id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15745	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-13.6.7-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> preset ""overall look"" ""publication 1 (silhouettes)""

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> alias nice cartoon suppressBackboneDisplay false; cartoon style width 1;
> size stickRadius 0.12

> lighting soft

> nice

Changed 0 bond radii  

> alias voltr5 vol transparency 0.5

> alias voltroff vol transparency 0

> alias cylinders cartoon style protein modeh tube rad 2 sides 24

> alias cartoonDefaults cartoon style protein modeh default

UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2922_005_volume_mask_refine.mrc""

Opened cryosparc_P120_J2922_005_volume_mask_refine.mrc as #1, grid size
200,200,200, pixel 1.04, shown at level 1, step 1, values float32  

> volume #1 level 0.9731

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2922_005_volume_map_sharp.mrc""

Opened cryosparc_P120_J2922_005_volume_map_sharp.mrc as #2, grid size
200,200,200, pixel 1.04, shown at level 0.0781, step 1, values float32  

> volume #1 level 0.1454

> volume #1 level 1

> ui tool show ""Side View""

> volume #1 level 1

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J3552_map_locres.mrc""

Opened cryosparc_P120_J3552_map_locres.mrc as #3, grid size 200,200,200, pixel
1.04, shown at level 5.73, step 1, values float32  

> volume #3 level 2.802

> volume #2 level 0.1843

> color sample #2 map #3 range 2.7,4.5 palette rainbow

Map values for surface ""surface"": minimum 2.75, mean 2.955, maximum 4.662  

> volume #2 level 0.231

> volume #2 level 0.07172

> volume #2 level 0.1703

> volume #2 level 0.14

> volume #2 level 0.17

> view locres_side

Expected an objects specifier or a view name or a keyword  

> view orient

> turn x -90

> ui tool show ""Color Key""

> ui mousemode right ""color key""

> key blue-white-red :min : :max white:

> key blue:min white: red:max white: white:

> key blue:2 white: red:max white: white:

> key blue:2. white: red:max white: white:

> key blue:2.7 white: red:max white: white:

> key blue:2.7 white: red: white: white:

> key blue:2.7 white:3 red: white: white:

> key blue:2.7 white:3. red: white: white:

> key blue:2.7 white:3.1 red: white: white:

> key blue:2.7 white:3.1 red:3 white: white:

> key blue:2.7 white:3.1 red:3. white: white:

> key blue:2.7 white:3.1 red:3.5 white: white:

> key blue:2.7 white:3.1 red:3.5 white:3 white:

> key blue:2.7 white:3.1 red:3.5 white:3. white:

> key blue:2.7 white:3.1 red:3.5 white:3.9 white:

> key blue:2.7 white:3.1 red:3.5 white:3.9 white:4

> key blue:2.7 white:3.1 red:3.5 white:3.9 white:4.

> key blue:2.7 white:3.1 red:3.5 white:3.9 white:4.3

> key rainbow :2.7 :3.1 :3.5 :3.9 :4.3

> color sample #2 map #3 range 2.7,4.3 palette rainbow

Map values for surface ""surface"": minimum 2.75, mean 2.971, maximum 4.766  

> key fontSize 40

> hide #!2 models

> key pos 0.0575451,0.553904 size 0.911327,0.0955666

> key pos 0.0523717,0.482386

> pwd

Current working directory is: /Users/bburendei/Desktop  

> cd ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing""

Current working directory is: /Users/bburendei/Dropbox (Scripps
Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing  

> save J2922_locresJ3552_colorkey.png supersample 3 transparentBackground true

> hide #4 models

> show #!2 models

> save J2922_locresJ3552_otherSide.png supersample 3 transparentBackground
> true

> turn y 90

> save J2922_locresJ3552_side.png supersample 3 transparentBackground true

> view initial

> color #2 #B2B2B2

> lighting soft

> preset ""overall look"" ""publication 1 (silhouettes)""

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> camera ortho

> color sample #2 map #3 range 2.7,4.3 palette rainbow

Map values for surface ""surface"": minimum 2.75, mean 2.971, maximum 4.766  

> save J2922_locresJ3552_side.png supersample 3 transparentBackground true

> turn y -90

> save J2922_locresJ3552_otherSide.png supersample 3 transparentBackground
> true

> turn y -90

> surface dust #2

> color #2 #B2B2B2

> save J2922_NC36_final_side.png supersample 3 transparentBackground true

> color sample #2 map #3 range 2.7,4.3 palette rainbow

Map values for surface ""surface"": minimum 2.75, mean 2.971, maximum 4.766  

> save J2922_locresJ3552_side.png supersample 3 transparentBackground true

> turn y -90

> save J2922_locresJ3552_otherSide.png supersample 3 transparentBackground
> true

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2704_class_04_00162_volume.mrc""

Opened cryosparc_P120_J2704_class_04_00162_volume.mrc as #5, grid size
100,100,100, pixel 2.09, shown at level 0.139, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2704_class_03_00162_volume.mrc""

Opened cryosparc_P120_J2704_class_03_00162_volume.mrc as #6, grid size
100,100,100, pixel 2.09, shown at level 0.151, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2704_class_02_00162_volume.mrc""

Opened cryosparc_P120_J2704_class_02_00162_volume.mrc as #7, grid size
100,100,100, pixel 2.09, shown at level 0.126, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2704_class_01_00162_volume.mrc""

Opened cryosparc_P120_J2704_class_01_00162_volume.mrc as #8, grid size
100,100,100, pixel 2.09, shown at level 0.15, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2704_class_00_00162_volume.mrc""

Opened cryosparc_P120_J2704_class_00_00162_volume.mrc as #9, grid size
100,100,100, pixel 2.09, shown at level 0.123, step 1, values float32  

> hide #!2 models

> tile

5 models tiled  

> color #B2B2B2

> lighting soft

> volume #5 level 0.2126

> volume #6 level 0.2515

> volume #7 level 0.2288

> volume #8 level 0.2354

> volume #9 level 0.2117

> volume #5-9 level 0.15

> volume #5-9 level 0.2

> volume #5-9 level 0.18

> volume #5-9 level 0.19

> volume #5-9 level 0.2

> save J2704_hetero_coll3.png supersample 3 transparentBackground true

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2723_class_04_00122_volume.mrc""

Opened cryosparc_P120_J2723_class_04_00122_volume.mrc as #10, grid size
100,100,100, pixel 2.09, shown at level 0.15, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2723_class_03_00122_volume.mrc""

Opened cryosparc_P120_J2723_class_03_00122_volume.mrc as #11, grid size
100,100,100, pixel 2.09, shown at level 0.156, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2723_class_02_00122_volume.mrc""

Opened cryosparc_P120_J2723_class_02_00122_volume.mrc as #12, grid size
100,100,100, pixel 2.09, shown at level 0.156, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2723_class_01_00122_volume.mrc""

Opened cryosparc_P120_J2723_class_01_00122_volume.mrc as #13, grid size
100,100,100, pixel 2.09, shown at level 0.159, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2723_class_00_00122_volume.mrc""

Opened cryosparc_P120_J2723_class_00_00122_volume.mrc as #14, grid size
100,100,100, pixel 2.09, shown at level 0.159, step 1, values float32  

> tile off

> view initial

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> tile

5 models tiled  

> lighting soft

> color #B2B2B2

> volume #14 level 0.2039

> volume #13 level 0.2518

> volume #12 level 0.2601

> volume #11 level 0.2174

> volume #10 level 0.2153

> volume #11 level 0.2349

> key pos 0.475164,0.446975 size 0.00838926,0.000748005

> save J2723_hetero_coll3.png supersample 3 transparentBackground true

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2725_002_volume_map_sharp.mrc""

Opened cryosparc_P120_J2725_002_volume_map_sharp.mrc as #15, grid size
100,100,100, pixel 2.09, shown at level 3.77, step 1, values float32  

> tile off

> view initial

> view orient

> hide #!10 models

> hide #!11 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> volume #15 level 6.365

> view orient

> turn y -90

> turn x -90

> turn y -90

> volume #15 level 7.107

> volume #15 level 6.489

> color #b2b2b2

> color #B2B2B2

> save J2725_NUref_coll3.png supersample 3 transparentBackground true

> hide #!15 models

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2527_class_02_00182_volume.mrc""

Opened cryosparc_P120_J2527_class_02_00182_volume.mrc as #16, grid size
128,128,128, pixel 1.63, shown at level 0.103, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2527_class_04_00182_volume.mrc""

Opened cryosparc_P120_J2527_class_04_00182_volume.mrc as #17, grid size
128,128,128, pixel 1.63, shown at level 0.0987, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2527_class_03_00182_volume.mrc""

Opened cryosparc_P120_J2527_class_03_00182_volume.mrc as #18, grid size
128,128,128, pixel 1.63, shown at level 0.0985, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2527_class_01_00182_volume.mrc""

Opened cryosparc_P120_J2527_class_01_00182_volume.mrc as #19, grid size
128,128,128, pixel 1.63, shown at level 0.0976, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2527_class_00_00182_volume.mrc""

Opened cryosparc_P120_J2527_class_00_00182_volume.mrc as #20, grid size
128,128,128, pixel 1.63, shown at level 0.117, step 1, values float32  

> view initial

> tile

5 models tiled  

> lighting soft

> color #B2B2B2

> volume #20 level 0.1445

> volume #19 level 0.1343

> volume #18 level 0.1302

> volume #17 level 0.128

> volume #16 level 0.1298

> save J2527_hetero_coll2.png supersample 3 transparentBackground true

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2537_class_04_00142_volume.mrc""

Opened cryosparc_P120_J2537_class_04_00142_volume.mrc as #21, grid size
128,128,128, pixel 1.63, shown at level 0.112, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2537_class_03_00142_volume.mrc""

Opened cryosparc_P120_J2537_class_03_00142_volume.mrc as #22, grid size
128,128,128, pixel 1.63, shown at level 0.114, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2537_class_02_00142_volume.mrc""

Opened cryosparc_P120_J2537_class_02_00142_volume.mrc as #23, grid size
128,128,128, pixel 1.63, shown at level 0.116, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2537_class_01_00142_volume.mrc""

Opened cryosparc_P120_J2537_class_01_00142_volume.mrc as #24, grid size
128,128,128, pixel 1.63, shown at level 0.112, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2537_class_00_00142_volume.mrc""

Opened cryosparc_P120_J2537_class_00_00142_volume.mrc as #25, grid size
128,128,128, pixel 1.63, shown at level 0.116, step 1, values float32  

> hide #!16 models

> hide #!17 models

> hide #!18 models

> hide #!19 models

> hide #!20 models

> hide #!21 models

> show #!21 models

> view initial

> select ~sel & ##selected

Nothing selected  

> tile off

> tile

5 models tiled  

> lighting soft

> volume #25 level 0.1585

> volume #24 level 0.1873

> volume #23 level 0.1609

> volume #22 level 0.1615

> volume #21 level 0.149

> save J2537_hetero_coll2.png supersample 3 transparentBackground true

> color #B2B2B2

> save J2537_hetero_coll2.png supersample 3 transparentBackground true

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2540_006_volume_map_sharp.mrc""

Opened cryosparc_P120_J2540_006_volume_map_sharp.mrc as #26, grid size
200,200,200, pixel 1.04, shown at level 0.0843, step 1, values float32  

> view initial

> tile off

> hide #!21 models

> hide #!22 models

> hide #!23 models

> hide #!24 models

> hide #!25 models

> select down

Nothing selected  

> save J2537_hetero_coll2.png supersample 3 transparentBackground true

> select down

Nothing selected  

> color #B2B2B2

> volume #26 level 0.162

> save J2540_NUref_coll2.png supersample 3 transparentBackground true

> hide #!26 models

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2484_class_04_00202_volume.mrc""

Opened cryosparc_P120_J2484_class_04_00202_volume.mrc as #27, grid size
128,128,128, pixel 1.63, shown at level 0.103, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2484_class_03_00202_volume.mrc""

Opened cryosparc_P120_J2484_class_03_00202_volume.mrc as #28, grid size
128,128,128, pixel 1.63, shown at level 0.104, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2484_class_02_00202_volume.mrc""

Opened cryosparc_P120_J2484_class_02_00202_volume.mrc as #29, grid size
128,128,128, pixel 1.63, shown at level 0.0963, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2484_class_01_00202_volume.mrc""

Opened cryosparc_P120_J2484_class_01_00202_volume.mrc as #30, grid size
128,128,128, pixel 1.63, shown at level 0.0965, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2484_class_00_00202_volume.mrc""

Opened cryosparc_P120_J2484_class_00_00202_volume.mrc as #31, grid size
128,128,128, pixel 1.63, shown at level 0.0877, step 1, values float32  

> view initial

> tile

5 models tiled  

> lighting soft

> color #B2B2B2

> volume #31 level 0.1001

> volume #30 level 0.1265

> volume #29 level 0.1236

> volume #28 level 0.1249

> volume #27 level 0.1298

> volume #26 level 0.166

> volume #27 level 0.1338

> volume #28 level 0.1349

> volume #29 level 0.1353

> save J2484_hetero_coll1.png supersample 3 transparentBackground true

> hide #!27 models

> hide #!28 models

> hide #!29 models

> hide #!30 models

> hide #!31 models

> tile off

No models found for tiling.  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2506_class_04_00122_volume.mrc""

Opened cryosparc_P120_J2506_class_04_00122_volume.mrc as #32, grid size
128,128,128, pixel 1.63, shown at level 0.101, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2506_class_03_00122_volume.mrc""

Opened cryosparc_P120_J2506_class_03_00122_volume.mrc as #33, grid size
128,128,128, pixel 1.63, shown at level 0.101, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2506_class_02_00122_volume.mrc""

Opened cryosparc_P120_J2506_class_02_00122_volume.mrc as #34, grid size
128,128,128, pixel 1.63, shown at level 0.102, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2506_class_01_00122_volume.mrc""

Opened cryosparc_P120_J2506_class_01_00122_volume.mrc as #35, grid size
128,128,128, pixel 1.63, shown at level 0.102, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2506_class_00_00122_volume.mrc""

Opened cryosparc_P120_J2506_class_00_00122_volume.mrc as #36, grid size
128,128,128, pixel 1.63, shown at level 0.11, step 1, values float32  

> tile off

> tile

5 models tiled  

> volume #36 level 0.1621

> tile

5 models tiled  

> tile spacingFactor 1

5 models tiled  

> tile spacingFactor 1.1

5 models tiled  

> volume #35 level 0.1622

> volume #34 level 0.1792

> volume #33 level 0.1406

> volume #32 level 0.1384

> color #B2B2B2

> lighting soft

> tile spacingFactor 1

5 models tiled  

> tile spacingFactor 1.1

5 models tiled  

> lighting soft

> save J2506_hetero_coll1.png supersample 3 transparentBackground true

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2530_005_volume_map_sharp.mrc""

Opened cryosparc_P120_J2530_005_volume_map_sharp.mrc as #37, grid size
200,200,200, pixel 1.04, shown at level 0.0821, step 1, values float32  

> tile off

> view initial

> hide #!32 models

> hide #!33 models

> hide #!34 models

> hide #!35 models

> hide #!36 models

> volume #37 level 0.1758

> color #B2B2B2

> lighting soft

> save J2530_NUref_coll1.png supersample 3 transparentBackground true

> hide #!37 models

> show #!27 models

> show #!28 models

> show #!29 models

> show #!30 models

> show #!31 models

> tile

5 models tiled  

> lighting soft

> hide #!28 models

> show #!28 models

> hide #!29 models

> hide #!31 models

> hide #!27 models

> hide #!28 models

> hide #!30 models

> show #!16 models

> show #!17 models

> show #!18 models

> show #!19 models

> show #!20 models

> tile

5 models tiled  

> lighting soft

> hide #!16 models

> hide #!19 models

> hide #!18 models

> hide #!17 models

> hide #!20 models

> show #!5 models

> show #!6 models

> show #!7 models

> show #!8 models

> show #!9 models

> tile

5 models tiled  

> lighting soft

> hide #!5 models

> hide #!9 models

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2756_004_volume_map_sharp.mrc""

Opened cryosparc_P120_J2756_004_volume_map_sharp.mrc as #38, grid size
200,200,200, pixel 1.04, shown at level 0.0777, step 1, values float32  

> tile off

> hide #!8 models

> hide #!7 models

> hide #!6 models

> volume #38 level 0.156

> view orient

> turn x -90

> turn y 90

> color #b2b2b2

> save J2756_NUref_merged.png supersample 3 transparentBackground true

> hide #!38 models

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2809_class_02_final_volume.mrc""

Opened cryosparc_P120_J2809_class_02_final_volume.mrc as #39, grid size
200,200,200, pixel 1.04, shown at level 0.029, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2809_class_01_final_volume.mrc""

Opened cryosparc_P120_J2809_class_01_final_volume.mrc as #40, grid size
200,200,200, pixel 1.04, shown at level 0.0522, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2809_class_00_final_volume.mrc""

Opened cryosparc_P120_J2809_class_00_final_volume.mrc as #41, grid size
200,200,200, pixel 1.04, shown at level 0.0322, step 1, values float32  

> view

> view initial

> tile

3 models tiled  

> lighting soft

> key pos 0.939082,0.123641 size 0.0096127,0.0246367

> tile columns 3

3 models tiled  

> volume #40 level 0.1011

> tile columns 3 spacingFactor 1

3 models tiled  

> volume #41 level 0.04092

> volume #39 level 0.03316

> lighting soft

> volume #40 level 0.1175

> color #b2b2b2

> tile columns 3 spacingFactor 0.9

3 models tiled  

> lighting soft

> tile columns 3 spacingFactor 1

3 models tiled  

> lighting soft

> save J2809_abInit_merged.png supersample 3 transparentBackground true

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2758_class_02_final_volume.mrc""

Opened cryosparc_P120_J2758_class_02_final_volume.mrc as #42, grid size
200,200,200, pixel 1.04, shown at level 0.0319, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2758_class_01_final_volume.mrc""

Opened cryosparc_P120_J2758_class_01_final_volume.mrc as #43, grid size
200,200,200, pixel 1.04, shown at level 0.0299, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2758_class_00_final_volume.mrc""

Opened cryosparc_P120_J2758_class_00_final_volume.mrc as #44, grid size
200,200,200, pixel 1.04, shown at level 0.0439, step 1, values float32  

> hide #!39 models

> hide #!40 models

> hide #!41 models

> tile columns 3 spacingFactor 1

3 models tiled  

> tile columns 3

3 models tiled  

> color #b2b2b2

> volume #43 level 0.06142

> volume #44 level 0.05758

> volume #42 level 0.04794

> lighting soft

> volume #43 level 0.06482

> volume #42 level 0.0565

> volume #44 level 0.06123

> volume #43 level 0.06738

> volume #42 level 0.05436

> save J2758_abInit_merged.png supersample 3 transparentBackground true

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2759_class_02_01600_volume.mrc""

Opened cryosparc_P120_J2759_class_02_01600_volume.mrc as #45, grid size
128,128,128, pixel 1.63, shown at level 0.0632, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2759_class_01_01600_volume.mrc""

Opened cryosparc_P120_J2759_class_01_01600_volume.mrc as #46, grid size
128,128,128, pixel 1.63, shown at level 0.0884, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2759_class_00_01600_volume.mrc""

Opened cryosparc_P120_J2759_class_00_01600_volume.mrc as #47, grid size
128,128,128, pixel 1.63, shown at level 0.0662, step 1, values float32  

> hide #!42 models

> hide #!43 models

> hide #!44 models

> tile off

> view initial

> tile columns 3

3 models tiled  

> lighting soft

> color #b2b2b2

> volume #46 level 0.1341

> volume #47 level 0.1393

> volume #45 level 0.1553

> volume #45 level 0.1653

> volume #47 level 0.1451

> volume #46 level 0.1382

> save J2759_abInit_merged.png supersample 3 transparentBackground true

> view initial

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2812_class_01_final_volume.mrc""

Opened cryosparc_P120_J2812_class_01_final_volume.mrc as #48, grid size
200,200,200, pixel 1.04, shown at level 0.049, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2812_class_00_final_volume.mrc""

Opened cryosparc_P120_J2812_class_00_final_volume.mrc as #49, grid size
200,200,200, pixel 1.04, shown at level 0.0516, step 1, values float32  

> view

> tile

2 models tiled  

> volume #48 level 0.1112

> volume #49 level 0.1113

> lighting soft

> volume #49 level 0.09486

> volume #48 level 0.1286

> volume #49 level 0.1113

> color #b2b2b2

> save J2812_abInit_merged_k2.png supersample 3 transparentBackground true

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2813_class_01_final_volume.mrc""

Opened cryosparc_P120_J2813_class_01_final_volume.mrc as #50, grid size
200,200,200, pixel 1.04, shown at level 0.0509, step 1, values float32  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2813_class_00_final_volume.mrc""

Opened cryosparc_P120_J2813_class_00_final_volume.mrc as #51, grid size
200,200,200, pixel 1.04, shown at level 0.0423, step 1, values float32  

> hide #!48 models

> hide #!49 models

> view initial

> tile

2 models tiled  

> volume #50 level 0.09709

> lighting soft

> volume #51 level 0.08004

> volume #50 level 0.1086

> color #b2b2b2

> save J2813_abInit_merged_k2.png supersample 3 transparentBackground true

> save ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/240805_NC36_processing.cxs""

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/240801_C11_processing.cxs""
> format session

> ui mousemode right translate

Opened cryosparc_P120_cryosparc_P120_J2126_class_05_00202_volume.mrc as #1,
grid size 256,256,256, pixel 1.15, shown at level 0.0983, step 1, values
float32  
Opened cryosparc_P120_cryosparc_P120_J2126_class_04_00202_volume.mrc as #2,
grid size 256,256,256, pixel 1.15, shown at level 0.103, step 1, values
float32  
Opened cryosparc_P120_cryosparc_P120_J2126_class_03_00202_volume.mrc as #3,
grid size 256,256,256, pixel 1.15, shown at level 0.104, step 1, values
float32  
Opened cryosparc_P120_cryosparc_P120_J2126_class_02_00202_volume.mrc as #4,
grid size 256,256,256, pixel 1.15, shown at level 0.128, step 1, values
float32  
Opened cryosparc_P120_cryosparc_P120_J2126_class_01_00202_volume.mrc as #5,
grid size 256,256,256, pixel 1.15, shown at level 0.149, step 1, values
float32  
Opened cryosparc_P120_cryosparc_P120_J2126_class_00_00202_volume.mrc as #6,
grid size 256,256,256, pixel 1.15, shown at level 0.109, step 1, values
float32  
Opened cryosparc_P120_cryosparc_P120_J2136_class_02_final_volume.mrc as #13,
grid size 256,256,256, pixel 1.15, shown at level 0.202, step 1, values
float32  
Opened cryosparc_P120_cryosparc_P120_J2136_class_01_final_volume.mrc as #14,
grid size 256,256,256, pixel 1.15, shown at level 0.212, step 1, values
float32  
Opened cryosparc_P120_cryosparc_P120_J2136_class_00_final_volume.mrc as #15,
grid size 256,256,256, pixel 1.15, shown at level 0.219, step 1, values
float32  
Opened cryosparc_P120_cryosparc_P120_J2132_class_00_00162_volume.mrc as #7,
grid size 256,256,256, pixel 1.15, shown at level 0.162, step 1, values
float32  
Opened cryosparc_P120_cryosparc_P120_J2132_class_05_00162_volume.mrc as #12,
grid size 256,256,256, pixel 1.15, shown at level 0.133, step 1, values
float32  
Opened cryosparc_P120_cryosparc_P120_J2132_class_04_00162_volume.mrc as #8,
grid size 256,256,256, pixel 1.15, shown at level 0.128, step 1, values
float32  
Opened cryosparc_P120_cryosparc_P120_J2132_class_03_00162_volume.mrc as #9,
grid size 256,256,256, pixel 1.15, shown at level 0.124, step 1, values
float32  
Opened cryosparc_P120_cryosparc_P120_J2132_class_02_00162_volume.mrc as #10,
grid size 256,256,256, pixel 1.15, shown at level 0.114, step 1, values
float32  
Opened cryosparc_P120_cryosparc_P120_J2132_class_01_00162_volume.mrc as #11,
grid size 256,256,256, pixel 1.15, shown at level 0.0912, step 1, values
float32  
Opened cryosparc_P120_cryosparc_P120_J2140_006_volume_map_sharp.mrc as #16,
grid size 256,256,256, pixel 1.15, shown at level 0.279, step 1, values
float32  
Opened cryosparc_P120_cryosparc_P120_J2142_010_volume_map_sharp.mrc as #17,
grid size 256,256,256, pixel 1.15, shown at level 0.397, step 1, values
float32  
Opened cryosparc_P120_cryosparc_P120_J2146_006_volume_map_sharp.mrc as #18,
grid size 256,256,256, pixel 1.15, shown at level 0.399, step 1, values
float32  
Opened cryosparc_P120_cryosparc_P120_J2188_cluster_000.mrc as #19, grid size
256,256,256, pixel 1.15, shown at level 0.0801, step 1, values float32  
Opened cryosparc_P120_J2188_cluster_001.mrc as #20, grid size 256,256,256,
pixel 1.15, shown at level 0.108, step 1, values float32  
Opened cryosparc_P120_J2188_cluster_002.mrc as #21, grid size 256,256,256,
pixel 1.15, shown at level 0.101, step 1, values float32  
Opened cryosparc_P120_J2188_cluster_003.mrc as #22, grid size 256,256,256,
pixel 1.15, shown at level 0.0954, step 1, values float32  
Opened cryosparc_P120_J2188_cluster_004.mrc as #23, grid size 256,256,256,
pixel 1.15, shown at level 0.0801, step 1, values float32  
Opened cryosparc_P120_J2235_map_locres.mrc as #24, grid size 256,256,256,
pixel 1.15, shown at level 2.98, step 1, values float32  
Opened cryosparc_P120_J2190_007_volume_map_sharp.mrc as #25, grid size
256,256,256, pixel 1.15, shown at level 0.35, step 1, values float32  
Opened cryosparc_P120_cryosparc_P120_J2157_007_volume_map.mrc as #27, grid
size 256,256,256, pixel 1.15, shown at level 0.248, step 1, values float32  
Opened cryosparc_P120_J2157_007_volume_map_sharp.mrc as #28, grid size
256,256,256, pixel 1.15, shown at level 0.281, step 1, values float32  
opened ChimeraX session  

> hide #!30 models

> show #!29 models

> hide #!29 models

> show #!28 models

> hide #!28 models

> show #!28 models

> hide #!28 models

> show #!2 models

> show #!1 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #!6 models

> tile

6 models tiled  

> tile columns 6

6 models tiled  

> hide #!6 models

> hide #!3 models

> hide #!2 models

> show #!6 models

> hide #!6 models

> hide #!4 models

> hide #!5 models

> hide #!1 models

> show #!20 models

> show #!22 models

> show #!19 models

> show #!21 models

> show #!23 models

> tile columns 5

5 models tiled  

> voltroff

> lighting soft

> hide #!20 models

> hide #!22 models

> show #!22 models

> show #!20 models

> hide #!20 models

> hide #!22 models

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/240805_NC36_processing.cxs""
> format session

Opened cryosparc_P120_J2922_005_volume_mask_refine.mrc as #1, grid size
200,200,200, pixel 1.04, shown at level 1, step 1, values float32  
Opened cryosparc_P120_J2922_005_volume_map_sharp.mrc as #2, grid size
200,200,200, pixel 1.04, shown at level 0.17, step 1, values float32  
Opened cryosparc_P120_J3552_map_locres.mrc as #3, grid size 200,200,200, pixel
1.04, shown at level 2.8, step 1, values float32  
Opened cryosparc_P120_J2704_class_04_00162_volume.mrc as #5, grid size
100,100,100, pixel 2.09, shown at level 0.2, step 1, values float32  
Opened cryosparc_P120_J2704_class_03_00162_volume.mrc as #6, grid size
100,100,100, pixel 2.09, shown at level 0.2, step 1, values float32  
Opened cryosparc_P120_J2704_class_02_00162_volume.mrc as #7, grid size
100,100,100, pixel 2.09, shown at level 0.2, step 1, values float32  
Opened cryosparc_P120_J2704_class_01_00162_volume.mrc as #8, grid size
100,100,100, pixel 2.09, shown at level 0.2, step 1, values float32  
Opened cryosparc_P120_J2704_class_00_00162_volume.mrc as #9, grid size
100,100,100, pixel 2.09, shown at level 0.2, step 1, values float32  
Opened cryosparc_P120_J2723_class_04_00122_volume.mrc as #10, grid size
100,100,100, pixel 2.09, shown at level 0.215, step 1, values float32  
Opened cryosparc_P120_J2723_class_03_00122_volume.mrc as #11, grid size
100,100,100, pixel 2.09, shown at level 0.235, step 1, values float32  
Opened cryosparc_P120_J2723_class_02_00122_volume.mrc as #12, grid size
100,100,100, pixel 2.09, shown at level 0.26, step 1, values float32  
Opened cryosparc_P120_J2723_class_01_00122_volume.mrc as #13, grid size
100,100,100, pixel 2.09, shown at level 0.252, step 1, values float32  
Opened cryosparc_P120_J2723_class_00_00122_volume.mrc as #14, grid size
100,100,100, pixel 2.09, shown at level 0.204, step 1, values float32  
Opened cryosparc_P120_J2725_002_volume_map_sharp.mrc as #15, grid size
100,100,100, pixel 2.09, shown at level 6.49, step 1, values float32  
Opened cryosparc_P120_J2527_class_02_00182_volume.mrc as #16, grid size
128,128,128, pixel 1.63, shown at level 0.13, step 1, values float32  
Opened cryosparc_P120_J2527_class_04_00182_volume.mrc as #17, grid size
128,128,128, pixel 1.63, shown at level 0.128, step 1, values float32  
Opened cryosparc_P120_J2527_class_03_00182_volume.mrc as #18, grid size
128,128,128, pixel 1.63, shown at level 0.13, step 1, values float32  
Opened cryosparc_P120_J2527_class_01_00182_volume.mrc as #19, grid size
128,128,128, pixel 1.63, shown at level 0.134, step 1, values float32  
Opened cryosparc_P120_J2527_class_00_00182_volume.mrc as #20, grid size
128,128,128, pixel 1.63, shown at level 0.144, step 1, values float32  
Opened cryosparc_P120_J2537_class_04_00142_volume.mrc as #21, grid size
128,128,128, pixel 1.63, shown at level 0.149, step 1, values float32  
Opened cryosparc_P120_J2537_class_03_00142_volume.mrc as #22, grid size
128,128,128, pixel 1.63, shown at level 0.162, step 1, values float32  
Opened cryosparc_P120_J2537_class_02_00142_volume.mrc as #23, grid size
128,128,128, pixel 1.63, shown at level 0.161, step 1, values float32  
Opened cryosparc_P120_J2537_class_01_00142_volume.mrc as #24, grid size
128,128,128, pixel 1.63, shown at level 0.187, step 1, values float32  
Opened cryosparc_P120_J2537_class_00_00142_volume.mrc as #25, grid size
128,128,128, pixel 1.63, shown at level 0.159, step 1, values float32  
Opened cryosparc_P120_J2540_006_volume_map_sharp.mrc as #26, grid size
200,200,200, pixel 1.04, shown at level 0.166, step 1, values float32  
Opened cryosparc_P120_J2484_class_04_00202_volume.mrc as #27, grid size
128,128,128, pixel 1.63, shown at level 0.134, step 1, values float32  
Opened cryosparc_P120_J2484_class_03_00202_volume.mrc as #28, grid size
128,128,128, pixel 1.63, shown at level 0.135, step 1, values float32  
Opened cryosparc_P120_J2484_class_02_00202_volume.mrc as #29, grid size
128,128,128, pixel 1.63, shown at level 0.135, step 1, values float32  
Opened cryosparc_P120_J2484_class_01_00202_volume.mrc as #30, grid size
128,128,128, pixel 1.63, shown at level 0.127, step 1, values float32  
Opened cryosparc_P120_J2484_class_00_00202_volume.mrc as #31, grid size
128,128,128, pixel 1.63, shown at level 0.1, step 1, values float32  
Opened cryosparc_P120_J2506_class_04_00122_volume.mrc as #32, grid size
128,128,128, pixel 1.63, shown at level 0.138, step 1, values float32  
Opened cryosparc_P120_J2506_class_03_00122_volume.mrc as #33, grid size
128,128,128, pixel 1.63, shown at level 0.141, step 1, values float32  
Opened cryosparc_P120_J2506_class_02_00122_volume.mrc as #34, grid size
128,128,128, pixel 1.63, shown at level 0.179, step 1, values float32  
Opened cryosparc_P120_J2506_class_01_00122_volume.mrc as #35, grid size
128,128,128, pixel 1.63, shown at level 0.162, step 1, values float32  
Opened cryosparc_P120_J2506_class_00_00122_volume.mrc as #36, grid size
128,128,128, pixel 1.63, shown at level 0.162, step 1, values float32  
Opened cryosparc_P120_J2530_005_volume_map_sharp.mrc as #37, grid size
200,200,200, pixel 1.04, shown at level 0.176, step 1, values float32  
Opened cryosparc_P120_J2756_004_volume_map_sharp.mrc as #38, grid size
200,200,200, pixel 1.04, shown at level 0.156, step 1, values float32  
Opened cryosparc_P120_J2809_class_02_final_volume.mrc as #39, grid size
200,200,200, pixel 1.04, shown at level 0.0332, step 1, values float32  
Opened cryosparc_P120_J2809_class_01_final_volume.mrc as #40, grid size
200,200,200, pixel 1.04, shown at level 0.117, step 1, values float32  
Opened cryosparc_P120_J2809_class_00_final_volume.mrc as #41, grid size
200,200,200, pixel 1.04, shown at level 0.0409, step 1, values float32  
Opened cryosparc_P120_J2758_class_02_final_volume.mrc as #42, grid size
200,200,200, pixel 1.04, shown at level 0.0544, step 1, values float32  
Opened cryosparc_P120_J2758_class_01_final_volume.mrc as #43, grid size
200,200,200, pixel 1.04, shown at level 0.0674, step 1, values float32  
Opened cryosparc_P120_J2758_class_00_final_volume.mrc as #44, grid size
200,200,200, pixel 1.04, shown at level 0.0612, step 1, values float32  
Opened cryosparc_P120_J2759_class_02_01600_volume.mrc as #45, grid size
128,128,128, pixel 1.63, shown at level 0.165, step 1, values float32  
Opened cryosparc_P120_J2759_class_01_01600_volume.mrc as #46, grid size
128,128,128, pixel 1.63, shown at level 0.138, step 1, values float32  
Opened cryosparc_P120_J2759_class_00_01600_volume.mrc as #47, grid size
128,128,128, pixel 1.63, shown at level 0.145, step 1, values float32  
Opened cryosparc_P120_J2812_class_01_final_volume.mrc as #48, grid size
200,200,200, pixel 1.04, shown at level 0.129, step 1, values float32  
Opened cryosparc_P120_J2812_class_00_final_volume.mrc as #49, grid size
200,200,200, pixel 1.04, shown at level 0.111, step 1, values float32  
Opened cryosparc_P120_J2813_class_01_final_volume.mrc as #50, grid size
200,200,200, pixel 1.04, shown at level 0.109, step 1, values float32  
Opened cryosparc_P120_J2813_class_00_final_volume.mrc as #51, grid size
200,200,200, pixel 1.04, shown at level 0.08, step 1, values float32  
opened ChimeraX session  

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2811_005_volume_map_sharp.mrc""

Opened cryosparc_P120_J2811_005_volume_map_sharp.mrc as #52, grid size
200,200,200, pixel 1.04, shown at level 0.0736, step 1, values float32  

> hide #!50 models

> hide #!51 models

> tile off

> view

> view initial

> volume #52 level 0.1573

> volume #52 level 0.1693

> view orient

> turn x -90

> turn y 90

> save J2811_NUref_merged.png supersample 3 transparentBackground true

> show #4 models

> hide #!52 models

> ui tool show ""Color Key""

> ui mousemode right ""color key""

> key pos 0.504457,0.0682585 size 0.0474474,0.830529

> save J2922_locresJ3552_colorkey.png supersample 3 transparentBackground true

> save ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/240805_NC36_processing_v2.cxs""

> open ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig3_cryoEM/final_maps_models/240709_zfO1_final_structures_maps_comparison_12.cxs""

> ui mousemode right translate

Opened emd_9360.map as #1, grid size 200,200,200, pixel 1.03, shown at level
3.67, step 1, values float32  
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc as #3,
grid size 256,256,256, pixel 1.15, shown at level 0.35, step 1, values float32  
Opened
zfO1_C11_1mM_final_cryosparc_P120_cryosparc_P120_J2190_007_volume_map.mrc as
#4, grid size 256,256,256, pixel 1.15, shown at level 0.176, step 1, values
float32  
Opened zfO1_NC2_1mM_final_cryosparc_P120_J3308_008_volume_map.mrc as #7, grid
size 200,200,200, pixel 1.07, shown at level 0.34, step 1, values float32  
Opened zfO1_NC2_1mM_final_cryosparc_P120_J3308_008_volume_map_sharp.mrc as #8,
grid size 200,200,200, pixel 1.07, shown at level 0.272, step 1, values
float32  
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map.mrc as #11,
grid size 200,200,200, pixel 1.07, shown at level 0.242, step 1, values
float32  
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc as
#12, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32  
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map.mrc as #15,
grid size 200,200,200, pixel 1.04, shown at level 0.0979, step 1, values
float32  
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc as
#16, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32  
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 0 as
#25.1, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32  
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 1 as
#25.2, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32  
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 2 as
#25.3, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32  
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 3 as
#25.4, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32  
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 4 as
#25.5, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32  
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 5 as
#25.6, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32  
Opened emd_9360.map 0 as #24.1, grid size 200,200,200, pixel 1.03, shown at
level 3.67, step 1, values float32  
Opened emd_9360.map 1 as #24.2, grid size 200,200,200, pixel 1.03, shown at
level 3.67, step 1, values float32  
Opened emd_9360.map 2 as #24.3, grid size 200,200,200, pixel 1.03, shown at
level 3.67, step 1, values float32  
Opened emd_9360.map 3 as #24.4, grid size 200,200,200, pixel 1.03, shown at
level 3.67, step 1, values float32  
Opened emd_9360.map 4 as #24.5, grid size 200,200,200, pixel 1.03, shown at
level 3.67, step 1, values float32  
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 0 as
#31.1, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values
float32  
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 1 as
#31.2, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values
float32  
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 2 as
#31.3, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values
float32  
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 3 as
#31.4, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values
float32  
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 4 as
#31.5, grid size 256,256,256, pixel 1.15, shown at level 0.35, step 1, values
float32  
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 5 as
#31.6, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values
float32  
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 0 as
#30.1, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32  
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 1 as
#30.2, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32  
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 2 as
#30.3, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32  
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 3 as
#30.4, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32  
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 4 as
#30.5, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32  
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 5 as
#30.6, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32  
opened ChimeraX session  

> view

> hide #!17 models

> hide #!5 models

> hide #!2 models

> show #!2 models

> show #!9 models

> hide #!9 models

> show #!13 models

> hide #!2 models

> select add #13

6846 atoms, 7036 bonds, 18 pseudobonds, 800 residues, 3 models selected  

> show #14 surfaces

> show #!14 models

> select subtract #13

Nothing selected  

> hide #!13 models

> hide #!14 models

> show #!14 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!14 models

> show #!14 models

> surface #14 transparency 0

> hide #14/B target s

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

37 atoms, 38 bonds, 1 residue, 1 model selected  

> show sphere sel

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show sel sphere

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> atom sel style phere

Unknown command: atom sel style phere  

> atom sel style sphere

Unknown command: atom sel style sphere  

> style sel sphere

Changed 37 atom styles  

> select clear

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> show #2/A surfaces

> show #!2 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> hide #!2 models

> style #13:NC2 stick

Changed 296 atom styles  

> select clear

> hide HC

> view list

Named views: 570central_modelComp2, CHS_in_dens_central, CLR_in_outer_molOnly,
C_dom_pocket_mirror2docked, C_domonly_side_comparison, Cdom_pocket,
F570_central_NC36_2copies_modelComp_view, F570central_densityComp,
F570central_modelComp, F570central_modelComp2, F570central_resi_comp,
F570central_site_allModels, F570outer, F570outer_resi_comp,
F570outer_site_modelComp2, NC2_central_molOnly, NC2_outer_molOnly,
NC36_in_Dens_outer, NC36_in_dens_central, N_dom_side_comparison,
N_domonly_side_comparison, all_models_aligned_Cdompocket_models,
all_models_aligned_F570central_models,
all_models_aligned_F570outer_site_models, c11_in_dens_Cdom,
c11_in_dens_central, central_site_45, outer_site_45, side_view,
side_view_NdomAligned, side_view_models, top_view  

> view F570outer_resi_comp

> view F570outer

> view F570outer_site_modelComp2

> camera mono

> show #!2 models

> hide #!13 models

> hide #2 surfaces

> show #!13 models

> hide #!2 models

> show #!2 models

> hide #!13 models

> show #!13 models

> hide #!2 models

> show #!23 models

> ui tool show Distances

> select #13/A:267@OE2

1 atom, 1 residue, 1 model selected  

> select add #13/A:609@O14

2 atoms, 2 residues, 1 model selected  

> distance #13/A:267@OE2 #13/A:609@O14

Distance already exists; modify distance properties with 'distance style'  

> show #23.1 models

> hide #23.1 models

> show #23.1 models

> show #23 target p

> show #!12 models

> hide #!12 models

> lighting simple

> lighting soft

> hide #13/A:111-140 target c

> show #13/A:111-140 target c

> transparency #13/A:111-140 0.9 target c

> transparency #13/A:111-140 90 target c

> hide #23.1 models

> show #!2 models

> hide #!13 models

> select add #13

6846 atoms, 7036 bonds, 18 pseudobonds, 800 residues, 3 models selected  

> select subtract #13

Nothing selected  

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!2 models

> hide #13/A:111-140 target c

> hide #13/A:111-140:C,CA,N,O

> show #13/A:111-140:C,CA,N,O

> hide #!13 cartoons

> show #!13 cartoons

> show #13/A:111-140@C,CA,N,O

> hide #13/A:111-140@C,CA,N,O

> hide #13/A:111-140 target c

> show #13/A:111-140 target c

> show #13/A:111-140@C,CA,N,O

> hide #13:CLR,CHS

> select clear

> view name outer_site_NC2_flat_view

> lighting soft

> preset ""overall look"" ""publication 1 (silhouettes)""

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> lighting soft

> lighting simple

> lighting soft

> preset ""overall look"" ""publication 1 (silhouettes)""

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> select ~sel & ##selected

Nothing selected  

> view outer_site_NC2_flat_view

> show #23.1 models

> hide #23.1 models

> show #23.1 models

> hide #23.1 models

> pwd

Current working directory is: /Users/bburendei/Dropbox (Scripps
Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing  

> cd ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig3_cryoEM""

Current working directory is: /Users/bburendei/Dropbox (Scripps
Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig3_cryoEM  

> save outer_site_NC2_flatView_2HBs.png supersample 3 transparentBackground
> true

> turn y 180

> transparency #13 0 target c

> save outer_site_NC2_flatView_2HBs_fromCdom.png supersample 3
> transparentBackground true

> cd images

Current working directory is: /Users/bburendei/Dropbox (Scripps
Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig3_cryoEM/images  

> view list

Named views: 570central_modelComp2, CHS_in_dens_central, CLR_in_outer_molOnly,
C_dom_pocket_mirror2docked, C_domonly_side_comparison, Cdom_pocket,
F570_central_NC36_2copies_modelComp_view, F570central_densityComp,
F570central_modelComp, F570central_modelComp2, F570central_resi_comp,
F570central_site_allModels, F570outer, F570outer_resi_comp,
F570outer_site_modelComp2, NC2_central_molOnly, NC2_outer_molOnly,
NC36_in_Dens_outer, NC36_in_dens_central, N_dom_side_comparison,
N_domonly_side_comparison, all_models_aligned_Cdompocket_models,
all_models_aligned_F570central_models,
all_models_aligned_F570outer_site_models, c11_in_dens_Cdom,
c11_in_dens_central, central_site_45, outer_site_45, outer_site_NC2_flat_view,
side_view, side_view_NdomAligned, side_view_models, top_view  

> view outer_site_NC2_flat_view

> view F570central_densityComp

> view F570central_resi_comp

> view F570central_modelComp2

> hide #13:Y01

> hide #!23 models

> show #!23 models

> show #!2 models

> view F570central_modelComp

> view F570central_densityComp

> view F570central_resi_comp

> view F570central_modelComp2

> hide #!2 models

> hide #!23 models

> show #!23 models

> select #13/A:607@H181

1 atom, 1 residue, 1 model selected  

> select #13/A:384@OE1

1 atom, 1 residue, 1 model selected  

> select add #13/A:607@H181

2 atoms, 2 residues, 1 model selected  

> distance #13/A:384@OE1 #13/A:607@H181

Distance between zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb #13/A
GLU 384 OE1 and NC2 607 H181: 2.037Å  

> show #23.1 models

> hide #23.1 models

> show #23.1 models

> show #!12 models

> hide #!12 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!13 models

> show #!13 models

> style sel sphere

Changed 2 atom styles  

> style sel sphere

Changed 2 atom styles  

> style sel stick

Changed 2 atom styles  

> select clear

> select add #13

6846 atoms, 7036 bonds, 19 pseudobonds, 800 residues, 3 models selected  

> style sel sphere

Changed 6846 atom styles  

> style sel stick

Changed 6846 atom styles  

> style sel ball

Changed 6846 atom styles  

> style sel stick

Changed 6846 atom styles  

> style sel sphere

Changed 6846 atom styles  

> lighting simple

> style sel stick

Changed 6846 atom styles  

> lighting soft

> select clear

> select #13/A:278@CB

1 atom, 1 residue, 1 model selected  

> select add #13/A:381@CG

2 atoms, 2 residues, 1 model selected  

> distance #13/A:278@CB #13/A:381@CG

Distance between zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb #13/A
VAL 278 CB and LEU 381 CG: 5.537Å  

> select add #13/A:275@CE

3 atoms, 3 residues, 1 model selected  

> select clear

> select #13/A:275@CE

1 atom, 1 residue, 1 model selected  

> select add #13/A:385@CG

2 atoms, 2 residues, 1 model selected  

> select subtract #13/A:385@CG

1 atom, 1 residue, 1 model selected  

> select add #13/A:385@CG

2 atoms, 2 residues, 1 model selected  

> select clear

> select add #13/A:385@CG

1 atom, 1 residue, 1 model selected  

> select add #13/A:275@CE

2 atoms, 2 residues, 1 model selected  

> distance #13/A:385@CG #13/A:275@CE

Distance between zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb #13/A
LEU 385 CG and MET 275 CE: 4.390Å  

> show HC

> hide HC

> select clear

> select #13/A:281@NZ

1 atom, 1 residue, 1 model selected  

> select add #13/A:607@O14

2 atoms, 2 residues, 1 model selected  

> distance #13/A:281@NZ #13/A:607@O14

Distance between zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb #13/A
LYS 281 NZ and NC2 607 O14: 4.723Å  

> select clear

> select #13/A:281@NZ

1 atom, 1 residue, 1 model selected  

> ui tool show ""Add Hydrogens""

> select clear

> hide #!23 models

> show #!23 models

> ui tool show Distances

> ~distance #13/A:385@CG #13/A:275@CE

> ~distance #13/A:278@CB #13/A:381@CG

> select #13/A:281@NZ

1 atom, 1 residue, 1 model selected  

> select clear

> preset ""overall look"" ""publication 1 (silhouettes)""

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> ~distance #13/A:281@NZ #13/A:607@O14

> view name central_site_flatView

> save central_site_NC2_flatView_HB.png supersample 3 transparentBackground
> true

> view central_site_flatView

> view name central_site_flatView

> save central_site_NC2_flatView_HB.png supersample 3 transparentBackground
> true

> ui mousemode right ""tape measure""

> marker segment #29 position 109.7,99.11,95.93 toPosition 107.4,96.8,92.97
> color yellow radius 0.2666 label 4.38 labelHeight 0.5331 labelColor yellow

> marker segment #29 position 109.4,91.97,100.8 toPosition 107.7,96.78,92.57
> color yellow radius 0.261 label 9.721 labelHeight 0.9721 labelColor yellow

> hide #!29 models

> show #!28 models

> hide #!28 models

> show #!29 models

> close #29

> marker segment #29 position 109.9,99.24,95.9 toPosition 107.7,96.7,92.66
> color yellow radius 0.2666 label 4.646 labelHeight 0.5331 labelColor yellow

> hide #!29 models

> ui mousemode right translate

> select add #13/A:277@CE2

1 atom, 1 residue, 1 model selected  

> select add #13/A:277@CG

2 atoms, 1 bond, 1 residue, 1 model selected  

> select add #13/A:277@CE1

3 atoms, 2 bonds, 1 residue, 1 model selected  

> select add #13/A:277@CZ

4 atoms, 2 bonds, 1 residue, 1 model selected  

> select clear

> select add #13/A:277@CD2

1 atom, 1 residue, 1 model selected  

> select add #13/A:277@CE2

2 atoms, 1 residue, 1 model selected  

> select add #13/A:277@CG

3 atoms, 1 residue, 1 model selected  

> select add #13/A:277@CD1

4 atoms, 1 residue, 1 model selected  

> select add #13/A:277@CE1

5 atoms, 1 residue, 1 model selected  

> select add #13/A:277@CZ

6 atoms, 1 residue, 1 model selected  

> define centroid sel name F277_centroid

Centroid 'F277_centroid' placed at [111.43766658 100.26916631 96.34250005]  

> define centroid sel name F277_centroid radius 0.2

Centroid 'F277_centroid' placed at [111.43766658 100.26916631 96.34250005]  

> select clear

> view list

Named views: 570central_modelComp2, CHS_in_dens_central, CLR_in_outer_molOnly,
C_dom_pocket_mirror2docked, C_domonly_side_comparison, Cdom_pocket,
F570_central_NC36_2copies_modelComp_view, F570central_densityComp,
F570central_modelComp, F570central_modelComp2, F570central_resi_comp,
F570central_site_allModels, F570outer, F570outer_resi_comp,
F570outer_site_modelComp2, NC2_central_molOnly, NC2_outer_molOnly,
NC36_in_Dens_outer, NC36_in_dens_central, N_dom_side_comparison,
N_domonly_side_comparison, all_models_aligned_Cdompocket_models,
all_models_aligned_F570central_models,
all_models_aligned_F570outer_site_models, c11_in_dens_Cdom,
c11_in_dens_central, central_site_45, central_site_flatView, outer_site_45,
outer_site_NC2_flat_view, side_view, side_view_NdomAligned, side_view_models,
top_view  

> view central_site_flatView

> select #!13/A:607@C10

1 atom, 1 residue, 1 model selected  

> select add #13.3

2 atoms, 2 residues, 2 models selected  

> distance #!13/A:607@C10 #13.3

Distance between zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb
#!13/A NC2 607 C10 and F277_centroid #13.3: 4.501Å  

> ~select #13.3

1 atom, 1 residue, 1 model selected  

> select #13.3

1 atom, 1 residue, 1 model selected  

> ~select #13.3

Nothing selected  

> transparency sel 100

> transparency sel 100 target a

> select #13.3

1 atom, 1 residue, 1 model selected  

> hide #13.3 models

> show #13.3 models

> transparency #13.3 1

> color #13.3 #aa5ee8e1

> color #13.3 #aa5ee800

> select clear

> save central_site_NC2_flatView_HB.png supersample 3 transparentBackground
> true

> view central_site_flatView

> hide #13.3 models

> show #13.3 models

> close #13.2

> select #13.3

1 atom, 1 residue, 1 model selected  

> ~select #13.3

Nothing selected  

> ui tool show Distances

> select #13.3

1 atom, 1 residue, 1 model selected  

> ~select #13.3

Nothing selected  

> view central_site_flatView

> hide #23.1 models

> save central_site_NC2_flatView_HB.png supersample 3 transparentBackground
> true

> distance save ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig3_cryoEM/final_maps_models/distances.txt""

> save central_site_NC2_flatView_HB.png supersample 3 transparentBackground
> trueview

Invalid ""transparentBackground"" argument: Expected true or false (or 1 or 0)  

> view

> hide #13.3 models

> hide #!13 models

> show #!14 models

> hide #!14 models

> show #!14 models

> save ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig3_cryoEM/final_maps_models/240807_zfO1_final_structures_maps_comparison_13.cxs""

> hide #!14 models

> show #!13 models

> hide #13.1 models

> hide atoms

> cartoon style width 2

> hide /B target c

> show #!2 models

> view orient

> view list

Named views: 570central_modelComp2, CHS_in_dens_central, CLR_in_outer_molOnly,
C_dom_pocket_mirror2docked, C_domonly_side_comparison, Cdom_pocket,
F570_central_NC36_2copies_modelComp_view, F570central_densityComp,
F570central_modelComp, F570central_modelComp2, F570central_resi_comp,
F570central_site_allModels, F570outer, F570outer_resi_comp,
F570outer_site_modelComp2, NC2_central_molOnly, NC2_outer_molOnly,
NC36_in_Dens_outer, NC36_in_dens_central, N_dom_side_comparison,
N_domonly_side_comparison, all_models_aligned_Cdompocket_models,
all_models_aligned_F570central_models,
all_models_aligned_F570outer_site_models, c11_in_dens_Cdom,
c11_in_dens_central, central_site_45, central_site_flatView, outer_site_45,
outer_site_NC2_flat_view, side_view, side_view_NdomAligned, side_view_models,
top_view  

> view side_view

> view side_view_NdomAligned

> view side_view_models

> view side_view_NdomAligned

> view side_view_models

> view side_view_NdomAligned

> view side_view_models

> show #!16 models

> hide #!16 models

> show #!17 models

> hide #!17 models

> show #!17 models

> show #!5 models

> hide #!5 models

> show #!5 models

> mmaker #5,13,17 to #2

No matrix compatible with both reference structure and all match structures  

> hide #!23 models

> mmaker #5 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_C11_1mM_final_bestModel1_w4copiesOfC11.pdb, chain A (#5), sequence
alignment score = 1579.5  
RMSD between 329 pruned atom pairs is 0.742 angstroms; (across all 354 pairs:
1.052)  
  

> mmaker #13 to #2

No matrix compatible with both reference structure and all match structures  

> close #13.3

> mmaker #13 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 1783.5  
RMSD between 351 pruned atom pairs is 0.732 angstroms; (across all 389 pairs:
1.990)  
  

> mmaker #5,13,17 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_C11_1mM_final_bestModel1_w4copiesOfC11.pdb, chain A (#5), sequence
alignment score = 1579.5  
RMSD between 329 pruned atom pairs is 0.742 angstroms; (across all 354 pairs:
1.052)  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 1783.5  
RMSD between 351 pruned atom pairs is 0.732 angstroms; (across all 389 pairs:
1.990)  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC36_1mM_final_240319_zfO1_NC36_bestModel_NC36_6copies.pdb, chain A
(#17), sequence alignment score = 1670.9  
RMSD between 358 pruned atom pairs is 0.679 angstroms; (across all 367 pairs:
1.167)  
  

> view side_view_models

> pwd

Current working directory is: /Users/bburendei/Dropbox (Scripps
Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig3_cryoEM/images  

> save all_models_alTo6nf4_Cdom_slanted_side_view.png supersample 3
> transparentBackground true

> save all_models_alTo6nf4_Ndom_slanted_side_view.png supersample 3
> transparentBackground true

> mmaker #13:1-300 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 833.6  
RMSD between 165 pruned atom pairs is 0.622 angstroms; (across all 183 pairs:
2.417)  
  

> mmaker #5,13,17:1-300 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_C11_1mM_final_bestModel1_w4copiesOfC11.pdb, chain A (#5), sequence
alignment score = 810.1  
RMSD between 163 pruned atom pairs is 0.668 angstroms; (across all 172 pairs:
0.956)  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 833.6  
RMSD between 165 pruned atom pairs is 0.622 angstroms; (across all 183 pairs:
2.417)  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC36_1mM_final_240319_zfO1_NC36_bestModel_NC36_6copies.pdb, chain A
(#17), sequence alignment score = 773.2  
RMSD between 164 pruned atom pairs is 0.611 angstroms; (across all 167 pairs:
1.283)  
  

> mmaker #5,13,17/A:1-300 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_C11_1mM_final_bestModel1_w4copiesOfC11.pdb, chain A (#5), sequence
alignment score = 810.1  
RMSD between 163 pruned atom pairs is 0.668 angstroms; (across all 172 pairs:
0.956)  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 833.6  
RMSD between 165 pruned atom pairs is 0.622 angstroms; (across all 183 pairs:
2.417)  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC36_1mM_final_240319_zfO1_NC36_bestModel_NC36_6copies.pdb, chain A
(#17), sequence alignment score = 773.2  
RMSD between 164 pruned atom pairs is 0.611 angstroms; (across all 167 pairs:
1.283)  
  

> mmaker #5:1-300 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_C11_1mM_final_bestModel1_w4copiesOfC11.pdb, chain A (#5), sequence
alignment score = 810.1  
RMSD between 163 pruned atom pairs is 0.668 angstroms; (across all 172 pairs:
0.956)  
  

> mmaker #5/A:1-300 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_C11_1mM_final_bestModel1_w4copiesOfC11.pdb, chain A (#5), sequence
alignment score = 810.1  
RMSD between 163 pruned atom pairs is 0.668 angstroms; (across all 172 pairs:
0.956)  
  

> hide #2,5,13,17:300-586

> hide #2,5,13,17:300-586 target c

> hide #!5 models

> hide #!17 models

> select #13/A:1-300

1508 atoms, 1548 bonds, 4 pseudobonds, 185 residues, 2 models selected  

> select #2/A:1-300

1647 atoms, 1692 bonds, 2 pseudobonds, 203 residues, 2 models selected  

> show #2,5,13,17:300-586 target c

> hide #2,5,13,17:1-300 target c

> hide /B target c

> mmaker #5,13,17/A:300-599 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_C11_1mM_final_bestModel1_w4copiesOfC11.pdb, chain A (#5), sequence
alignment score = 803.4  
RMSD between 174 pruned atom pairs is 0.646 angstroms; (across all 182 pairs:
0.853)  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 974.9  
RMSD between 195 pruned atom pairs is 0.511 angstroms; (across all 206 pairs:
1.101)  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC36_1mM_final_240319_zfO1_NC36_bestModel_NC36_6copies.pdb, chain A
(#17), sequence alignment score = 921.7  
RMSD between 197 pruned atom pairs is 0.599 angstroms; (across all 200 pairs:
0.908)  
  

> rmsd

Missing or invalid ""atoms"" argument: empty atom specifier  

> show #!17 models

> hide #!13 models

> show #!13 models

> hide #!17 models

> show #2,5,13,17/A target c

> select clear

> show #!17 models

> hide #!13 models

> hide #!17 models

> show #!13 models

> transparency #2 0 target c

> mmaker #13 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 1783.5  
RMSD between 351 pruned atom pairs is 0.732 angstroms; (across all 389 pairs:
1.990)  
  

> mmaker #13/A:1-300 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 833.6  
RMSD between 165 pruned atom pairs is 0.622 angstroms; (across all 183 pairs:
2.417)  
  

> rmsd #13 #2

Missing required ""to"" argument  

> rmsd #13 to #2

Number of atoms from first atom spec (6846) differs from number in second
(6960)  

> rmsd #13@CA to #2@CA

Number of atoms from first atom spec (782) differs from number in second (842)  

> rmsd #13/A@CA to #2@CA

Number of atoms from first atom spec (391) differs from number in second (842)  

> rmsd #13/A@CA to #2/A@CA

Number of atoms from first atom spec (391) differs from number in second (421)  

> select #2/A:300-599

1700 atoms, 1739 bonds, 1 pseudobond, 218 residues, 2 models selected  
value: None default: None  

> define axis sel name axis

Axis '6nf4.cif #2/axis' centered at [120.65083896 118.77276092 100.9266898 ]
with direction [ 0.00180921 -0.03751698 0.99929435], radius 10.7681, and
length 60.0678  

> select #13/A:300-599

1613 atoms, 1649 bonds, 3 pseudobonds, 206 residues, 2 models selected  
value: None default: None  

> define axis sel name axis_NC2

Axis 'zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb #13/axis_NC2'
centered at [121.3391677 118.7759146 101.6475822] with direction [-0.13294866
-0.06416798 0.98904354], radius 10.2564, and length 56.0317  
value: None default: None  

> define axis sel name axis_apo radius 1

Axis 'zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb #13/axis_apo'
centered at [121.3391677 118.7759146 101.6475822] with direction [-0.13294866
-0.06416798 0.98904354], radius 1, and length 56.0317  

> close #13.3

> close #2.3

> close #13.2

> select #2/A:300-599

1700 atoms, 1739 bonds, 1 pseudobond, 218 residues, 2 models selected  
value: None default: None  

> define axis sel name axis_apo radius 0.1

Axis '6nf4.cif #2/axis_apo' centered at [120.65083896 118.77276092 100.9266898
] with direction [ 0.00180921 -0.03751698 0.99929435], radius 0.1, and length
60.0678  

> select #13/A:300-599

1613 atoms, 1649 bonds, 3 pseudobonds, 206 residues, 2 models selected  
value: None default: None  

> define axis sel name axis_C2.2 radius 0.1

Axis 'zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb #13/axis_C2.2'
centered at [121.3391677 118.7759146 101.6475822] with direction [-0.13294866
-0.06416798 0.98904354], radius 0.1, and length 56.0317  

> select clear

> select #13.2

1 model selected  

> select add #2.3

2 models selected  
Either three or four atoms must be selected!  

> select clear

> select add #13.2

1 model selected  

> select add #2.3

2 models selected  

> select clear

> color #2.3 #bffdb78a

> color #2.3 #bffdb7bc

> color #2.3 #bffdb7

> color #2.3 #bffdb7bd

> color #2.3 #bffdb7c9

> color #2.3 #bffdb7d4

> color #2.3 #bffdb7

> color #2.3 #bffdb703

> color #2.3 #bffdb7

> transparency #2.3 0

> select clear

> view side_view_models

> select #2/A:1-300

1647 atoms, 1692 bonds, 2 pseudobonds, 203 residues, 2 models selected  
value: None default: None  

> define axis sel name axis_N_apo radius 0.1

Axis '6nf4.cif #2/axis_N_apo' centered at [118.54776471 90.8364824
103.97076155] with direction [0.27118103 0.20100905 0.94130559], radius 0.1,
and length 61.1241  

> select #13/A:1-300

1508 atoms, 1548 bonds, 4 pseudobonds, 185 residues, 2 models selected  
value: None default: None  

> define axis sel name axis_N_C2.2 radius 0.1

Axis 'zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb #13/axis_N_C2.2'
centered at [116.76259877 90.30409579 101.24155364] with direction [0.35270227
0.21681833 0.9102697 ], radius 0.1, and length 56.3703  

> select clear

> mmaker #13 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 1783.5  
RMSD between 351 pruned atom pairs is 0.732 angstroms; (across all 389 pairs:
1.990)  
  

> mmaker #13/A:1-300 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 833.6  
RMSD between 165 pruned atom pairs is 0.622 angstroms; (across all 183 pairs:
2.417)  
  

> mmaker #13 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 1783.5  
RMSD between 351 pruned atom pairs is 0.732 angstroms; (across all 389 pairs:
1.990)  
  

> mmaker #13/A:1-300 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 833.6  
RMSD between 165 pruned atom pairs is 0.622 angstroms; (across all 183 pairs:
2.417)  
  

> mmaker #13/A:300-599 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 974.9  
RMSD between 195 pruned atom pairs is 0.511 angstroms; (across all 206 pairs:
1.101)  
  

> mmaker #13/A:1-300 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 833.6  
RMSD between 165 pruned atom pairs is 0.622 angstroms; (across all 183 pairs:
2.417)  
  

> camera ortho

> select #2.3

1 model selected  

> select clear

> ui mousemode right ""mark point""

> marker #28 position 122.4,112.2,132.2 color yellow radius 1

> marker #28 position 110.8,133.1,118.3 color yellow radius 1

> select #2.3

1 model selected  

> select #13.2

1 model selected  

> select #2.3

1 model selected  

> select #13.2

1 model selected  

> select #2.3

1 model selected  

> marker #28 position 136.5,129.1,114.2 color yellow radius 1

> ui mousemode right translate

> select #2.3

1 model selected  

> select #13.2

1 model selected  

> select #2.3

1 model selected  

> select #2.4

1 model selected  

> select #2.3

1 model selected  

> ~select #2.3

Nothing selected  

> select #13.2

1 model selected  

> select add #2.3

2 models selected  
Either three or four atoms must be selected!  
Exactly two atoms must be selected!  

> select #2.4

1 model selected  

> select #2.3

1 model selected  

> select add #13.2

2 models selected  
No atoms selected  

> ~select #13.2

1 model selected  

> ~select #2.3

Nothing selected  

> morph #13,2 frames 60 wrap true

Computed 121 frame morph #32  

> coordset #32 1,121

> morph #2,13 frames 60

Computed 61 frame morph #33  

> coordset #33 1,61

> hide #!32 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!13 models

> hide #!13 models

> show #!13 models

> show #13:NC2

> hide /B

> mmaker #13 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 1783.5  
RMSD between 351 pruned atom pairs is 0.732 angstroms; (across all 389 pairs:
1.990)  
  

> morph #2,13 frames 60

Computed 61 frame morph #34  

> coordset #34 1,61

> hide #!33 models

> show #!13 models

> mmaker #13/A:300-586 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 974.9  
RMSD between 195 pruned atom pairs is 0.511 angstroms; (across all 206 pairs:
1.101)  
  

> morph #2,13 frames 60

Computed 61 frame morph #35  

> coordset #35 1,61

> show #!33 models

> hide #!33 models

> hide #!34 models

> hide #!35 models

> show #!35 models

> show #!34 models

> hide #!35 models

> hide #!34 models

> show #!13 models

> show #!2 models

> mmaker #13 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 1783.5  
RMSD between 351 pruned atom pairs is 0.732 angstroms; (across all 389 pairs:
1.990)  
  

> hide #!13 models

> show #!34 models

> show #!13 models

> hide #!2 models

> hide #!13 models

> show #!13 models

> show #13 atoms

> hide /B

> show #!2 models

> show #2/A atoms

> transparency #2 0

> transparency #2 0 target ca

> select clear

> hide #!2 models

> show #34/A atoms

> hide atoms

> hide #!34 models

> hide #13.2 models

> show #13.2 models

> hide #13.2 models

> show #!2 models

> hide #2.3 models

> hide #2.2 models

> show #2.2 models

> hide #2.2 models

> transparency #2 50 target c

> transparency #2 90 target c

> transparency #2 70 target c

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> show #!34 models

> show #34/A atoms

> hide #!13 models

> hide #!34 models

> show #!13 models

> view orient

> turn z 90

> turn x 180

> turn z 180

> ui tool show ""Side View""

> camera mono

> preset ""overall look"" ""publication 1 (silhouettes)""

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> lighting simple

> lighting soft

> transparency #2 00 target c

> transparency #2 80 target c

> transparency #2 90 target c

> save apo_vs_NC2_bottom_view.png supersample 3 transparentBackground true

> mmaker #13/A:1-300 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 833.6  
RMSD between 165 pruned atom pairs is 0.622 angstroms; (across all 183 pairs:
2.417)  
  

> show #13/A:NC2

> preset ""overall look"" ""publication 1 (silhouettes)""

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> hide HC

> style #13/A:NC2 sphere

Changed 148 atom styles  

> hide #13:608

> camera ortho

> mmaker #13 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 1783.5  
RMSD between 351 pruned atom pairs is 0.732 angstroms; (across all 389 pairs:
1.990)  
  

> view name bottom_view

> save apo_vs_NC2_bottom_view.png supersample 3 transparentBackground true

> hide #13:610

> view side_view

> view bottom_view

> transparency #2 0 target c

> save apo_vs_NC2_bottom_view.png supersample 3 transparentBackground true

> view side_view

> camera mono

> camera ortho

> view bottom_view

> view side_view

> view bottom_view

> view side_view

> save apo_vs_NC2_models_side_view.png supersample 3 transparentBackground
> true

> view bottom_view

> turn x 180

> lighting soft

> lighting simple

> lighting soft

> preset ""overall look"" ""publication 1 (silhouettes)""

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> hide #23.1 models

> show #23.1 models

> hide #23.1 models

> view bottom_view

> turn x 180

> show #!22 models

> hide #!22 models

> show #!22 models

> hide #!22 models

> show #!34 models

> hide #!2 models

> save ""/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig3_cryoEM/final_maps_models/240807_zfO1_final_structures_maps_comparison_14.cxs""

> hide #!34 models

> show #!2 models

> save apo_vs_NC2_models_top_view.png supersample 3 transparentBackground true

> camera orho

Expected one of '360', '360sbs', '360tb', 'crosseye', 'dome', 'mono', 'ortho',
'sbs', 'stereo', 'tb', or 'walleye' or a keyword  

> camera ortho

> clip off

> show #!34 models

> hide #!2 models

> hide #!13 models

> show #!13 models

> hide #!34 models

> view list

Named views: 570central_modelComp2, CHS_in_dens_central, CLR_in_outer_molOnly,
C_dom_pocket_mirror2docked, C_domonly_side_comparison, Cdom_pocket,
F570_central_NC36_2copies_modelComp_view, F570central_densityComp,
F570central_modelComp, F570central_modelComp2, F570central_resi_comp,
F570central_site_allModels, F570outer, F570outer_resi_comp,
F570outer_site_modelComp2, NC2_central_molOnly, NC2_outer_molOnly,
NC36_in_Dens_outer, NC36_in_dens_central, N_dom_side_comparison,
N_domonly_side_comparison, all_models_aligned_Cdompocket_models,
all_models_aligned_F570central_models,
all_models_aligned_F570outer_site_models, bottom_view, c11_in_dens_Cdom,
c11_in_dens_central, central_site_45, central_site_flatView, outer_site_45,
outer_site_NC2_flat_view, side_view, side_view_NdomAligned, side_view_models,
top_view  

> view C_dom_pocket_mirror2docked

> show #13/A atoms

> style #13:NC2 stick

Changed 296 atom styles  

> hide HC


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> preset ""overall look"" ""publication 1 (silhouettes)""

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> alias nice cartoon suppressBackboneDisplay false; cartoon style width 1;
> size stickRadius 0.12

> lighting soft

> nice

Changed 0 bond radii  

> alias voltr5 vol transparency 0.5

> alias voltroff vol transparency 0

> alias cylinders cartoon style protein modeh tube rad 2 sides 24

> alias cartoonDefaults cartoon style protein modeh default

UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac
      Model Identifier: Mac14,2
      Model Number: Z15S000D5LL/A
      Chip: Unknown
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.121.1
      OS Loader Version: 8422.141.2.700.1

Software:

    System Software Overview:

      System Version: macOS 13.6.7 (22G720)
      Kernel Version: Darwin 22.6.0
      Time since boot: 6 days, 4 hours, 19 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      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: No
          Connection Type: Internal
        DELL P2721Q:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes


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