Save command history: No space left on device

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/lilyh/Downloads/Class3D_Job147/run_it025_class001.mrc

Opened run_it025_class001.mrc as #1, grid size 256,256,256, pixel 1.09, shown
at level 5.66e-07, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job147/run_it025_class004.mrc

Opened run_it025_class004.mrc as #2, grid size 256,256,256, pixel 1.09, shown
at level 1.49e-06, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job147/run_it025_class003.mrc

Opened run_it025_class003.mrc as #3, grid size 256,256,256, pixel 1.09, shown
at level 1.86e-06, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job147/run_it025_class002.mrc

Opened run_it025_class002.mrc as #4, grid size 256,256,256, pixel 1.09, shown
at level 9.88e-07, step 1, values float32  

> color red

> open C:/Users/lilyh/Downloads/Class3D_Job148/run_it025_class004.mrc

Opened run_it025_class004.mrc as #5, grid size 256,256,256, pixel 1.09, shown
at level 7.05e-07, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job148/run_it025_class003.mrc

Opened run_it025_class003.mrc as #6, grid size 256,256,256, pixel 1.09, shown
at level 6.04e-07, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job148/run_it025_class002.mrc

Opened run_it025_class002.mrc as #7, grid size 256,256,256, pixel 1.09, shown
at level 1.46e-06, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job148/run_it025_class001.mrc

Opened run_it025_class001.mrc as #8, grid size 256,256,256, pixel 1.09, shown
at level 1.79e-06, step 1, values float32  

> select add #5

2 models selected  

> select add #6

4 models selected  

> select add #7

6 models selected  

> select add #8

8 models selected  

> color #5.1#6.1#7.1#8.1 orange

> tile

8 models tiled  

> volume level 0.03

> volume level 0.3

> volume level 0.03

> volume #6 level 0.0006345

> volume level 0.000635

> select clear

> set bgColor white

> lighting flat

> lighting full

[Repeated 1 time(s)]

> lighting soft

> volume showOutlineBox true

> volume showOutlineBox false

> volume #2 level 0.002014

> volume level 0.00201

> volume #3 level 0.003119

> volume level 0.00312

> open C:/Users/lilyh/Downloads/Class3D_Job148/run_it025_class003.mrc

Opened run_it025_class003.mrc as #9, grid size 256,256,256, pixel 1.09, shown
at level 6.04e-07, step 1, values float32  

> volume #9 level 0.00312

> select #9

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #9,1,0,0,179.4,0,1,0,-149.38,0,0,1,0

> select clear

> volume #9 level 0.0006087

> ui mousemode right "rotate selected models"

> select #9

2 models selected  

> view matrix models
> #9,0.66964,0.16837,-0.72334,329.01,-0.57203,-0.50424,-0.64693,242.97,-0.47367,0.84699,-0.24135,169.56

> view matrix models
> #9,0.4012,0.45178,-0.79682,344.13,0.51845,0.60515,0.60415,-276.98,0.75514,-0.6555,0.0085597,141.95

> volume #9 level 0.0008467

> volume #9 level 0.0009658

> volume #9 level 0.00312

> select clear

> close #9

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!4 models

> show #!4 models

> volume #1 level 0.00361

> volume #2 level 0.00381

> volume #3 level 0.003397

> volume level 0.0034

> select clear

Drag select of 1 run_it025_class001.mrc , 2 run_it025_class004.mrc , 3
run_it025_class003.mrc  

> color #1.1#2.1#3.1 orange red

> select clear

Drag select of 4 run_it025_class002.mrc  

> color #4.1 orange red

> select clear

> save C:\Users\lilyh\Desktop\image106.png supersample 3

> open "C:/Users/lilyh/Downloads/cryosparc_P122_J482_003_volume_map (1).mrc"

Opened cryosparc_P122_J482_003_volume_map (1).mrc as #9, grid size
256,256,256, pixel 1.09, shown at level 0.00334, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J505_mask.mrc

Opened cryosparc_P122_J505_mask.mrc as #10, grid size 256,256,256, pixel 1.09,
shown at level 5e-05, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J520_mask.mrc

Opened cryosparc_P122_J520_mask.mrc as #11, grid size 256,256,256, pixel 1.09,
shown at level 5e-05, step 1, values float32  

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> volume #9 level 0.0579

> ~tile

> volume #9 level 0.08961

> select #10

2 models selected  

> select #9

2 models selected  

> color #9.1 dark gray

> select #10

2 models selected  

> color #10.1 red

> transparency #10.1 80

> select clear

> hide #!11 models

> hide #!10 models

> show #!10 models

> save C:\Users\lilyh\Desktop\image107.png supersample 3

> hide #!10 models

> show #!11 models

> select #11

2 models selected  

> transparency #11.1 50

> color #11.1 orange

> show #!10 models

> select #10

2 models selected  

> surface style #10 mesh

> select clear

> select #11

2 models selected  

> transparency #11.1 70

> select clear

> save C:\Users\lilyh\Desktop\image108.png supersample 3

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!11 models

> show #!11 models

> hide #!10 models

> hide #!11 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> hide #!9 models

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> open C:/Users/lilyh/Downloads/Class3D_Job151/run_it025_class004.mrc

Opened run_it025_class004.mrc as #12, grid size 256,256,256, pixel 1.09, shown
at level 1.52e-06, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job151/run_it025_class003.mrc

Opened run_it025_class003.mrc as #13, grid size 256,256,256, pixel 1.09, shown
at level 5.8e-07, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job151/run_it025_class002.mrc

Opened run_it025_class002.mrc as #14, grid size 256,256,256, pixel 1.09, shown
at level 1.22e-06, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job151/run_it025_class001.mrc

Opened run_it025_class001.mrc as #15, grid size 256,256,256, pixel 1.09, shown
at level 6.64e-08, step 1, values float32  

> tile

4 models tiled  

> volume level 0.0034

> lighting flat

> lighting full

> lighting shadows false

> lighting soft

> color #12-15 yellow

> color #12-15 #ffff00ff

> color #12-15 #ffff7fff

> color #12-15 #eaea75ff

> color #12-15 #f0f078ff

> color #12-15 #f3f379ff

> color #12-15 #ffff7fff

> color #12-15 #f9ff7eff

> color #12-15 #fdff7cff

> color #12-15 #f2ff7cff

> color #12-15 #eaff80ff

> color #12-15 #e1ff80ff

> color #12-15 #ddff81ff

> color #12-15 #d7ff81ff

> color #12-15 #ddff81ff

> color #12-15 #e2ff81ff

> color #12-15 #e4ff81ff

> color #12-15 #e8ff81ff

> color #12-15 #eeff81ff

> color #12-15 #f5ff81ff

> color #12-15 #f9ff81ff

> color #12-15 #fdff81ff

> color #12-15 #ffff81ff

> color #12-15 #fffb81ff

> color #12-15 #fff581ff

> color #12-15 #fff585ff

> color #12-15 #fff587ff

> color #12-15 #fff58cff

> color #12-15 #fff68eff

> color #12-15 #fff690ff

> color #12-15 #fff692ff

> color #12-15 #fff695ff

> color #12-15 #fff799ff

> color #12-15 #fff79bff

> color #12-15 #fff79cff

> color #12-15 #fff7a1ff

> color #12-15 #fff7a4ff

> color #12-15 #fff8a5ff

> color #12-15 #fff7a4ff

> color #12-15 #fff7a1ff

> color #12-15 #fff79eff

> color #12-15 #fff79dff

> select clear

> hide #!12 models

> show #!12 models

> hide #!13 models

> show #!13 models

> hide #!14 models

> show #!14 models

> hide #!15 models

> show #!15 models

> hide #!12 models

> show #!12 models

> save C:\Users\lilyh\Desktop\image109.png supersample 3

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> open C:/Users/lilyh/Downloads/Class3D_Job153/run_it025_class004.mrc

Opened run_it025_class004.mrc as #16, grid size 256,256,256, pixel 1.09, shown
at level 5.91e-07, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job153/run_it025_class003.mrc

Opened run_it025_class003.mrc as #17, grid size 256,256,256, pixel 1.09, shown
at level 1.36e-06, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job153/run_it025_class002.mrc

Opened run_it025_class002.mrc as #18, grid size 256,256,256, pixel 1.09, shown
at level 2.03e-06, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job153/run_it025_class001.mrc

Opened run_it025_class001.mrc as #19, grid size 256,256,256, pixel 1.09, shown
at level 1.39e-06, step 1, values float32  

> volume level 0.0034

> tile

4 models tiled  

> lighting shadows true

> lighting soft

> color #16-19 #aaff00ff

> color #16-19 #aaff7fff

> color #16-19 #55ff7fff

> color #16-19 #aaff7fff

> color #16-19 #a5ff7cff

> color #16-19 #9fff7cff

> color #16-19 #98ff7cff

> color #16-19 #8dff7cff

> color #16-19 #89ff7cff

> color #16-19 #85ff7cff

> color #16-19 #83ff7cff

> color #16-19 #83ff7dff

> color #16-19 #7dff7dff

> color #16-19 #7eff7eff

> color #16-19 #80ff7eff

> color #16-19 #8bff7eff

> color #16-19 #a7ff7eff

> color #16-19 #b2ff7eff

> color #16-19 #b8ff7eff

> color #16-19 #c3ff7eff

> color #16-19 #cbff7eff

> color #16-19 #ceff7eff

> color #16-19 #c7ff7eff

> color #16-19 #c3ff7eff

> color #16-19 #bcff7eff

> color #16-19 #b8ff7eff

> color #16-19 #b6ff7eff

> color #16-19 #b2ff7eff

> volume level 0.0034

Drag select of 16 run_it025_class004.mrc , 18 run_it025_class002.mrc  

> ui mousemode right "translate selected models"

> view matrix models
> #16,-0.6562,-0.45162,0.60451,183.48,0.02297,-0.81271,-0.58222,328.58,0.75423,-0.36817,0.54368,6.3905,#18,-0.6562,-0.45162,0.60451,180.08,0.02297,-0.81271,-0.58222,284.5,0.75423,-0.36817,0.54368,15.049

> select clear

Drag select of 17 run_it025_class003.mrc , 19 run_it025_class001.mrc  

> view matrix models
> #17,-0.6562,-0.45162,0.60451,251.73,0.02297,-0.81271,-0.58222,328.24,0.75423,-0.36817,0.54368,16.337,#19,-0.6562,-0.45162,0.60451,252.14,0.02297,-0.81271,-0.58222,284.47,0.75423,-0.36817,0.54368,17.484

> select clear

> save C:\Users\lilyh\Desktop\image110.png supersample 3

> show #!15 models

> show #!14 models

> show #!13 models

> show #!12 models

> tile

8 models tiled  

> hide #!12 models

> show #!12 models

> hide #!13 models

> show #!13 models

> hide #!14 models

> show #!14 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!17 models

> show #!17 models

> hide #17.1 models

> show #17.1 models

> hide #!18 models

> show #!18 models

> hide #!19 models

> show #!19 models

> lighting soft

> lighting flat

> lighting soft

> lighting shadows true intensity 0.5

> lighting soft

> save C:\Users\lilyh\Desktop\image111.png supersample 3

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> hide #!16 models

> hide #17.1 models

> hide #!17 models

> hide #!18 models

> hide #!19 models

> open C:/Users/lilyh/Downloads/Refine3D_Job156/run_class001.mrc

Opened run_class001.mrc as #20, grid size 256,256,256, pixel 1.09, shown at
level 0.000529, step 1, values float32  

> volume #20 level 0.003905

> volume #20 level 0.006828

> close #20

> open C:/Users/lilyh/Downloads/Class3D_Job155/run_it025_class004.mrc

Opened run_it025_class004.mrc as #20, grid size 256,256,256, pixel 1.09, shown
at level 1.56e-06, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job155/run_it025_class003.mrc

Opened run_it025_class003.mrc as #21, grid size 256,256,256, pixel 1.09, shown
at level 3.1e-07, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job155/run_it025_class002.mrc

Opened run_it025_class002.mrc as #22, grid size 256,256,256, pixel 1.09, shown
at level 7.18e-07, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job155/run_it025_class001.mrc

Opened run_it025_class001.mrc as #23, grid size 256,256,256, pixel 1.09, shown
at level 5.85e-07, step 1, values float32  

> volume level 0.0034

> color #20-23 #aaffffff

> tile

4 models tiled  

> lighting full

[Repeated 1 time(s)]

> lighting soft

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> tile

8 models tiled  
Drag select of 1 run_it025_class001.mrc , 2 run_it025_class004.mrc , 3
run_it025_class003.mrc  
Drag select of 24 run_it025_class001.mrc , 22 run_it025_class004.mrc , 24
run_it025_class003.mrc , 26 run_it025_class002.mrc  

> lighting soft

> lighting shadows true intensity 0.5

> lighting flat

> lighting soft

> select clear

> save C:\Users\lilyh\Desktop\image112.png supersample 3

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> hide #!21 models

> hide #!20 models

> hide #!22 models

> hide #!23 models

> open C:/Users/lilyh/Downloads/Class3D_Job157/run_it025_class001.mrc

Opened run_it025_class001.mrc as #24, grid size 256,256,256, pixel 1.09, shown
at level 1.46e-06, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job157/run_it025_class004.mrc

Opened run_it025_class004.mrc as #25, grid size 256,256,256, pixel 1.09, shown
at level 7.72e-07, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job157/run_it025_class003.mrc

Opened run_it025_class003.mrc as #26, grid size 256,256,256, pixel 1.09, shown
at level 6.08e-07, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job157/run_it025_class002.mrc

Opened run_it025_class002.mrc as #27, grid size 256,256,256, pixel 1.09, shown
at level 1.24e-07, step 1, values float32  

> tile

4 models tiled  

> lighting soft

> color #24-27 medium blue

> color #24-27 cornflower blue

> volume level 0.0034

> hide #!24 models

> show #!24 models

> close #24

> close #25

> close #27

> close #26

> open C:/Users/lilyh/Downloads/Class3D_Job159/run_it025_class004.mrc

Opened run_it025_class004.mrc as #24, grid size 256,256,256, pixel 1.09, shown
at level 5.08e-07, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job159/run_it025_class003.mrc

Opened run_it025_class003.mrc as #25, grid size 256,256,256, pixel 1.09, shown
at level 1.05e-06, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job159/run_it025_class002.mrc

Opened run_it025_class002.mrc as #26, grid size 256,256,256, pixel 1.09, shown
at level 1.65e-07, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job159/run_it025_class001.mrc

Opened run_it025_class001.mrc as #27, grid size 256,256,256, pixel 1.09, shown
at level 6.48e-07, step 1, values float32  

> volume level 0.0034

> tile

4 models tiled  

> lighting soft

Drag select of 24 run_it025_class004.mrc , 26 run_it025_class002.mrc  

> ui mousemode right "translate selected models"

> view matrix models
> #24,0.047067,0.35787,0.93259,-78.153,-0.47244,-0.81462,0.33644,248.36,0.88011,-0.45642,0.13073,75.285,#26,0.047067,0.35787,0.93259,-79.854,-0.47244,-0.81462,0.33644,205.82,0.88011,-0.45642,0.13073,77.026

Drag select of 25 run_it025_class003.mrc , 27 run_it025_class001.mrc  

> view matrix models
> #25,0.047067,0.35787,0.93259,-19.723,-0.47244,-0.81462,0.33644,246.64,0.88011,-0.45642,0.13073,78.834,#27,0.047067,0.35787,0.93259,-21.918,-0.47244,-0.81462,0.33644,206.87,0.88011,-0.45642,0.13073,83.489

> select clear

Drag select of 24 run_it025_class004.mrc , 25 run_it025_class003.mrc , 26
run_it025_class002.mrc , 27 run_it025_class001.mrc  
No visible atoms or bonds selected  
Drag select of 24 run_it025_class004.mrc , 25 run_it025_class003.mrc , 26
run_it025_class002.mrc , 27 run_it025_class001.mrc  
No visible atoms or bonds selected  

> select add #24

8 models selected  

> select add #25

8 models selected  

> select add #26

8 models selected  

> select add #27

8 models selected  
No visible atoms or bonds selected  
[Repeated 2 time(s)]

> ui tool show "Color Actions"

> color #24.1#25.1#26.1#27.1 cornflower blue

> select clear

> save C:\Users\lilyh\Desktop\image113.png supersample 3

> show #!16 models

> show #!18 models

> hide #!18 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> hide #!27 models

> hide #!26 models

> hide #!25 models

> hide #!24 models

> open C:/Users/lilyh/Downloads/Class3D_Job160/run_it025_class004.mrc

Opened run_it025_class004.mrc as #28, grid size 256,256,256, pixel 1.09, shown
at level 1.09e-07, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job160/run_it025_class003.mrc

Opened run_it025_class003.mrc as #29, grid size 256,256,256, pixel 1.09, shown
at level 7.5e-07, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job160/run_it025_class002.mrc

Opened run_it025_class002.mrc as #30, grid size 256,256,256, pixel 1.09, shown
at level 1.35e-07, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job160/run_it025_class001.mrc

Opened run_it025_class001.mrc as #31, grid size 256,256,256, pixel 1.09, shown
at level 1.45e-06, step 1, values float32  

> tile

4 models tiled  

> volume level 0.0034

> lighting simple

> lighting soft

> lighting flat

> lighting soft

> lighting shadows true intensity 0.5

> lighting simple

[Repeated 1 time(s)]

> lighting soft

> color #28-31 #0055ffff

> color #28-31 #aa55ffff

> select clear

Drag select of 28 run_it025_class004.mrc  

> ui mousemode right "translate selected models"

> view matrix models
> #28,-0.5539,-0.11417,0.82472,109.62,-0.36195,-0.85903,-0.36202,348.85,0.74979,-0.49903,0.43449,48.626

> select clear

> save C:\Users\lilyh\Desktop\image114.png supersample 3

> show #!27 models

> show #!26 models

> show #!25 models

> show #!24 models

> show #!16 models

> tile

9 models tiled  
Drag select of 68 run_it025_class004.mrc , 54 run_it025_class003.mrc , 56
run_it025_class002.mrc , 58 run_it025_class001.mrc  

> lighting full

> lighting soft

> lighting full

> lighting soft

> select clear

> save C:\Users\lilyh\Desktop\image115.png supersample 3

> show volume

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

> show all

> tile

31 models tiled  

> hide #!9 models

> hide #!10 models

> close #9

> close #10

> close #11

> tile

28 models tiled  

> close #6

> close #7

> close #8

> tile

25 models tiled  

> close #5

> tile

24 models tiled  

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting flat

[Repeated 1 time(s)]

> lighting full

> lighting soft

[Repeated 1 time(s)]

> select clear

[Repeated 1 time(s)]

> close #20

> close #21

> close #22

> close #23

> tile

20 models tiled  

> lighting soft

> select clear

> save C:/Users/lilyh/Desktop/Vac17_focused_3D_Relion.cxs includeMaps true

> save C:\Users\lilyh\Desktop\image116.png supersample 3

> open C:/Users/lilyh/Downloads/cryosparc_P122_J540_class_00_00031_volume.mrc

Opened cryosparc_P122_J540_class_00_00031_volume.mrc as #5, grid size
100,100,100, pixel 2.78, shown at level 0.0542, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J541_class_02_00031_volume.mrc

Opened cryosparc_P122_J541_class_02_00031_volume.mrc as #6, grid size
100,100,100, pixel 2.78, shown at level 0.0674, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J541_class_01_00031_volume.mrc

Opened cryosparc_P122_J541_class_01_00031_volume.mrc as #7, grid size
100,100,100, pixel 2.78, shown at level 0.0663, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J541_class_00_00031_volume.mrc

Opened cryosparc_P122_J541_class_00_00031_volume.mrc as #8, grid size
100,100,100, pixel 2.78, shown at level 0.0729, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J540_class_01_00031_volume.mrc

Opened cryosparc_P122_J540_class_01_00031_volume.mrc as #9, grid size
100,100,100, pixel 2.78, shown at level 0.0571, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J540_class_02_00031_volume.mrc

Opened cryosparc_P122_J540_class_02_00031_volume.mrc as #10, grid size
100,100,100, pixel 2.78, shown at level 0.0555, step 1, values float32  

> ~tile

> volume level 0.35

> close #5

> close #6

> close #7

> close #10

> close #9

> close #8

> open C:/Users/lilyh/Downloads/cryosparc_P122_J521_004_volume_map_sharp.mrc

Opened cryosparc_P122_J521_004_volume_map_sharp.mrc as #5, grid size
256,256,256, pixel 1.09, shown at level 0.0396, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J482_003_volume_map_sharp.mrc

Opened cryosparc_P122_J482_003_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.09, shown at level 0.0359, step 1, values float32  

> volume level 0.35

> volume #5 level 0.4689

> open "C:/Users/lilyh/Downloads/cryosparc_P122_J482_003_volume_map (1).mrc"

Opened cryosparc_P122_J482_003_volume_map (1).mrc as #7, grid size
256,256,256, pixel 1.09, shown at level 0.00334, step 1, values float32  

> volume #7 level 0.1708

> volume #7 level 0.2

> volume #7 level 0.1556

> volume #6 level 0.2471

> volume #5 level 0.4635

> hide #!1 models

> show #!1 models

> close session

> open "C:/Users/lilyh/Downloads/cryosparc_P122_J482_003_volume_map (1).mrc"

Opened cryosparc_P122_J482_003_volume_map (1).mrc as #1, grid size
256,256,256, pixel 1.09, shown at level 0.00334, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J521_004_volume_map_sharp.mrc

Opened cryosparc_P122_J521_004_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.09, shown at level 0.0396, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J482_003_volume_map_sharp.mrc

Opened cryosparc_P122_J482_003_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.09, shown at level 0.0359, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job151/run_it025_class001.mrc

Opened run_it025_class001.mrc as #4, grid size 256,256,256, pixel 1.09, shown
at level 6.64e-08, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job151/run_it025_class004.mrc

Opened run_it025_class004.mrc as #5, grid size 256,256,256, pixel 1.09, shown
at level 1.52e-06, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job151/run_it025_class003.mrc

Opened run_it025_class003.mrc as #6, grid size 256,256,256, pixel 1.09, shown
at level 5.8e-07, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job151/run_it025_class002.mrc

Opened run_it025_class002.mrc as #7, grid size 256,256,256, pixel 1.09, shown
at level 1.22e-06, step 1, values float32  

> ~tile

> volume level 0.3

> hide #!3 models

> show #!3 models

> hide #!3 models

> volume #2 level 0.4567

> volume #1 level 0.1934

> volume #3 level 0.2255

> volume #2 level 0.4675

> volume #3 color #7a7a7a

> volume #!2-7 appearance chest

> lighting soft

> lighting shadows true intensity 0.5

> lighting soft

> style ball

Changed 0 atom styles  

> set bgColor white

> volume #2 color #aaff7f

> volume #4 level 0.01084

> volume #4 level 0.005243

> volume #5 level 0.00524

> volume #6 level 0.00524

> volume #7 level 0.00524

> volume #7 level 0.0034

> volume #6 level 0.0034

> volume #5 level 0.0034

> volume #4 level 0.0034

> volume #1 level 0.1071

> select #1

2 models selected  

> transparency #1.1 50

> select clear

[Repeated 1 time(s)]

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!2 models

> lighting flat

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting full

> lighting soft

> show #!7 models

> show #!6 models

> hide #!7 models

> hide #!6 models

> show #!5 models

> show #!4 models

> hide #!5 models

> hide #5.1 models

> hide #!4 models

> show #!4 models

> show #!2 models

> hide #!4 models

> hide #!2 models

> show #!4 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #5.1 models

> hide #!4 models

> show #!4 models

> show #!6 models

> show #!7 models

> show #!2 models

> hide #!7 models

> hide #!6 models

> hide #5.1 models

> hide #!5 models

> hide #!4 models

> open
> C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb

Chain information for
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
#8  
---  
Chain | Description  
B | No description available  
C | No description available  
  

> open
> C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb

Chain information for
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
#9  
---  
Chain | Description  
B | No description available  
C | No description available  
  
Drag select of 260 residues  

> ui mousemode right "translate selected models"

> view matrix models
> #8,1,0,0,48.272,0,1,0,164.59,0,0,1,125.11,#9,1,0,0,48.272,0,1,0,164.59,0,0,1,125.11

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.79558,0.33084,-0.50755,47.489,0.60106,-0.32581,0.72978,163.29,0.076068,-0.88566,-0.45806,124.13,#9,0.79558,0.33084,-0.50755,47.489,0.60106,-0.32581,0.72978,163.29,0.076068,-0.88566,-0.45806,124.13

Drag select of 13 residues  

> view matrix models
> #8,-0.68742,0.37563,-0.62157,42.22,-0.72534,-0.39814,0.56157,158.83,-0.036534,0.83689,0.54615,119.84

Drag select of 35 residues  

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.68742,0.37563,-0.62157,44.71,-0.72534,-0.39814,0.56157,169,-0.036534,0.83689,0.54615,136.84,#9,0.79558,0.33084,-0.50755,49.979,0.60106,-0.32581,0.72978,173.46,0.076068,-0.88566,-0.45806,141.13

> fitmap #8 inMap #1

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#8) to map cryosparc_P122_J482_003_volume_map (1).mrc (#1) using 4737 atoms  
average map value = -0.0001557, steps = 220  
shifted from previous position = 34.4  
rotated from previous position = 13.7 degrees  
atoms outside contour = 4737, contour level = 0.10714  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#8) relative to cryosparc_P122_J482_003_volume_map (1).mrc (#1) coordinates:  
Matrix rotation and translation  
-0.59337904 0.39472638 -0.70149301 15.58357562  
-0.77494843 -0.51576627 0.36529460 153.90466178  
-0.21761501 0.76037905 0.61193748 126.40547452  
Axis 0.29794421 -0.36490591 -0.88208442  
Axis point 49.43314375 37.01777903 0.00000000  
Rotation angle (degrees) 138.46958829  
Shift along axis -163.01798392  
  

> fitmap #9 inMap #1

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#9) to map cryosparc_P122_J482_003_volume_map (1).mrc (#1) using 4737 atoms  
average map value = -0.0005607, steps = 188  
shifted from previous position = 28.5  
rotated from previous position = 23.5 degrees  
atoms outside contour = 4737, contour level = 0.10714  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#9) relative to cryosparc_P122_J482_003_volume_map (1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.55684007 0.19458370 -0.80750626 31.45155338  
0.82481919 -0.24422806 0.50992742 150.98828914  
-0.09799213 -0.94999467 -0.29649234 147.12942730  
Axis -0.83842948 -0.40747214 0.36194262  
Axis point 0.00000000 123.41655057 32.72092284  
Rotation angle (degrees) 119.46818259  
Shift along axis -34.64102022  
  

> ui mousemode right "translate selected models"

Drag select of 980 residues  

> view matrix models
> #8,-0.59338,0.39473,-0.70149,135.36,-0.77495,-0.51577,0.36529,146.11,-0.21762,0.76038,0.61194,89.887,#9,0.55684,0.19458,-0.80751,151.23,0.82482,-0.24423,0.50993,143.19,-0.097992,-0.94999,-0.29649,110.61

> fitmap #9 inMap #1

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#9) to map cryosparc_P122_J482_003_volume_map (1).mrc (#1) using 4737 atoms  
average map value = 0.1296, steps = 268  
shifted from previous position = 35.4  
rotated from previous position = 28.5 degrees  
atoms outside contour = 2247, contour level = 0.10714  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#9) relative to cryosparc_P122_J482_003_volume_map (1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.21655754 0.37106564 -0.90300231 140.08778531  
0.94719644 0.14418810 0.28640655 135.91408502  
0.23647781 -0.91734406 -0.32024703 143.18623375  
Axis -0.68597216 -0.64934682 0.32831526  
Axis point 0.00000000 83.02464481 84.91999610  
Rotation angle (degrees) 118.66912068  
Shift along axis -137.34147382  
  

> fitmap #8 inMap #1

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#8) to map cryosparc_P122_J482_003_volume_map (1).mrc (#1) using 4737 atoms  
average map value = 0.05356, steps = 284  
shifted from previous position = 19.7  
rotated from previous position = 22.9 degrees  
atoms outside contour = 3710, contour level = 0.10714  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#8) relative to cryosparc_P122_J482_003_volume_map (1).mrc (#1) coordinates:  
Matrix rotation and translation  
-0.59328132 0.11780182 -0.79632912 140.10884055  
-0.78557228 -0.30071813 0.54078171 138.46098801  
-0.17576553 0.94640974 0.27095230 106.75620040  
Axis 0.34709426 -0.53101375 -0.77301356  
Axis point 111.00925700 -4.44760771 0.00000000  
Rotation angle (degrees) 144.24505627  
Shift along axis -107.41770462  
  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.59328,0.1178,-0.79633,138.1,-0.78557,-0.30072,0.54078,139.58,-0.17577,0.94641,0.27095,102.83,#9,0.21656,0.37107,-0.903,138.07,0.9472,0.14419,0.28641,137.03,0.23648,-0.91734,-0.32025,139.26

Drag select of 12 residues  

> view matrix models
> #8,-0.59328,0.1178,-0.79633,156.85,-0.78557,-0.30072,0.54078,137.86,-0.17577,0.94641,0.27095,136.96

> fitmap #8 inMap #1

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#8) to map cryosparc_P122_J482_003_volume_map (1).mrc (#1) using 4737 atoms  
average map value = 0.1286, steps = 168  
shifted from previous position = 17.5  
rotated from previous position = 29.6 degrees  
atoms outside contour = 2258, contour level = 0.10714  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#8) relative to cryosparc_P122_J482_003_volume_map (1).mrc (#1) coordinates:  
Matrix rotation and translation  
-0.82721618 0.18944314 -0.52898462 140.58045518  
-0.50731220 -0.65654110 0.55820085 134.80884922  
-0.24155282 0.73011311 0.63920823 142.51790837  
Axis 0.22237576 -0.37180515 -0.90128239  
Axis point 96.80068636 18.67151445 0.00000000  
Rotation angle (degrees) 157.26089928  
Shift along axis -147.30982056  
  

> fitmap #9 inMap #1

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#9) to map cryosparc_P122_J482_003_volume_map (1).mrc (#1) using 4737 atoms  
average map value = 0.1296, steps = 68  
shifted from previous position = 4.56  
rotated from previous position = 0.0414 degrees  
atoms outside contour = 2247, contour level = 0.10714  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#9) relative to cryosparc_P122_J482_003_volume_map (1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.21598263 0.37072598 -0.90327947 140.09571243  
0.94733734 0.14445566 0.28580509 135.91222227  
0.23643919 -0.91743929 -0.32000265 143.18785790  
Axis -0.68569713 -0.64949550 0.32859555  
Axis point 0.00000000 83.01705196 84.95176759  
Rotation angle (degrees) 118.67117648  
Shift along axis -137.28671147  
  

> select clear

> hide #8 models

> hide #9 models

> show #9 models

> hide #9 models

> volume #2 level 0.5323

> volume #7 color #aaaaff

> volume #7 color #ff5500

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!6 models

> hide #!6 models

> hide #!2 models

> show #!6 models

> volume #6 level 0.00389

> volume #6 level 0.0034

> volume #7 level 0.004435

> volume #4 level 0.004406

> volume #6 level 0.004456

> volume #5 level 0.003186

> hide #!7 models

> hide #!6 models

> hide #5.1 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #5.1 models

> show #!6 models

> hide #5.1 models

> volume level 0.00319

> volume #1 level 0.08883

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #8 models

> select #8/B:18

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel atoms

> select clear

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> hide #8 models

> show #8 models

> hide #8 models

> show #!7 models

> show #5.1 models

> show #!4 models

> save C:\Users\lilyh\Desktop\image117.png supersample 3

> save C:\Users\lilyh\Desktop\image118.png supersample 3

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!7 models

> hide #!6 models

> show #!6 models

> hide #5.1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #2 level 0.6781

> hide #!6 models

> volume #2 level 0.6509

> volume #1 level 0.1349

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> volume #2 level 0.5094

> save C:\Users\lilyh\Desktop\image119.png supersample 3

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> open C:/Users/lilyh/Downloads/cryosparc_P122_J507_004_volume_map_sharp.mrc

Opened cryosparc_P122_J507_004_volume_map_sharp.mrc as #10, grid size
256,256,256, pixel 1.09, shown at level 0.0356, step 1, values float32  

> volume #10 level 0.5011

> volume #1 level 0.1412

> volume #10 level 0.5574

> volume #2 level 0.557

> show #!6 models

> volume #10 color #aaff7f

> volume #10 color #ffaaff

> volume #10 color #aa557f

> open C:/Users/lilyh/Downloads/cryosparc_P122_J482_003_volume_map_sharp.mrc

Opened cryosparc_P122_J482_003_volume_map_sharp.mrc as #11, grid size
256,256,256, pixel 1.09, shown at level 0.0359, step 1, values float32  

> volume #11 level 0.2754

> hide #!1 models

> volume #11 level 0.2933

> volume #10 level 0.5318

> save C:\Users\lilyh\Desktop\image120.png supersample 3

> show #!6 models

> hide #!6 models

> show #!6 models

> save C:\Users\lilyh\Desktop\image121.png supersample 3

> hide #!6 models

> save C:\Users\lilyh\Desktop\image122.png supersample 3

> open "C:/Users/lilyh/Downloads/cryosparc_P122_J506_003_volume_map_sharp
> (1).mrc"

Opened cryosparc_P122_J506_003_volume_map_sharp (1).mrc as #12, grid size
256,256,256, pixel 1.09, shown at level 0.0511, step 1, values float32  

> volume #12 level 0.421

> volume #12 level 0.4848

> close #12

> open C:/Users/lilyh/Downloads/cryosparc_P122_J534_class_02_00031_volume.mrc

Opened cryosparc_P122_J534_class_02_00031_volume.mrc as #12, grid size
100,100,100, pixel 2.78, shown at level 0.0675, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J534_class_01_00031_volume.mrc

Opened cryosparc_P122_J534_class_01_00031_volume.mrc as #13, grid size
100,100,100, pixel 2.78, shown at level 0.0686, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J534_class_00_00031_volume.mrc

Opened cryosparc_P122_J534_class_00_00031_volume.mrc as #14, grid size
100,100,100, pixel 2.78, shown at level 0.0664, step 1, values float32  

> volume #12 level 0.2438

> volume #13 level 0.2523

> volume #14 level 0.2188

> show #9 models

> open C:/Users/lilyh/Downloads/cryosparc_P122_J535_class_02_00031_volume.mrc

Opened cryosparc_P122_J535_class_02_00031_volume.mrc as #15, grid size
100,100,100, pixel 2.78, shown at level 0.057, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J535_class_01_00031_volume.mrc

Opened cryosparc_P122_J535_class_01_00031_volume.mrc as #16, grid size
100,100,100, pixel 2.78, shown at level 0.0563, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J535_class_00_00031_volume.mrc

Opened cryosparc_P122_J535_class_00_00031_volume.mrc as #17, grid size
100,100,100, pixel 2.78, shown at level 0.0561, step 1, values float32  

> volume #17 level 0.1619

> volume #16 level 0.1707

> volume #15 level 0.1911

> volume #17 level 0.1892

> open C:/Users/lilyh/Downloads/cryosparc_P122_J513_class_01_00031_volume.mrc

Opened cryosparc_P122_J513_class_01_00031_volume.mrc as #18, grid size
100,100,100, pixel 2.78, shown at level 0.0579, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J513_class_02_00031_volume.mrc

Opened cryosparc_P122_J513_class_02_00031_volume.mrc as #19, grid size
100,100,100, pixel 2.78, shown at level 0.0563, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J513_class_00_00031_volume.mrc

Opened cryosparc_P122_J513_class_00_00031_volume.mrc as #20, grid size
100,100,100, pixel 2.78, shown at level 0.0611, step 1, values float32  

> hide #!15 models

> hide #!16 models

> hide #!17 models

> volume #20 level 0.168

> volume #19 level 0.1494

> volume #18 level 0.1919

> volume #20 level 0.1253

> show #!17 models

> hide #!17 models

> show #!16 models

> hide #!16 models

> show #!15 models

> hide #!15 models

> hide #!11 models

> hide #!10 models

> hide #9 models

> hide #!5 models

> hide #!20 models

> hide #!19 models

> volume #18 level 0.1369

> show #!19 models

> volume #19 level 0.1315

> volume #20 level 0.1502

> hide #!19 models

> show #!19 models

> tile

3 models tiled  

> volume #!18-20 planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume #!18-20 planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume #!18-20 planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume #18 region 0,0,0,99,99,99 step 1

> volume #18 style surface region 0,0,0,99,99,99 step 1

> volume #19 region 0,0,0,99,99,99 step 1

> volume #19 style surface region 0,0,0,99,99,99 step 1

> volume #20 level -0.03735,0 level 0.1826,0.8 level 1.122,1

> volume #20 region 0,0,0,99,99,99 step 1

> volume #20 style surface region 0,0,0,99,99,99 step 1

> lighting flat

> lighting soft

> open "C:/Users/lilyh/Downloads/cryosparc_P122_J510_class_00_00031_volume
> (1).mrc"

Opened cryosparc_P122_J510_class_00_00031_volume (1).mrc as #21, grid size
100,100,100, pixel 2.78, shown at level 0.0528, step 1, values float32  

> open "C:/Users/lilyh/Downloads/cryosparc_P122_J510_class_02_00031_volume
> (1).mrc"

Opened cryosparc_P122_J510_class_02_00031_volume (1).mrc as #22, grid size
100,100,100, pixel 2.78, shown at level 0.052, step 1, values float32  

> open "C:/Users/lilyh/Downloads/cryosparc_P122_J510_class_01_00031_volume
> (1).mrc"

Opened cryosparc_P122_J510_class_01_00031_volume (1).mrc as #23, grid size
100,100,100, pixel 2.78, shown at level 0.0559, step 1, values float32  

> tile

6 models tiled  

> volume level 0.15

Drag select of 21 cryosparc_P122_J510_class_00_00031_volume (1).mrc , 22
cryosparc_P122_J510_class_02_00031_volume (1).mrc , 23
cryosparc_P122_J510_class_01_00031_volume (1).mrc  

> color #21.1#22.1#23.1 dark gray

Drag select of 18 cryosparc_P122_J513_class_01_00031_volume.mrc , 19
cryosparc_P122_J513_class_02_00031_volume.mrc , 20
cryosparc_P122_J513_class_00_00031_volume.mrc  

> color #18.1#19.1#20.1 cornflower blue

Drag select of 18 cryosparc_P122_J513_class_01_00031_volume.mrc , 19
cryosparc_P122_J513_class_02_00031_volume.mrc , 20
cryosparc_P122_J513_class_00_00031_volume.mrc , 21
cryosparc_P122_J510_class_00_00031_volume (1).mrc , 22
cryosparc_P122_J510_class_02_00031_volume (1).mrc , 23
cryosparc_P122_J510_class_01_00031_volume (1).mrc  

> lighting soft

> lighting shadows true intensity 0.5

> lighting soft

Drag select of 21 cryosparc_P122_J510_class_00_00031_volume (1).mrc , 22
cryosparc_P122_J510_class_02_00031_volume (1).mrc , 23
cryosparc_P122_J510_class_01_00031_volume (1).mrc  

> ui mousemode right "translate selected models"

> view matrix models
> #21,1,0,0,29.909,0,1,0,140.61,0,0,1,2.181,#22,1,0,0,-28.528,0,1,0,167.93,0,0,1,-276.02,#23,1,0,0,-87.313,0,1,0,196.91,0,0,1,-554.6

Drag select of 18 cryosparc_P122_J513_class_01_00031_volume.mrc , 21
cryosparc_P122_J510_class_00_00031_volume (1).mrc  

> view matrix models
> #18,0.92111,0.38436,0.061799,-60.026,-0.3739,0.91767,-0.13443,96.536,-0.10838,0.10072,0.98899,-58.625,#21,1,0,0,17.422,0,1,0,152.14,0,0,1,-60.779

Drag select of 20 cryosparc_P122_J513_class_00_00031_volume.mrc , 23
cryosparc_P122_J510_class_01_00031_volume (1).mrc  

> view matrix models
> #20,0.92111,0.38436,0.061799,-141.34,-0.3739,0.91767,-0.13443,127.57,-0.10838,0.10072,0.98899,-444.33,#23,1,0,0,-64.293,0,1,0,184.44,0,0,1,-444.32

Drag select of 18 cryosparc_P122_J513_class_01_00031_volume.mrc , 21
cryosparc_P122_J510_class_00_00031_volume (1).mrc  

> view matrix models
> #18,0.92111,0.38436,0.061799,-65.853,-0.3739,0.91767,-0.13443,93.567,-0.10838,0.10072,0.98899,-82.506,#21,1,0,0,11.595,0,1,0,149.17,0,0,1,-84.66

> select clear

> hide #!19 models

> show #!19 models

> open C:/Users/lilyh/Downloads/cryosparc_P122_J514_class_01_00031_volume.mrc

Opened cryosparc_P122_J514_class_01_00031_volume.mrc as #24, grid size
100,100,100, pixel 2.78, shown at level 0.0498, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J514_class_00_00031_volume.mrc

Opened cryosparc_P122_J514_class_00_00031_volume.mrc as #25, grid size
100,100,100, pixel 2.78, shown at level 0.0491, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J514_class_02_00031_volume.mrc

Opened cryosparc_P122_J514_class_02_00031_volume.mrc as #26, grid size
100,100,100, pixel 2.78, shown at level 0.0495, step 1, values float32  

> volume level 0.15

> tile

9 models tiled  
Drag select of 24 cryosparc_P122_J514_class_01_00031_volume.mrc , 25
cryosparc_P122_J514_class_00_00031_volume.mrc , 26
cryosparc_P122_J514_class_02_00031_volume.mrc  

> ui mousemode right "rotate selected models"

> view matrix models
> #24,-0.96661,0.23993,-0.090029,218.35,0.22146,0.95886,0.17757,293.36,0.12893,0.15171,-0.97998,-126.14,#25,-0.96661,0.23993,-0.090029,265.93,0.22146,0.95886,0.17757,273.88,0.12893,0.15171,-0.97998,19.103,#26,-0.96661,0.23993,-0.090029,316.72,0.22146,0.95886,0.17757,255.13,0.12893,0.15171,-0.97998,164.38

> select clear

Drag select of 24 cryosparc_P122_J514_class_01_00031_volume.mrc , 25
cryosparc_P122_J514_class_00_00031_volume.mrc , 26
cryosparc_P122_J514_class_02_00031_volume.mrc  

> ui mousemode right "rotate selected models"

> view matrix models
> #24,-0.68697,0.72668,-0.0011518,87.673,0.70213,0.66335,-0.25882,336.47,-0.18732,-0.17861,-0.96592,-31.413,#25,-0.68697,0.72668,-0.0011518,148.68,0.70213,0.66335,-0.25882,306.7,-0.18732,-0.17861,-0.96592,106.83,#26,-0.68697,0.72668,-0.0011518,212.77,0.70213,0.66335,-0.25882,275.9,-0.18732,-0.17861,-0.96592,245.56

> view matrix models
> #24,-0.84324,0.34721,0.41035,140.03,0.35169,0.93369,-0.067337,316.29,-0.40652,0.087531,-0.90944,-56.464,#25,-0.84324,0.34721,0.41035,163.14,0.35169,0.93369,-0.067337,293.46,-0.40652,0.087531,-0.90944,94.085,#26,-0.84324,0.34721,0.41035,189.14,0.35169,0.93369,-0.067337,271,-0.40652,0.087531,-0.90944,246.14

> tile

9 models tiled  

> select #24

2 models selected  

> view matrix models
> #24,-0.9732,0.13667,-0.18492,325.59,0.13697,0.99051,0.011225,285.97,0.1847,-0.014405,-0.98269,186.63

> select #25

2 models selected  

> view matrix models
> #25,-0.97124,0.20972,-0.11275,274.21,0.20827,0.97776,0.02458,290.19,0.1154,0.00038985,-0.99332,48.306

> select clear

> select #26

2 models selected  

> view matrix models
> #26,-0.95822,0.18981,-0.21398,261.28,0.18598,0.98182,0.038061,306.44,0.21731,-0.0033254,-0.9761,-116.46

> select clear

Drag select of 24 cryosparc_P122_J514_class_01_00031_volume.mrc , 25
cryosparc_P122_J514_class_00_00031_volume.mrc , 26
cryosparc_P122_J514_class_02_00031_volume.mrc  

> color #24.1#25.1#26.1 gray

> select clear

> show #9 models

> hide #9 models

> ui mousemode right select

> save C:\Users\lilyh\Desktop\image123.png supersample 3

> ~tile

> hide #!26 models

> hide #!25 models

> hide #!24 models

> hide #!20 models

> hide #!19 models

> hide #!18 models

> show #!17 models

> hide #!17 models

> show #!6 models

> show #!10 models

> show #!11 models

> hide #!11 models

> show #!11 models

Drag select of 10 cryosparc_P122_J507_004_volume_map_sharp.mrc , 11
cryosparc_P122_J482_003_volume_map_sharp.mrc  
Drag select of 21 cryosparc_P122_J510_class_00_00031_volume (1).mrc , 22
cryosparc_P122_J510_class_02_00031_volume (1).mrc , 23
cryosparc_P122_J510_class_01_00031_volume (1).mrc  

> ui mousemode right "rotate selected models"

> view matrix models
> #21,0.97291,0.23052,-0.017584,-41.237,-0.23116,0.97119,-0.057973,54.578,0.0037132,0.060467,0.99816,-96.273,#22,0.97291,0.23052,-0.017584,-41.237,-0.23116,0.97119,-0.057973,54.578,0.0037132,0.060467,0.99816,-96.273,#23,0.97291,0.23052,-0.017584,-41.237,-0.23116,0.97119,-0.057973,54.578,0.0037132,0.060467,0.99816,-96.273

> ui mousemode right "translate selected models"

> view matrix models
> #21,0.97291,0.23052,-0.017584,-23.174,-0.23116,0.97119,-0.057973,41.586,0.0037132,0.060467,0.99816,-7.629,#22,0.97291,0.23052,-0.017584,-23.174,-0.23116,0.97119,-0.057973,41.586,0.0037132,0.060467,0.99816,-7.629,#23,0.97291,0.23052,-0.017584,-23.174,-0.23116,0.97119,-0.057973,41.586,0.0037132,0.060467,0.99816,-7.629

> fitmap #21 inMap #11

Fit map cryosparc_P122_J510_class_00_00031_volume (1).mrc in map
cryosparc_P122_J482_003_volume_map_sharp.mrc using 3844 points  
correlation = 0.8682, correlation about mean = 0.8339, overlap = 394.1  
steps = 84, shift = 3.79, angle = 13.9 degrees  
  
Position of cryosparc_P122_J510_class_00_00031_volume (1).mrc (#21) relative
to cryosparc_P122_J482_003_volume_map_sharp.mrc (#11) coordinates:  
Matrix rotation and translation  
0.99999770 -0.00113062 0.00180339 -0.16379964  
0.00113007 0.99999924 0.00030748 -0.21275999  
-0.00180374 -0.00030544 0.99999829 0.30589603  
Axis -0.14250878 0.83869044 0.52563257  
Axis point 167.84735995 0.00000000 90.58973462  
Rotation angle (degrees) 0.12321195  
Shift along axis 0.00569203  
  

> fitmap #23 inMap #11

Fit map cryosparc_P122_J510_class_01_00031_volume (1).mrc in map
cryosparc_P122_J482_003_volume_map_sharp.mrc using 3850 points  
correlation = 0.8692, correlation about mean = 0.8367, overlap = 395.1  
steps = 96, shift = 3.78, angle = 13.9 degrees  
  
Position of cryosparc_P122_J510_class_01_00031_volume (1).mrc (#23) relative
to cryosparc_P122_J482_003_volume_map_sharp.mrc (#11) coordinates:  
Matrix rotation and translation  
0.99999724 -0.00120749 0.00200091 -0.16756740  
0.00120548 0.99999869 0.00100615 -0.33521827  
-0.00200212 -0.00100374 0.99999746 0.44164081  
Axis -0.39503510 0.78678090 0.47426056  
Axis point 217.66418739 0.00000000 81.69243662  
Rotation angle (degrees) 0.14575657  
Shift along axis 0.01190449  
  

> fitmap #22 inMap #11

Fit map cryosparc_P122_J510_class_02_00031_volume (1).mrc in map
cryosparc_P122_J482_003_volume_map_sharp.mrc using 3885 points  
correlation = 0.868, correlation about mean = 0.8378, overlap = 394.7  
steps = 88, shift = 3.77, angle = 13.8 degrees  
  
Position of cryosparc_P122_J510_class_02_00031_volume (1).mrc (#22) relative
to cryosparc_P122_J482_003_volume_map_sharp.mrc (#11) coordinates:  
Matrix rotation and translation  
0.99999742 -0.00044905 0.00221325 -0.29811604  
0.00044722 0.99999949 0.00082670 -0.19350796  
-0.00221362 -0.00082571 0.99999718 0.44077115  
Axis -0.34357548 0.92044951 0.18635610  
Axis point 198.40582146 0.00000000 133.92316790  
Rotation angle (degrees) 0.13778116  
Shift along axis 0.00645145  
  

> fitmap #24 inMap #11

Fit map cryosparc_P122_J514_class_01_00031_volume.mrc in map
cryosparc_P122_J482_003_volume_map_sharp.mrc using 3837 points  
correlation = 0.3865, correlation about mean = 0.1375, overlap = 127.6  
steps = 488, shift = 48.7, angle = 50.9 degrees  
  
Position of cryosparc_P122_J514_class_01_00031_volume.mrc (#24) relative to
cryosparc_P122_J482_003_volume_map_sharp.mrc (#11) coordinates:  
Matrix rotation and translation  
-0.87435716 -0.46943886 -0.12299046 342.58917502  
-0.47102628 0.75998173 0.44784138 46.36316524  
-0.11676365 0.44950505 -0.88561357 176.49363820  
Axis 0.25063484 -0.93807816 -0.23914755  
Axis point 177.33207737 0.00000000 82.64004135  
Rotation angle (degrees) 179.80983969  
Shift along axis 0.16449149  
  

> volume #6 level 0.002529

> volume #10 level 0.4262

> show #9 models

> show #8 models

> hide #!23 models

> hide #!22 models

> hide #!21 models

> hide #!10 models

> hide #!6 models

> show #!23 models

> volume #23 level 0.2683

> volume #22 level 0.2389

> volume #21 level 0.2202

> show #!22 models

> show #!23 models

> hide #!11 models

> volume #21 level 0.2266

> volume #22 level 0.227

> volume #23 level 0.227

> save C:\Users\lilyh\Desktop\image124.png supersample 3

> show #!17 models

> hide #!17 models

> show #!17 models

> show #!16 models

> show #!15 models

> hide #!23 models

> hide #!22 models

> hide #!21 models

> volume #15 level 0.1672

> volume #15 level 0.227

> volume #16 level 0.227

> volume #17 level 0.227

> hide #!17 models

> hide #!16 models

> hide #!15 models

> open C:/Users/lilyh/Downloads/cryosparc_P122_J549_class_00_00031_volume.mrc

Opened cryosparc_P122_J549_class_00_00031_volume.mrc as #27, grid size
100,100,100, pixel 2.78, shown at level 0.0661, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J549_class_02_00031_volume.mrc

Opened cryosparc_P122_J549_class_02_00031_volume.mrc as #28, grid size
100,100,100, pixel 2.78, shown at level 0.0634, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J549_class_01_00031_volume.mrc

Opened cryosparc_P122_J549_class_01_00031_volume.mrc as #29, grid size
100,100,100, pixel 2.78, shown at level 0.0648, step 1, values float32  

> volume #27 level 0.1598

> volume #27 level 0.227

> volume #27 level 0.2062

> volume #28 level 0.1752

> volume #29 level 0.1892

> volume #19 change image level -0.03572,0 level 0.1738,0.8 level 1.116,1

> volume #18 change image level -0.03663,0 level 0.1745,0.8 level 1.134,1

Drag select of 18 cryosparc_P122_J513_class_01_00031_volume.mrc , 19
cryosparc_P122_J513_class_02_00031_volume.mrc , 20
cryosparc_P122_J513_class_00_00031_volume.mrc  

> ui mousemode right "rotate selected models"

> view matrix models
> #18,0.98908,0.13745,0.053101,-42.594,-0.13165,0.98619,-0.10051,44.188,-0.066182,0.092418,0.99352,-91.271,#19,0.98908,0.13745,0.053101,-42.594,-0.13165,0.98619,-0.10051,44.188,-0.066182,0.092418,0.99352,-91.271,#20,0.98908,0.13745,0.053101,-42.594,-0.13165,0.98619,-0.10051,44.188,-0.066182,0.092418,0.99352,-91.271

> ui mousemode right "translate selected models"

> view matrix models
> #18,0.98908,0.13745,0.053101,-24.002,-0.13165,0.98619,-0.10051,31.413,-0.066182,0.092418,0.99352,-1.8236,#19,0.98908,0.13745,0.053101,-24.002,-0.13165,0.98619,-0.10051,31.413,-0.066182,0.092418,0.99352,-1.8236,#20,0.98908,0.13745,0.053101,-24.002,-0.13165,0.98619,-0.10051,31.413,-0.066182,0.092418,0.99352,-1.8236

> fitmap #18 inMap #21

Fit map cryosparc_P122_J513_class_01_00031_volume.mrc in map
cryosparc_P122_J510_class_00_00031_volume (1).mrc using 3531 points  
correlation = 0.9852, correlation about mean = 0.937, overlap = 818.5  
steps = 64, shift = 3.15, angle = 10.4 degrees  
  
Position of cryosparc_P122_J513_class_01_00031_volume.mrc (#18) relative to
cryosparc_P122_J510_class_00_00031_volume (1).mrc (#21) coordinates:  
Matrix rotation and translation  
0.99998737 -0.00487273 -0.00123410 0.93607583  
0.00487290 0.99998812 0.00012815 -0.63986405  
0.00123346 -0.00013417 0.99999924 -0.25009704  
Axis -0.02608453 -0.24536670 0.96907935  
Axis point 137.30468320 191.16118119 0.00000000  
Rotation angle (degrees) 0.28810121  
Shift along axis -0.10977963  
  

> fitmap #19 inMap #21

Fit map cryosparc_P122_J513_class_02_00031_volume.mrc in map
cryosparc_P122_J510_class_00_00031_volume (1).mrc using 3459 points  
correlation = 0.9911, correlation about mean = 0.9625, overlap = 817.8  
steps = 76, shift = 3.07, angle = 10.3 degrees  
  
Position of cryosparc_P122_J513_class_02_00031_volume.mrc (#19) relative to
cryosparc_P122_J510_class_00_00031_volume (1).mrc (#21) coordinates:  
Matrix rotation and translation  
0.99999505 -0.00102057 -0.00297896 0.65883504  
0.00102279 0.99999920 0.00074681 -0.18621108  
0.00297820 -0.00074985 0.99999529 -0.36137254  
Axis -0.23120724 -0.92027206 0.31566209  
Axis point 111.60487742 0.00000000 213.60106474  
Rotation angle (degrees) 0.18544544  
Shift along axis -0.09503419  
  

> fitmap #20 inMap #21

Fit map cryosparc_P122_J513_class_00_00031_volume.mrc in map
cryosparc_P122_J510_class_00_00031_volume (1).mrc using 3482 points  
correlation = 0.9896, correlation about mean = 0.9563, overlap = 820.3  
steps = 60, shift = 3.09, angle = 10.2 degrees  
  
Position of cryosparc_P122_J513_class_00_00031_volume.mrc (#20) relative to
cryosparc_P122_J510_class_00_00031_volume (1).mrc (#21) coordinates:  
Matrix rotation and translation  
0.99999754 -0.00087826 -0.00204103 0.49941442  
0.00087765 0.99999957 -0.00030151 -0.06366800  
0.00204129 0.00029972 0.99999788 -0.41357419  
Axis 0.13407012 -0.91033414 0.39155708  
Axis point 195.76000615 0.00000000 246.88280533  
Rotation angle (degrees) 0.12846926  
Shift along axis -0.03702220  
  

> fitmap #22 inMap #21

Fit map cryosparc_P122_J510_class_02_00031_volume (1).mrc in map
cryosparc_P122_J510_class_00_00031_volume (1).mrc using 2977 points  
correlation = 0.9922, correlation about mean = 0.955, overlap = 787.2  
steps = 40, shift = 0.0417, angle = 0.0138 degrees  
  
Position of cryosparc_P122_J510_class_02_00031_volume (1).mrc (#22) relative
to cryosparc_P122_J510_class_00_00031_volume (1).mrc (#21) coordinates:  
Matrix rotation and translation  
0.99999958 0.00078079 0.00047614 -0.13384199  
-0.00078094 0.99999965 0.00030881 0.06917322  
-0.00047590 -0.00030918 0.99999984 0.14858538  
Axis -0.32009729 0.49312790 -0.80892682  
Axis point 115.79670913 189.20825354 0.00000000  
Rotation angle (degrees) 0.05530802  
Shift along axis -0.04324099  
  

> fitmap #23 inMap #21

Fit map cryosparc_P122_J510_class_01_00031_volume (1).mrc in map
cryosparc_P122_J510_class_00_00031_volume (1).mrc using 2979 points  
correlation = 0.9944, correlation about mean = 0.9665, overlap = 789.7  
steps = 40, shift = 0.0122, angle = 0.199 degrees  
  
Position of cryosparc_P122_J510_class_01_00031_volume (1).mrc (#23) relative
to cryosparc_P122_J510_class_00_00031_volume (1).mrc (#21) coordinates:  
Matrix rotation and translation  
0.99999393 -0.00327470 0.00118935 0.29050043  
0.00327499 0.99999461 -0.00024230 -0.43631200  
-0.00118855 0.00024619 0.99999926 0.14361836  
Axis 0.06993302 0.34042547 0.93766725  
Axis point 134.04127686 88.32435076 0.00000000  
Rotation angle (degrees) 0.20010857  
Shift along axis 0.00645009  
  

> fitmap #27 inMap #21

Fit map cryosparc_P122_J549_class_00_00031_volume.mrc in map
cryosparc_P122_J510_class_00_00031_volume (1).mrc using 2861 points  
correlation = 0.9924, correlation about mean = 0.9594, overlap = 799.2  
steps = 44, shift = 0.098, angle = 0.0573 degrees  
  
Position of cryosparc_P122_J549_class_00_00031_volume.mrc (#27) relative to
cryosparc_P122_J510_class_00_00031_volume (1).mrc (#21) coordinates:  
Matrix rotation and translation  
0.99999529 0.00150375 -0.00268668 0.27160752  
-0.00150382 0.99999894 -0.00002031 0.30438763  
0.00268665 0.00002436 0.99999642 -0.43536963  
Axis 0.00725437 -0.87258645 -0.48840583  
Axis point 171.45570900 0.00000000 100.92925358  
Rotation angle (degrees) 0.17641211  
Shift along axis -0.05099712  
  

> fitmap #278in #21

Missing or invalid "atomsOrMap" argument: only initial part "#278" of atom
specifier valid  

> fitmap #28 inMap #21

Fit map cryosparc_P122_J549_class_02_00031_volume.mrc in map
cryosparc_P122_J510_class_00_00031_volume (1).mrc using 3187 points  
correlation = 0.9887, correlation about mean = 0.9458, overlap = 812.9  
steps = 40, shift = 0.0783, angle = 0.119 degrees  
  
Position of cryosparc_P122_J549_class_02_00031_volume.mrc (#28) relative to
cryosparc_P122_J510_class_00_00031_volume (1).mrc (#21) coordinates:  
Matrix rotation and translation  
0.99999703 -0.00072491 -0.00233975 0.50430132  
0.00072235 0.99999921 -0.00109376 0.08179126  
0.00234054 0.00109207 0.99999670 -0.56387928  
Axis 0.40746574 -0.87246047 0.26978584  
Axis point 239.15502653 0.00000000 218.36493337  
Rotation angle (degrees) 0.15368079  
Shift along axis -0.01800077  
  

> fitmap #29 inMap #21

Fit map cryosparc_P122_J549_class_01_00031_volume.mrc in map
cryosparc_P122_J510_class_00_00031_volume (1).mrc using 3060 points  
correlation = 0.9868, correlation about mean = 0.9335, overlap = 806.6  
steps = 44, shift = 0.105, angle = 0.245 degrees  
  
Position of cryosparc_P122_J549_class_01_00031_volume.mrc (#29) relative to
cryosparc_P122_J510_class_00_00031_volume (1).mrc (#21) coordinates:  
Matrix rotation and translation  
0.99999317 -0.00282414 -0.00239730 0.78329290  
0.00282702 0.99999535 0.00120206 -0.48850983  
0.00239390 -0.00120882 0.99999644 -0.26422500  
Axis -0.30943374 -0.61494617 0.72532197  
Axis point 202.30267331 262.22460773 0.00000000  
Rotation angle (degrees) 0.22320350  
Shift along axis -0.13361820  
  

> select clear

> hide #9 models

> hide #8 models

> tile

9 models tiled  
Drag select of 27 cryosparc_P122_J549_class_00_00031_volume.mrc , 28
cryosparc_P122_J549_class_02_00031_volume.mrc , 29
cryosparc_P122_J549_class_01_00031_volume.mrc  

> color #27.1#28.1#29.1 light gray

> color #27.1#28.1#29.1 dim gray

> select clear

> lighting soft

> lighting flat

> lighting soft

Drag select of 27 cryosparc_P122_J549_class_00_00031_volume.mrc , 28
cryosparc_P122_J549_class_02_00031_volume.mrc , 29
cryosparc_P122_J549_class_01_00031_volume.mrc  
Drag select of 21 cryosparc_P122_J510_class_00_00031_volume (1).mrc , 22
cryosparc_P122_J510_class_02_00031_volume (1).mrc , 23
cryosparc_P122_J510_class_01_00031_volume (1).mrc  

> select clear

> show #!26 models

> show #!25 models

> show #!24 models

> tile

12 models tiled  

> select #24

2 models selected  

> ui mousemode right "rotate selected models"

[Repeated 1 time(s)]

> view matrix models
> #24,-0.84731,0.038394,-0.52972,337.66,-0.036697,0.99077,0.13051,152.88,0.52984,0.13002,-0.83807,-124.39

> select clear

> select #25

2 models selected  

> view matrix models
> #25,-0.82929,-0.025865,-0.55822,333.67,-0.068492,0.9961,0.055598,177.44,0.5546,0.08434,-0.82783,-271.33

> select clear

Drag select of 27 cryosparc_P122_J549_class_00_00031_volume.mrc , 28
cryosparc_P122_J549_class_02_00031_volume.mrc , 29
cryosparc_P122_J549_class_01_00031_volume.mrc  
No visible atoms or bonds selected  

> color #27.1#28.1#29.1 lime

> color #27.1#28.1#29.1 light gray

> select clear

> save C:\Users\lilyh\Desktop\image125.png supersample 3

Drag select of 27 cryosparc_P122_J549_class_00_00031_volume.mrc , 28
cryosparc_P122_J549_class_02_00031_volume.mrc , 29
cryosparc_P122_J549_class_01_00031_volume.mrc  

> color #27.1#28.1#29.1 medium blue

> select clear

Drag select of 27 cryosparc_P122_J549_class_00_00031_volume.mrc , 28
cryosparc_P122_J549_class_02_00031_volume.mrc , 29
cryosparc_P122_J549_class_01_00031_volume.mrc  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #27,-0.7941,0.56332,-0.22823,204.39,0.5355,0.82606,0.17569,-179.55,0.2875,0.017299,-0.95762,224.97,#28,-0.79276,0.56484,-0.22911,185.65,0.53727,0.82505,0.17499,-167.44,0.28787,0.015631,-0.95754,78.415,#29,-0.79158,0.56703,-0.22777,173.02,0.53902,0.82352,0.17685,-156.49,0.28785,0.017224,-0.95752,-70.598

> select clear

[Repeated 1 time(s)]

> select #21

2 models selected  

> view matrix models
> #21,-0.79263,0.56451,-0.23035,215.1,0.53626,0.82525,0.17715,87.026,0.2901,0.016886,-0.95685,-53.236

> select #24

2 models selected  
Drag select of 21 cryosparc_P122_J510_class_00_00031_volume (1).mrc , 24
cryosparc_P122_J514_class_01_00031_volume.mrc , 25
cryosparc_P122_J514_class_00_00031_volume.mrc  

> view matrix models
> #21,-0.79263,0.56451,-0.23035,256.41,0.53626,0.82525,0.17715,222.66,0.2901,0.016886,-0.95685,100.04,#24,-0.87796,0.44865,-0.16701,277.44,0.42107,0.88969,0.1765,229.98,0.22778,0.084635,-0.97003,96.802,#25,-0.88373,0.40867,-0.22804,278.05,0.39003,0.91245,0.12371,248.94,0.25864,0.020386,-0.96576,-47.626

> select #21

2 models selected  

> view matrix models
> #21,-0.79263,0.56451,-0.23035,215.09,0.53626,0.82525,0.17715,89.159,0.2901,0.016886,-0.95685,-56.931

Drag select of 26 cryosparc_P122_J514_class_02_00031_volume.mrc  

> ui mousemode right "rotate selected models"

> view matrix models
> #26,-0.90457,0.4177,-0.085275,292.05,0.36426,0.8612,0.35447,207.44,0.2215,0.28958,-0.93117,216.55

> view matrix models
> #26,-0.90849,0.41789,-0.0040277,281.07,0.30314,0.66559,0.68198,195.83,0.28767,0.61835,-0.73136,135.05

> view matrix models
> #26,-0.9081,0.41867,-0.0082793,281.52,0.30698,0.67903,0.66684,195.63,0.28481,0.60302,-0.74515,139.45

> view matrix models
> #26,-0.94964,0.27299,0.15384,283.88,0.065522,-0.30712,0.94941,321.34,0.30643,0.91168,0.27377,-49.003

> view matrix models
> #26,-0.99252,0.12202,0.0049363,331.23,0.12173,0.98534,0.11955,259.8,0.009723,0.11925,-0.99282,278.79

Drag select of 21 cryosparc_P122_J510_class_00_00031_volume (1).mrc , 22
cryosparc_P122_J510_class_02_00031_volume (1).mrc , 23
cryosparc_P122_J510_class_01_00031_volume (1).mrc  

> ui mousemode right "translate selected models"

> view matrix models
> #21,-0.79263,0.56451,-0.23035,205.65,0.53626,0.82525,0.17715,39.617,0.2901,0.016886,-0.95685,-60.862,#22,-0.79296,0.56397,-0.23055,231.95,0.53554,0.82561,0.17766,21.22,0.29054,0.017409,-0.95671,236.97,#23,-0.7905,0.56705,-0.23143,221.61,0.53875,0.82353,0.17759,27.051,0.29129,0.015701,-0.95651,85.606

Drag select of 24 cryosparc_P122_J514_class_01_00031_volume.mrc , 25
cryosparc_P122_J514_class_00_00031_volume.mrc , 26
cryosparc_P122_J514_class_02_00031_volume.mrc  

> view matrix models
> #24,-0.87796,0.44865,-0.16701,260.59,0.42107,0.88969,0.1765,135.3,0.22778,0.084635,-0.97003,100.1,#25,-0.88373,0.40867,-0.22804,261.2,0.39003,0.91245,0.12371,154.26,0.25864,0.020386,-0.96576,-44.332,#26,-0.99252,0.12202,0.0049363,314.38,0.12173,0.98534,0.11955,165.12,0.009723,0.11925,-0.99282,282.08

> select clear

> save C:\Users\lilyh\Desktop\image126.png supersample 3

> show #9 models

> molmap #9 10

Opened
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
map 10 as #30, grid size 40,51,41, pixel 3.33, shown at level 0.0534, step 1,
values float32  

> select #30

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #30,0.16233,0.29077,-0.94292,140.16,0.95098,-0.301,0.070898,134.84,-0.26321,-0.90821,-0.32538,145.61

> view matrix models
> #30,0.16168,0.40195,0.90128,144.21,0.96958,0.10535,-0.22092,134.68,-0.18375,0.90958,-0.37269,147.58

> hide #9 models

> hide #!30 models

> close session

> open C:/Users/lilyh/Downloads/Class3D_Job171/run_it025_class003.mrc

Opened run_it025_class003.mrc as #1, grid size 256,256,256, pixel 1.09, shown
at level 0.000507, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job171/run_it025_class002.mrc

Opened run_it025_class002.mrc as #2, grid size 256,256,256, pixel 1.09, shown
at level 0.000511, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job171/run_it025_class001.mrc

Opened run_it025_class001.mrc as #3, grid size 256,256,256, pixel 1.09, shown
at level 0.000505, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job171/run_it025_class004.mrc

Opened run_it025_class004.mrc as #4, grid size 256,256,256, pixel 1.09, shown
at level 0.000511, step 1, values float32  

> volume level 0.3

> volume #1 level 0.006789

> tile

1 model tiled  

> tile

1 model tiled  

> volume level 0.00679

> tile

4 models tiled  

> volume #1 level 0.005695

> volume level 0.00569

> close session

> open C:/Users/lilyh/Downloads/run_it016_class001.mrc

Opened run_it016_class001.mrc as #1, grid size 256,256,256, pixel 1.09, shown
at level 0.00271, step 1, values float32  

> open C:/Users/lilyh/Downloads/run_it016_class005.mrc

Opened run_it016_class005.mrc as #2, grid size 256,256,256, pixel 1.09, shown
at level 0.00283, step 1, values float32  

> open C:/Users/lilyh/Downloads/run_it016_class004.mrc

Opened run_it016_class004.mrc as #3, grid size 256,256,256, pixel 1.09, shown
at level 0.00277, step 1, values float32  

> open C:/Users/lilyh/Downloads/run_it016_class003.mrc

Opened run_it016_class003.mrc as #4, grid size 256,256,256, pixel 1.09, shown
at level 0.00278, step 1, values float32  

> open C:/Users/lilyh/Downloads/run_it016_class002.mrc

Opened run_it016_class002.mrc as #5, grid size 256,256,256, pixel 1.09, shown
at level 0.00274, step 1, values float32  

> volume level 0.00569

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> volume #1 level 0.008511

> show #!2 models

> hide #!1 models

> volume #1 level 0.01015

> hide #!1 models

> volume #2 level 0.009196

> hide #!2 models

> show #!3 models

> volume #3 level 0.009482

> hide #!3 models

> show #!4 models

> volume #4 level 0.006495

> hide #!4 models

> show #!5 models

> volume #5 level 0.006699

> volume #5 level 0.00796

> close session

> open C:/Users/lilyh/Downloads/Class3D_Job172/run_it025_class002.mrc

Opened run_it025_class002.mrc as #1, grid size 256,256,256, pixel 1.09, shown
at level 0.000511, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job172/run_it025_class001.mrc

Opened run_it025_class001.mrc as #2, grid size 256,256,256, pixel 1.09, shown
at level 0.000505, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job172/run_it025_class004.mrc

Opened run_it025_class004.mrc as #3, grid size 256,256,256, pixel 1.09, shown
at level 0.000511, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job172/run_it025_class003.mrc

Opened run_it025_class003.mrc as #4, grid size 256,256,256, pixel 1.09, shown
at level 0.000507, step 1, values float32  

> volume level 0.00569

> hide #!4 models

> hide #!3 models

> hide #!2 models

> tile

1 model tiled  

> show #!3 models

> show #!4 models

> show #!2 models

> tile

4 models tiled  

> volume #1 level 0.006258

> close session

> open
> C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb

Chain information for
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
#1  
---  
Chain | Description  
B | No description available  
C | No description available  
  

> open
> C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb

Chain information for
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
#2  
---  
Chain | Description  
B | No description available  
C | No description available  
  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J482_003_volume_map_sharp.mrc

Opened cryosparc_P122_J482_003_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.09, shown at level 0.0359, step 1, values float32  

> ~tile

> volume #3 level 0.1907

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

Drag select of 3 cryosparc_P122_J482_003_volume_map_sharp.mrc  

> view matrix models #3,1,0,0,-166.29,0,1,0,-175.89,0,0,1,-100.88

Drag select of 4 residues  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.97633,-0.14064,0.16431,-5.2566,0.021158,-0.81816,-0.5746,5.6834,0.21524,-0.55752,0.80177,2.3439

Drag select of 3 cryosparc_P122_J482_003_volume_map_sharp.mrc  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,-134.31,0,1,0,-151.91,0,0,1,-130.5

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.87002,0.44753,0.20683,-208.17,0.2944,-0.13511,-0.94608,98.666,-0.39545,0.88401,-0.2493,-27.679

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.87002,0.44753,0.20683,-212.56,0.2944,-0.13511,-0.94608,116.66,-0.39545,0.88401,-0.2493,-30.3

> fitmap #1 inMap #3

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#1) to map cryosparc_P122_J482_003_volume_map_sharp.mrc (#3) using 4737 atoms  
average map value = 0.1856, steps = 156  
shifted from previous position = 7.64  
rotated from previous position = 26.9 degrees  
atoms outside contour = 2745, contour level = 0.19069  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#1) relative to cryosparc_P122_J482_003_volume_map_sharp.mrc (#3)
coordinates:  
Matrix rotation and translation  
-0.83214070 0.17998909 -0.52454334 140.52207659  
-0.49786038 -0.65912186 0.56364293 134.67261516  
-0.24428840 0.73017959 0.63809159 142.54394458  
Axis 0.22140877 -0.37259604 -0.90119384  
Axis point 96.40388725 19.11225562 0.00000000  
Rotation angle (degrees) 157.90866282  
Shift along axis -147.52538930  
  

> fitmap #2 inMap #3

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#2) to map cryosparc_P122_J482_003_volume_map_sharp.mrc (#3) using 4737 atoms  
average map value = 0.1868, steps = 232  
shifted from previous position = 4.35  
rotated from previous position = 48.8 degrees  
atoms outside contour = 2724, contour level = 0.19069  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#2) relative to cryosparc_P122_J482_003_volume_map_sharp.mrc (#3)
coordinates:  
Matrix rotation and translation  
0.22180925 0.37383074 -0.90058379 140.05335003  
0.94562907 0.14284690 0.29219918 135.77559386  
0.23787864 -0.91643073 -0.32182045 143.26005403  
Axis -0.68825231 -0.64829556 0.32560962  
Axis point 0.00000000 83.08323191 84.71542206  
Rotation angle (degrees) 118.59284157  
Shift along axis -137.76790527  
  

> hide #1 models

> hide #2 models

> hide #!3 models

> show #1 models

> molmap #1 10 onGrid #3

Opened
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
map 10 as #4, grid size 256,256,256, pixel 1.09, shown at level 0.0546, step
1, values float32  

> hide #1 models

> show #2 models

> hide #!4 models

> molmap #2 10 onGrid #3

Opened
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
map 10 as #5, grid size 256,256,256, pixel 1.09, shown at level 0.0528, step
1, values float32  

> hide #2 models

> show #2 models

> hide #2 models

> show #!4 models

> hide #!5 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!4 models

> show #!4 models

> close #4

> close #5

> molmap #2 6 onGrid #3

Opened
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
map 6 as #4, grid size 256,256,256, pixel 1.09, shown at level 0.0793, step 1,
values float32  

> volume #4 level 0.3144

> close #4

> molmap #2 8 onGrid #3

Opened
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
map 8 as #4, grid size 256,256,256, pixel 1.09, shown at level 0.0638, step 1,
values float32  

> molmap #2 9 onGrid #3

Opened
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
map 9 as #4, grid size 256,256,256, pixel 1.09, shown at level 0.0578, step 1,
values float32  

> molmap #1 9 onGrid #3

Opened
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
map 9 as #5, grid size 256,256,256, pixel 1.09, shown at level 0.0601, step 1,
values float32  

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> save C:/Users/lilyh/Desktop/Mask_Generation_J65/rank2_molmap9A.mrc models #4

> save C:/Users/lilyh/Desktop/Mask_Generation_J65/rank1_molmap9A.mrc models #5

> hide #!5 models

> hide #!4 models

> show #2 models

> combine #1 #2

Remapping chain ID 'B' in
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
#2 to 'D'  
Remapping chain ID 'C' in
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
#2 to 'E'  

> hide #2 models

> hide #6 models

> show #6 models

> hide #6 models

> show #2 models

> show #1 models

> hide #1 models

> hide #2 models

> show #6 models

> hide #6 models

> show #6 models

> hide #6 models

> show #!5 models

> hide #5.1 models

> hide #!5 models

> show #6 models

> select add #6

9474 atoms, 9646 bonds, 1170 residues, 3 models selected  

> select subtract #6

2 models selected  

> select add #6

9474 atoms, 9646 bonds, 1170 residues, 3 models selected  

> hide #6 models

> show #6 models

> hide #6 models

> open C:/Users/lilyh/Downloads/cryosparc_P104_J3813_003_volume_map.mrc

Opened cryosparc_P104_J3813_003_volume_map.mrc as #7, grid size 256,256,256,
pixel 1.09, shown at level 0.00684, step 1, values float32  

> volume #7 level 0.1148

> volume #7 level 0.1211

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class001.mrc

Opened run_it025_class001.mrc as #8, grid size 256,256,256, pixel 1.09, shown
at level 0.00129, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class005.mrc

Opened run_it025_class005.mrc as #9, grid size 256,256,256, pixel 1.09, shown
at level 0.00106, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class004.mrc

Opened run_it025_class004.mrc as #10, grid size 256,256,256, pixel 1.09, shown
at level 0.00094, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class003.mrc

Opened run_it025_class003.mrc as #11, grid size 256,256,256, pixel 1.09, shown
at level 0.00107, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class002.mrc

Opened run_it025_class002.mrc as #12, grid size 256,256,256, pixel 1.09, shown
at level 0.00137, step 1, values float32  

> titile

Unknown command: titile  

> tile

5 models tiled  

> volume level 0.003

> volume #12 level 0.005901

> volume level 0.0059

> volume #11 level 0.003133

> volume #9 level 0.003281

> volume level 0.00328

> open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class006.mrc

Opened run_it025_class006.mrc as #13, grid size 256,256,256, pixel 1.09, shown
at level 0.00103, step 1, values float32  

> volume level 0.00328

> tile

6 models tiled  

> select #13

2 models selected  

> select #13

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #13,-0.3926,0.33493,0.85656,-255.41,-0.81533,-0.55768,-0.15564,282.95,0.42556,-0.75948,0.49202,-170.95

> view matrix models
> #13,-0.79801,-0.50365,0.33094,-10.132,0.46274,-0.86389,-0.1989,152.61,0.38608,-0.0055828,0.92245,-329.17

> select clear

> volume #12 level 0.004396

> volume #11 level 0.006833

> volume #13 level 0.002836

> volume #10 level 0.003457

> volume #9 level 0.002396

> volume #8 level 0.003082

> volume #13 level 0.007239

> volume #13 level 0.007165

> volume #13 level 0.005574

> volume #11 level 0.004612

> volume level 0.004

> volume #8 level 0.002216

> volume #8 level 0.005916

> ~tile

> hide #!8 models

> hide #!9 models

> hide #!10 models

> hide #!12 models

> fitmap #11 inMap #13

Fit map run_it025_class003.mrc in map run_it025_class006.mrc using 43937
points  
correlation = 0.98, correlation about mean = 0.7752, overlap = 1.881  
steps = 68, shift = 0.168, angle = 3.81 degrees  
  
Position of run_it025_class003.mrc (#11) relative to run_it025_class006.mrc
(#13) coordinates:  
Matrix rotation and translation  
0.99800934 -0.06302882 0.00217236 8.74105301  
0.06296948 0.99779424 0.02101206 -11.26954788  
-0.00349194 -0.02083345 0.99977686 3.50822058  
Axis -0.31489768 0.04262519 0.94816799  
Axis point 183.70273900 133.34854015 0.00000000  
Rotation angle (degrees) 3.80971165  
Shift along axis 0.09347853  
  

> volume #13 level 0.005221

> volume #11 level 0.005572

> volume #11 level 0.007348

> volume #13 level 0.007441

> tile

2 models tiled  

> hide #!11 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!9 models

> volume #9 level 0.003558

> volume #9 level 0.002741

> show #1 models

> hide #1 models

> close session

> open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class006.mrc

Opened run_it025_class006.mrc as #1, grid size 256,256,256, pixel 1.09, shown
at level 0.00103, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class005.mrc

Opened run_it025_class005.mrc as #2, grid size 256,256,256, pixel 1.09, shown
at level 0.00106, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class004.mrc

Opened run_it025_class004.mrc as #3, grid size 256,256,256, pixel 1.09, shown
at level 0.00094, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class003.mrc

Opened run_it025_class003.mrc as #4, grid size 256,256,256, pixel 1.09, shown
at level 0.00107, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class002.mrc

Opened run_it025_class002.mrc as #5, grid size 256,256,256, pixel 1.09, shown
at level 0.00137, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class001.mrc

Opened run_it025_class001.mrc as #6, grid size 256,256,256, pixel 1.09, shown
at level 0.00129, step 1, values float32  

> open
> C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb

Chain information for
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
#7  
---  
Chain | Description  
B | No description available  
C | No description available  
  

> open
> C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb

Chain information for
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
#8  
---  
Chain | Description  
B | No description available  
C | No description available  
  

> ~tile

> ui mousemode right "translate selected models"

Drag select of 1153 residues  

> ui mousemode right "translate selected models"

> view matrix models
> #7,1,0,0,137.53,0,1,0,146,0,0,1,0,#8,1,0,0,137.53,0,1,0,146,0,0,1,0

> view matrix models
> #7,1,0,0,114.21,0,1,0,131.39,0,0,1,140.78,#8,1,0,0,114.21,0,1,0,131.39,0,0,1,140.78

> select up

9403 atoms, 9574 bonds, 1162 residues, 2 models selected  

> volume level 0.004

> hide #!1 models

> hide #!2 models

> hide #!3 models

> show #!2 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> volume #2 level 0.002844

> select #2

2 models selected  

> select clear

> ui mousemode right "rotate selected models"

Drag select of 3 residues  

> view matrix models
> #7,-0.26975,0.35466,-0.89524,106.01,-0.92422,-0.35631,0.13733,134.33,-0.27028,0.86444,0.4239,134.69

Drag select of 5 residues  

> view matrix models
> #8,-0.23883,0.13926,-0.96102,120.55,0.97103,0.042055,-0.23522,124.36,0.0076582,-0.98936,-0.14527,138.34

> fitmap #7 inMap #2

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#7) to map run_it025_class005.mrc (#2) using 4737 atoms  
average map value = 0.003537, steps = 300  
shifted from previous position = 27.6  
rotated from previous position = 60 degrees  
atoms outside contour = 2044, contour level = 0.0028435  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#7) relative to run_it025_class005.mrc (#2) coordinates:  
Matrix rotation and translation  
0.67041123 0.22239462 -0.70787668 131.93155495  
-0.74176984 0.22410593 -0.63210285 137.33856533  
0.01806309 0.94885043 0.31520876 142.44349169  
Axis 0.79485896 -0.36498215 -0.48475484  
Axis point 0.00000000 4.25911866 203.78217280  
Rotation angle (degrees) 83.98072869  
Shift along axis -14.30931872  
  

> fitmap #8 inMap #2

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#8) to map run_it025_class005.mrc (#2) using 4737 atoms  
average map value = 0.004346, steps = 364  
shifted from previous position = 21.6  
rotated from previous position = 35.2 degrees  
atoms outside contour = 1606, contour level = 0.0028435  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#8) relative to run_it025_class005.mrc (#2) coordinates:  
Matrix rotation and translation  
0.26484965 0.37638631 -0.88779952 139.78430774  
0.93516327 0.12431824 0.33168451 136.13979180  
0.23521118 -0.91808404 -0.31905701 142.80814378  
Axis -0.70581293 -0.63422582 0.31557204  
Axis point 0.00000000 85.31235050 82.36563740  
Rotation angle (degrees) 117.70663459  
Shift along axis -139.93868660  
  
Drag select of 7 residues  

> ui mousemode right "rotate selected models"

> view matrix models
> #7,-0.9098,0.34259,-0.23432,127.82,-0.39996,-0.5728,0.71549,145.72,0.1109,0.74467,0.65815,144.6

> fitmap #7 inMap #2

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#7) to map run_it025_class005.mrc (#2) using 4737 atoms  
average map value = 0.004441, steps = 184  
shifted from previous position = 16.8  
rotated from previous position = 21.8 degrees  
atoms outside contour = 1577, contour level = 0.0028435  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#7) relative to run_it025_class005.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.81810596 0.20765135 -0.53626815 140.57361684  
-0.52497845 -0.65032553 0.54906677 135.16355895  
-0.23473442 0.73072403 0.64104768 142.16276519  
Axis 0.22349149 -0.37097458 -0.90134867  
Axis point 97.41629186 17.89919390 0.00000000  
Rotation angle (degrees) 156.02063833  
Shift along axis -146.86345505  
  

> select clear

> open C:/Users/lilyh/Downloads/cryosparc_P122_J505_mask.mrc

Opened cryosparc_P122_J505_mask.mrc as #9, grid size 256,256,256, pixel 1.09,
shown at level 5e-05, step 1, values float32  

> select #9

2 models selected  

> transparency #9.1 50

> select clear

> volume #2 level 0.004442

> volume #2 level 0.005905

> hide #7 models

> show #7 models

> hide #!9 models

> volume #2 level 0.003388

> volume #2 level 0.003864

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!4 models

> volume #4 level 0.003795

> hide #!4 models

> show #!5 models

> volume #5 level 0.006975

> volume #5 level 0.005339

> volume #6 level 0.005784

> open
> C:/Users/lilyh/Downloads/cryosparc_P104_J3423_class_02_00122_volume_sharp.mrc

Opened cryosparc_P104_J3423_class_02_00122_volume_sharp.mrc as #10, grid size
128,128,128, pixel 2.17, shown at level 0.0672, step 1, values float32  

> open
> C:/Users/lilyh/Downloads/cryosparc_P104_J3423_class_01_00122_volume_sharp.mrc

Opened cryosparc_P104_J3423_class_01_00122_volume_sharp.mrc as #11, grid size
128,128,128, pixel 2.17, shown at level 0.0692, step 1, values float32  

> volume #10 level 0.2801

> hide #8 models

> hide #7 models

> volume #10 level 0.1828

> volume #11 level 0.1865

> select #10

2 models selected  

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #10,-0.89307,-0.23379,0.38441,244.31,-0.23294,0.97123,0.049517,29.763,-0.38493,-0.045323,-0.92183,320.44

> fitmap #10 inMap #11

Fit map cryosparc_P104_J3423_class_02_00122_volume_sharp.mrc in map
cryosparc_P104_J3423_class_01_00122_volume_sharp.mrc using 8257 points  
correlation = 0.9071, correlation about mean = 0.5993, overlap = 1160  
steps = 196, shift = 2.97, angle = 62.1 degrees  
  
Position of cryosparc_P104_J3423_class_02_00122_volume_sharp.mrc (#10)
relative to cryosparc_P104_J3423_class_01_00122_volume_sharp.mrc (#11)
coordinates:  
Matrix rotation and translation  
-0.71707819 0.69697322 0.00521346 140.85245041  
0.69697654 0.71709246 -0.00145090 -54.78773595  
-0.00474977 0.00259325 -0.99998535 273.87631528  
Axis 0.37610463 0.92657715 0.00030830  
Axis point 81.94288839 0.00000000 136.74420261  
Rotation angle (degrees) 179.69195567  
Shift along axis 2.29463106  
  

> select clear

> show #8 models

> hide #8 models

> show #7 models

> hide #7 models

> show #8 models

> show #7 models

> fitmap #7 inMap #10

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#7) to map cryosparc_P104_J3423_class_02_00122_volume_sharp.mrc (#10) using
4737 atoms  
average map value = 0.2848, steps = 184  
shifted from previous position = 5.22  
rotated from previous position = 31.3 degrees  
atoms outside contour = 1714, contour level = 0.1828  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#7) relative to cryosparc_P104_J3423_class_02_00122_volume_sharp.mrc (#10)
coordinates:  
Matrix rotation and translation  
0.66845251 -0.31728464 0.67268246 136.65439192  
-0.70035335 -0.57296099 0.42570046 134.37842005  
0.25035259 -0.75567596 -0.60520857 131.31049403  
Axis -0.90059359 0.32195291 -0.29202312  
Axis point 0.00000000 111.70347316 7.72215948  
Rotation angle (degrees) 139.01301011  
Shift along axis -118.15224739  
  

> fitmap #8 inMap #10

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#8) to map cryosparc_P104_J3423_class_02_00122_volume_sharp.mrc (#10) using
4737 atoms  
average map value = 0.2896, steps = 196  
shifted from previous position = 3.65  
rotated from previous position = 29.1 degrees  
atoms outside contour = 1716, contour level = 0.1828  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#8) relative to cryosparc_P104_J3423_class_02_00122_volume_sharp.mrc (#10)
coordinates:  
Matrix rotation and translation  
0.00075152 -0.37212803 0.92818110 137.57900910  
0.97707992 0.19785664 0.07853393 135.30883867  
-0.21287147 0.90684810 0.36374751 130.60755963  
Axis 0.42444358 0.58469655 0.69135923  
Axis point 27.47524782 36.09958021 0.00000000  
Rotation angle (degrees) 102.63986242  
Shift along axis 227.80588093  
  

> hide #7 models

> hide #8 models

> show #8 models

> show #7 models

> hide #!11 models

> show #!11 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> select #11

2 models selected  

> transparency #11.1 40

> select clear

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!2 models

> volume #2 level 0.003626

> fitmap #2 inMap #11

Fit map run_it025_class005.mrc in map
cryosparc_P104_J3423_class_01_00122_volume_sharp.mrc using 50478 points  
correlation = 0.9061, correlation about mean = 0.4069, overlap = 116.1  
steps = 104, shift = 2.12, angle = 26.6 degrees  
  
Position of run_it025_class005.mrc (#2) relative to
cryosparc_P104_J3423_class_01_00122_volume_sharp.mrc (#11) coordinates:  
Matrix rotation and translation  
0.89449861 0.44705699 0.00350577 -49.12452265  
-0.44699715 0.89418161 0.02515531 74.93541992  
0.00811106 -0.02406845 0.99967741 1.93985496  
Axis -0.05497282 -0.00514317 -0.99847461  
Axis point 134.14963204 141.49583994 0.00000000  
Rotation angle (degrees) 26.59685498  
Shift along axis 0.37821183  
  

> hide #7 models

> hide #8 models

> volume #2 level 0.003898

> volume #11 level 0.1809

> volume #2 level 0.003388

> open C:/Users/lilyh/Downloads/cryosparc_P104_J3410_class_00_final_volume.mrc

Opened cryosparc_P104_J3410_class_00_final_volume.mrc as #12, grid size
128,128,128, pixel 2.17, shown at level 0.025, step 1, values float32  

> volume #12 level 0.1722

> volume #12 level 0.1402

> hide #!12 models

> hide #!11 models

> volume #2 level 0.002912

> show #!3 models

> close session

> open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class005.mrc

Opened run_it025_class005.mrc as #1, grid size 256,256,256, pixel 1.09, shown
at level 0.00106, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class004.mrc

Opened run_it025_class004.mrc as #2, grid size 256,256,256, pixel 1.09, shown
at level 0.00094, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class003.mrc

Opened run_it025_class003.mrc as #3, grid size 256,256,256, pixel 1.09, shown
at level 0.00107, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class002.mrc

Opened run_it025_class002.mrc as #4, grid size 256,256,256, pixel 1.09, shown
at level 0.00137, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class001.mrc

Opened run_it025_class001.mrc as #5, grid size 256,256,256, pixel 1.09, shown
at level 0.00129, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class006.mrc

Opened run_it025_class006.mrc as #6, grid size 256,256,256, pixel 1.09, shown
at level 0.00103, step 1, values float32  

> volume level 0.003

> tile

6 models tiled  

> hide #!6 models

> hide #!5 models

> close session

> open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class004.mrc

Opened run_it025_class004.mrc as #1, grid size 256,256,256, pixel 1.09, shown
at level 0.00105, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class003.mrc

Opened run_it025_class003.mrc as #2, grid size 256,256,256, pixel 1.09, shown
at level 0.00126, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class002.mrc

Opened run_it025_class002.mrc as #3, grid size 256,256,256, pixel 1.09, shown
at level 0.00117, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class001.mrc

Opened run_it025_class001.mrc as #4, grid size 256,256,256, pixel 1.09, shown
at level 0.000995, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class005.mrc

Opened run_it025_class005.mrc as #5, grid size 256,256,256, pixel 1.09, shown
at level 0.000954, step 1, values float32  

> volume level 0.003

> tile

5 models tiled  

> volume #3 level 0.006424

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class003.mrc

Opened run_it025_class003.mrc as #6, grid size 256,256,256, pixel 1.09, shown
at level 0.00128, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class002.mrc

Opened run_it025_class002.mrc as #7, grid size 256,256,256, pixel 1.09, shown
at level 0.000939, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class001.mrc

Opened run_it025_class001.mrc as #8, grid size 256,256,256, pixel 1.09, shown
at level 0.000951, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class004.mrc

Opened run_it025_class004.mrc as #9, grid size 256,256,256, pixel 1.09, shown
at level 0.00102, step 1, values float32  

> volume level 0.003

> tile

4 models tiled  

> volume #6 level 0.002824

> volume #9 level 0.004489

> volume #8 level 0.006079

> volume #7 level 0.005781

> close session

> open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class005.mrc

Opened run_it025_class005.mrc as #1, grid size 256,256,256, pixel 1.09, shown
at level 0.0011, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class004.mrc

Opened run_it025_class004.mrc as #2, grid size 256,256,256, pixel 1.09, shown
at level 0.000697, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class003.mrc

Opened run_it025_class003.mrc as #3, grid size 256,256,256, pixel 1.09, shown
at level 0.000861, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class002.mrc

Opened run_it025_class002.mrc as #4, grid size 256,256,256, pixel 1.09, shown
at level 0.00113, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class001.mrc

Opened run_it025_class001.mrc as #5, grid size 256,256,256, pixel 1.09, shown
at level 0.000747, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class006.mrc

Opened run_it025_class006.mrc as #6, grid size 256,256,256, pixel 1.09, shown
at level 0.000788, step 1, values float32  

> volume level 0.003

> tile

6 models tiled  

> close session

> open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class004.mrc

Opened run_it025_class004.mrc as #1, grid size 256,256,256, pixel 1.09, shown
at level 0.00102, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class003.mrc

Opened run_it025_class003.mrc as #2, grid size 256,256,256, pixel 1.09, shown
at level 0.00128, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class002.mrc

Opened run_it025_class002.mrc as #3, grid size 256,256,256, pixel 1.09, shown
at level 0.000939, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class001.mrc

Opened run_it025_class001.mrc as #4, grid size 256,256,256, pixel 1.09, shown
at level 0.000951, step 1, values float32  

> volume level 0.003

> tile

4 models tiled  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #2 level 0.003843

> volume #2 level 0.002895

> volume #4 level 0.003456

> volume #3 level 0.003193

> volume #1 level 0.006309

> volume #3 level 0.001957

> volume #3 level 0.005626

> volume #4 level 0.006535

> hide #!3 models

> hide #!4 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> volume #2 level 0.003281

> volume #2 level 0.003879

> volume #2 level 0.003773

> volume #2 level 0.003351

> open C:/Users/lilyh/Downloads/cryosparc_P122_J505_mask.mrc

Opened cryosparc_P122_J505_mask.mrc as #5, grid size 256,256,256, pixel 1.09,
shown at level 5e-05, step 1, values float32  

> close session

> t~ile

Unknown command: t~ile  

> ~tile

No models found for tiling.  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J505_mask.mrc

Opened cryosparc_P122_J505_mask.mrc as #1, grid size 256,256,256, pixel 1.09,
shown at level 5e-05, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class003.mrc

Opened run_it025_class003.mrc as #2, grid size 256,256,256, pixel 1.09, shown
at level 0.00128, step 1, values float32  

> volume #2 level 0.004269

> volume #2 level 0.005218

> select add #1

2 models selected  

> transparency #1.1 40

> volume #2 level 0.007081

> volume #2 level 0.005886

> hide #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!2 models

> close session

> open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class003.mrc

Opened run_it025_class003.mrc as #1, grid size 256,256,256, pixel 1.09, shown
at level 0.00126, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class002.mrc

Opened run_it025_class002.mrc as #2, grid size 256,256,256, pixel 1.09, shown
at level 0.00117, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class001.mrc

Opened run_it025_class001.mrc as #3, grid size 256,256,256, pixel 1.09, shown
at level 0.000995, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class005.mrc

Opened run_it025_class005.mrc as #4, grid size 256,256,256, pixel 1.09, shown
at level 0.000954, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class004.mrc

Opened run_it025_class004.mrc as #5, grid size 256,256,256, pixel 1.09, shown
at level 0.00105, step 1, values float32  

> tile

5 models tiled  

> volume level 0.003

> hide #!1 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 456, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
  
See log for complete Python traceback.  
  

> close session

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 456, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
  
See log for complete Python traceback.  
  

> open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class004.mrc

Opened run_it025_class004.mrc as #1, grid size 256,256,256, pixel 1.09, shown
at level 0.00158, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class003.mrc

Opened run_it025_class003.mrc as #2, grid size 256,256,256, pixel 1.09, shown
at level 0.00159, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class002.mrc

Opened run_it025_class002.mrc as #3, grid size 256,256,256, pixel 1.09, shown
at level 0.0016, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class001.mrc

Opened run_it025_class001.mrc as #4, grid size 256,256,256, pixel 1.09, shown
at level 0.00158, step 1, values float32  

> volume level 0.003

> tile

4 models tiled  

> volume level 0.004

> volume #1 level 0.004881

> volume level 0.003

> ~tile

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 456, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
  
See log for complete Python traceback.  
  

> hide #!2 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 456, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
  
See log for complete Python traceback.  
  

> show #!2 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 456, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
  
See log for complete Python traceback.  
  

> close session

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 456, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
  
See log for complete Python traceback.  
  

> open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class003.mrc

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 456, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
  
See log for complete Python traceback.  
  
Opened run_it025_class003.mrc as #1, grid size 256,256,256, pixel 1.09, shown
at level 0.00128, step 1, values float32  

> volume #1 level 0.003667

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 456, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
  
See log for complete Python traceback.  
  

> close session

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 456, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.14756 Core Profile Forward-Compatible Context 20.40.68.03 27.20.14068.3000
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: Microsoft Corporation
Model: Surface Laptop 4
OS: Microsoft Windows 11 Home (Build 22621)
Memory: 8,002,093,056
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 Microsoft Surface (R) Edition
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.2.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0