id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
17084	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-15.3.1-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 0x00000001f6b6c840 (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.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.surface._surface, 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.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif (total: 52)


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===== 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/sahtelis/Downloads/cryosparc_P7_J57_class_00_final_volume.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J57_class_01_final_volume.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J57_class_02_final_volume.mrc

Opened cryosparc_P7_J57_class_00_final_volume.mrc as #1.1, grid size
192,192,192, pixel 1.84, shown at level 0.35, step 1, values float32  
Opened cryosparc_P7_J57_class_01_final_volume.mrc as #1.2, grid size
192,192,192, pixel 1.84, shown at level 0.376, step 1, values float32  
Opened cryosparc_P7_J57_class_02_final_volume.mrc as #1.3, grid size
192,192,192, pixel 1.84, shown at level 0.403, step 1, values float32  

> surface dust #1.1 size 18.4

> surface dust #1.2 size 18.4

> surface dust #1.3 size 18.4

> tile

3 models tiled  

> volume #1.1 level 1.375

> volume #1.2 level 1.264

> volume #1.3 level 1.327

> volume #1.3 level 1.024

> volume #1.2 level 0.9118

> volume #1.1 level 1.017

> volume #1.3 level 0.9289

> volume #1.3 level 1.056

> volume #1.2 level 1.004

> volume #1.1 level 1.03

> volume #1.2 level 1.28

> volume #1.3 level 1.242

> volume #1.2 level 1.128

> volume #1.2 level 0.9443

> volume #1.2 level 0.6683

> volume #1.3 level 0.8228

> volume #1.1 level 0.6777

> volume #1.2 level 0.9876

> volume #1.3 level 1.2

> volume #1.1 level 0.9872

> volume #1.3 level 0.9024

> volume #1.1 level 0.4593

> volume #1.2 level 0.3545

> volume #1.3 level 0.3397

> volume #1.3 level 0.3927

> volume #1.2 level 0.4086

> volume #1.3 level 0.4193

> volume #1.3 level 0.5892

> volume #1.2 level 0.5114

> volume #1.1 level 0.5321

> volume #1.1 level 0.4835

> volume #1.2 level 0.4411

> volume #1.3 level 0.4458

> volume #1.3 level 0.4565

> volume #1.2 level 0.4519

> volume #1.1 level 0.4653

> open /Users/sahtelis/Downloads/cryosparc_P7_J60_class_00_final_volume.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J63_class_00_final_volume.mrc

Opened cryosparc_P7_J60_class_00_final_volume.mrc as #2.1, grid size
128,128,128, pixel 2.76, shown at level 0.629, step 1, values float32  
Opened cryosparc_P7_J63_class_00_final_volume.mrc as #2.2, grid size
192,192,192, pixel 1.84, shown at level 0.336, step 1, values float32  

> hide #!1 models

> tile

2 models tiled  

> volume #2.1 level 1.062

> surface dust #2.1 size 27.6

> surface dust #2.2 size 18.4

> volume #2.1 level 0.6813

> volume #2.2 level 0.5765

> open /Users/sahtelis/Downloads/cryosparc_P7_J62_class_00_final_volume.mrc

Opened cryosparc_P7_J62_class_00_final_volume.mrc as #3, grid size
128,128,128, pixel 2.76, shown at level 0.936, step 1, values float32  

> tile

2 models tiled  

> surface dust #2.1 size 27.6

> surface dust #2.2 size 18.4

> surface dust #3 size 27.6

> volume #3 level 1.79

> volume #3 level 0.6009

> volume #3 level 0.7926

> hide #!3 models

> tile

2 models tiled  

> tile

2 models tiled  

> tile

2 models tiled  

> tile

2 models tiled  

> untile

Unknown command: untile  

> undo tile

Expected fewer arguments  

> tile

2 models tiled  

> close #2

> open /Users/sahtelis/Downloads/cryosparc_P7_J60_class_00_final_volume.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J63_class_00_final_volume.mrc

Opened cryosparc_P7_J60_class_00_final_volume.mrc as #2.1, grid size
128,128,128, pixel 2.76, shown at level 0.629, step 1, values float32  
Opened cryosparc_P7_J63_class_00_final_volume.mrc as #2.2, grid size
192,192,192, pixel 1.84, shown at level 0.336, step 1, values float32  

> tile

2 models tiled  

> surface dust #2.1 size 27.6

> surface dust #2.2 size 18.4

> volume #2.1 level 0.7559

> volume #2.2 level 0.4901

> volume #2.1 level 0.5021

> hide #!2 models

> show #!2 models

> volume #2.2 level 0.4098

> volume #2.1 level 0.7485

> volume #2.2 level 0.4469

> hide #!2 models

> show #!3 models

> volume #3 level 2.001

> volume #3 level 0.3612

> volume #3 level 1.732

> volume #3 level 1.972

> hide #!3 models

> show #!2 models

> open /Users/sahtelis/Downloads/cryosparc_P7_J64_005_volume_map_sharp.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J65_003_volume_map_sharp.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J66_005_volume_map_sharp.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J67_004_volume_map_sharp.mrc

Opened cryosparc_P7_J64_005_volume_map_sharp.mrc as #4.1, grid size
192,192,192, pixel 1.84, shown at level 0.653, step 1, values float32  
Opened cryosparc_P7_J65_003_volume_map_sharp.mrc as #4.2, grid size
192,192,192, pixel 1.84, shown at level 0.336, step 1, values float32  
Opened cryosparc_P7_J66_005_volume_map_sharp.mrc as #4.3, grid size
192,192,192, pixel 1.84, shown at level 0.552, step 1, values float32  
Opened cryosparc_P7_J67_004_volume_map_sharp.mrc as #4.4, grid size
192,192,192, pixel 1.84, shown at level 0.319, step 1, values float32  

> hide #!2 models

> surface dust #4.1 size 18.4

> surface dust #4.2 size 18.4

> surface dust #4.3 size 18.4

> surface dust #4.4 size 18.4

> tile

4 models tiled  

> hide #!4.1 models

> show #!4.1 models

> hide #!4.2 models

> show #!4.2 models

> hide #!4.3 models

> show #!4.3 models

> hide #!4.4 models

> show #!4.4 models

> hide #!4.3 models

> hide #!4.4 models

> hide #!4.1 models

> hide #!4.2 models

> show #!4.3 models

> show #!4.4 models

> volume #4.3 level 2.365

> volume #4.4 level 2.081

> volume #4.3 level 1.825

> volume #4.4 level 1.524

> volume #4.4 level 1.64

> volume #4.3 level 2.3

> volume #4.3 level 2.279

> volume #4.3 level 2.3

> show #!4.2 models

> show #!4.1 models

> volume #4.2 level 1.529

> volume #4.1 level 1.57

> hide #!4.1 models

> hide #!4.3 models

> tile

2 models tiled  

> volume #4.2 level 1.724

> volume #4.4 level 1.71

> hide #!4 models

> hide #!4.2 models

> hide #!4.4 models

> show #!4.4 models

> volume #4.4 level 1.13

> volume #4.4 level 1.662

> volume #4.4 level 0.8381

> volume #4.4 level 0.8115

> volume #4.4 level 1.635

> open /Users/sahtelis/Desktop/7z1t.pdb

7z1t.pdb title:  
CONNEXIN43 gap junction channel structure In digitonin [more info...]  
  
Chain information for 7z1t.pdb #5  
---  
Chain | Description | UniProt  
A B C D E F G H I J K L | gap junction α-1 protein | CXA1_HUMAN 1-382  
  

> volume #!4.4 style surface

> volume #!4.4 hide

> volume show

> show #!1 models

> hide #!1 models

> hide #!1.1 models

> hide #!1.2 models

> hide #!1.3 models

> show #!2 models

> hide #!2 models

> hide #!2.1 models

> hide #!2.2 models

> hide #!3 models

> hide #!4 models

> show #!4 models

> hide #!4.1 models

> hide #!4.2 models

> hide #!4.3 models

> open /Users/sahtelis/Desktop/7z1tchainA.pdb

Summary of feedback from opening /Users/sahtelis/Desktop/7z1tchainA.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 7 7 ASP B 3 ALA B 16 1 14  
Start residue of secondary structure not found: HELIX 8 8 GLY B 21 TRP B 45 1
25  
Start residue of secondary structure not found: HELIX 9 9 GLY B 60 PHE B 70 1
11  
Start residue of secondary structure not found: HELIX 10 10 SER B 73 LYS B 105
1 33  
Start residue of secondary structure not found: HELIX 11 11 LEU B 152 TYR B
177 1 26  
94 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (54 )  
Cannot find LINK/SSBOND residue CYS (61 )  
Cannot find LINK/SSBOND residue CYS (65 )  
Cannot find LINK/SSBOND residue CYS (54 )  
Cannot find LINK/SSBOND residue CYS (61 )  
28 messages similar to the above omitted  
  
7z1tchainA.pdb title:  
CONNEXIN43 gap junction channel structure In digitonin [more info...]  
  
Chain information for 7z1tchainA.pdb #6  
---  
Chain | Description | UniProt  
A | gap junction α-1 protein | CXA1_HUMAN 1-382  
  

> show surfaces

> close #5

> close #6

> open /Users/sahtelis/Desktop/7xkt_hc.cif

Summary of feedback from opening /Users/sahtelis/Desktop/7xkt_hc.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
notes | Fetching CCD MC3 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/3/MC3/MC3.cif  
Fetching CCD Y01 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/Y01/Y01.cif  
Fetching CCD LHG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/LHG/LHG.cif  
  
Chain information for 7xkt_hc.cif #5  
---  
Chain | Description  
A B C D E F | No description available  
  

> hide surfaces

> hide cartoons

> hide atoms

> show cartoons

Computing secondary structure  

> hide #!5 models

> show #!5 models

> select add #5

18966 atoms, 18930 bonds, 6 pseudobonds, 1272 residues, 2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models
> #5,0.8524,0.41992,0.31158,-12.605,-0.5228,0.69591,0.49233,-138.06,-0.010091,-0.58256,0.81273,-34.332

> ui mousemode right ""rotate selected models""

> view matrix models
> #5,0.98036,-0.19475,0.031083,117.36,-0.195,-0.93366,0.30041,127.42,-0.029484,-0.30057,-0.9533,177.59

> view matrix models
> #5,0.74418,0.18754,-0.64111,189.61,-0.15865,-0.88269,-0.44237,220.76,-0.64886,0.43091,-0.62713,109.18

> select subtract #5

Nothing selected  

> ui tool show ""Fit in Map""

> fitmap #5 inMap #4.4

Fit molecule 7xkt_hc.cif (#5) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 18966 atoms  
average map value = 0.5724, steps = 200  
shifted from previous position = 64.2  
rotated from previous position = 39.9 degrees  
atoms outside contour = 17245, contour level = 1.6351  
  
Position of 7xkt_hc.cif (#5) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
-0.61552418 0.14481519 0.77469904 154.21370152  
-0.78511236 -0.02690356 -0.61876881 442.56279472  
-0.06876496 -0.98909293 0.13025598 296.34728696  
Axis -0.28291804 0.64438465 -0.71044057  
Axis point 128.93936736 312.92729733 0.00000000  
Rotation angle (degrees) 139.12034108  
Shift along axis 31.01370062  
  

> select add #5

18966 atoms, 18930 bonds, 6 pseudobonds, 1272 residues, 2 models selected  

> view matrix models
> #5,0.2288,0.12665,-0.9652,316.61,0.80979,-0.57503,0.11651,-132.16,-0.54027,-0.80827,-0.23413,302.56

> fitmap #5 inMap #4.4

Fit molecule 7xkt_hc.cif (#5) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 18966 atoms  
average map value = 0.6793, steps = 92  
shifted from previous position = 18.2  
rotated from previous position = 11.1 degrees  
atoms outside contour = 16455, contour level = 1.6351  
  
Position of 7xkt_hc.cif (#5) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
0.51387715 0.54390899 0.66339532 -102.68423211  
0.41983313 -0.83382607 0.35843310 234.22235985  
0.74811127 0.09432475 -0.65683516 50.24853943  
Axis -0.86920631 -0.27880845 -0.40834573  
Axis point 0.00000000 135.84988044 38.90786482  
Rotation angle (degrees) 171.26149982  
Shift along axis 3.43183173  
  

> view matrix models
> #5,0.3255,0.016047,-0.94541,299.16,0.70431,-0.67123,0.2311,-113.35,-0.63087,-0.74108,-0.22979,312.51

> select subtract #5

Nothing selected  

> ui mousemode right ""rotate selected models""

> ui mousemode right ""translate selected models""

> volume #4.2 level 1.689

> hide #!4.2 models

> volume #4.4 level 1.614

> fitmap #5 inMap #4.4

Fit molecule 7xkt_hc.cif (#5) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 18966 atoms  
average map value = 0.8518, steps = 92  
shifted from previous position = 7.94  
rotated from previous position = 12.9 degrees  
atoms outside contour = 14862, contour level = 1.614  
  
Position of 7xkt_hc.cif (#5) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
-0.60635327 -0.65152280 0.45590986 345.25131768  
0.79505755 -0.48603771 0.36283729 97.17638955  
-0.01480739 0.58248214 0.81270865 -120.31319948  
Axis 0.14290357 0.30625428 0.94116252  
Axis point 154.96258807 155.33579194 0.00000000  
Rotation angle (degrees) 129.77997564  
Shift along axis -34.13594227  
  

> transparency #5#4.4#!4 50

> volume #4.4 color #35a6ff80

> volume #4.4 color #17caff80

> volume #4.4 color #a0f8ff80

> volume #4.4 color #cdffe680

> volume #4.4 color #fff6da80

> volume #4.4 color #ffd2cf80

> volume #4.4 color #fff2d180

> volume #4.4 color #ffecaf80

> volume #4.4 color #ffedaf80

> volume #4.4 color #ffc88980

> volume #4.4 color #f3bf8280

> volume #4.4 color #bbf39980

> volume #4.4 color #d4f3d380

> volume #4.4 color #f3e4eb80

> volume #4.4 color #f3c7d280

> volume #4.4 color #e8e6f380

> volume #4.4 color #cbeff380

> volume #4.4 color #abf3e780

> volume #4.4 color #a9f3b980

> volume #4.4 color #d0f3bc80

> volume #4.4 color #d8f38f80

> volume #4.4 color #f3b40e80

> volume #4.4 color #f39a2c80

> volume #4.4 color #f3851e80

> volume #4.4 color #f3ae3e80

> volume #4.4 color #ff9300

> volume #4.4 color #ff930000

> volume #4.4 color #ffd479

> volume #4.4 color #ffd479b1

> volume #4.4 color #b8a065b1

> volume #4.4 color #fddc8bb1

> volume #4.4 color #fddca3b1

> volume #4.4 color #fdf4a9b1

> volume #4.4 color #fdec91b1

> volume #4.4 color #fdad48b1

> volume #4.4 color #fdd071b1

> volume #4.4 color #fdb93db1

> volume #4.4 color #fde280b1

> volume #4.4 color #fde496b1

> volume #4.4 color #fdfba7b1

> volume #4.4 color #fdfba7b0

> transparency #5#4.4#!4 50

> volume #4.4 level 1.74

> volume #4.4 level 1.72

> volume #4.4 level 1.75

> volume #4.4 level 1.76

> volume #4.4 level 1.8

> volume #4.4 level 1.78

> hide #!5 models

> volume #4.4 level 1.632

> show #!5 models

> fitmap #5 inMap #4.4

Fit molecule 7xkt_hc.cif (#5) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 18966 atoms  
average map value = 0.7167, steps = 72  
shifted from previous position = 4.12  
rotated from previous position = 6.51 degrees  
atoms outside contour = 16051, contour level = 1.6325  
  
Position of 7xkt_hc.cif (#5) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
0.28586009 0.79388086 -0.53669100 45.49067633  
0.69081258 -0.55887081 -0.45873899 252.61093618  
-0.66412502 -0.23961771 -0.70818173 371.66516288  
Axis 0.80077662 0.46570642 -0.37666209  
Axis point -0.00000000 96.89956632 207.09099291  
Rotation angle (degrees) 172.13624231  
Shift along axis 14.07822915  
  

> vop zflip #4.4

> volume zflip #4.4

Expected a density maps specifier or a keyword  

> hide #!4.4 models

> show #!4.4 models

> volume flip #4.4 axis z

Opened cryosparc_P7_J67_004_volume_map_sharp.mrc z flip as #6, grid size
192,192,192, pixel 1.84, shown at step 1, values float32  

> show #!4.4 models

> hide #!4.4 models

> volume #6 level 1.822

> volume #6 level 1.63

> surface dust #6 size 18.4

> select add #6

2 models selected  

> view matrix models
> #6,-0.73501,0.54622,-0.40176,355.14,-0.28565,-0.78681,-0.54712,250.18,-0.61496,-0.28738,0.73433,5.439

> ui mousemode right ""rotate selected models""

> view matrix models
> #6,-0.60677,0.60469,-0.51592,343.55,0.037632,-0.62648,-0.77853,208.11,-0.79399,-0.4918,0.35737,143.79

> fitmap #5 inMap #6

Fit molecule 7xkt_hc.cif (#5) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
z flip (#6) using 18966 atoms  
average map value = 0.5998, steps = 236  
shifted from previous position = 72.7  
rotated from previous position = 31.4 degrees  
atoms outside contour = 16479, contour level = 1.63  
  
Position of 7xkt_hc.cif (#5) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc z flip (#6) coordinates:  
Matrix rotation and translation  
0.47911822 0.67247616 -0.56411133 38.27920023  
0.61041856 -0.71709479 -0.33639900 242.16503432  
-0.63074159 -0.18316913 -0.75406509 439.39665538  
Axis 0.85967429 0.37381955 -0.34816527  
Axis point 0.00000000 101.61647778 234.02536835  
Rotation angle (degrees) 174.88696574  
Shift along axis -29.54898799  
  

> select subtract #6

Nothing selected  

> select add #5

18966 atoms, 18930 bonds, 6 pseudobonds, 1272 residues, 2 models selected  

> ui mousemode right ""move picked models""

> view matrix models
> #5,-0.4873,-0.46869,0.7368,298.21,-0.1449,-0.78866,-0.59752,154.4,0.86113,-0.39793,0.31639,-210.66

> ui mousemode right ""rotate selected models""

> view matrix models
> #5,-0.049266,0.057094,0.99715,84.261,-0.6753,-0.73749,0.0088614,152.55,0.73589,-0.67294,0.074889,-102.19

> ui mousemode right ""move picked models""

> view matrix models
> #5,-0.049266,0.057094,0.99715,98.119,-0.6753,-0.73749,0.0088614,215,0.73589,-0.67294,0.074889,-39.931

> select subtract #5

Nothing selected  

> fitmap #5 inMap #6

Fit molecule 7xkt_hc.cif (#5) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
z flip (#6) using 18966 atoms  
average map value = 0.7654, steps = 68  
shifted from previous position = 3.24  
rotated from previous position = 12.4 degrees  
atoms outside contour = 15659, contour level = 1.63  
  
Position of 7xkt_hc.cif (#5) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc z flip (#6) coordinates:  
Matrix rotation and translation  
0.99283680 0.11947854 0.00002515 -26.07392941  
0.11947854 -0.99283681 0.00000157 335.81667011  
0.00002515 0.00000145 -1.00000002 331.24300049  
Axis -0.99846569 -0.03316596 -0.04434287  
Axis point 0.00000000 168.34138776 166.20048022  
Rotation angle (degrees) 179.99999671  
Shift along axis 0.20797394  
  

> fitmap #5 inMap #6

Fit molecule 7xkt_hc.cif (#5) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
z flip (#6) using 18966 atoms  
average map value = 0.7655, steps = 64  
shifted from previous position = 2.57  
rotated from previous position = 0.0234 degrees  
atoms outside contour = 15668, contour level = 1.63  
  
Position of 7xkt_hc.cif (#5) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc z flip (#6) coordinates:  
Matrix rotation and translation  
0.99287853 0.11913128 -0.00010406 -26.02315062  
0.11913129 -0.99287852 0.00016898 335.86498218  
-0.00008319 -0.00018017 -1.00000000 331.29727092  
Axis -0.99821856 -0.05966323 0.00003233  
Axis point 0.00000000 168.72470020 165.63348742  
Rotation angle (degrees) 179.98997951  
Shift along axis 5.94871123  
  

> select add #4.4

2 models selected  

> show #!4.4 models

> select subtract #4.4

Nothing selected  

> hide #!6 models

> select add #4.4

2 models selected  

> view matrix models
> #4.4,-0.32306,-0.67855,0.6597,362.45,-0.29054,0.73453,0.61323,-305.43,-0.90068,0.0064394,-0.43444,182.43

> ui mousemode right ""rotate selected models""

> view matrix models
> #4.4,-0.49055,-0.86665,-0.090968,548.45,-0.7065,0.33443,0.62371,-163,-0.51012,0.37023,-0.77634,105.29

> view matrix models
> #4.4,0.22647,-0.33611,-0.91419,463.18,-0.96844,0.022593,-0.24822,81.442,0.10408,0.94155,-0.32038,-178.95

> view matrix models
> #4.4,0.40737,0.55028,-0.72886,244.24,-0.84212,-0.082485,-0.53295,124.42,-0.35339,0.83089,0.4298,-201.71

> ui mousemode right ""move picked models""

> view matrix models
> #4.4,0.40737,0.55028,-0.72886,234.72,-0.84212,-0.082485,-0.53295,189.45,-0.35339,0.83089,0.4298,-159.02

> fitmap #5 inMap #4.4

Fit molecule 7xkt_hc.cif (#5) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 18966 atoms  
average map value = 0.4857, steps = 152  
shifted from previous position = 38.9  
rotated from previous position = 16.6 degrees  
atoms outside contour = 17620, contour level = 1.6325  
  
Position of 7xkt_hc.cif (#5) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
-0.07893603 -0.95686739 -0.27959610 385.74632356  
0.86370561 0.07440324 -0.49847452 61.99410107  
0.49777685 -0.28083631 0.82057860 47.74021013  
Axis 0.10928234 -0.39034107 0.91416149  
Axis point 147.10731505 230.22553263 0.00000000  
Rotation angle (degrees) 95.27735786  
Shift along axis 61.59867755  
  

> ui mousemode right ""rotate selected models""

> view matrix models
> #4.4,0.96249,0.14734,-0.22783,125.62,-0.27082,0.47085,-0.83961,41.118,-0.016435,0.86982,0.4931,-235.81

> fitmap #5 inMap #4.4

Fit molecule 7xkt_hc.cif (#5) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 18966 atoms  
average map value = 0.5113, steps = 84  
shifted from previous position = 12.7  
rotated from previous position = 14.7 degrees  
atoms outside contour = 17391, contour level = 1.6325  
  
Position of 7xkt_hc.cif (#5) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
0.11558659 -0.62034417 -0.77576602 333.75096726  
0.74598613 0.56989296 -0.34456752 -18.07339258  
0.65585402 -0.53888329 0.52864011 96.91881240  
Axis -0.09771952 -0.71994784 0.68711426  
Axis point 118.12436676 0.00000000 301.47267680  
Rotation angle (degrees) 83.85414504  
Shift along axis 46.99221421  
  

> view matrix models
> #4.4,0.91897,0.1579,-0.36133,153.35,-0.39279,0.44712,-0.80361,60.947,0.034669,0.88043,0.47291,-243.39

> ui mousemode right ""translate selected models""

> view matrix models
> #4.4,0.91897,0.1579,-0.36133,142.81,-0.39279,0.44712,-0.80361,51.369,0.034669,0.88043,0.47291,-240.67

> fitmap #5 inMap #4.4

Fit molecule 7xkt_hc.cif (#5) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 18966 atoms  
average map value = 0.65, steps = 144  
shifted from previous position = 11.9  
rotated from previous position = 33.5 degrees  
atoms outside contour = 16663, contour level = 1.6325  
  
Position of 7xkt_hc.cif (#5) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
0.72263721 0.64286025 -0.25402012 -70.45284079  
-0.63351844 0.46896315 -0.61540882 291.95129201  
-0.27649578 0.60564372 0.74615403 31.46511131  
Axis 0.69121653 0.01272308 -0.72253570  
Axis point 316.79798245 173.46352377 0.00000000  
Rotation angle (degrees) 62.03856370  
Shift along axis -67.71831428  
  

> ui mousemode right ""rotate selected models""

> view matrix models
> #4.4,0.89649,0.29775,-0.32809,116.62,-0.43456,0.7353,-0.52009,-38.688,0.086389,0.60883,0.78858,-253.64

> ui mousemode right ""move picked models""

> view matrix models
> #4.4,0.89649,0.29775,-0.32809,114.57,-0.43456,0.7353,-0.52009,-41.704,0.086389,0.60883,0.78858,-259.58

> fitmap #5 inMap #4.4

Fit molecule 7xkt_hc.cif (#5) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 18966 atoms  
average map value = 0.7166, steps = 88  
shifted from previous position = 15  
rotated from previous position = 7.39 degrees  
atoms outside contour = 16057, contour level = 1.6325  
  
Position of 7xkt_hc.cif (#5) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
0.87628795 0.45183657 0.16722203 -121.80696468  
-0.40592220 0.87935997 -0.24890415 109.54566851  
-0.25951234 0.15023256 0.95398301 94.78581748  
Axis 0.38457502 0.41116584 -0.82646519  
Axis point 269.28341221 275.10139351 0.00000000  
Rotation angle (degrees) 31.26065018  
Shift along axis -80.13965733  
  

> select subtract #4.4

Nothing selected  

> hide #!5 models

> volume #4.4 level 0.9371

> show #!5 models

> volume #4.4 level 1.064

> fitmap #5 inMap #4.4

Fit molecule 7xkt_hc.cif (#5) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 18966 atoms  
average map value = 0.6963, steps = 64  
shifted from previous position = 5.15  
rotated from previous position = 11 degrees  
atoms outside contour = 12500, contour level = 1.0635  
  
Position of 7xkt_hc.cif (#5) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
0.50078182 0.86555967 -0.00490740 -26.47564613  
-0.84900993 0.49229477 0.19190638 184.52595356  
0.16852230 -0.09193680 0.98140099 45.17090403  
Axis -0.16251764 -0.09929914 -0.98169634  
Axis point 138.05615722 121.17139683 0.00000000  
Rotation angle (degrees) 60.84074470  
Shift along axis -58.36462085  
  

> volume #4.4 level 1.19

> volume #6 level 2.283

> hide #!6 models

> close #6

> volume #4.4 level 1.654

> fitmap #5 inMap #4.4

Fit molecule 7xkt_hc.cif (#5) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 18966 atoms  
average map value = 0.6963, steps = 64  
shifted from previous position = 7.02  
rotated from previous position = 12.9 degrees  
atoms outside contour = 16222, contour level = 1.6536  
  
Position of 7xkt_hc.cif (#5) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
-0.37901441 -0.24834420 -0.89144448 458.76527946  
-0.60597313 -0.66144647 0.44191081 314.50816349  
-0.69938878 0.70768195 0.10020784 186.01299683  
Axis 0.54775691 -0.39582866 -0.73707669  
Axis point 324.43098753 68.51412956 -0.00000000  
Rotation angle (degrees) 165.95998197  
Shift along axis -10.30533662  
  

> select add #5

18966 atoms, 18930 bonds, 6 pseudobonds, 1272 residues, 2 models selected  

> view matrix models
> #5,0.3696,-0.92806,-0.045825,328.57,0.52585,0.24957,-0.81314,-119.18,0.76608,0.27644,0.58026,-256.71

> ui mousemode right ""rotate selected models""

> view matrix models
> #5,0.36281,-0.93023,-0.055179,331.58,0.49812,0.24364,-0.83217,-110.25,0.78755,0.27444,0.55176,-256.07

> view matrix models
> #5,0.38616,-0.89394,-0.22749,346.06,0.74094,0.4475,-0.50075,-240.4,0.54945,0.024813,0.83516,-208.87

> fitmap #5 inMap #4.4

Fit molecule 7xkt_hc.cif (#5) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 18966 atoms  
average map value = 0.6963, steps = 88  
shifted from previous position = 6.22  
rotated from previous position = 12.2 degrees  
atoms outside contour = 16213, contour level = 1.6536  
  
Position of 7xkt_hc.cif (#5) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
-0.83021338 0.55173039 0.07961990 262.41957050  
-0.55426057 -0.83225310 -0.01224846 410.31362222  
0.05950607 -0.05429901 0.99675005 55.06427355  
Axis -0.03798698 0.01817012 -0.99911302  
Axis point 192.32920433 166.32987596 0.00000000  
Rotation angle (degrees) 146.39347475  
Shift along axis -57.52851173  
  

> ui mousemode right ""translate selected models""

> view matrix models
> #5,-0.21448,-0.10001,-0.97159,420.24,0.27828,0.94726,-0.15893,-299.42,0.93625,-0.30446,-0.17534,-69.786

> select subtract #5

Nothing selected  

> fitmap #5 inMap #4.4

Fit molecule 7xkt_hc.cif (#5) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 18966 atoms  
average map value = 0.6952, steps = 64  
shifted from previous position = 4.39  
rotated from previous position = 7.98 degrees  
atoms outside contour = 16232, contour level = 1.6536  
  
Position of 7xkt_hc.cif (#5) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
-0.72775568 0.65720445 0.19609687 208.46124737  
-0.66019246 -0.74875328 0.05928281 398.93185142  
0.18578910 -0.08631828 0.97879088 39.81487244  
Axis -0.10984959 0.00777675 -0.99391780  
Axis point 178.16850471 161.12510323 0.00000000  
Rotation angle (degrees) 138.49164092  
Shift along axis -59.36969870  
  

> select add #5

18966 atoms, 18930 bonds, 6 pseudobonds, 1272 residues, 2 models selected  

> ui mousemode right ""move picked models""

> view matrix models
> #5,-0.17136,-0.51495,-0.83991,470.21,-0.55394,0.75537,-0.3501,-84.132,0.81473,0.40527,-0.4147,-140.97

> view matrix models
> #4.4,-0.83864,0.5434,-0.037344,332.6,-0.40164,-0.66326,-0.63148,216.77,-0.36791,-0.51459,0.77449,20.601

> view matrix models
> #5,0.85783,-0.5134,-0.023542,159.46,0.29844,0.53491,-0.79045,-131.3,0.41841,0.67104,0.61208,-266.21

> ui mousemode right ""rotate selected models""

> view matrix models
> #5,0.84133,-0.50241,-0.19936,186.33,0.21303,0.64718,-0.73197,-144.8,0.49677,0.57336,0.65152,-268.49

> view matrix models
> #5,-0.77197,-0.54159,0.33279,409.21,-0.16642,0.67747,0.71648,-294.23,-0.61349,0.49772,-0.61312,133.66

> view matrix models
> #5,-0.77262,-0.53125,0.34763,405.26,-0.17838,0.70714,0.68421,-292.71,-0.6093,0.46662,-0.64111,142.68

> ui mousemode right ""translate selected models""

> view matrix models
> #5,-0.77262,-0.53125,0.34763,409.77,-0.17838,0.70714,0.68421,-294.62,-0.6093,0.46662,-0.64111,142.47

> fitmap #5 inMap #4.4

Fit molecule 7xkt_hc.cif (#5) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 18966 atoms  
average map value = 0.6963, steps = 60  
shifted from previous position = 4.8  
rotated from previous position = 6.27 degrees  
atoms outside contour = 16218, contour level = 1.6536  
  
Position of 7xkt_hc.cif (#5) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
-0.85351581 -0.32901920 0.40405090 370.27321780  
0.37739228 -0.92500923 0.04396595 238.48115154  
0.35928518 0.19001132 0.91367930 -29.18907324  
Axis 0.20207232 0.06193906 0.97741001  
Axis point 165.70201991 154.40632128 0.00000000  
Rotation angle (degrees) 158.81570125  
Shift along axis 61.06357375  
  

> select subtract #5

Nothing selected  

> hide #!5 models

> show #!2.2 models

> volume #2.2 level 1.25

> volume #2.2 level 0.3402

> volume #2.2 level 0.6658

> volume #2.2 level 0.5367

> volume #2.2 level 0.2953

> volume #2.2 level 0.5086

> show #!2.1 models

> tile

2 models tiled  

> volume #2.2 level 0.4469

> volume #2.2 level 0.5423

> volume #2.2 level 0.4413

> volume #4.4 level 0.8949

> volume #4.4 level 1.632

> hide #!2.1 models

> hide #!2.2 models

> volume #4.4 level 1.19

> volume #4.4 level 1

> volume #4.4 level 1.717

> open /Users/sahtelis/Downloads/cryosparc_P7_J69_class_00_final_volume.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J69_class_01_final_volume.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J69_class_02_final_volume.mrc

Opened cryosparc_P7_J69_class_00_final_volume.mrc as #6.1, grid size
128,128,128, pixel 2.76, shown at level 0.268, step 1, values float32  
Opened cryosparc_P7_J69_class_01_final_volume.mrc as #6.2, grid size
128,128,128, pixel 2.76, shown at level 0.569, step 1, values float32  
Opened cryosparc_P7_J69_class_02_final_volume.mrc as #6.3, grid size
128,128,128, pixel 2.76, shown at level 0.235, step 1, values float32  

> hide #!4 models

> surface dust #6.1 size 27.6

> surface dust #6.2 size 27.6

> surface dust #6.3 size 27.6

> tile

1 model tiled  

> tile

1 model tiled  

> tile

1 model tiled  

> hide #!6.2 models

> hide #!6.3 models

> volume #6.1 level 1.042

> volume #6.1 level 1.189

> hide #!6.1 models

> show #!6.2 models

> volume #6.2 level 1.498

> volume #6.2 level 0.4916

> volume #6.2 level 1.731

> hide #!6.2 models

> show #!6.3 models

> volume #6.3 level 0.9611

> volume #6.3 level 1.935

> volume #6.3 level 1.353

> show #!6.2 models

> show #!6.1 models

> hide #!6.1 models

> hide #!6.2 models

> hide #!6.3 models

> hide #!6 models

> open
> /Users/sahtelis/Downloads/cryosparc_P7_J70_class_00_00122_volume_sharp.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J70_class_01_00122_volume_sharp.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J70_class_02_00122_volume_sharp.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J70_class_03_00122_volume_sharp.mrc

Opened cryosparc_P7_J70_class_00_00122_volume_sharp.mrc as #7.1, grid size
192,192,192, pixel 1.84, shown at level 0.187, step 1, values float32  
Opened cryosparc_P7_J70_class_01_00122_volume_sharp.mrc as #7.2, grid size
192,192,192, pixel 1.84, shown at level 0.3, step 1, values float32  
Opened cryosparc_P7_J70_class_02_00122_volume_sharp.mrc as #7.3, grid size
192,192,192, pixel 1.84, shown at level 0.176, step 1, values float32  
Opened cryosparc_P7_J70_class_03_00122_volume_sharp.mrc as #7.4, grid size
192,192,192, pixel 1.84, shown at level 0.399, step 1, values float32  

> surface dust #7.1 size 18.4

> surface dust #7.2 size 18.4

> surface dust #7.3 size 18.4

> surface dust #7.4 size 18.4

> tile

1 model tiled  

> tile

1 model tiled  

> hide #!7.4 models

> hide #!7.3 models

> hide #!7.2 models

> volume #7.1 level 0.6203

> volume #7.1 level 1.154

> hide #!7.1 models

> show #!7.2 models

> volume #7.2 level 0.8123

> volume #7.2 level 0.8014

> hide #!7.2 models

> show #!7.3 models

> volume #7.3 level 0.9403

> hide #!7.3 models

> show #!7.4 models

> volume #7.4 level 0.7427

> volume #7.4 level 0.3562

> volume #7.4 level 0.8228

> volume #7.4 level 0.7851

> hide #!7.4 models

> show #!7.3 models

> hide #!7.3 models

> show #!7.2 models

> hide #!7.2 models

> show #!7.3 models

> volume #7.3 level 0.6306

> hide #!7.3 models

> show #!7.1 models

> volume #7.1 level 0.6381

> hide #!7.1 models

> show #!7.4 models

> volume #7.4 level 0.8322

> hide #!7.4 models

> show #!6 models

> show #!6.1 models

> hide #!6.1 models

> show #!6.2 models

> hide #!6 models

> hide #!6.2 models

> hide #!7 models

> open
> /Users/sahtelis/Downloads/cryosparc_P7_J71_class_02_00102_volume_sharp.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J71_class_01_00102_volume_sharp.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J71_class_00_00102_volume_sharp.mrc

Opened cryosparc_P7_J71_class_02_00102_volume_sharp.mrc as #8.1, grid size
192,192,192, pixel 1.84, shown at level 0.413, step 1, values float32  
Opened cryosparc_P7_J71_class_01_00102_volume_sharp.mrc as #8.2, grid size
192,192,192, pixel 1.84, shown at level 0.184, step 1, values float32  
Opened cryosparc_P7_J71_class_00_00102_volume_sharp.mrc as #8.3, grid size
192,192,192, pixel 1.84, shown at level 0.199, step 1, values float32  

> surface dust #8.1 size 18.4

> surface dust #8.2 size 18.4

> surface dust #8.3 size 18.4

> hide #!8.2 models

> hide #!8.3 models

> hide #!8.1 models

> show #!8.3 models

> volume #8.3 level 0.8805

> hide #!8.3 models

> show #!8.2 models

> volume #8.2 level 0.8651

> hide #!8.2 models

> show #!8.1 models

> volume #8.1 level 0.6133

> volume #8.1 level 0.5256

> volume #8.1 level 0.8667

> volume #8.1 level 0.3891

> hide #!8.1 models

> show #!8.2 models

> hide #!8.2 models

> show #!8.3 models

> hide #!8.3 models

> show #!8.1 models

> hide #!8.1 models

> show #!4 models

> hide #!4.4 models

> show #!4.4 models

> show #!2.2 models

> hide #!2.2 models

> volume #4.4 level 0.8106

> volume #4.4 color #fdda7980

> volume #4.4 color #fdc65280

> volume #4.4 color #fdd66580

> volume #4.4 color #fdc43b80

> volume #4.4 color #fdc15080

> volume #4.4 color #fdd56b80

> volume #4.4 color #fdd47a80

> volume #4.4 color #fdce8480

> volume #4.4 color #fde19780

> volume #4.4 level 0.916

> volume #4.4 level 0.9581

> ui tool show ""Render/Select by Attribute""

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

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

> volume #4.4 level 1.675

> volume #4.4 level 1.611

> surface dust #4.4 size 18.4

> surface dust #4.4 size 20

> surface dust #4.4 size 50

> surface dust #4.4 size 90

> surface dust #4.4 size 60

> surface dust #4.4 size 70

> surface dust #4.4 size 80

> surface dust #4.4 size 85

> surface dust #4.4 size 80

> surface dust #4.4 size 20

> surface dust #4.4 size 18

> surface dust #4.4 size 19

> surface dust #4.4 size 20

> toolshed show

> help help:user/preferences.html#startup

> lighting full

> lighting soft

> lighting simple

> lighting full

> set bgColor white

> set bgColor #ffffff00

> set bgColor black

> set bgColor transparent

> lighting soft

> lighting simple

> lighting full

> ui tool show ""Selection Inspector""

> lighting simple

> preset ""initial styles"" ""original look""

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> lighting simple

> lighting full

> volume #4.4 level 1.675

> volume #4.4 level 1.717

> volume #4.4 level 1.6

> volume #4.4 level 1.65

> volume #4.4 level 1.68

> volume #4.4 level 1.69

> volume #4.4 level 1.7

> volume #4.4 level 1.75

> volume #4.4 level 1.7

> volume #4.4 level 1.72

> volume #4.4 level 1.71

> volume #4.4 level 1.7

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

> show #!5 models

> hide atoms

> show cartoons

> show surfaces

> hide surfaces

> select add #5

18966 atoms, 18930 bonds, 6 pseudobonds, 1272 residues, 2 models selected  

> view matrix models
> #5,-0.53149,0.61498,-0.5825,438.68,-0.84623,-0.41594,0.33299,-194.5,-0.037502,0.66992,0.74149,-408.29

> ui mousemode right ""rotate selected models""

> view matrix models
> #5,-0.0012646,0.26104,-0.96533,462.86,-0.049671,-0.96415,-0.26066,-152.43,-0.99876,0.047619,0.014186,-12.705

> view matrix models
> #5,0.19168,0.1068,-0.97563,457.33,0.019283,-0.99428,-0.10505,-182.4,-0.98127,0.0013222,-0.19264,22.968

> select subtract #5

6 models selected  

> select add #5

18966 atoms, 18930 bonds, 6 pseudobonds, 1272 residues, 2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models
> #5,0.28607,0.023172,-0.95793,470.2,0.066169,-0.9978,-0.0043758,-151.15,-0.95592,-0.062134,-0.28697,99.46

> view matrix models
> #5,-0.75644,0.44566,-0.47873,506.92,0.108,-0.63678,-0.76345,-113.94,-0.64508,-0.62921,0.43355,37.24

> fitmap #5 inMap #4.4

Fit molecule 7xkt_hc.cif (#5) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 18966 atoms  
average map value = 0.007541, steps = 80  
shifted from previous position = 5.02  
rotated from previous position = 7.86 degrees  
atoms outside contour = 18966, contour level = 1.7  
  
Position of 7xkt_hc.cif (#5) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
0.33680089 -0.88799692 -0.31309204 41.34051812  
0.89450652 0.19793818 0.40084732 -18.02005043  
-0.29397831 -0.41506859 0.86098479 128.20273529  
Axis -0.41618599 -0.00974961 0.90922723  
Axis point 61.46928879 47.29693297 0.00000000  
Rotation angle (degrees) 78.58804147  
Shift along axis 99.53576236  
  

> transparency (#!5 & sel) 50

> transparency (#!5 & sel) 0

> select subtract #5

6 models selected  

> transparency #5#4.4#!2,4,8 100

> transparency #5#4.4#!2,4,8 50

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows true

> lighting flat

> graphics silhouettes false

> lighting simple

> lighting flat

> lighting simple

> ui tool show ""Side View""

> view

> view orient

> undo

> set bgColor gray

> set bgColor #80808000

> graphics silhouettes false

> transparency #5#4.4#!2,4,8 80

> lighting simple

> graphics silhouettes true

> fitmap #5 inMap #4.4

Fit molecule 7xkt_hc.cif (#5) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 18966 atoms  
average map value = -0.0006071, steps = 240  
shifted from previous position = 25.1  
rotated from previous position = 18.6 degrees  
atoms outside contour = 18966, contour level = 1.7  
  
Position of 7xkt_hc.cif (#5) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
-0.88368620 0.35003567 0.31076313 -67.63545033  
0.40010872 0.22031493 0.88959224 -0.99786545  
0.24292327 0.91045941 -0.33474160 -14.71891343  
Axis 0.24023383 0.78100789 0.57646715  
Axis point -33.66441913 0.00000000 -6.13571137  
Rotation angle (degrees) 177.51080574  
Shift along axis -25.51263396  
  

> select add #5

18966 atoms, 18930 bonds, 6 pseudobonds, 1272 residues, 2 models selected  

> view matrix models
> #5,0.87453,0.41806,-0.24582,176.73,-0.48362,0.71384,-0.50651,-305.13,-0.036275,0.56184,0.82645,-336.68

> volume #4.4 level 1.721

> lighting simple

> view sel

> undo

> view

> graphics silhouettes false

> lighting simple

> lighting full

> lighting simple

> lighting flat

> lighting simple

> volume #4.4 level 0.9414

> fitmap #5 inMap #4.4

Fit molecule 7xkt_hc.cif (#5) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 18966 atoms  
average map value = 0.001578, steps = 2000  
shifted from previous position = 4.07  
rotated from previous position = 9.12 degrees  
atoms outside contour = 18966, contour level = 0.94136  
  
Position of 7xkt_hc.cif (#5) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
-0.51206609 -0.85678418 0.06090293 124.45089017  
-0.85019138 0.49547377 -0.17798975 341.00026602  
0.12232300 -0.14292164 -0.98214584 293.04165041  
Axis 0.49368875 -0.86467166 0.09281349  
Axis point 156.36665152 0.00000000 167.14634766  
Rotation angle (degrees) 177.96463149  
Shift along axis -206.21504417  
  

> volume #4.4 level 1.51

> volume #4.4 level 1.658

> fitmap #5 inMap #4.4

Fit molecule 7xkt_hc.cif (#5) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 18966 atoms  
average map value = -0.0006391, steps = 2000  
shifted from previous position = 12.1  
rotated from previous position = 12.5 degrees  
atoms outside contour = 18966, contour level = 1.6579  
  
Position of 7xkt_hc.cif (#5) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
0.52913100 -0.84015807 0.11897379 -72.12214886  
-0.39878037 -0.12245270 0.90883415 223.05117365  
-0.74899570 -0.52833673 -0.39983208 439.66259380  
Axis -0.82787035 0.49998662 0.25425196  
Axis point 0.00000000 218.54936460 180.19139574  
Rotation angle (degrees) 119.77378648  
Shift along axis 283.01546680  
  

> ui mousemode right ""rotate selected models""

> view matrix models
> #5,0.34861,0.31425,-0.88301,385.22,0.45768,-0.87923,-0.13221,-241.4,-0.81792,-0.35805,-0.45034,161.23

> view matrix models
> #5,0.38412,0.28431,-0.87842,383.53,0.38982,-0.91239,-0.12484,-224.08,-0.83695,-0.29447,-0.4613,154.73

> select subtract #5

6 models selected  

> open /Users/sahtelis/Desktop/cx43_hc.pdb

Chain information for cx43_hc.pdb #9  
---  
Chain | Description  
A B C D E F | No description available  
  

> hide atoms

> show cartoons

Computing secondary structure  

> select add #9

10620 atoms, 10680 bonds, 6 pseudobonds, 1374 residues, 2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models
> #9,0.88568,0.20454,-0.41681,317.55,-0.34234,0.89413,-0.28867,-365.24,0.31364,0.39836,0.86194,-400.41

> ui mousemode right ""rotate selected models""

> view matrix models
> #9,0.59286,-0.26685,-0.75981,453.34,-0.70528,0.28337,-0.64983,-199.45,0.38871,0.92114,-0.020202,-397.23

> view matrix models
> #9,0.3224,-0.31098,-0.89406,508.58,-0.62442,0.64,-0.44778,-277.72,0.71145,0.70263,0.012151,-414.38

> ui mousemode right ""translate selected models""

> view matrix models
> #9,0.3224,-0.31098,-0.89406,488.18,-0.62442,0.64,-0.44778,-233.35,0.71145,0.70263,0.012151,-380.54

> ui mousemode right ""rotate selected models""

> view matrix models
> #9,0.95807,-0.25635,0.12803,297.79,0.2832,0.91515,-0.28687,-408.33,-0.043625,0.31109,0.94938,-314.87

> fitmap #9 inMap #4.4

Fit molecule cx43_hc.pdb (#9) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 10620 atoms  
average map value = 0.6122, steps = 216  
shifted from previous position = 58.2  
rotated from previous position = 36.7 degrees  
atoms outside contour = 9461, contour level = 1.6579  
  
Position of cx43_hc.pdb (#9) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
-0.49243214 0.84988060 -0.18765296 -118.84709668  
-0.38821303 -0.02150938 0.92131866 150.00432361  
0.77897453 0.52653620 0.34052663 -203.93624006  
Axis -0.24375336 -0.59683173 -0.76444502  
Axis point 42.15848415 186.52774312 0.00000000  
Rotation angle (degrees) 125.92370386  
Shift along axis 95.34008189  
  

> hide #!5 models

> transparency (#!9 & sel) 50

> transparency (#!9 & sel) 0

> hide #!4.4 models

> show #!4.4 models

> graphics silhouettes false

> lighting simple

> lighting full

> lighting simple

> transparency (#!9 & sel) 50

> transparency #4.4 50

> view matrix models
> #9,-0.42486,0.59194,-0.68491,453.33,0.86947,0.47745,-0.1267,-406.72,0.25201,-0.64934,-0.71753,-111.82

> view matrix models
> #9,-0.42997,0.15854,-0.88882,531.92,0.90279,0.086606,-0.42128,-330.44,0.010188,-0.98355,-0.18036,-85.14

> fitmap #9 inMap #4.4

Fit molecule cx43_hc.pdb (#9) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 10620 atoms  
average map value = 0.7049, steps = 132  
shifted from previous position = 16.3  
rotated from previous position = 25.2 degrees  
atoms outside contour = 9065, contour level = 1.6579  
  
Position of cx43_hc.pdb (#9) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
0.82642417 -0.51278181 -0.23254678 -105.39186735  
0.55080140 0.82194698 0.14498649 -28.51897805  
0.11679467 -0.24790741 0.96171774 -79.63973309  
Axis -0.33115663 -0.29444778 0.89645736  
Axis point -4.96546686 -221.99277267 0.00000000  
Rotation angle (degrees) 36.38545748  
Shift along axis -28.09505944  
  

> volume #4.4 level 1.595

> select subtract #9

Nothing selected  

> volume #4.4 level 1.489

> volume #4.4 level 1.595

> fitmap #9 inMap #4.4

Fit molecule cx43_hc.pdb (#9) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 10620 atoms  
average map value = 0.7049, steps = 64  
shifted from previous position = 2.28  
rotated from previous position = 0.0256 degrees  
atoms outside contour = 8868, contour level = 1.5946  
  
Position of cx43_hc.pdb (#9) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
0.83694867 0.48793107 0.24787151 -288.30358578  
0.01717986 -0.47611464 0.87921544 147.98378509  
0.54701175 -0.73159977 -0.40686608 59.66868359  
Axis -0.94495597 -0.17548528 -0.27615779  
Axis point 0.00000000 137.23762323 16.19091160  
Rotation angle (degrees) 121.53477769  
Shift along axis 229.98724839  
  

> select add #9

10620 atoms, 10680 bonds, 6 pseudobonds, 1374 residues, 2 models selected  

> view matrix models
> #9,-0.46171,0.085394,-0.88291,554,0.55788,0.80181,-0.21418,-388.55,0.68964,-0.59145,-0.41784,-213.17

> select subtract #9

Nothing selected  

> select add #9

10620 atoms, 10680 bonds, 6 pseudobonds, 1374 residues, 2 models selected  

> view matrix models
> #9,-0.27349,-0.94951,-0.15372,598.97,0.68365,-0.079461,-0.72547,-237.93,0.67663,-0.3035,0.67087,-353.82

> view matrix models
> #9,-0.23221,-0.96568,-0.11634,592.02,0.76913,-0.10908,-0.62971,-254.58,0.59541,-0.2357,0.76807,-361.25

> view matrix models
> #9,-0.2405,-0.9646,-0.10817,592.22,0.69679,-0.093988,-0.71109,-239.11,0.67576,-0.24639,0.69473,-363.68

> volume flip #4.4 axis z

Opened cryosparc_P7_J67_004_volume_map_sharp.mrc z flip as #10, grid size
192,192,192, pixel 1.84, shown at step 1, values float32  

> hide #!8 models

> select add #10

10620 atoms, 10680 bonds, 6 pseudobonds, 1374 residues, 4 models selected  

> select subtract #9

2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models
> #10,-0.56124,-0.82675,0.038649,625.08,0.78196,-0.54497,-0.30257,-285.19,0.27121,-0.13959,0.95234,-350.22

> volume #10 level 0.6885

> select subtract #10

Nothing selected  

> hide #!9 models

> volume #10 level 2.164

> surface dust #10 size 18.4

> volume #10 level 1.616

> show #!9 models

> fitmap #9 inMap #10

Fit molecule cx43_hc.pdb (#9) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
z flip (#10) using 10620 atoms  
average map value = -0.002056, steps = 140  
shifted from previous position = 3.23  
rotated from previous position = 5.75 degrees  
atoms outside contour = 10620, contour level = 1.6157  
  
Position of cx43_hc.pdb (#9) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc z flip (#10) coordinates:  
Matrix rotation and translation  
0.52589008 -0.81646204 0.23838927 176.59101156  
-0.80263367 -0.56911852 -0.17855918 386.30223849  
0.28145852 -0.09743675 -0.95461367 380.18240997  
Axis 0.87339406 -0.46369943 0.14888133  
Axis point 0.00000000 235.03487761 180.37362114  
Rotation angle (degrees) 177.33817443  
Shift along axis 31.70747692  
  

> tile

2 models tiled  

> select add #10

2 models selected  

> view matrix models
> #10,-0.15698,0.29012,0.94403,263.56,-0.59456,-0.79101,0.14423,-105.98,0.78858,-0.53864,0.29667,-418.19

> view matrix models
> #10,-0.15698,0.29012,0.94403,257.92,-0.59456,-0.79101,0.14423,-100.07,0.78858,-0.53864,0.29667,-414.69

> view matrix models
> #10,0.087351,0.18399,0.97904,212.81,-0.94759,0.31854,0.024682,-186.6,-0.30732,-0.92988,0.20217,-116.41

> view matrix models
> #10,0.087351,0.18399,0.97904,200.11,-0.94759,0.31854,0.024682,-190.08,-0.30732,-0.92988,0.20217,-123.98

> ui mousemode right ""rotate selected models""

> view matrix models
> #10,0.44364,-0.38622,0.80871,269.8,-0.85794,0.077827,0.50782,-253.89,-0.25907,-0.91912,-0.29683,-40.943

> view matrix models
> #10,0.36826,0.0059344,0.92971,191.19,-0.9185,0.15725,0.36281,-230.06,-0.14405,-0.98754,0.06336,-116.64

> ui mousemode right ""translate selected models""

> view matrix models
> #10,0.36826,0.0059344,0.92971,180.56,-0.9185,0.15725,0.36281,-157.26,-0.14405,-0.98754,0.06336,-53.274

> select subtract #10

Nothing selected  

> fitmap #9 inMap #10

Fit molecule cx43_hc.pdb (#9) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
z flip (#10) using 10620 atoms  
average map value = 0.7925, steps = 52  
shifted from previous position = 3.26  
rotated from previous position = 5.21 degrees  
atoms outside contour = 8781, contour level = 1.6157  
  
Position of cx43_hc.pdb (#9) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc z flip (#10) coordinates:  
Matrix rotation and translation  
0.61441797 -0.78898076 -0.00002218 200.21958080  
-0.78898076 -0.61441797 0.00007508 366.09458649  
-0.00007288 -0.00002863 -1.00000003 285.44769665  
Axis -0.89839759 0.43918306 -0.00000835  
Axis point 0.00000000 231.99070521 142.71690359  
Rotation angle (degrees) 179.99669295  
Shift along axis -19.09662915  
  

> show #!4.4 models

> hide #!9 models

> fitmap #4.4 inMap #10

Fit map cryosparc_P7_J67_004_volume_map_sharp.mrc in map
cryosparc_P7_J67_004_volume_map_sharp.mrc z flip using 9494 points  
correlation = 0.6563, correlation about mean = 0.08955, overlap = 2.559e+04  
steps = 72, shift = 3.96, angle = 8.86 degrees  
  
Position of cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc z flip (#10) coordinates:  
Matrix rotation and translation  
0.93266190 -0.25499085 0.25518893 302.83609457  
0.31891898 0.91342835 -0.25286237 82.40014130  
-0.16861925 0.31721968 0.93324128 111.34443861  
Axis 0.62425166 0.46407874 0.62844315  
Axis point 279.02793231 386.21777076 0.00000000  
Rotation angle (degrees) 27.16872460  
Shift along axis 297.25973767  
  

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!9 models

> show #!10 models

> hide #!9 models

> hide #!4.4 models

> show #!9 models

> hide #!10 models

> show #!4.4 models

> select add #4.4

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #4.4,-0.3084,0.24527,0.91909,133.61,-0.39058,-0.91364,0.11275,137.82,0.86737,-0.32421,0.37757,-162.37

> fitmap #9 inMap #4.4

Fit molecule cx43_hc.pdb (#9) to map cryosparc_P7_J67_004_volume_map_sharp.mrc
(#4.4) using 10620 atoms  
average map value = 0.9609, steps = 104  
shifted from previous position = 2.51  
rotated from previous position = 13.2 degrees  
atoms outside contour = 8179, contour level = 1.5946  
  
Position of cx43_hc.pdb (#9) relative to
cryosparc_P7_J67_004_volume_map_sharp.mrc (#4.4) coordinates:  
Matrix rotation and translation  
-0.19368557 -0.98058146 -0.03076084 145.20681676  
-0.98035581 0.19464157 -0.03189263 535.44352464  
0.03726048 0.02397923 -0.99901776 282.93365497  
Axis 0.63471839 -0.77273928 0.00256349  
Axis point 288.46426767 0.00000000 147.32500772  
Rotation angle (degrees) 177.47741941  
Shift along axis -320.86750904  
  

> select subtract #4.4

Nothing selected  

> volume #10 level 1.6

> volume #10 level 1.8

> volume #10 level 1.822

> volume #4.4 level 1.55

> volume #4.4 level 1.617

> volume #4.4 level 1.6

> volume #4.4 level 1.64

> volume #4.4 level 1.6

> volume #4.4 level 1.622

> volume #4.4 level 1.6

> select add #9

10620 atoms, 10680 bonds, 6 pseudobonds, 1374 residues, 2 models selected  

> ui mousemode right ""move picked models""

> view matrix models
> #9,0.087966,-0.24709,-0.96499,535.69,-0.98313,0.13445,-0.12405,-97.461,0.16039,0.95962,-0.23109,-370.26

> select subtract #9

Nothing selected  

> select add #9

10620 atoms, 10680 bonds, 6 pseudobonds, 1374 residues, 2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #9,0.14263,-0.33644,-0.93084,537.12,-0.98929,-0.019095,-0.14469,-73.937,0.030904,0.94151,-0.33556,-340.4

> select subtract #9

Nothing selected  

> transparency #9#4.4#!2,4 70

> transparency #9#4.4#!2,4 40

> transparency #9#4.4#!2,4 50

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

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

> hide #!9 models

> volume #4.4 level 1.136

> volume #4.4 level 1.6

> hide #!4.4 models

> open /Users/sahtelis/Downloads/cryosparc_P7_J72_class_00_final_volume.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J72_class_01_final_volume.mrc

Opened cryosparc_P7_J72_class_00_final_volume.mrc as #11.1, grid size
192,192,192, pixel 1.84, shown at level 0.425, step 1, values float32  
Opened cryosparc_P7_J72_class_01_final_volume.mrc as #11.2, grid size
192,192,192, pixel 1.84, shown at level 0.372, step 1, values float32  

> ui mousemode right ""translate selected models""

> surface dust #11.1 size 18.4

> surface dust #11.2 size 18.4

> tile

1 model tiled  

> hide #!11.2 models

> volume #11.1 level 0.6635

> hide #!11.1 models

> show #!11.2 models

> volume #11.2 level 0.6959

> volume #11.2 level 0.4785

> volume #11.2 level 0.3565

> volume #11.2 level 0.4202

> hide #!11.2 models

> show #!11.1 models

> volume #11.1 level 0.515

> hide #!11.1 models

> show #!11.2 models

> volume #11.2 level 0.4573

> hide #!11.2 models

> show #!11.1 models

> volume #11.1 level 0.796

> volume #11.1 level 1.194

> volume #11.1 level 0.5627

> volume #11.1 level 0.4779

> volume #11.1 level 0.5044

> hide #!11 models

> hide #!11.1 models

> show #!8.3 models

> hide #!8.3 models

> show #!8.2 models

> hide #!8.2 models

> show #!8.1 models

> volume #8.1 level 0.4044

> volume #8.1 level 0.7778

> volume #8.1 level 0.7113

> volume #8.1 level 0.6141

> show #!7.4 models

> show #!7.3 models

> show #!7.2 models

> show #!7.1 models

> hide #!7.2 models

> hide #!7.3 models

> hide #!7.4 models

> hide #!8 models

> hide #!8.1 models

> hide #!7.1 models

> show #!7.2 models

> hide #!7.2 models

> show #!7.3 models

> hide #!7.3 models

> show #!7.4 models

> volume #7.4 level 0.5453

> hide #!7.4 models

> show #!4.4 models

> volume #4.4 level 1.65

> volume #4.4 level 1.7

> volume #4.4 level 1.75

> volume #4.4 level 1.7

> volume #4.4 level 1.8

> volume #4.4 level 1.7

> volume #4.4 level 1.75

> volume #4.4 level 1.7

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

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

> open /Users/sahtelis/Downloads/cryosparc_P7_J10_036_class_averages.mrc

Opened cryosparc_P7_J10_036_class_averages.mrc as #12, grid size 128,128,100,
pixel 2.76,2.76,2.76, shown at level 2.87, step 1, values float32  

> close #12

> hide #!7 models

> hide #!4.4 models

> open
> /Users/sahtelis/Downloads/cryosparc_P7_J73_class_00_00102_volume_sharp.mrc.download
> /Users/sahtelis/Downloads/cryosparc_P7_J73_class_01_00102_volume_sharp.mrc.download
> /Users/sahtelis/Downloads/cryosparc_P7_J73_class_02_00102_volume_sharp.mrc.download

Unrecognized file suffix '.download'  

> open
> /Users/sahtelis/Downloads/cryosparc_P7_J73_class_00_00102_volume_sharp.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J73_class_01_00102_volume_sharp.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J73_class_02_00102_volume_sharp.mrc

Opened cryosparc_P7_J73_class_00_00102_volume_sharp.mrc as #12.1, grid size
192,192,192, pixel 1.84, shown at level 0.462, step 1, values float32  
Opened cryosparc_P7_J73_class_01_00102_volume_sharp.mrc as #12.2, grid size
192,192,192, pixel 1.84, shown at level 0.269, step 1, values float32  
Opened cryosparc_P7_J73_class_02_00102_volume_sharp.mrc as #12.3, grid size
192,192,192, pixel 1.84, shown at level 0.365, step 1, values float32  

> surface dust #12.1 size 18.4

> surface dust #12.2 size 18.4

> surface dust #12.3 size 18.4

> hide #!12.1 models

> hide #!12.2 models

> hide #!12.3 models

> show #!12.1 models

> volume #12.1 level 0.6682

> hide #!12.1 models

> show #!12.2 models

> volume #12.2 level 0.7314

> hide #!12.2 models

> show #!12.3 models

> volume #12.3 level 0.6036

> open /Users/sahtelis/Downloads/cryosparc_P7_J75_005_volume_map_sharp.mrc

Opened cryosparc_P7_J75_005_volume_map_sharp.mrc as #13, grid size
192,192,192, pixel 1.84, shown at level 0.317, step 1, values float32  

> hide #!12.3 models

> surface dust #13 size 18.4

> volume #13 level 1.458

> volume #13 level 2.112

> volume #13 level 1.441

> volume #13 level 1.324

> volume #13 level 1.491

> volume #13 level 0.9544

> show #!4.4 models

> volume #10 level 1.291

> volume #10 level 1.999

> close #10

> volume #4.4 level 1.213

> volume #4.4 level 1.103

> hide #!4.4 models

> hide #!13 models

> show #!12.3 models

> volume #12.3 level 0.882

> volume #12.3 level 0.6931

> volume #12.3 level 0.7925

> hide #!12.3 models

> open /Users/sahtelis/Downloads/cryosparc_P7_J78_003_volume_map_sharp.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J80_003_volume_map_sharp.mrc

Opened cryosparc_P7_J78_003_volume_map_sharp.mrc as #10.1, grid size
192,192,192, pixel 1.84, shown at level 0.339, step 1, values float32  
Opened cryosparc_P7_J80_003_volume_map_sharp.mrc as #10.2, grid size
192,192,192, pixel 1.84, shown at level 0.332, step 1, values float32  

> surface dust #10.1 size 18.4

> surface dust #10.2 size 18.4

> hide #!10.2 models

> volume #10.1 level 0.8122

> volume #10.1 level 1.246

> show #!10.2 models

> hide #!10.1 models

> volume #10.2 level 1.177

> volume #10.2 level 0.7165

> volume #10.2 level 0.7293

> volume #10.2 level 0.6204

> volume #10.2 level 0.4796

> show #!4.4 models

> hide #!10 models

> hide #!10.2 models

> hide #!12 models

> transparency #4.4#!2,4 0

> volume #4.4 level 1.612

> hide #!4.4 models

> hide #!4 models

> close #10.2

> show #!10.1 models

> volume #10.1 level 0.7086

> open /Users/sahtelis/Downloads/cryosparc_P7_J78_003_volume_mask_refine.mrc

Opened cryosparc_P7_J78_003_volume_mask_refine.mrc as #14, grid size
192,192,192, pixel 1.84, shown at level 1, step 1, values float32  

> volume #14 level 1

> volume #14 level 0.7072

> tile

2 models tiled  

> select add #14

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #14,0.46778,0.80653,-0.36151,-40.324,0.36487,-0.54876,-0.75215,231.63,-0.80501,0.21994,-0.55098,542.7

> view matrix models
> #14,0.57675,0.81432,0.065068,-141.19,0.52967,-0.31212,-0.78869,167.6,-0.62194,0.48934,-0.61134,474.13

> view matrix models
> #14,0.52929,0.84836,0.011824,-128.8,0.66467,-0.40594,-0.62724,129.95,-0.52732,0.33985,-0.77874,515.31

> view matrix models
> #14,0.50711,0.84339,0.17757,-155.18,0.67185,-0.25777,-0.69439,115.14,-0.53987,0.47143,-0.69735,478.97

> select subtract #14

Nothing selected  

> select add #14

2 models selected  

> view matrix models
> #14,0.57689,0.81506,0.05368,-139.2,0.68374,-0.4459,-0.57764,124.31,-0.44687,0.36994,-0.81452,502.51

> view matrix models
> #14,0.51193,0.85409,0.091939,-141.82,0.79133,-0.42724,-0.43733,75.616,-0.33424,0.29664,-0.89459,510.63

> hide #!14 models

> select subtract #14

Nothing selected  

> hide #!10 models

> hide #!10.1 models

> show #!4.2 models

> volume #4.2 level 1.073

> select add #4.2

2 models selected  

> view matrix models
> #4.2,0.69512,0.1048,-0.71121,212.56,0.52777,-0.74613,0.40589,25.914,-0.48812,-0.6575,-0.57396,384.85

> ui mousemode right ""translate selected models""

> view matrix models
> #4.2,0.69512,0.1048,-0.71121,127.36,0.52777,-0.74613,0.40589,47.052,-0.48812,-0.6575,-0.57396,270.16

> select subtract #4.2

Nothing selected  

> volume #4.2 level 1.763

> volume #4.2 level 1.502

> show #!4.1 models

> hide #!4.2 models

> volume #4.1 level 1.445

> hide #!4.1 models

> show #!4.3 models

> volume #4.3 level 1.806

> volume #4.3 level 1.6

> hide #!4.3 models

> show #!4.4 models

> volume #4.4 level 1.191

> volume #4.4 level 1.501

> volume #4.4 level 1.457

> volume #4.4 level 1.413

> volume #4.4 level 1.501

> volume #4.4 level 1.7

> volume #4.4 level 1.6

> hide #!4.4 models

> open /Users/sahtelis/Downloads/cryosparc_P7_J83_005_volume_map_sharp.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J84_004_volume_map_sharp.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J85_002_volume_map_sharp.mrc
> /Users/sahtelis/Downloads/cryosparc_P7_J86_002_volume_map_sharp.mrc

Opened cryosparc_P7_J83_005_volume_map_sharp.mrc as #15.1, grid size
192,192,192, pixel 1.84, shown at level 0.35, step 1, values float32  
Opened cryosparc_P7_J84_004_volume_map_sharp.mrc as #15.2, grid size
192,192,192, pixel 1.84, shown at level 0.493, step 1, values float32  
Opened cryosparc_P7_J85_002_volume_map_sharp.mrc as #15.3, grid size
192,192,192, pixel 1.84, shown at level 0.317, step 1, values float32  
Opened cryosparc_P7_J86_002_volume_map_sharp.mrc as #15.4, grid size
192,192,192, pixel 1.84, shown at level 0.334, step 1, values float32  

> hide #!15.2 models

> hide #!15.3 models

> hide #!15.4 models

> volume #15.1 level 1.281

> volume #15.1 level 0.9304

> volume #15.1 level 0.8235

> hide #!15.1 models

> show #!15.2 models

> volume #15.2 level 1.22

> hide #!15.2 models

> show #!15.3 models

> volume #15.3 level 0.715

> volume #15.3 level 0.5822

> hide #!15.3 models

> show #!15.4 models

> volume #15.4 level 1.138

> hide #!15.4 models

> show #!15.2 models

> show #!15.1 models

> hide #!15.2 models

> volume #15.1 level 1.48

> volume #15.1 level 0.9762

> hide #!15.1 models

> show #!4.4 models

> view


===== 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 - 89.3
OpenGL renderer: Apple M3
OpenGL vendor: Apple

Python: 3.11.4
Locale: 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 Air
      Model Identifier: Mac15,12
      Model Number: MC8G4KS/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.81.4
      OS Loader Version: 11881.81.4

Software:

    System Software Overview:

      System Version: macOS 15.3.1 (24D70)
      Kernel Version: Darwin 24.3.0
      Time since boot: 16 days, 23 hours, 46 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 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