id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
18735	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Current thread 0x000000020c56e0c0 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 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, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, 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, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.pdb._pdbio (total: 52)


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  ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=9.9G written=5672K(0%) resident=5672K(0%) swapped_out=0K(0%) unallocated=9.9G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               256K        2 \nActivity Tracing                   256K        1 \nCG image                           832K       44 \nColorSync                          624K       33 \nCoreAnimation                     1424K       88 \nCoreGraphics                        64K        4 \nCoreUI image data                 5504K       53 \nFoundation                          48K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                             8.8G      254 \nMALLOC guard page                  288K       18 \nMach message                        64K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                       56.7M       45 \nStack                            203.5M       45 \nVM_ALLOCATE                      575.5M      251 \nVM_ALLOCATE (reserved)           352.0M        4         reserved VM address space (unallocated)\n__AUTH                            5520K      696 \n__AUTH_CONST                      77.4M      943 \n__CTF                               824        1 \n__DATA                            34.0M     1082 \n__DATA_CONST                      36.8M     1099 \n__DATA_DIRTY                      2777K      342 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       647.5M      150 \n__OBJC_RO                         61.4M        1 \n__OBJC_RW                         2396K        1 \n__TEXT                             1.3G     1069 \n__TEXT (graphics)                 39.6M       50 \n__TPRO_CONST                       128K        2 \ndyld private memory               2720K       24 \nmapped file                      726.4M       98 \npage table in kernel              5672K        1 \nshared memory                     3264K       29 \n===========                     =======  ======= \nTOTAL                             12.9G     6442 \nTOTAL, minus reserved VM space    12.5G     6442 \n"",
  ""legacyInfo"" : {
  ""threadTriggered"" : {
    ""name"" : ""CrBrowserMain"",
    ""queue"" : ""com.apple.main-thread""
  }
},
  ""logWritingSignature"" : ""32d1ed4969a2b0ff5987e5394586d293cbb52de8"",
  ""trialInfo"" : {
  ""rollouts"" : [
    {
      ""rolloutId"" : ""60da5e84ab0ca017dace9abf"",
      ""factorPackIds"" : {

      },
      ""deploymentId"" : 240000008
    },
    {
      ""rolloutId"" : ""6410af69ed1e1e7ab93ed169"",
      ""factorPackIds"" : {

      },
      ""deploymentId"" : 240000011
    }
  ],
  ""experiments"" : [

  ]
}
}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/uozumilab2/Library/CloudStorage/GoogleDrive-
> yuki.muraoka.d4@tohoku.ac.jp/共有ドライブ/01_魚住研
> (科学論文・work)/論文・ファイル交換用/2025_GORK_K濃度_奏音&村岡/Cryo-EM関連
> (村岡)/CryoSPARC_150K_22C/J73_3D
> Class/cryosparc_P17_J85_004_volume_map_sharp.mrc""

Opened cryosparc_P17_J85_004_volume_map_sharp.mrc as #1, grid size
448,448,448, pixel 0.825, shown at level 0.0551, step 2, values float32  

> open ""/Users/uozumilab2/Library/CloudStorage/GoogleDrive-
> yuki.muraoka.d4@tohoku.ac.jp/共有ドライブ/01_魚住研
> (科学論文・work)/論文・ファイル交換用/2025_GORK_K濃度_奏音&村岡/Cryo-EM関連
> (村岡)/CryoSPARC_150K_22C/J73_3D
> Class/cryosparc_P17_J92_003_volume_map_sharp.mrc""

Opened cryosparc_P17_J92_003_volume_map_sharp.mrc as #2, grid size
448,448,448, pixel 0.825, shown at level 0.0581, step 2, values float32  

> open ""/Users/uozumilab2/Library/CloudStorage/GoogleDrive-
> yuki.muraoka.d4@tohoku.ac.jp/共有ドライブ/01_魚住研
> (科学論文・work)/論文・ファイル交換用/2025_GORK_K濃度_奏音&村岡/Cryo-EM関連
> (村岡)/CryoSPARC_150K_22C/J73_3D
> Class/cryosparc_P17_J93_004_volume_map_sharp.mrc""

Opened cryosparc_P17_J93_004_volume_map_sharp.mrc as #3, grid size
448,448,448, pixel 0.825, shown at level 0.0581, step 2, values float32  

> open ""/Users/uozumilab2/Library/CloudStorage/GoogleDrive-
> yuki.muraoka.d4@tohoku.ac.jp/共有ドライブ/01_魚住研
> (科学論文・work)/論文・ファイル交換用/2025_GORK_K濃度_奏音&村岡/Cryo-EM関連
> (村岡)/CryoSPARC_150K_22C/J73_3D
> Class/cryosparc_P17_J94_011_volume_map_sharp.mrc""

Opened cryosparc_P17_J94_011_volume_map_sharp.mrc as #4, grid size
448,448,448, pixel 0.825, shown at level 0.0515, step 2, values float32  

> open ""/Users/uozumilab2/Library/CloudStorage/GoogleDrive-
> yuki.muraoka.d4@tohoku.ac.jp/共有ドライブ/01_魚住研
> (科学論文・work)/論文・ファイル交換用/2025_GORK_K濃度_奏音&村岡/Cryo-EM関連
> (村岡)/CryoSPARC_150K_22C/J73_3D
> Class/cryosparc_P17_J86_009_volume_map_sharp.mrc""

Opened cryosparc_P17_J86_009_volume_map_sharp.mrc as #5, grid size
448,448,448, pixel 0.825, shown at level 0.0519, step 2, values float32  

> open ""/Users/uozumilab2/Library/CloudStorage/GoogleDrive-
> yuki.muraoka.d4@tohoku.ac.jp/共有ドライブ/01_魚住研
> (科学論文・work)/論文・ファイル交換用/2025_GORK_K濃度_奏音&村岡/Cryo-EM関連
> (村岡)/CryoSPARC_150K_22C/J73_3D
> Class/cryosparc_P17_J87_012_volume_map_sharp.mrc""

Opened cryosparc_P17_J87_012_volume_map_sharp.mrc as #6, grid size
448,448,448, pixel 0.825, shown at level 0.0528, step 2, values float32  

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> open ""/Users/uozumilab2/Library/CloudStorage/GoogleDrive-
> yuki.muraoka.d4@tohoku.ac.jp/共有ドライブ/01_魚住研
> (科学論文・work)/論文・ファイル交換用/2025_GORK_K濃度_奏音&村岡/Cryo-EM関連
> (村岡)/CryoSPARC_150K_22C/J73_3D
> Class/cryosparc_P17_J88_009_volume_map_sharp.mrc""

Opened cryosparc_P17_J88_009_volume_map_sharp.mrc as #7, grid size
448,448,448, pixel 0.825, shown at level 0.0494, step 2, values float32  

> open ""/Users/uozumilab2/Library/CloudStorage/GoogleDrive-
> yuki.muraoka.d4@tohoku.ac.jp/共有ドライブ/01_魚住研
> (科学論文・work)/論文・ファイル交換用/2025_GORK_K濃度_奏音&村岡/Cryo-EM関連
> (村岡)/CryoSPARC_150K_22C/J73_3D
> Class/cryosparc_P17_J89_013_volume_map_sharp.mrc""

Opened cryosparc_P17_J89_013_volume_map_sharp.mrc as #8, grid size
448,448,448, pixel 0.825, shown at level 0.052, step 2, values float32  

> open ""/Users/uozumilab2/Library/CloudStorage/GoogleDrive-
> yuki.muraoka.d4@tohoku.ac.jp/共有ドライブ/01_魚住研
> (科学論文・work)/論文・ファイル交換用/2025_GORK_K濃度_奏音&村岡/Cryo-EM関連
> (村岡)/CryoSPARC_150K_22C/J73_3D
> Class/cryosparc_P17_J90_011_volume_map_sharp.mrc""

Opened cryosparc_P17_J90_011_volume_map_sharp.mrc as #9, grid size
448,448,448, pixel 0.825, shown at level 0.0544, step 2, values float32  

> open ""/Users/uozumilab2/Library/CloudStorage/GoogleDrive-
> yuki.muraoka.d4@tohoku.ac.jp/共有ドライブ/01_魚住研
> (科学論文・work)/論文・ファイル交換用/2025_GORK_K濃度_奏音&村岡/Cryo-EM関連
> (村岡)/CryoSPARC_150K_22C/J73_3D
> Class/cryosparc_P17_J91_004_volume_map_sharp.mrc""

Opened cryosparc_P17_J91_004_volume_map_sharp.mrc as #10, grid size
448,448,448, pixel 0.825, shown at level 0.0563, step 2, values float32  

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> show #!1 models

> volume #1 step 1

> surface dust #1 size 8.25

> hide #!1 models

> show #!2 models

> volume #2 step 1

> surface dust #2 size 8.25

> hide #!2 models

> volume #3 step 1

> show #!3 models

> surface dust #3 size 8.25

> hide #!3 models

> show #!4 models

> volume #4 step 1

> surface dust #4 size 8.25

> hide #!4 models

> show #!5 models

> volume #5 step 1

> surface dust #5 size 8.25

> hide #!5 models

> show #!6 models

> volume #6 step 1

> surface dust #6 size 8.25

> hide #!6 models

> show #!7 models

> volume #7 step 1

> surface dust #7 size 8.25

> hide #!7 models

> show #!8 models

> volume #8 step 1

> surface dust #8 size 8.25

> hide #!8 models

> show #!9 models

> volume #9 step 1

> surface dust #9 size 8.25

> hide #!9 models

> show #!10 models

> volume #10 step 1

> surface dust #10 size 8.25

> hide #!10 models

> show #!1 models

> volume #1 level 0.09254

> hide #!1 models

> show #!2 models

> volume #2 level 0.09078

> hide #!2 models

> show #!3 models

> volume #3 level 0.101

> hide #!3 models

> show #!4 models

> volume #4 level 0.09256

> hide #!4 models

> show #!5 models

> volume #5 level 0.07505

> volume #5 level 0.1008

> hide #!5 models

> show #!6 models

> volume #6 level 0.09509

> hide #!6 models

> show #!7 models

> volume #7 level 0.09016

> hide #!7 models

> show #!8 models

> volume #8 level 0.09118

> volume #8 level 0.09464

> hide #!8 models

> show #!9 models

> volume #9 level 0.09334

> volume #9 level 0.07

> volume #9 level 0.09983

> hide #!9 models

> show #!10 models

> volume #10 level 0.06798

> volume #10 level 0.09239

> volume #7 level 0.09

> hide #!10 models

> show #!7 models

> volume #1 level 0.09

> hide #!7 models

> show #!1 models

> hide #!1 models

> show #!2 models

> volume #2 level 0.09

> hide #!2 models

> show #!3 models

> volume #3 level 0.09

> hide #!3 models

> show #!4 models

> volume #4 level 0.09

> hide #!4 models

> show #!5 models

> volume #5 level 0.09

> hide #!5 models

> show #!6 models

> volume #6 level 0.09

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!8 models

> volume #8 level 0.09

> hide #!8 models

> show #!9 models

> volume #9 level 0.09

> hide #!9 models

> show #!10 models

> volume #10 level 0.09

> hide #!10 models

> show #!1 models

> set bgColor white

> set bgColor #ffffff00

> save /Users/uozumilab2/Desktop/image1.png supersample 3

> hide #!1 models

> show #!2 models

> save /Users/uozumilab2/Desktop/image2.png supersample 3

> hide #!2 models

> show #!3 models

> save /Users/uozumilab2/Desktop/image3.png supersample 3

> hide #!3 models

> show #!4 models

> save /Users/uozumilab2/Desktop/image4.png supersample 3

> hide #!4 models

> show #!5 models

> save /Users/uozumilab2/Desktop/image5.png supersample 3

> hide #!5 models

> show #!6 models

> save /Users/uozumilab2/Desktop/image6.png supersample 3

> hide #!6 models

> show #!7 models

> save /Users/uozumilab2/Desktop/image7.png supersample 3

> hide #!7 models

> show #!8 models

> save /Users/uozumilab2/Desktop/image8.png supersample 3

> hide #!8 models

> show #!9 models

> save /Users/uozumilab2/Desktop/image9.png supersample 3

> hide #!9 models

> show #!10 models

> save /Users/uozumilab2/Desktop/image10.png supersample 3

> volume #10 level 0.01

> volume #10 level 0.04

> volume #10 level 0.05

> volume #9 level 0.05

> hide #!10 models

> show #!9 models

> hide #!9 models

> show #!1 models

> volume #1 level 0.05

> volume #2 level 0.05

> volume #3 level 0.05

> volume #4 level 0.05

> volume #5 level 0.05

> volume #6 level 0.05

> volume #7 level 0.05

> volume #8 level 0.05

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!1 models

> turn y 90

> view orient

> ui tool show ""Side View""

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!2 models

> show #!1 models

> turn y 90

> turn x 90

> hide #!2 models

> turn y 90

> turn y 10

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!8 models

> show #!9 models

> hide #!8 models

> hide #!9 models

> show #!10 models

> hide #!10 models

> show #!1 models

> save /Users/uozumilab2/Desktop/image1.png supersample 3

> hide #!1 models

> show #!2 models

> show #!1 models

> select add #2

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.21839,0.97517,-0.036731,-28.644,-0.97586,0.21818,-0.009868,326.73,-0.0016092,0.037999,0.99928,-6.5845

> fitmap #2 inMap #1

Fit map cryosparc_P17_J92_003_volume_map_sharp.mrc in map
cryosparc_P17_J85_004_volume_map_sharp.mrc using 1159088 points  
correlation = 0.9089, correlation about mean = 0.6679, overlap = 5976  
steps = 68, shift = 0.931, angle = 3.22 degrees  
  
Position of cryosparc_P17_J92_003_volume_map_sharp.mrc (#2) relative to
cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.25846076 0.96602175 0.00007346 -41.49098775  
-0.96602176 0.25846076 -0.00003058 315.55988283  
-0.00004853 -0.00006306 1.00000000 -0.30844972  
Axis -0.00001681 0.00006314 -1.00000000  
Axis point 184.79838080 184.80560309 0.00000000  
Rotation angle (degrees) 75.02125128  
Shift along axis 0.32907104  
  

> turn x 90

> select subtract #2

Nothing selected  

> hide #!1 models

> save /Users/uozumilab2/Desktop/image2.png supersample 3

> hide #!2 models

> show #!3 models

> show #!1 models

> select ~sel & ##selected

Nothing selected  

> select down

Nothing selected  

> turn x -90

> select add #3

2 models selected  

> view matrix models
> #3,0.77789,0.62818,-0.016757,-71.388,-0.62837,0.77783,-0.011417,159.67,0.0058623,0.019411,0.99979,-4.6258

> fitmap #3 inMap #1

Fit map cryosparc_P17_J93_004_volume_map_sharp.mrc in map
cryosparc_P17_J85_004_volume_map_sharp.mrc using 1133741 points  
correlation = 0.9465, correlation about mean = 0.7769, overlap = 6901  
steps = 100, shift = 0.919, angle = 6.42 degrees  
  
Position of cryosparc_P17_J93_004_volume_map_sharp.mrc (#3) relative to
cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.84231178 0.53899059 0.00008646 -70.47272760  
-0.53899059 0.84231179 -0.00002221 128.74734890  
-0.00008480 -0.00002790 1.00000000 -0.38680135  
Axis -0.00000528 0.00015887 -0.99999999  
Axis point 184.79775712 184.81427456 0.00000000  
Rotation angle (degrees) 32.61495056  
Shift along axis 0.40762767  
  

> select subtract #3

Nothing selected  

> turn x 90

> hide #!1 models

> volume #3 level 0.04322

> volume #3 level 0.05

> save /Users/uozumilab2/Desktop/image3.png supersample 3

> hide #!3 models

> show #!4 models

> show #!1 models

> turn x -90

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> turn x 90

> hide #!1 models

> show #!1 models

> hide #!4 models

> show #!4 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> fitmap #1 inMap #4

Fit map cryosparc_P17_J85_004_volume_map_sharp.mrc in map
cryosparc_P17_J94_011_volume_map_sharp.mrc using 1042243 points  
correlation = 0.8973, correlation about mean = 0.5035, overlap = 5669  
steps = 56, shift = 0.364, angle = 0.967 degrees  
  
Position of cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) relative to
cryosparc_P17_J94_011_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99985771 0.01686916 -0.00000694 -3.07909934  
-0.01686916 0.99985771 -0.00000001 3.14503024  
0.00000694 0.00000013 1.00000000 0.36302770  
Axis 0.00000427 -0.00041143 -0.99999992  
Axis point 184.87493376 184.08762582 0.00000000  
Rotation angle (degrees) 0.96657787  
Shift along axis -0.36433478  
  

> hide #!1 models

> save /Users/uozumilab2/Desktop/image4.png supersample 3

> hide #!4 models

> show #!5 models

> show #!1 models

> turn x -90

> select add #5

2 models selected  

> view matrix models
> #5,0.61829,0.7856,-0.023507,-69.616,-0.78593,0.61819,-0.012409,218.45,0.004783,0.026147,0.99965,-5.6404

> fitmap #5 inMap #1

Fit map cryosparc_P17_J86_009_volume_map_sharp.mrc in map
cryosparc_P17_J85_004_volume_map_sharp.mrc using 956200 points  
correlation = 0.8835, correlation about mean = 0.4981, overlap = 5570  
steps = 120, shift = 0.833, angle = 11.5 degrees  
  
Position of cryosparc_P17_J86_009_volume_map_sharp.mrc (#5) relative to
cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.77271076 0.63475829 -0.00001580 -75.30664248  
-0.63475829 0.77271076 -0.00000450 159.31066717  
0.00000935 0.00001350 1.00000000 -0.41824436  
Axis 0.00001418 -0.00001981 -1.00000000  
Axis point 184.80280856 184.81103885 0.00000000  
Rotation angle (degrees) 39.40205947  
Shift along axis 0.41402097  
  

> select subtract #5

Nothing selected  

> turn x 90

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> save /Users/uozumilab2/Desktop/image5.png supersample 3

> hide #!5 models

> show #!6 models

> show #!1 models

> turn x -90

> select add #6

2 models selected  

> view matrix models
> #6,0.62926,0.77685,-0.02308,-70.182,-0.77718,0.62916,-0.012392,214.77,0.0048945,0.025735,0.99966,-5.588

> fitmap #6 inMap #1

Fit map cryosparc_P17_J87_012_volume_map_sharp.mrc in map
cryosparc_P17_J85_004_volume_map_sharp.mrc using 992914 points  
correlation = 0.8894, correlation about mean = 0.5052, overlap = 5645  
steps = 60, shift = 0.8, angle = 1.93 degrees  
  
Position of cryosparc_P17_J87_012_volume_map_sharp.mrc (#6) relative to
cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.65840925 0.75266012 0.00004024 -75.96680112  
-0.75266012 0.65840925 -0.00000944 202.21774655  
-0.00003360 -0.00002407 1.00000000 -0.15421395  
Axis -0.00000972 0.00004906 -1.00000000  
Axis point 184.79960514 184.80138827 0.00000000  
Rotation angle (degrees) 48.82133441  
Shift along axis 0.16487213  
  

> select subtract #6

Nothing selected  

> turn x 90

> hide #!1 models

> show #!1 models

> hide #!1 models

> save /Users/uozumilab2/Desktop/image6.png supersample 3

> hide #!6 models

> show #!7 models

> show #!1 models

> turn x -90

> hide #!1 models

> save /Users/uozumilab2/Desktop/image7.png supersample 3

> hide #!7 models

> show #!8 models

> show #!1 models

> turn x -90

> undo

> turn x -90

> select add #8

2 models selected  

> view matrix models
> #8,-0.91104,-0.41042,-0.039498,437.56,0.40873,-0.91157,0.044439,268.1,-0.054244,0.024342,0.99823,5.909

> select subtract #8

Nothing selected  

> fitmap #1 inMap #8

Fit map cryosparc_P17_J85_004_volume_map_sharp.mrc in map
cryosparc_P17_J89_013_volume_map_sharp.mrc using 1042243 points  
correlation = 0.9097, correlation about mean = 0.5305, overlap = 5841  
steps = 104, shift = 1.93, angle = 7.37 degrees  
  
Position of cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) relative to
cryosparc_P17_J89_013_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.95780920 0.28740483 0.00005167 308.67743001  
-0.28740483 -0.95780920 -0.00001131 414.91853351  
0.00004624 -0.00002568 0.99999999 0.38613934  
Axis -0.00002501 0.00000945 -1.00000000  
Axis point 184.79356578 184.80246870 0.00000000  
Rotation angle (degrees) 163.29734922  
Shift along axis -0.38993909  
  

> turn x -90

> hide #!1 models

> show #!1 models

> hide #!1 models

> save /Users/uozumilab2/Desktop/image8.png supersample 3

> hide #!8 models

> show #!9 models

> show #!1 models

> turn x -90

> fitmap #1 inMap #9

Fit map cryosparc_P17_J85_004_volume_map_sharp.mrc in map
cryosparc_P17_J90_011_volume_map_sharp.mrc using 1042243 points  
correlation = 0.9001, correlation about mean = 0.506, overlap = 6055  
steps = 104, shift = 1.95, angle = 7.16 degrees  
  
Position of cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) relative to
cryosparc_P17_J90_011_volume_map_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.99978055 0.02094856 0.00003510 -3.83295378  
-0.02094856 0.99978055 -0.00001338 3.91247392  
-0.00003538 0.00001265 1.00000000 0.15375152  
Axis 0.00062132 0.00168223 -0.99999839  
Axis point 184.84087475 184.90167151 0.00000000  
Rotation angle (degrees) 1.20035369  
Shift along axis -0.14955106  
  

> hide #!1 models

> turn x -90

> save /Users/uozumilab2/Desktop/image9.png supersample 3

> hide #!9 models

> show #!10 models

> show #!1 models

> turn x -90

> select add #10

2 models selected  

> view matrix models
> #10,-0.37088,0.92732,-0.050327,92.879,-0.92853,-0.37126,0.0019041,424.59,-0.016918,0.047436,0.99873,-5.3645

> fitmap #10 inMap #1

Fit map cryosparc_P17_J91_004_volume_map_sharp.mrc in map
cryosparc_P17_J85_004_volume_map_sharp.mrc using 1090866 points  
correlation = 0.9531, correlation about mean = 0.7872, overlap = 6824  
steps = 140, shift = 1.58, angle = 14.3 degrees  
  
Position of cryosparc_P17_J91_004_volume_map_sharp.mrc (#10) relative to
cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.11549341 0.99330825 0.00003435 22.58241347  
-0.99330825 -0.11549341 -0.00002197 389.70596942  
-0.00001785 -0.00003666 1.00000000 -0.35214737  
Axis -0.00000740 0.00002628 -1.00000000  
Axis point 184.80103765 184.79855038 0.00000000  
Rotation angle (degrees) 96.63208510  
Shift along axis 0.36222148  
  

> select subtract #10

Nothing selected  

> turn x 90

> hide #!1 models

> save /Users/uozumilab2/Desktop/image10.png supersample 3

> hide #!10 models

> show #!1 models

> turn x -90

> save /Users/uozumilab2/Desktop/image11.png supersample 3

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> save /Users/uozumilab2/Desktop/image12.png supersample 3

> hide #!3 models

> show #!4 models

> save /Users/uozumilab2/Desktop/image13.png supersample 3

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!4 models

> show #!5 models

> save /Users/uozumilab2/Desktop/image14.png supersample 3

> hide #!5 models

> show #!6 models

> save /Users/uozumilab2/Desktop/image15.png supersample 3

> hide #!6 models

> show #!7 models

> save /Users/uozumilab2/Desktop/image16.png supersample 3

> hide #!7 models

> show #!8 models

> save /Users/uozumilab2/Desktop/image17.png supersample 3

> hide #!8 models

> show #!9 models

> save /Users/uozumilab2/Desktop/image18.png supersample 3

> hide #!9 models

> show #!10 models

> save /Users/uozumilab2/Desktop/image19.png supersample 3

> hide #!10 models

> show #!4 models

> view

> ui tool show ""Side View""

> hide #!4 models

> hide #!9 models

> show #!4 models

> hide #!4 models

> show #!5 models

> show #!6 models

> show #!7 models

> show #!8 models

> show #!9 models

> show #!10 models

> show #!4 models

> show #!3 models

> show #!2 models

> show #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> save /Users/uozumilab2/Desktop/image20.png supersample 3

> hide #!1 models

> show #!2 models

> save /Users/uozumilab2/Desktop/image21.png supersample 3

> hide #!2 models

> show #!3 models

> save /Users/uozumilab2/Desktop/image22.png supersample 3

> hide #!3 models

> show #!4 models

> save /Users/uozumilab2/Desktop/image23.png supersample 3

> hide #!4 models

> show #!5 models

> save /Users/uozumilab2/Desktop/image24.png supersample 3

> hide #!5 models

> show #!6 models

> save /Users/uozumilab2/Desktop/image25.png supersample 3

> hide #!6 models

> show #!7 models

> save /Users/uozumilab2/Desktop/image26.png supersample 3

> hide #!7 models

> show #!8 models

> save /Users/uozumilab2/Desktop/image27.png supersample 3

> hide #!8 models

> show #!9 models

> save /Users/uozumilab2/Desktop/image28.png supersample 3

> hide #!9 models

> show #!10 models

> save /Users/uozumilab2/Desktop/image29.png supersample 3

> show #!9 models

> show #!8 models

> hide #!9 models

> hide #!8 models

> show #!7 models

> hide #!7 models

> show #!6 models

> hide #!6 models

> show #!5 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!5 models

> hide #!5 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

> hide #!10 models

> show #!10 models

> show #!9 models

> hide #!9 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!7 models

> hide #!7 models

> show #!6 models

> hide #!6 models

> show #!5 models

> hide #!5 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!10 models

> show #!1 models

> hide #!1 models

> hide #!2 models

> show #!3 models

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #!4 models

> open /Users/uozumilab2/Downloads/9L9U-assembly1.cif.gz

File reader requires uncompressed file;
'/Users/uozumilab2/Downloads/9L9U-assembly1.cif.gz' is compressed  

> open /Users/uozumilab2/Downloads/9L9U.cif

9L9U.cif title:  
Arabidopsis GORK WT1 [more info...]  
  
Chain information for 9L9U.cif #11  
---  
Chain | Description | UniProt  
A B C D | Potassium channel GORK | GORK_ARATH 2-820  
  

> volume #4 level 0.08996

> select add #11

21836 atoms, 22345 bonds, 2692 residues, 1 model selected  

> view matrix models
> #11,0.9973,-0.0030636,-0.073386,14.477,0.0012426,0.99969,-0.024847,4.4479,0.07344,0.024689,0.99699,-14.873

> ui mousemode right ""translate selected models""

> view matrix models
> #11,0.9973,-0.0030636,-0.073386,44.268,0.0012426,0.99969,-0.024847,25.649,0.07344,0.024689,0.99699,-9.765

> view matrix models
> #11,0.9973,-0.0030636,-0.073386,37.293,0.0012426,0.99969,-0.024847,23.896,0.07344,0.024689,0.99699,4.9111

> view matrix models
> #11,0.9973,-0.0030636,-0.073386,36.524,0.0012426,0.99969,-0.024847,23.46,0.07344,0.024689,0.99699,6.9891

> ui mousemode right ""rotate selected models""

> view matrix models
> #11,0.5586,-0.82549,-0.080874,236.84,0.82757,0.56123,-0.012445,-39.13,0.055662,-0.059977,0.99665,23.236

> ui mousemode right ""translate selected models""

> view matrix models
> #11,0.5586,-0.82549,-0.080874,238.29,0.82757,0.56123,-0.012445,-31.828,0.055662,-0.059977,0.99665,23.553

> view matrix models
> #11,0.5586,-0.82549,-0.080874,237.69,0.82757,0.56123,-0.012445,-31.904,0.055662,-0.059977,0.99665,27.775

> fitmap #11 inMap #4

Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J94_011_volume_map_sharp.mrc
(#4) using 21836 atoms  
average map value = 0.08035, steps = 2000  
shifted from previous position = 3.6  
rotated from previous position = 6.79 degrees  
atoms outside contour = 14758, contour level = 0.089962  
  
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J94_011_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.48947063 -0.87201611 0.00252961 244.54001690  
0.87201612 0.48945810 -0.00431944 -29.24784000  
0.00252848 0.00432010 0.99998747 26.67111281  
Axis 0.00495371 0.00000065 0.99998773  
Axis point 147.18253319 194.10293925 0.00000000  
Rotation angle (degrees) 60.69502962  
Shift along axis 27.88214688  
  

> transparency #4.1 50

> select subtract #11

Nothing selected  

> volume #4 level 0.08108

> volume #4 level 0.06998

> hide #!4 models

> hide #11 models

> open /Users/uozumilab2/Downloads/9LA0.cif

9LA0.cif title:  
Arabidopsis GORK WT5 [more info...]  
  
Chain information for 9LA0.cif #12  
---  
Chain | Description | UniProt  
A B C D | Potassium channel GORK | GORK_ARATH 2-820  
  

> show #!4 models

> volume #4 level 0.09551

> select add #12

21944 atoms, 22460 bonds, 2704 residues, 1 model selected  

> view matrix models #12,1,0,0,30.488,0,1,0,33.189,0,0,1,-1.3523

> view matrix models #12,1,0,0,30.977,0,1,0,29.448,0,0,1,27.556

> ui mousemode right ""rotate selected models""

> view matrix models
> #12,0.9178,-0.37059,-0.14251,128.25,0.38888,0.91145,0.13428,-42.514,0.080127,-0.17866,0.98064,46.543

> view matrix models
> #12,0.55709,-0.80017,-0.2222,267.16,0.83024,0.54269,0.12724,-52.832,0.018772,-0.25536,0.96666,70.819

> ui mousemode right ""translate selected models""

> view matrix models
> #12,0.55709,-0.80017,-0.2222,256.99,0.83024,0.54269,0.12724,-51.957,0.018772,-0.25536,0.96666,69.042

> view matrix models
> #12,0.55709,-0.80017,-0.2222,255.68,0.83024,0.54269,0.12724,-50.259,0.018772,-0.25536,0.96666,69.666

> view matrix models
> #12,0.55709,-0.80017,-0.2222,255.77,0.83024,0.54269,0.12724,-50.297,0.018772,-0.25536,0.96666,68.727

> ui mousemode right ""rotate selected models""

> view matrix models
> #12,0.55555,-0.82478,-0.10533,238.46,0.82714,0.56113,-0.031238,-23.662,0.084867,-0.069767,0.99395,24.162

> ui mousemode right ""translate selected models""

> view matrix models
> #12,0.55555,-0.82478,-0.10533,238.27,0.82714,0.56113,-0.031238,-31.329,0.084867,-0.069767,0.99395,23.894

> view matrix models
> #12,0.55555,-0.82478,-0.10533,238.33,0.82714,0.56113,-0.031238,-31.327,0.084867,-0.069767,0.99395,23.663

> fitmap #12 inMap #4

Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J94_011_volume_map_sharp.mrc
(#4) using 21944 atoms  
average map value = 0.07179, steps = 2000  
shifted from previous position = 8.72  
rotated from previous position = 7.7 degrees  
atoms outside contour = 16036, contour level = 0.095512  
  
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J94_011_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.50309993 -0.86420599 0.00620231 240.71249764  
0.86421754 0.50311646 0.00136631 -30.79714710  
-0.00430126 0.00467275 0.99997983 27.96715983  
Axis 0.00191294 0.00607684 0.99997971  
Axis point 147.26102230 193.80155398 0.00000000  
Rotation angle (degrees) 59.79481813  
Shift along axis 28.23991177  
  

> select subtract #12

Nothing selected  

> select add #12

21944 atoms, 22460 bonds, 2704 residues, 1 model selected  

> view matrix models
> #12,0.5031,-0.86421,0.0062023,240.42,0.86422,0.50312,0.0013663,-30.815,-0.0043013,0.0046728,0.99998,26.914

> view matrix models
> #12,0.5031,-0.86421,0.0062023,239.73,0.86422,0.50312,0.0013663,-31.281,-0.0043013,0.0046728,0.99998,26.533

> fitmap #12 inMap #4

Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J94_011_volume_map_sharp.mrc
(#4) using 21944 atoms  
average map value = 0.07158, steps = 2000  
shifted from previous position = 1.71  
rotated from previous position = 0.274 degrees  
atoms outside contour = 16050, contour level = 0.095512  
  
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J94_011_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.50322986 -0.86414973 0.00222580 241.12022280  
0.86415260 0.50322819 -0.00129768 -30.21436053  
0.00000131 0.00257646 0.99999668 27.61855575  
Axis 0.00224158 0.00128709 0.99999666  
Axis point 146.84021313 194.53961587 0.00000000  
Rotation angle (degrees) 59.78624859  
Shift along axis 28.12006572  
  

> select subtract #12

Nothing selected  

> hide #12 models

> show #11 models

> view

> fitmap #11 inMap #4

Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J94_011_volume_map_sharp.mrc
(#4) using 21836 atoms  
average map value = 0.0804, steps = 2000  
shifted from previous position = 0.411  
rotated from previous position = 0.332 degrees  
atoms outside contour = 15399, contour level = 0.095512  
  
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J94_011_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.48969651 -0.87189244 0.00095120 244.94607476  
0.87189158 0.48969738 0.00124112 -29.98918017  
-0.00154793 0.00022157 0.99999878 28.21878535  
Axis -0.00058468 0.00143316 0.99999880  
Axis point 148.13504908 194.25404443 0.00000000  
Rotation angle (degrees) 60.67937541  
Shift along axis 28.03255797  
  

> volume #4 level 0.08552

> fitmap #11 inMap #4

Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J94_011_volume_map_sharp.mrc
(#4) using 21836 atoms  
average map value = 0.08019, steps = 2000  
shifted from previous position = 0.354  
rotated from previous position = 0.0647 degrees  
atoms outside contour = 14056, contour level = 0.085521  
  
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J94_011_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.48975829 -0.87185824 -0.00017355 244.82122570  
0.87185763 0.48975768 0.00130095 -30.15912233  
-0.00104924 -0.00078846 0.99999914 28.37790838  
Axis -0.00119825 0.00050220 0.99999916  
Axis point 148.20634470 194.10701492 0.00000000  
Rotation angle (degrees) 60.67535250  
Shift along axis 28.06938147  
  

> hide #11 models

> show #11 models

> hide #11 models

> show #!1 models

> hide #!4 models

> show #11 models

> transparency #1.1 50

> volume #1 level 0.09901

> hide #11 models

> show #12 models

> hide #12 models

> show #11 models

> hide #!1 models

> show #!2 models

> transparency #2.1 50

> volume #2 level 0.05601

> volume #2 level 0.07068

> hide #!2 models

> show #!3 models

> transparency #3.1 50

> volume #3 level 0.09518

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!5 models

> transparency #5.1 50

> volume #5 level 0.08609

> fitmap #11 inMap #5

Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J86_009_volume_map_sharp.mrc
(#5) using 21836 atoms  
average map value = 0.08371, steps = 2000  
shifted from previous position = 0.471  
rotated from previous position = 0.396 degrees  
atoms outside contour = 13749, contour level = 0.086085  
  
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J86_009_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.18854667 -0.98205718 0.00372226 368.89610343  
0.98205539 -0.18852754 0.00495720 58.90982444  
-0.00416650 0.00459012 0.99998078 28.16331907  
Axis -0.00018689 0.00401642 0.99999192  
Axis point 160.15969433 181.80624398 0.00000000  
Rotation angle (degrees) 100.86798412  
Shift along axis 28.33075581  
  

> volume #5 level 0.08093

> hide #!5 models

> show #!6 models

> transparency #6.1 50

> volume #6 level 0.07232

> volume #6 level 0.06645

> volume #6 level 0.07584

> hide #!6 models

> show #!7 models

> transparency #7.1 50

> volume #7 level 0.0848

> hide #!7 models

> show #!8 models

> transparency #8.1 50

> volume #8 level 0.08803

> fitmap #11 inMap #8

Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J89_013_volume_map_sharp.mrc
(#8) using 21836 atoms  
average map value = 0.08195, steps = 2000  
shifted from previous position = 0.754  
rotated from previous position = 7.02 degrees  
atoms outside contour = 14343, contour level = 0.088031  
  
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J89_013_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.19683143 0.98043723 -0.00047197 61.33981057  
-0.98043690 -0.19683086 0.00104141 370.41851312  
0.00092813 0.00066772 0.99999934 27.55524391  
Axis -0.00019057 -0.00071402 -0.99999973  
Axis point 182.38152037 160.07697775 0.00000000  
Rotation angle (degrees) 101.35173302  
Shift along axis -27.83141248  
  

> volume #8 level 0.08342

> hide #!8 models

> show #!9 models

> transparency #9.1 50

> volume #9 level 0.09021

> volume #9 level 0.08632

> hide #!9 models

> show #!10 models

> transparency #10.1 50

> volume #10 level 0.08608

> fitmap #11 inMap #10

Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J91_004_volume_map_sharp.mrc
(#10) using 21836 atoms  
average map value = 0.0748, steps = 100  
shifted from previous position = 0.811  
rotated from previous position = 7.46 degrees  
atoms outside contour = 14299, contour level = 0.086082  
  
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J91_004_volume_map_sharp.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.93258114 -0.36095219 -0.00243413 389.10299366  
0.36093541 -0.93257473 0.00547641 274.01040811  
-0.00424673 0.00422864 0.99998204 27.97315722  
Axis -0.00172848 0.00251091 0.99999535  
Axis point 168.99392239 173.31077389 0.00000000  
Rotation angle (degrees) 158.84172756  
Shift along axis 27.98848463  
  

> view orient

> fitmap #11 inMap #10

Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J91_004_volume_map_sharp.mrc
(#10) using 21836 atoms  
average map value = 0.0748, steps = 28  
shifted from previous position = 0.015  
rotated from previous position = 0.00553 degrees  
atoms outside contour = 14299, contour level = 0.086082  
  
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J91_004_volume_map_sharp.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.93259818 -0.36090821 -0.00242805 389.09908210  
0.36089182 -0.93259209 0.00539237 274.02005349  
-0.00421053 0.00415266 0.99998251 27.98156603  
Axis -0.00171753 0.00246948 0.99999548  
Axis point 168.99414628 173.31103546 0.00000000  
Rotation angle (degrees) 158.84442047  
Shift along axis 27.98983917  
  

> hide #!10 models

> show #!5 models

> undo

> show #!5 models

> view orient

> ui tool show ""Side View""

> transparency #5.1 0

> volume #!5 style mesh

> volume #!5 style surface

> volume #!5 style image

> volume #!5 style surface

> volume #!5 style mesh

> volume #!5 style surface

> volume #!5 style mesh

> volume #!5 style image

> volume #!5 style mesh

> volume #!5 style surface

> volume #!5 showOutlineBox true

> transparency #5.1 50

> volume #!5 showOutlineBox false

> volume #!5 style mesh

> volume #!5 style surface

> hide #11 models

> show #12 models

> fitmap #12 inMap #5

Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J86_009_volume_map_sharp.mrc
(#5) using 21944 atoms  
average map value = 0.07408, steps = 2000  
shifted from previous position = 0.529  
rotated from previous position = 0.483 degrees  
atoms outside contour = 14188, contour level = 0.08093  
  
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J86_009_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.17148280 -0.98516145 0.00711053 366.04943852  
0.98517789 -0.17144550 0.00556400 55.71901988  
-0.00426237 0.00795927 0.99995924 27.61974939  
Axis 0.00121564 0.00577195 0.99998260  
Axis point 159.64732348 181.68680593 0.00000000  
Rotation angle (degrees) 99.87414412  
Shift along axis 28.38586101  
  

> hide #12 models

> volume #5 level 0.08

> volume #5 change image level -0.005746,0 level 0.05178,0.8 level 0.4066,1

> show #11 models

> volume #5 level 0.09

> volume #5 level 0.05

> volume #5 level 0.09

> undo

> show #11 models

> view orient

> fitmap #11 inMap #5

Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J86_009_volume_map_sharp.mrc
(#5) using 21836 atoms  
average map value = 0.08378, steps = 2000  
shifted from previous position = 0.121  
rotated from previous position = 0.521 degrees  
atoms outside contour = 14347, contour level = 0.09  
  
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J86_009_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.18871694 -0.98203093 0.00107831 369.28206341  
0.98202319 -0.18871070 0.00432742 59.11782565  
-0.00404617 0.00187558 0.99999005 28.19901947  
Axis -0.00124835 0.00260912 0.99999582  
Axis point 160.26921285 182.07385197 0.00000000  
Rotation angle (degrees) 100.87802359  
Shift along axis 27.89215469  
  

> ui tool show ""Show Sequence Viewer""

> sequence chain #11/A #11/B #11/C #11/D #12/A #12/B #12/C #12/D

Alignment identifier is 1  

> select #11/A-D:511-512 #12/A-D:511-512

152 atoms, 144 bonds, 16 residues, 2 models selected  

> select #11/A-D:511-519 #12/A-D:511-519

608 atoms, 600 bonds, 72 residues, 2 models selected  
Potassium Channel GORK [ID: 1] region 8 chains [519-527] RMSD: 6.546  
  

> color (#11 & sel) red

> select add #11

22140 atoms, 22645 bonds, 2728 residues, 2 models selected  

> select add #12

43780 atoms, 44805 bonds, 5396 residues, 2 models selected  

> select subtract #11

21944 atoms, 22460 bonds, 2704 residues, 1 model selected  

> select subtract #12

Nothing selected  

> volume #1 level 0.09

> volume #2 level 0.09

> volume #3 level 0.09

> volume #4 level 0.09

> volume #6 level 0.09

> volume #7 level 0.09

> volume #8 level 0.09

> volume #9 level 0.09

> volume #10 level 0.09

> save /Users/uozumilab2/Desktop/image1.png supersample 3

> hide #!5 models

> show #!1 models

> save /Users/uozumilab2/Desktop/image1.png supersample 3

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #2 level 0.05

> volume #1 level 0.05

> hide #!2 models

> show #!1 models

> hide #!1 models

> volume #3 level 0.05

> volume #4 level 0.05

> volume #5 level 0.05

> volume #6 level 0.05

> volume #7 level 0.05

> volume #8 level 0.05

> volume #9 level 0.05

> volume #10 level 0.05

> show #!1 models

> volume #1 level 0.06

> volume #1 level 0.07

> volume #1 level 0.08

> volume #1 level 0.09

> save /Users/uozumilab2/Desktop/image1.png supersample 3

> hide #!1 models

> show #!2 models

> volume #2 level 0.06

> volume #2 level 0.07

> volume #2 level 0.08

> volume #2 level 0.05

> volume #2 level 0.06

> volume #2 level 0.09

> volume #2 level 0.05

> save /Users/uozumilab2/Desktop/image2.png supersample 3

> hide #!2 models

> show #!3 models

> volume #3 level 0.09

> volume #4 level 0.09

> volume #5 level 0.09

> volume #6 level 0.09

> volume #7 level 0.09

> volume #8 level 0.09

> volume #9 level 0.09

> volume #10 level 0.09

> save /Users/uozumilab2/Desktop/image2.png supersample 3

> hide #!3 models

> show #!4 models

> save /Users/uozumilab2/Desktop/image3.png supersample 3

> hide #!4 models

> show #!5 models

> save /Users/uozumilab2/Desktop/image4.png supersample 3

> hide #!5 models

> show #!6 models

> save /Users/uozumilab2/Desktop/image5.png supersample 3

> hide #!6 models

> show #!7 models

> save /Users/uozumilab2/Desktop/image6.png supersample 3

> hide #!7 models

> show #!8 models

> save /Users/uozumilab2/Desktop/image7.png supersample 3

> hide #!8 models

> show #!9 models

> save /Users/uozumilab2/Desktop/image8.png supersample 3

> fitmap #11 inMap #9

Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J90_011_volume_map_sharp.mrc
(#9) using 21836 atoms  
average map value = 0.08549, steps = 2000  
shifted from previous position = 0.478  
rotated from previous position = 0.453 degrees  
atoms outside contour = 14092, contour level = 0.09  
  
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J90_011_volume_map_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.48761455 -0.87305662 -0.00204759 245.65931372  
0.87305901 0.48761301 0.00122888 -30.01779299  
-0.00007445 -0.00238689 0.99999715 28.30342300  
Axis -0.00207074 -0.00113002 0.99999722  
Axis point 148.40598626 194.34692887 0.00000000  
Rotation angle (degrees) 60.81623085  
Shift along axis 27.82856780  
  

> hide #!9 models

> show #!10 models

> fitmap #11 inMap #10

Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J91_004_volume_map_sharp.mrc
(#10) using 21836 atoms  
average map value = 0.0748, steps = 48  
shifted from previous position = 0.4  
rotated from previous position = 0.489 degrees  
atoms outside contour = 14961, contour level = 0.09  
  
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J91_004_volume_map_sharp.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.93259707 -0.36091101 -0.00243967 389.09971033  
0.36089450 -0.93259097 0.00540756 274.02777352  
-0.00422686 0.00416261 0.99998240 27.98060976  
Axis -0.00172476 0.00247599 0.99999545  
Axis point 168.99364652 173.31518114 0.00000000  
Rotation angle (degrees) 158.84425132  
Shift along axis 27.98786816  
  

> hide #!10 models

> show #!1 models

> fitmap #11 inMap #1

Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J85_004_volume_map_sharp.mrc
(#1) using 21836 atoms  
average map value = 0.07957, steps = 84  
shifted from previous position = 0.164  
rotated from previous position = 0.154 degrees  
atoms outside contour = 13862, contour level = 0.09  
  
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.46838416 -0.88351193 0.00479113 249.43621126  
0.88351855 0.46839448 0.00125602 -28.52533883  
-0.00335384 0.00364475 0.99998773 27.72112460  
Axis 0.00135182 0.00460936 0.99998846  
Axis point 148.51058363 192.92085980 0.00000000  
Rotation angle (degrees) 62.07060324  
Shift along axis 27.92651425  
  

> save /Users/uozumilab2/Desktop/image1.png supersample 3

> hide #!1 models

> show #!2 models

> fitmap #11 inMap #2

Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J92_003_volume_map_sharp.mrc
(#2) using 21836 atoms  
average map value = 0.06074, steps = 120  
shifted from previous position = 0.747  
rotated from previous position = 1.24 degrees  
atoms outside contour = 8755, contour level = 0.05  
  
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J92_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.73280010 -0.68044374 0.00057594 407.50866351  
0.68044226 -0.73279607 0.00287364 192.49988169  
-0.00153331 0.00249770 0.99999570 27.35154803  
Axis -0.00027625 0.00154990 0.99999876  
Axis point 165.97058019 176.24151103 0.00000000  
Rotation angle (degrees) 137.12166393  
Shift along axis 27.53729629  
  

> save /Users/uozumilab2/Desktop/image2.png supersample 3

> hide #!2 models

> show #!3 models

> fitmap #11 inMap #3

Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J93_004_volume_map_sharp.mrc
(#3) using 21836 atoms  
average map value = 0.07199, steps = 44  
shifted from previous position = 0.314  
rotated from previous position = 0.142 degrees  
atoms outside contour = 15368, contour level = 0.09  
  
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J93_004_volume_map_sharp.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.08403690 -0.99646224 0.00089893 354.88117594  
0.99646230 -0.08403610 0.00089980 40.72620654  
-0.00082107 0.00097137 0.99999919 27.86137784  
Axis 0.00003591 0.00086306 0.99999963  
Axis point 158.73308781 183.45667504 0.00000000  
Rotation angle (degrees) 94.82064536  
Shift along axis 27.90926032  
  

> save /Users/uozumilab2/Desktop/image2.png supersample 3

> hide #!3 models

> show #!4 models

> fitmap #11 inMap #4

Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J94_011_volume_map_sharp.mrc
(#4) using 21836 atoms  
average map value = 0.08023, steps = 2000  
shifted from previous position = 0.447  
rotated from previous position = 1.54 degrees  
atoms outside contour = 14788, contour level = 0.09  
  
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J94_011_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.48944822 -0.87201097 0.00610822 244.29229162  
0.87202360 0.48946270 0.00105376 -30.11457588  
-0.00390864 0.00481075 0.99998079 27.57199436  
Axis 0.00215415 0.00574339 0.99998119  
Axis point 147.97196306 193.44342631 0.00000000  
Rotation angle (degrees) 60.69583421  
Shift along axis 27.92475879  
  

> save /Users/uozumilab2/Desktop/image3.png supersample 3

> hide #!4 models

> show #!5 models

> fitmap #11 inMap #5

Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J86_009_volume_map_sharp.mrc
(#5) using 21836 atoms  
average map value = 0.08382, steps = 2000  
shifted from previous position = 0.571  
rotated from previous position = 0.427 degrees  
atoms outside contour = 14308, contour level = 0.09  
  
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J86_009_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.18857013 -0.98205797 -0.00185779 369.55313334  
0.98205777 -0.18857320 0.00163930 59.51404927  
-0.00196021 -0.00151533 0.99999693 28.73218084  
Axis -0.00160613 0.00005215 0.99999871  
Axis point 160.21346018 182.44686607 0.00000000  
Rotation angle (degrees) 100.86952953  
Shift along axis 28.14169734  
  

> save /Users/uozumilab2/Desktop/image4.png supersample 3

> hide #!5 models

> show #!6 models

> fitmap #11 inMap #6

Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J87_012_volume_map_sharp.mrc
(#6) using 21836 atoms  
average map value = 0.08248, steps = 2000  
shifted from previous position = 0.31  
rotated from previous position = 0.651 degrees  
atoms outside contour = 14745, contour level = 0.09  
  
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J87_012_volume_map_sharp.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.35694611 -0.93412417 -0.00122969 388.34936101  
0.93411415 -0.35694801 0.00434374 93.02447560  
-0.00449653 0.00040181 0.99998981 28.28765327  
Axis -0.00210996 0.00174861 0.99999625  
Axis point 162.20211864 180.17746706 0.00000000  
Rotation angle (degrees) 110.91313503  
Shift along axis 27.63080797  
  

> save /Users/uozumilab2/Desktop/image5.png supersample 3

> hide #!6 models

> show #!7 models

> fitmap #11 inMap #7

Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J88_009_volume_map_sharp.mrc
(#7) using 21836 atoms  
average map value = 0.08656, steps = 2000  
shifted from previous position = 0.577  
rotated from previous position = 3.55 degrees  
atoms outside contour = 13674, contour level = 0.09  
  
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J88_009_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.53604381 -0.84418288 0.00350765 232.71001494  
0.84418877 0.53604584 -0.00041358 -32.86953052  
-0.00153112 0.00318282 0.99999376 28.07683083  
Axis 0.00213008 0.00298438 0.99999328  
Axis point 146.30635837 195.18237933 0.00000000  
Rotation angle (degrees) 57.58541494  
Shift along axis 28.47423851  
  

> save /Users/uozumilab2/Desktop/image6.png supersample 3

> hide #!7 models

> show #!8 models

> save /Users/uozumilab2/Desktop/image7.png supersample 3

> fitmap #11 inMap #8

Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J89_013_volume_map_sharp.mrc
(#8) using 21836 atoms  
average map value = 0.08199, steps = 2000  
shifted from previous position = 0.731  
rotated from previous position = 4.79 degrees  
atoms outside contour = 14668, contour level = 0.09  
  
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J89_013_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.19689966 0.98042102 -0.00226852 61.79924268  
-0.98040026 -0.19691042 -0.00645019 371.30478268  
-0.00677059 0.00095401 0.99997662 28.73732717  
Axis 0.00377603 0.00229599 -0.99999023  
Axis point 183.05322918 160.33182754 0.00000000  
Rotation angle (degrees) 101.35671540  
Shift along axis -27.65117702  
  

> save /Users/uozumilab2/Desktop/image7.png supersample 3

> hide #!8 models

> show #!9 models

> fitmap #11 inMap #9

Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J90_011_volume_map_sharp.mrc
(#9) using 21836 atoms  
average map value = 0.08547, steps = 2000  
shifted from previous position = 0.783  
rotated from previous position = 7.25 degrees  
atoms outside contour = 14170, contour level = 0.09  
  
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J90_011_volume_map_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.48744965 -0.87314518 0.00321498 244.91335655  
0.87313702 0.48745939 0.00388303 -30.17217173  
-0.00495763 0.00091434 0.99998729 28.21234402  
Axis -0.00169999 0.00467995 0.99998760  
Axis point 148.29094824 193.50022734 0.00000000  
Rotation angle (degrees) 60.82700556  
Shift along axis 27.65444012  
  

> save /Users/uozumilab2/Desktop/image8.png supersample 3

> hide #!9 models

> show #!10 models

> fitmap #11 inMap #10

Fit molecule 9L9U.cif (#11) to map cryosparc_P17_J91_004_volume_map_sharp.mrc
(#10) using 21836 atoms  
average map value = 0.0748, steps = 44  
shifted from previous position = 0.327  
rotated from previous position = 0.274 degrees  
atoms outside contour = 14959, contour level = 0.09  
  
Position of 9L9U.cif (#11) relative to
cryosparc_P17_J91_004_volume_map_sharp.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.93259620 -0.36091339 -0.00242011 389.09830628  
0.36089640 -0.93258945 0.00554036 274.00874153  
-0.00425656 0.00429351 0.99998172 27.96526138  
Axis -0.00172738 0.00254422 0.99999527  
Axis point 168.99475196 173.30485046 0.00000000  
Rotation angle (degrees) 158.84411601  
Shift along axis 27.99014385  
  

> save /Users/uozumilab2/Desktop/image9.png supersample 3

> hide #!10 models

> show #!1 models

> hide #11 models

> show #12 models

> ui tool show ""Show Sequence Viewer""

> sequence chain #11/A #11/B #11/C #11/D #12/A #12/B #12/C #12/D

Alignment identifier is 2  

> select #11/A-D:511 #12/A-D:511

64 atoms, 56 bonds, 8 residues, 2 models selected  

> select #11/A-D:511-519 #12/A-D:511-519

608 atoms, 600 bonds, 72 residues, 2 models selected  
Potassium Channel GORK [ID: 2] region 8 chains [519-527] RMSD: 6.782  
  

> color (#12 & sel) red

> select add #12

22248 atoms, 22760 bonds, 2740 residues, 2 models selected  

> select add #11

43780 atoms, 44805 bonds, 5396 residues, 2 models selected  

> select subtract #12

21836 atoms, 22345 bonds, 2692 residues, 1 model selected  

> select subtract #11

Nothing selected  

> fitmap #12 inMap #1

Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J85_004_volume_map_sharp.mrc
(#1) using 21944 atoms  
average map value = 0.07121, steps = 100  
shifted from previous position = 0.462  
rotated from previous position = 1.48 degrees  
atoms outside contour = 14955, contour level = 0.09  
  
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.46720793 -0.88406548 0.01204087 248.68145727  
0.88414676 0.46718147 -0.00509639 -27.42986720  
-0.00111973 0.01302697 0.99991452 25.69845366  
Axis 0.01024872 0.00744229 0.99991978  
Axis point 147.14177537 192.29130247 0.00000000  
Rotation angle (degrees) 62.15041770  
Shift along axis 28.04091842  
  

> turn x -90

> fitmap #12 inMap #1

Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J85_004_volume_map_sharp.mrc
(#1) using 21944 atoms  
average map value = 0.07121, steps = 120  
shifted from previous position = 0.00565  
rotated from previous position = 0.00152 degrees  
atoms outside contour = 14953, contour level = 0.09  
  
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J85_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.46720047 -0.88406963 0.01202563 248.68717876  
0.88415069 0.46717426 -0.00507631 -27.43182441  
-0.00113025 0.01300413 0.99991480 25.70909608  
Axis 0.01022440 0.00743959 0.99992005  
Axis point 147.14626746 192.29364096 0.00000000  
Rotation angle (degrees) 62.15088367  
Shift along axis 28.04563662  
  

> save /Users/uozumilab2/Desktop/image10.png supersample 3

> hide #!1 models

> show #!2 models

> fitmap #12 inMap #2

Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J92_003_volume_map_sharp.mrc
(#2) using 21944 atoms  
average map value = 0.05803, steps = 124  
shifted from previous position = 0.648  
rotated from previous position = 1.73 degrees  
atoms outside contour = 9873, contour level = 0.05  
  
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J92_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.73915103 -0.67353415 0.00273842 406.93546898  
0.67353572 -0.73912652 0.00645135 194.08179893  
-0.00232116 0.00661295 0.99997544 26.80555828  
Axis 0.00011996 0.00375597 0.99999294  
Axis point 165.90385242 175.78960718 0.00000000  
Rotation angle (degrees) 137.65914874  
Shift along axis 27.58315076  
  

> save /Users/uozumilab2/Desktop/image11.png supersample 3

> hide #!2 models

> show #!3 models

> fitmap #12 inMap #3

Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J93_004_volume_map_sharp.mrc
(#3) using 21944 atoms  
average map value = 0.06628, steps = 88  
shifted from previous position = 0.278  
rotated from previous position = 0.328 degrees  
atoms outside contour = 16154, contour level = 0.09  
  
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J93_004_volume_map_sharp.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.08742467 -0.99615148 0.00625699 354.51215608  
0.99616983 -0.08743300 -0.00106940 41.65531474  
0.00161235 0.00613953 0.99997985 26.54050968  
Axis 0.00361832 0.00233125 0.99999074  
Axis point 158.15811125 183.13088179 0.00000000  
Rotation angle (degrees) 95.01628656  
Shift along axis 27.92011250  
  

> save /Users/uozumilab2/Desktop/image12.png supersample 3

> hide #!3 models

> show #!4 models

> save /Users/uozumilab2/Desktop/image13.png supersample 3

> fitmap #12 inMap #4

Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J94_011_volume_map_sharp.mrc
(#4) using 21944 atoms  
average map value = 0.07184, steps = 2000  
shifted from previous position = 0.54  
rotated from previous position = 2.62 degrees  
atoms outside contour = 15525, contour level = 0.09  
  
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J94_011_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.50293282 -0.86429959 0.00669356 240.69525495  
0.86431505 0.50294975 0.00102354 -30.75045030  
-0.00425117 0.00527057 0.99997707 27.64475099  
Axis 0.00245684 0.00633136 0.99997694  
Axis point 147.20375154 193.74787661 0.00000000  
Rotation angle (degrees) 59.80597466  
Shift along axis 28.04077089  
  

> save /Users/uozumilab2/Desktop/image13.png supersample 3

> hide #!4 models

> show #!5 models

> fitmap #12 inMap #5

Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J86_009_volume_map_sharp.mrc
(#5) using 21944 atoms  
average map value = 0.07405, steps = 2000  
shifted from previous position = 0.38  
rotated from previous position = 0.46 degrees  
atoms outside contour = 15311, contour level = 0.09  
  
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J86_009_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.17162995 -0.98510950 0.01012090 365.61365910  
0.98516119 -0.17161289 0.00253717 56.03432857  
-0.00076251 0.01040617 0.99994556 26.36568994  
Axis 0.00399378 0.00552369 0.99997677  
Axis point 159.26127505 181.61028305 0.00000000  
Rotation angle (degrees) 99.88368829  
Shift along axis 28.13477304  
  

> save /Users/uozumilab2/Desktop/image14.png supersample 3

> hide #!5 models

> show #!6 models

> fitmap #12 inMap #6

Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J87_012_volume_map_sharp.mrc
(#6) using 21944 atoms  
average map value = 0.07811, steps = 2000  
shifted from previous position = 0.457  
rotated from previous position = 1.12 degrees  
atoms outside contour = 15331, contour level = 0.09  
  
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J87_012_volume_map_sharp.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.34777074 -0.93757586 0.00264782 386.79983897  
0.93757837 -0.34776431 0.00260647 91.54528181  
-0.00152295 0.00338899 0.99999310 27.39241129  
Axis 0.00041731 0.00222422 0.99999744  
Axis point 161.57376957 180.27752509 0.00000000  
Rotation angle (degrees) 110.35103856  
Shift along axis 27.75737279  
  

> save /Users/uozumilab2/Desktop/image15.png supersample 3

> hide #!6 models

> show #!7 models

> fitmap #12 inMap #7

Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J88_009_volume_map_sharp.mrc
(#7) using 21944 atoms  
average map value = 0.07629, steps = 2000  
shifted from previous position = 0.12  
rotated from previous position = 3.81 degrees  
atoms outside contour = 14967, contour level = 0.09  
  
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J88_009_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.54819789 -0.83634016 0.00377009 229.64803023  
0.83634773 0.54819844 -0.00097848 -33.10891427  
-0.00124841 0.00368951 0.99999241 27.39975913  
Axis 0.00279069 0.00300023 0.99999161  
Axis point 145.50808289 195.88823287 0.00000000  
Rotation angle (degrees) 56.75677295  
Shift along axis 27.94107077  
  

> save /Users/uozumilab2/Desktop/image16.png supersample 3

> hide #!7 models

> show #!8 models

> fitmap #12 inMap #8

Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J89_013_volume_map_sharp.mrc
(#8) using 21944 atoms  
average map value = 0.07614, steps = 2000  
shifted from previous position = 1.18  
rotated from previous position = 4.27 degrees  
atoms outside contour = 15422, contour level = 0.09  
  
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J89_013_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.20612135 0.97851575 -0.00457254 63.74864348  
-0.97849527 -0.20607525 0.00894351 370.39223812  
0.00780907 0.00631766 0.99994955 25.60633775  
Axis -0.00134174 -0.00632667 -0.99997909  
Axis point 182.03763380 159.27025069 0.00000000  
Rotation angle (degrees) 101.89527713  
Shift along axis -28.03468387  
  

> save /Users/uozumilab2/Desktop/image17.png supersample 3

> hide #!8 models

> show #!9 models

> fitmap #12 inMap #9

Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J90_011_volume_map_sharp.mrc
(#9) using 21944 atoms  
average map value = 0.08055, steps = 2000  
shifted from previous position = 0.845  
rotated from previous position = 7.2 degrees  
atoms outside contour = 14864, contour level = 0.09  
  
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J90_011_volume_map_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.49723377 -0.86755629 0.01023045 241.74523457  
0.86761293 0.49723143 -0.00295176 -29.98732725  
-0.00252608 0.01034379 0.99994331 26.29190399  
Axis 0.00766196 0.00735134 0.99994362  
Axis point 146.82380141 193.31684751 0.00000000  
Rotation angle (degrees) 60.18479327  
Shift along axis 27.92221782  
  

> save /Users/uozumilab2/Desktop/image18.png supersample 3

> hide #!9 models

> show #!10 models

> fitmap #12 inMap #10

Fit molecule 9LA0.cif (#12) to map cryosparc_P17_J91_004_volume_map_sharp.mrc
(#10) using 21944 atoms  
average map value = 0.06788, steps = 52  
shifted from previous position = 0.202  
rotated from previous position = 0.954 degrees  
atoms outside contour = 15891, contour level = 0.09  
  
Position of 9LA0.cif (#12) relative to
cryosparc_P17_J91_004_volume_map_sharp.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.93330556 -0.35906053 0.00403379 387.88850244  
0.35908314 -0.93324084 0.01099192 273.59329509  
-0.00018227 0.01170729 0.99993145 26.04765414  
Axis 0.00099612 0.00587067 0.99998227  
Axis point 168.53851925 172.73999988 0.00000000  
Rotation angle (degrees) 158.95640412  
Shift along axis 28.03974965  
  

> save /Users/uozumilab2/Desktop/image19.png supersample 3


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac16,6
      Model Number: MX2G3J/A
      Chip: Apple M4 Max
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 36 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
      Time since boot: 6日 17時間 37分

Graphics/Displays:

    Apple M4 Max:

      Chipset Model: Apple M4 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    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: 2.3
    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: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    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-MutationScores: 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: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    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: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    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: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX