grid size 256,256,256, pixel 2.1, shown
at level 0.00316, step 1, values float32  
Opened PflBC13.mrc as #482, grid size 256,256,256, pixel 2.1, shown at level
0.00615, step 1, values float32  
Opened New_IM_Bottom2.mrc as #483, grid size 256,256,256, pixel 2.1, shown at
level 0.0072, step 1, values float32  
Opened New_IM_Bottom2.mrc gaussian as #484, grid size 256,256,256, pixel 2.1,
shown at level 0.0072, step 1, values float32  
Opened PflB_C13.mrc as #507, grid size 256,256,256, pixel 2.1, shown at level
0.0015, step 1, values float32  
Opened PflB_monomer.mrc as #508, grid size 256,256,256, pixel 2.1, shown at
level 0.00116, step 1, values float32  
Opened Unknown-ring.mrc as #509, grid size 256,256,256, pixel 2.1, shown at
level 0.000608, step 1, values float32  
Opened PflB_C13.mrc gaussian as #510, grid size 256,256,256, pixel 2.1, shown
at level 0.00108, step 1, values float32  
Opened PflB_monomer.mrc gaussian as #511, grid size 256,256,256, pixel 2.1,
shown at level 0.000387, step 1, values float32  
Opened Unknown-ring.mrc gaussian as #512, grid size 256,256,256, pixel 2.1,
shown at level 0.00109, step 1, values float32  
Opened 0838-disk.mrc gaussian as #513, grid size 240,240,240, pixel 4.3, shown
at level 0.0153, step 1, values float32  
Opened 0838-top.mrc gaussian as #514, grid size 240,240,240, pixel 4.3, shown
at level 0.00979, step 1, values float32  
Opened FlgV_monomer.mrc gaussian as #259.1, grid size 160,160,160, pixel 4.2,
shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.2, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.3, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.4, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.5, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.6, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.7, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.8, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.9, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.10, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.11, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.12, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.13, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.14, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.15, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.16, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.17, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.18, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.19, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.20, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.21, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgY-with-joints.mrc as #93, grid size 220,220,220, pixel 4.3, shown at
level 2.81, step 1, values float32  
Opened Cage_1unit.mrc copy as #85, grid size 240,240,240, pixel 2.1, shown at
level 0.0446, step 1, values float32  
Opened FliL.mrc copy as #114, grid size 240,240,240, pixel 2.1, shown at level
0.0732, step 1, values float32  
Opened PflA_new.mrc as #68, grid size 240,240,240, pixel 2.1, shown at level
0.162, step 1, values float32  
Opened Unknown_near_PflA.mrc as #69, grid size 240,240,240, pixel 2.1, shown
at level 0.127, step 1, values float32  
Opened PflB_new.mrc as #70, grid size 240,240,240, pixel 2.1, shown at level
0.0467, step 1, values float32  
Opened Top-cage.mrc as #71, grid size 240,240,240, pixel 2.1, shown at level
0.143, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #20, grid size 240,240,240, pixel 2.1,
shown at level 0.15, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #21, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #22, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #23, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #24, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #25, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #26, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #28, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #29, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #30, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #31, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #32, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #33, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #34, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #35, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #36, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #37, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Top-cage.mrc copy as #58, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #59, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #73, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #74, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #75, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #76, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #77, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #78, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #79, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #80, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #81, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #82, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #83, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #84, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #86, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #121, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #122, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #123, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened volume sum as #144, grid size 642,583,278, pixel 2.1, shown at level
0.162, step 1, values float32  
Opened FlgY-with-joints.mrc copy as #143, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32  
Opened FlgY-with-joints.mrc copy as #145, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32  
Opened 1x_Cage-units.mrc as #89, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened PilNO_PL-ring.mrc as #95, grid size 120,120,120, pixel 8.59, shown at
level 6.53e-05, step 1, values float32  
Opened New_PL-ring.mrc as #96, grid size 240,240,240, pixel 4.3, shown at
level 0.0141, step 1, values float32  
Opened Outer-ring-near-PL.mrc as #97, grid size 240,240,240, pixel 4.3, shown
at level 0.0141, step 1, values float32  
Opened Hpwt-L0.08-Global-PL.mrc as #115, grid size 240,240,240, pixel 4.3,
shown at level 0.0148, step 1, values float32  
Opened Hpwt-L0.08-rev.mrc as #142, grid size 240,240,240, pixel 4.3, shown at
level 0.0425, step 1, values float32  
Opened New_PL-ring.mrc gaussian as #165, grid size 240,240,240, pixel 4.3,
shown at level 0.0105, step 1, values float32  
Opened FlgY-with-joints.mrc copy as #173, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32  
Opened Hp-C1-4.296A-msk.mrc as #174, grid size 220,220,220, pixel 4.3, shown
at level 0.0868, step 1, values float32  
Opened Hp-C1-4.296A-msk.mrc as #1, grid size 220,220,220, pixel 4.3, shown at
level 0.000693, step 1, values float32  
opened ChimeraX session  

> close session

> open
> /Users/shoichitachiyama/Desktop/fold_2024_10_31_17_26flbb/fold_2024_10_31_17_26flbb_model_0.cif

Chain information for fold_2024_10_31_17_26flbb_model_0.cif #1  
---  
Chain | Description  
A B | .  
  

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> split #1

Split fold_2024_10_31_17_26flbb_model_0.cif (#1) into 2 models  
Chain information for fold_2024_10_31_17_26flbb_model_0.cif A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for fold_2024_10_31_17_26flbb_model_0.cif B #1.2  
---  
Chain | Description  
B | No description available  
  

> color #1.1 #a7db9dff

> color #1.2 #53db3fff

> color #1.2 #37912aff

> color #1.2 #41ab31ff

> save /Users/shoichitachiyama/Desktop/FlbB.png supersample 2
> transparentBackground true

> open
> /Users/shoichitachiyama/Downloads/cryosparc_P3_J334_011_volume_map_sharp.mrc

Opened cryosparc_P3_J334_011_volume_map_sharp.mrc as #2, grid size
100,100,100, pixel 4.27, shown at level 8.46, step 1, values float32  

> volume #2 level 8.459

> volume #2 level 8.572

> volume #2 level 8.459

> volume #2 level 8.347

> volume #2 level 8.234

> volume #2 level 8.121

> volume #2 level 8.009

> volume #2 level 7.896

> volume #2 level 7.783

> volume #2 level 7.671

> volume #2 level 7.445

> volume #2 level 7.107

> volume #2 level 6.995

> volume #2 level 6.882

> volume #2 level 6.769

> volume #2 level 6.544

> volume #2 level 6.319

> volume #2 level 6.206

> volume #2 level 6.094

> volume #2 level 5.981

> volume #2 level 5.643

> volume #2 level 5.418

> volume #2 level 5.192

> volume #2 level 4.967

> volume #2 level 4.854

> volume #2 level 4.742

> volume #2 level 4.516

> volume #2 level 4.404

> volume #2 level 4.291

> view

> ui tool show ""Side View""

> view orient

> volume #2 level 2.939

> surface dust #2 size 42.7

> open
> ""/Users/shoichitachiyama/Downloads/cryosparc_P3_J334_011_volume_map_sharp
> (1).mrc""

Opened cryosparc_P3_J334_011_volume_map_sharp (1).mrc as #3, grid size
100,100,100, pixel 4.27, shown at level 8.46, step 1, values float32  

> hide #!2 models

> volume #3 level 8.459

> volume #3 level 2.827

[deleted to fit within ticket limits]

> set bgColor #ffffff00

opened ChimeraX session  

> color #313 #454545ff models

> color #316 #454545ff models

> color #484 #454545ff models

> save /Users/shoichitachiyama/Desktop/Model-half.png supersample 2
> transparentBackground true

> view name SideP1

> save ""/Volumes/Backup-95/Chimera-2023/For_New England 2024/Model-half.cxs""
> includeMaps true

> hide #!16 models

> show #!16 models

> hide #!16 models

> hide #!53 models

> hide #!52 models

> hide #!58-80 models

> hide #!122 models

> hide #!97 models

> hide #!513 models

> hide #!514 models

> hide #!316 models

> hide #!259 models

> show #!259 models

> hide #!312 models

> turn x -40

> turn x 40

> show #!185.1 models

> show #!185.13 models

> show #!185.14 models

> show #!185.44 models

> show #!185.47 models

> show #!185.48 models

> show #!185.51 models

> show #!185.52 models

> show #!184.8 models

> show #!184.9 models

> show #!184.10 models

> show #!184.11 models

> show #!184.12 models

> show #!184.13 models

> show #!184.26 models

> show #!184.27 models

> show #!184.28 models

> show #!184.29 models

> show #!184.30 models

Cell requested for row 91 is out of bounds for table with 161 rows! Resizing
table model.  

> show #!183.8 models

> show #!183.9 models

> show #!183.10 models

> show #!183.11 models

> show #!183.12 models

> show #!183.13 models

Cell requested for row 77 is out of bounds for table with 244 rows! Resizing
table model.  

> show #!167.6 models

> show #!167.7 models

> show #!167.8 models

> show #!167.9 models

> show #!167.10 models

> show #!167.11 models

> show #!167.12 models

> show #!168.6 models

> show #!168.7 models

> show #!168.8 models

> show #!168.9 models

> show #!168.10 models

> show #!168.11 models

> show #!168.12 models

> show #!169.6 models

> show #!169.7 models

> show #!169.8 models

> show #!169.9 models

> show #!169.10 models

> show #!169.11 models

> show #!169.12 models

> save /Users/shoichitachiyama/Desktop/Model-40tilt-half.png supersample 2
> transparentBackground true

> save ""/Volumes/Backup-95/Chimera-2023/For_New England 2024/Model-40tilted-
> half.cxs"" includeMaps true

> close session

> open ""/Volumes/Backup-95/Chimera-2023/For_New England 2024/Model-half.cxs""
> format session

Opened 0838-bottom.mrc as #16, grid size 240,240,240, pixel 4.3, shown at
level 0.0144, step 1, values float32  
Opened Hpwt-L0.08-Global-Rod-no-MS.mrc as #113, grid size 240,240,240, pixel
4.3, shown at level 0.0151, step 1, values float32  
Opened Disk.mrc gaussian as #312, grid size 250,250,250, pixel 4.3, shown at
level 0.0186, step 1, values float32  
Opened IM-old-maps.mrc gaussian as #313, grid size 120,120,120, pixel 8.8,
shown at level 0.0702, step 1, values float32  
Opened OM.mrc copy gaussian as #316, grid size 240,240,240, pixel 4.3, shown
at level 0.0323, step 1, values float32  
Opened New_FliF.mrc gaussian as #479, grid size 256,256,256, pixel 2.1, shown
at level 0.0115, step 1, values float32  
Opened New_FlhA.mrc gaussian as #481, grid size 256,256,256, pixel 2.1, shown
at level 0.00316, step 1, values float32  
Opened PflBC13.mrc as #482, grid size 256,256,256, pixel 2.1, shown at level
0.00615, step 1, values float32  
Opened New_IM_Bottom2.mrc as #483, grid size 256,256,256, pixel 2.1, shown at
level 0.0072, step 1, values float32  
Opened New_IM_Bottom2.mrc gaussian as #484, grid size 256,256,256, pixel 2.1,
shown at level 0.0072, step 1, values float32  
Opened PflB_C13.mrc as #507, grid size 256,256,256, pixel 2.1, shown at level
0.0015, step 1, values float32  
Opened PflB_monomer.mrc as #508, grid size 256,256,256, pixel 2.1, shown at
level 0.00116, step 1, values float32  
Opened Unknown-ring.mrc as #509, grid size 256,256,256, pixel 2.1, shown at
level 0.000608, step 1, values float32  
Opened PflB_C13.mrc gaussian as #510, grid size 256,256,256, pixel 2.1, shown
at level 0.00108, step 1, values float32  
Opened PflB_monomer.mrc gaussian as #511, grid size 256,256,256, pixel 2.1,
shown at level 0.000387, step 1, values float32  
Opened Unknown-ring.mrc gaussian as #512, grid size 256,256,256, pixel 2.1,
shown at level 0.00109, step 1, values float32  
Opened 0838-disk.mrc gaussian as #513, grid size 240,240,240, pixel 4.3, shown
at level 0.0153, step 1, values float32  
Opened 0838-top.mrc gaussian as #514, grid size 240,240,240, pixel 4.3, shown
at level 0.00979, step 1, values float32  
Opened FlgV_monomer.mrc gaussian as #259.1, grid size 160,160,160, pixel 4.2,
shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.2, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.3, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.4, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.5, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.6, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.7, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.8, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.9, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.10, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.11, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.12, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.13, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.14, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.15, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.16, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.17, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.18, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.19, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.20, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.21, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgY-with-joints.mrc as #93, grid size 220,220,220, pixel 4.3, shown at
level 2.81, step 1, values float32  
Opened Cage_1unit.mrc copy as #85, grid size 240,240,240, pixel 2.1, shown at
level 0.0446, step 1, values float32  
Opened FliL.mrc copy as #114, grid size 240,240,240, pixel 2.1, shown at level
0.0732, step 1, values float32  
Opened PflA_new.mrc as #68, grid size 240,240,240, pixel 2.1, shown at level
0.162, step 1, values float32  
Opened Unknown_near_PflA.mrc as #69, grid size 240,240,240, pixel 2.1, shown
at level 0.127, step 1, values float32  
Opened PflB_new.mrc as #70, grid size 240,240,240, pixel 2.1, shown at level
0.0467, step 1, values float32  
Opened Top-cage.mrc as #71, grid size 240,240,240, pixel 2.1, shown at level
0.143, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #20, grid size 240,240,240, pixel 2.1,
shown at level 0.15, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #21, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #22, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #23, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #24, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #25, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #26, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #28, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #29, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #30, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #31, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #32, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #33, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #34, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #35, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #36, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #37, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Top-cage.mrc copy as #58, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #59, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #73, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #74, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #75, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #76, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #77, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #78, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #79, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #80, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #81, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #82, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #83, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #84, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #86, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #121, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #122, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #123, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened volume sum as #144, grid size 642,583,278, pixel 2.1, shown at level
0.162, step 1, values float32  
Opened FlgY-with-joints.mrc copy as #143, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32  
Opened FlgY-with-joints.mrc copy as #145, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32  
Opened 1x_Cage-units.mrc as #89, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened PilNO_PL-ring.mrc as #95, grid size 120,120,120, pixel 8.59, shown at
level 6.53e-05, step 1, values float32  
Opened New_PL-ring.mrc as #96, grid size 240,240,240, pixel 4.3, shown at
level 0.0141, step 1, values float32  
Opened Outer-ring-near-PL.mrc as #97, grid size 240,240,240, pixel 4.3, shown
at level 0.0141, step 1, values float32  
Opened Hpwt-L0.08-Global-PL.mrc as #115, grid size 240,240,240, pixel 4.3,
shown at level 0.0148, step 1, values float32  
Opened Hpwt-L0.08-rev.mrc as #142, grid size 240,240,240, pixel 4.3, shown at
level 0.0425, step 1, values float32  
Opened New_PL-ring.mrc gaussian as #165, grid size 240,240,240, pixel 4.3,
shown at level 0.0105, step 1, values float32  
Opened FlgY-with-joints.mrc copy as #173, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32  
Opened Hp-C1-4.296A-msk.mrc as #174, grid size 220,220,220, pixel 4.3, shown
at level 0.0868, step 1, values float32  
Opened Hp-C1-4.296A-msk.mrc as #1, grid size 220,220,220, pixel 4.3, shown at
level 0.000693, step 1, values float32  
opened ChimeraX session  

> lighting simple

> hide #!52 models

> show #!52 models

> hide #!53 models

> show #!53 models

> hide #!65 models

> show #!65 models

> view name SideP1

> turn y 3 120 models #65 center #481

Invalid ""center"" argument: Center argument has no object bounds  

> hide #!67 models

> show #!67 models

> turn y 3 120 models #65 center #67

> view name SideP1

> turn y 3 120 models #172#52#182#65 center #67

> view name SideP1

> turn y -12 120 models #167.13 center #167.13

> view name SideP1

> close session

> open ""/Volumes/Backup-95/Chimera-2023/For_New England 2024/Model-half.cxs""
> format session

Opened 0838-bottom.mrc as #16, grid size 240,240,240, pixel 4.3, shown at
level 0.0144, step 1, values float32  
Opened Hpwt-L0.08-Global-Rod-no-MS.mrc as #113, grid size 240,240,240, pixel
4.3, shown at level 0.0151, step 1, values float32  
Opened Disk.mrc gaussian as #312, grid size 250,250,250, pixel 4.3, shown at
level 0.0186, step 1, values float32  
Opened IM-old-maps.mrc gaussian as #313, grid size 120,120,120, pixel 8.8,
shown at level 0.0702, step 1, values float32  
Opened OM.mrc copy gaussian as #316, grid size 240,240,240, pixel 4.3, shown
at level 0.0323, step 1, values float32  
Opened New_FliF.mrc gaussian as #479, grid size 256,256,256, pixel 2.1, shown
at level 0.0115, step 1, values float32  
Opened New_FlhA.mrc gaussian as #481, grid size 256,256,256, pixel 2.1, shown
at level 0.00316, step 1, values float32  
Opened PflBC13.mrc as #482, grid size 256,256,256, pixel 2.1, shown at level
0.00615, step 1, values float32  
Opened New_IM_Bottom2.mrc as #483, grid size 256,256,256, pixel 2.1, shown at
level 0.0072, step 1, values float32  
Opened New_IM_Bottom2.mrc gaussian as #484, grid size 256,256,256, pixel 2.1,
shown at level 0.0072, step 1, values float32  
Opened PflB_C13.mrc as #507, grid size 256,256,256, pixel 2.1, shown at level
0.0015, step 1, values float32  
Opened PflB_monomer.mrc as #508, grid size 256,256,256, pixel 2.1, shown at
level 0.00116, step 1, values float32  
Opened Unknown-ring.mrc as #509, grid size 256,256,256, pixel 2.1, shown at
level 0.000608, step 1, values float32  
Opened PflB_C13.mrc gaussian as #510, grid size 256,256,256, pixel 2.1, shown
at level 0.00108, step 1, values float32  
Opened PflB_monomer.mrc gaussian as #511, grid size 256,256,256, pixel 2.1,
shown at level 0.000387, step 1, values float32  
Opened Unknown-ring.mrc gaussian as #512, grid size 256,256,256, pixel 2.1,
shown at level 0.00109, step 1, values float32  
Opened 0838-disk.mrc gaussian as #513, grid size 240,240,240, pixel 4.3, shown
at level 0.0153, step 1, values float32  
Opened 0838-top.mrc gaussian as #514, grid size 240,240,240, pixel 4.3, shown
at level 0.00979, step 1, values float32  
Opened FlgV_monomer.mrc gaussian as #259.1, grid size 160,160,160, pixel 4.2,
shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.2, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.3, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.4, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.5, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.6, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.7, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.8, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.9, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.10, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.11, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.12, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.13, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.14, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.15, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.16, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.17, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.18, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.19, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.20, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgV_monomer.mrc copy gaussian as #259.21, grid size 160,160,160, pixel
4.2, shown at level 0.015, step 1, values float32  
Opened FlgY-with-joints.mrc as #93, grid size 220,220,220, pixel 4.3, shown at
level 2.81, step 1, values float32  
Opened Cage_1unit.mrc copy as #85, grid size 240,240,240, pixel 2.1, shown at
level 0.0446, step 1, values float32  
Opened FliL.mrc copy as #114, grid size 240,240,240, pixel 2.1, shown at level
0.0732, step 1, values float32  
Opened PflA_new.mrc as #68, grid size 240,240,240, pixel 2.1, shown at level
0.162, step 1, values float32  
Opened Unknown_near_PflA.mrc as #69, grid size 240,240,240, pixel 2.1, shown
at level 0.127, step 1, values float32  
Opened PflB_new.mrc as #70, grid size 240,240,240, pixel 2.1, shown at level
0.0467, step 1, values float32  
Opened Top-cage.mrc as #71, grid size 240,240,240, pixel 2.1, shown at level
0.143, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #20, grid size 240,240,240, pixel 2.1,
shown at level 0.15, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #21, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #22, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #23, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #24, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #25, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #26, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #28, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #29, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #30, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #31, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #32, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #33, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #34, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #35, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #36, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #37, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32  
Opened Top-cage.mrc copy as #58, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #59, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #73, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #74, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #75, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #76, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #77, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #78, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #79, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #80, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #81, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #82, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #83, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #84, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #86, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #121, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #122, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened Top-cage.mrc copy as #123, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened volume sum as #144, grid size 642,583,278, pixel 2.1, shown at level
0.162, step 1, values float32  
Opened FlgY-with-joints.mrc copy as #143, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32  
Opened FlgY-with-joints.mrc copy as #145, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32  
Opened 1x_Cage-units.mrc as #89, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32  
Opened PilNO_PL-ring.mrc as #95, grid size 120,120,120, pixel 8.59, shown at
level 6.53e-05, step 1, values float32  
Opened New_PL-ring.mrc as #96, grid size 240,240,240, pixel 4.3, shown at
level 0.0141, step 1, values float32  
Opened Outer-ring-near-PL.mrc as #97, grid size 240,240,240, pixel 4.3, shown
at level 0.0141, step 1, values float32  
Opened Hpwt-L0.08-Global-PL.mrc as #115, grid size 240,240,240, pixel 4.3,
shown at level 0.0148, step 1, values float32  
Opened Hpwt-L0.08-rev.mrc as #142, grid size 240,240,240, pixel 4.3, shown at
level 0.0425, step 1, values float32  
Opened New_PL-ring.mrc gaussian as #165, grid size 240,240,240, pixel 4.3,
shown at level 0.0105, step 1, values float32  
Opened FlgY-with-joints.mrc copy as #173, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32  
Opened Hp-C1-4.296A-msk.mrc as #174, grid size 220,220,220, pixel 4.3, shown
at level 0.0868, step 1, values float32  
Opened Hp-C1-4.296A-msk.mrc as #1, grid size 220,220,220, pixel 4.3, shown at
level 0.000693, step 1, values float32  
opened ChimeraX session  

> view name SideP1

> movie record

> turn y 3 120 models #172#52#182#65 center #67

> turn y -12 120 models #167.1 center #167.1

> turn y -12 120 models #167.2 center #167.2

> turn y -12 120 models #167.3 center #167.3

> turn y -12 120 models #167.4 center #167.4

> turn y -12 120 models #167.5 center #167.5

> turn y -12 120 models #167.13 center #167.13

> turn y -12 120 models #167.14 center #167.14

> turn y -12 120 models #167.15 center #167.15

> turn y -12 120 models #167.16 center #167.16

> turn y -12 120 models #167.17 center #167.17

> turn y -12 120 models #167.18 center #167.18

> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/Hp_rotate.mov

Movie encoding failed because no images were recorded.  

> view SideP1

> movie record

> turn y 3 120 models #172#52#182#65 center #67

> turn y -12 120 models #167.1 center #167.1

> turn y -12 120 models #167.2 center #167.2

> turn y -12 120 models #167.3 center #167.3

> turn y -12 120 models #167.4 center #167.4

> turn y -12 120 models #167.5 center #167.5

> turn y -12 120 models #167.13 center #167.13

> turn y -12 120 models #167.14 center #167.14

> turn y -12 120 models #167.15 center #167.15

> turn y -12 120 models #167.16 center #167.16

> turn y -12 120 models #167.17 center #167.17

> turn y -12 120 models #167.18 center #167.18

> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/Hp_rotate.mov

Movie encoding failed because no images were recorded.  

> view SideP1

> movie record

> turn y 3 120 models #172#52#182#65 center #67

> turn y -12 120 models #167.1 center #167.1

> turn y -12 120 models #167.2 center #167.2

> turn y -12 120 models #167.3 center #167.3

> turn y -12 120 models #167.4 center #167.4

> turn y -12 120 models #167.5 center #167.5

> turn y -12 120 models #167.13 center #167.13

> turn y -12 120 models #167.14 center #167.14

> turn y -12 120 models #167.15 center #167.15

> turn y -12 120 models #167.16 center #167.16

> turn y -12 120 models #167.17 center #167.17

> turn y -12 120 models #167.18 center #167.18

> movie stop

> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/Hp_rotate.mov

Movie encoding failed because no images were recorded.  

> view SideP1

> movie record

> turn y 3 120 models #172#52#182#65 center #67

> turn y -12 120 models #167.1 center #167.1

> turn y -12 120 models #167.2 center #167.2

> turn y -12 120 models #167.3 center #167.3

> turn y -12 120 models #167.4 center #167.4

> turn y -12 120 models #167.5 center #167.5

> turn y -12 120 models #167.13 center #167.13

> turn y -12 120 models #167.14 center #167.14

> turn y -12 120 models #167.15 center #167.15

> turn y -12 120 models #167.16 center #167.16

> turn y -12 120 models #167.17 center #167.17

> turn y -12 120 models #167.18 center #167.18

> movie stop

> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/Hp_rotate.mov

Movie encoding failed because no images were recorded.  

> view SideP1

> movie record

> view SideP1

> wait 10

> turn y 3 120 models #172#52#182#65 center #67

> turn y -12 120 models #167.1 center #167.1

> turn y -12 120 models #167.2 center #167.2

> turn y -12 120 models #167.3 center #167.3

> turn y -12 120 models #167.4 center #167.4

> turn y -12 120 models #167.5 center #167.5

> turn y -12 120 models #167.13 center #167.13

> turn y -12 120 models #167.14 center #167.14

> turn y -12 120 models #167.15 center #167.15

> turn y -12 120 models #167.16 center #167.16

> turn y -12 120 models #167.17 center #167.17

> turn y -12 120 models #167.18 center #167.18

> movie stop

> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/Hp_rotate.mov

Movie saved to /Users/shoichitachiyama/Desktop/Hp_rotate.mov  
  

> view SideP1

> movie record

> turn y 3 120 models #172#52#182#65 center #67

> turn y -12 120 models #167.1 center #167.1

> turn y -12 120 models #167.2 center #167.2

> turn y -12 120 models #167.3 center #167.3

> turn y -12 120 models #167.4 center #167.4

> turn y -12 120 models #167.5 center #167.5

> turn y -12 120 models #167.13 center #167.13

> turn y -12 120 models #167.14 center #167.14

> turn y -12 120 models #167.15 center #167.15

> turn y -12 120 models #167.16 center #167.16

> turn y -12 120 models #167.17 center #167.17

> turn y -12 120 models #167.18 center #167.18

> wait 240

> movie stop

> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/Hp_rotate.mov

Movie saved to /Users/shoichitachiyama/Desktop/Hp_rotate.mov  
  

> lighting soft

> lighting simple

> show #!72 models

> hide #!72 models

> hide #!172 models

> show #!170 models

> show #171 models

> hide #!170 models

> show #!172 models

> hide #171 models

> select add #172

280839 atoms, 284349 bonds, 35529 residues, 40 models selected  

> hide sel cartoons

> hide sel surfaces

> show sel cartoons

> select subtract #172

234 models selected  

> turn x 90

> select add #172.28

7201 atoms, 7291 bonds, 911 residues, 1 model selected  

> ui mousemode right ""translate selected models""

> view matrix models
> #172.28,-0.51825,0.84298,-0.14421,1043.1,0.82082,0.53762,0.1929,190.19,0.24014,-0.018402,-0.97056,227.61

> turn x 90

> view matrix models
> #172.28,-0.51825,0.84298,-0.14421,1043.1,0.82082,0.53762,0.1929,192.35,0.24014,-0.018402,-0.97056,232.64

> show sel surfaces

> select add #172

280839 atoms, 284349 bonds, 35529 residues, 46 models selected  

> select subtract #172.28

273638 atoms, 277058 bonds, 34618 residues, 273 models selected  

> select add #172

280839 atoms, 284349 bonds, 35529 residues, 268 models selected  

> select subtract #172

234 models selected  

> select add #172.28

7201 atoms, 7291 bonds, 911 residues, 1 model selected  

> hide sel surfaces

> save ""/Volumes/Backup-95/Chimera-2023/For_New England 2024/Shifted-8uox-
> mono.pdb"" selectedOnly true

> select add #172

280839 atoms, 284349 bonds, 35529 residues, 46 models selected  

> select subtract #172

234 models selected  

> hide #!172 models

> open ""/Volumes/Backup-95/Chimera-2023/For_New England 2024/Shifted-8uox-
> mono.pdb""

Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/For_New
England 2024/Shifted-8uox-mono.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 78 1 77  
Start residue of secondary structure not found: HELIX 2 2 LEU A 79 ILE A 81 1
3  
Start residue of secondary structure not found: HELIX 3 3 LYS A 107 LEU A 118
1 12  
Start residue of secondary structure not found: HELIX 4 4 ASN A 119 MET A 121
1 3  
Start residue of secondary structure not found: HELIX 5 5 GLU A 154 ILE A 156
1 3  
14 messages similar to the above omitted  
  
Chain information for Shifted-8uox-mono.pdb #2  
---  
Chain | Description  
A1 | No description available  
B1 | No description available  
C1 | No description available  
D1 E1 | No description available  
F1 | No description available  
  

> select add #2

7201 atoms, 7291 bonds, 911 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> turn x -90

> show #!113 models

> sym #2 C39 copies true center #113

Made 39 copies for Shifted-8uox-mono.pdb symmetry C39  

> select subtract #2

Nothing selected  

> color #3 #727272ff models

> select add #3

280839 atoms, 284349 bonds, 35529 residues, 40 models selected  

> hide sel cartoons

> show sel surfaces

> view SideP1

> select subtract #3

234 models selected  

> hide #!113 models

> lighting soft

> movie record

> turn y 3 120 models #172#52#182#65 center #67

> turn y -12 120 models #167.1 center #167.1

> turn y -12 120 models #167.2 center #167.2

> turn y -12 120 models #167.3 center #167.3

> turn y -12 120 models #167.4 center #167.4

> turn y -12 120 models #167.5 center #167.5

> turn y -12 120 models #167.13 center #167.13

> turn y -12 120 models #167.14 center #167.14

> turn y -12 120 models #167.15 center #167.15

> turn y -12 120 models #167.16 center #167.16

> turn y -12 120 models #167.17 center #167.17

> turn y -12 120 models #167.18 center #167.18

> wait 120

> movie stop

> view SideP1

> movie record

> turn y 3 120 models #3#52#182#65 center #67

> turn y -12 120 models #167.1 center #167.1

> turn y -12 120 models #167.2 center #167.2

> turn y -12 120 models #167.3 center #167.3

> turn y -12 120 models #167.4 center #167.4

> turn y -12 120 models #167.5 center #167.5

> turn y -12 120 models #167.13 center #167.13

> turn y -12 120 models #167.14 center #167.14

> turn y -12 120 models #167.15 center #167.15

> turn y -12 120 models #167.16 center #167.16

> turn y -12 120 models #167.17 center #167.17

> turn y -12 120 models #167.18 center #167.18

> wait 120

> movie stop

> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/Hp_rotate.mov

Movie saved to /Users/shoichitachiyama/Desktop/Hp_rotate.mov  
  

> view SideP1

> set bgColor black

> set bgColor transparent

> movie record

> turn y 3 120 models #3#52#182#65 center #67

> turn y -12 120 models #167.1 center #167.1

> turn y -12 120 models #167.2 center #167.2

> turn y -12 120 models #167.3 center #167.3

> turn y -12 120 models #167.4 center #167.4

> turn y -12 120 models #167.5 center #167.5

> turn y -12 120 models #167.13 center #167.13

> turn y -12 120 models #167.14 center #167.14

> turn y -12 120 models #167.15 center #167.15

> turn y -12 120 models #167.16 center #167.16

> turn y -12 120 models #167.17 center #167.17

> turn y -12 120 models #167.18 center #167.18

> wait 120

> movie stop

> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/Hp_rotate.mov

Movie saved to /Users/shoichitachiyama/Desktop/Hp_rotate.mov  
  

> view SideP1

> save /Users/shoichitachiyama/Desktop/New-side1.png supersample 2
> transparentBackground true

> save ""/Volumes/Backup-95/Chimera-2023/For_New England 2024/Model-half-
> ShiftCring.cxs"" includeMaps true

> close session

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/For-FlgY_Local-Segment/Send-to-
> Jun_Sep20-2024/FlgY_Local-model09202024.cxs

> set bgColor #ffffff00

opened ChimeraX session  

> close session

> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/For-FlgY_Local-
> Segment/Fig3_FlgY_Loca-Sep17-2024l.cxs

Opened 13X_FlgY-ring.mrc as #1, grid size 220,220,220, pixel 2.15, shown at
level 0.539, step 1, values float32  
Opened FliF_local.mrc as #2, grid size 220,220,220, pixel 2.15, shown at level
0.378, step 1, values float32  
Opened Internal-ring_local.mrc as #3, grid size 220,220,220, pixel 2.15, shown
at level 0.299, step 1, values float32  
Opened Unknown_near_PflA.mrc as #4, grid size 240,240,240, pixel 2.1, shown at
level 0.147, step 1, values float32  
Opened Rod_local.mrc as #5, grid size 220,220,220, pixel 2.15, shown at level
0.482, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27.1, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27.2, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27.3, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27.4, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27.5, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27.6, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27.7, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27.8, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27.9, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27.10, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27.11, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27.12, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27.13, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27.14, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27.15, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27.16, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27.17, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32  
Opened Unknown_near_PflA.mrc copy as #27.18, grid size 240,240,240, pixel 2.1,
shown at level 0.147, step 1, values float32  
Opened 1X_FlgY_region.mrc as #10, grid size 220,220,220, pixel 2.15, shown at
level 0.539, step 1, values float32  
Opened 3X_FlgY_region.mrc as #11, grid size 220,220,220, pixel 2.15, shown at
level 0.539, step 1, values float32  
opened ChimeraX session  

> hide #!13 models

> hide #!27 models

> show #!10 models

> hide #!8 models

> hide #!1 models

> show #!13 models

> show #!11 models

> hide #!10 models

> hide #!13.6 models

> show #!13.6 models

> hide #!13.7 models

> show #!13.7 models

> hide #!13.8 models

> show #!13.8 models

> hide #!13.9 models

> hide #!13.10 models

> hide #!13.11 models

> hide #!13.12 models

> hide #!13.13 models

> hide #!13.1 models

> view orient

> turn x -12 120 models #13 center #13

> select add #13.6

2624 atoms, 2640 bonds, 326 residues, 3 models selected  

> select add #13.7

5248 atoms, 5280 bonds, 652 residues, 8 models selected  

> select add #13.8

7872 atoms, 7920 bonds, 978 residues, 13 models selected  

> select add #13

34112 atoms, 34320 bonds, 4238 residues, 46 models selected  

> select subtract #13

26 models selected  

> select add #13

34112 atoms, 34320 bonds, 4238 residues, 40 models selected  

> select subtract #13

26 models selected  

> turn x -3 120 models #13#11 center #13

> movie record

> turn x -3 120 models #13#11 center #13

> movie stop

> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/FlgY_rotate.mov

Movie encoding failed because no images were recorded.  

> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/FlgY_rotate.mov

Movie encoding failed because no images were recorded.  

> movie record

> turn x -3 120 models #13#11 center #13

> movie stop

> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/FlgY_rotate.mov

Movie encoding failed because no images were recorded.  

> movie record

> turn x -3 120 models #13#11 center #13

> wait 120

> movie stop

> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/FlgY_rotate.mov

Movie saved to /Users/shoichitachiyama/Desktop/FlgY_rotate.mov  
  

> set bgColor black

> set bgColor transparent

> color #11 #72727200 models

> color #11 #72727266 models

> movie record

> turn x -3 120 models #13#11 center #13

> wait 120

> movie stop

> movie encode quality high framerate 10 output
> /Users/shoichitachiyama/Desktop/FlgY_rotate.mov

Movie saved to /Users/shoichitachiyama/Desktop/FlgY_rotate.mov  
  

> hide #!13.8 models

> hide #!13 models

> show #!13 models

> hide #!11 models

> show #!8 models

> show #!13.1 models

> show #!13.2 models

> show #!13.3 models

> show #!13.4 models

> show #!13.5 models

> show #!13.8 models

> show #!13.10 models

> hide #!13.10 models

> show #!13.11 models

> show #!13.13 models

> show #!13.10 models

> show #!13.9 models

> show #!13.12 models

> hide #!13 models

> show #!12 models

> hide #!12 models

> show #!6 models

> hide #!6 models

> show #!1 models

> hide #!1 models

> show #!11 models

> hide #!11 models

> show #!12 models

> hide #!12 models

> show #!27 models

> hide #!27 models

> show #!12 models

> hide #!12 models

> show #!13 models

> show #!6 models

> hide #!13 models

> select add #6

41236 atoms, 41678 bonds, 5174 residues, 53 models selected  

> show sel surfaces

> show #!13 models

> hide #!13 models

> select subtract #6

52 models selected  


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: 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: 10151.41.12
      OS Loader Version: 10151.41.12

Software:

    System Software Overview:

      System Version: macOS 14.1.1 (23B81)
      Kernel Version: Darwin 23.1.0
      Time since boot: 6 days, 21 hours, 56 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
}}}
"	defect	assigned	normal		Window Toolkit								all	ChimeraX