ChimeraX bug report submission

[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.  
  

> open C:/Users/lilyh/Downloads/Class3D_Job214/run_it025_class001.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.  
  
File size 42254336 too small for grid size (256,256,256)  

> open C:/Users/lilyh/Downloads/Class3D_Job214/run_it025_class001.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.  
  
File size 42254336 too small for grid size (256,256,256)  

> open "C:\Users\lilyh\Downloads\cryodrgn training test
> J65\test_kmeans20\vol_001.mrc" format 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 vol_001.mrc as #1, grid size 128,128,128, pixel 1.09, shown at level
0.011, step 1, values float32  

> volume #1 level 0.05401

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.  
  

> volume #1 level 0.05062

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/Refine3D_Job216/run_class001.mrc

Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.09, shown at
level 0.00114, step 1, values float32  

> volume #1 level 0.002668

> volume #1 level 0.00279

[Repeated 1 time(s)]

> volume #1 level 0.002887

> volume #1 level 0.004101

> volume #1 level 0.002862

> close session

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

Opened run_it025_class003.mrc as #1, 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 #2, 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 #3, 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_class004.mrc

Opened run_it025_class004.mrc as #4, grid size 256,256,256, pixel 1.09, shown
at level 0.00158, step 1, values float32  

> tile

4 models tiled  

> volume level 0.34

> volume level 0.035

> volume level

Missing "level" keyword's argument  

> volume #1 level 0.0058

> volume level 0.005

> volume #3 level 0.00611

> close session

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

Opened run_it025_class003.mrc as #1, 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 #2, 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 #3, 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 #4, grid size 256,256,256, pixel 1.09, shown
at level 0.00102, step 1, values float32  

> volume level 0.005

> tile

4 models tiled  

> 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  

> tile

5 models tiled  

> volume level 0.005

> volume level 0.003

> hide #!3 models

> show #!3 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  

> volume level 0.003

> tile

6 models tiled  

> 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  

> tile

6 models tiled  

> volume level 0.004

> volume level 0.003

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 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  

> volume level 0.003

> tile

6 models tiled  

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!5 models

> hide #!6 models

> ~tile

> close session

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

Opened run_it025_class005.mrc as #1, 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 #2, 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 #3, 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 #4, 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 #5, grid size 256,256,256, pixel 1.09, shown
at level 0.000995, step 1, values float32  

> tile

5 models tiled  

> volume level 0.005

Drag select of 1 run_it025_class005.mrc , 2 run_it025_class004.mrc , 3
run_it025_class003.mrc , 4 run_it025_class002.mrc , 5 run_it025_class001.mrc  

> color #1.1#2.1#3.1#4.1#5.1 yellow

> select clear

> 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 0.005

> tile

9 models tiled  

> volume #1 level 0.008094

> close session

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

Opened run_it025_class001.mrc as #1, 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 #2, 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 #3, 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 #4, grid size 256,256,256, pixel 1.09, shown
at level 0.000939, step 1, values float32  

> color dark gray

> 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  

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

Opened run_it025_class004.mrc as #6, 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 #7, 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 #8, 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 #9, grid size 256,256,256, pixel 1.09, shown
at level 0.000995, step 1, values float32  

> tile

9 models tiled  

> volume level 0.005

> volume #1 level 0.003593

> volume level 0.003

> close session

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

Opened run_it025_class003.mrc as #1, 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 #2, 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 #3, 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_class004.mrc

Opened run_it025_class004.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  

> ~tile

> volume level 0.006

> volume level 0.004

> open C:/Users/lilyh/Downloads/Class3D_Job214/run_it025_class001.mrc

File size 42254336 too small for grid size (256,256,256)  

> open C:/Users/lilyh/Downloads/Class3D_Job214/run_it025_class002.mrc

MRC file is truncated. Failed reading 1 values, type int32  

> hide #!3 models

> hide #!4 models

> hide #!2 models

> volume #1 level 0.007255

> hide #!1 models

> close session

> open C:/Users/lilyh/Downloads/cryosparc_P122_J561_class_02_final_volume.mrc

Opened cryosparc_P122_J561_class_02_final_volume.mrc as #1, grid size
128,128,128, pixel 2.17, shown at level 0.0361, step 1, values float32  

> volume #1 level 0.2064

> volume #1 level 0.1013

> volume #1 level 0.3732

> close #1

> open
> C:/Users/lilyh/Downloads/cryosparc_P104_J3831_class_00_00064_volume_sharp.mrc

Opened cryosparc_P104_J3831_class_00_00064_volume_sharp.mrc as #1, grid size
128,128,128, pixel 2.17, shown at level 0.069, step 1, values float32  

> volume #1 level 0.3242

> volume #1 level 0.5218

> volume #1 level 0.2542

> volume #1 level 0.1843

> volume #1 level 0.2584

> close session

> open C:/Users/lilyh/Downloads/cryosparc_P104_J3840_class_00_00014_volume.mrc

Opened cryosparc_P104_J3840_class_00_00014_volume.mrc as #1, grid size
100,100,100, pixel 2.78, shown at level 0.0938, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P104_J3840_class_02_00014_volume.mrc

Opened cryosparc_P104_J3840_class_02_00014_volume.mrc as #2, grid size
100,100,100, pixel 2.78, shown at level 0.0776, step 1, values float32  

> volume level 0.3

> volume level 0.01

> volume level 0.2

> select clear

> hide #!2 models

> volume #1 level 0.1793

> show #!2 models

> hide #!1 models

> volume #2 level 0.1643

> show #!1 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
#3  
---  
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
#4  
---  
Chain | Description  
B | No description available  
C | No description available  
  
Drag select of 664 residues  

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> view matrix models
> #3,1,0,0,-6.5711,0,1,0,148.71,0,0,1,146.56,#4,1,0,0,-6.5711,0,1,0,148.71,0,0,1,146.56

> view matrix models
> #3,1,0,0,140.73,0,1,0,142.06,0,0,1,166.35,#4,1,0,0,140.73,0,1,0,142.06,0,0,1,166.35

Drag select of 11 residues  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.57291,0.56028,-0.59821,131.63,-0.81897,-0.42042,0.39057,146.37,-0.03267,0.71368,0.69971,162.45

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.57291,0.56028,-0.59821,135.24,-0.81897,-0.42042,0.39057,134.9,-0.03267,0.71368,0.69971,142.91

Drag select of 4 residues  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.84866,0.014175,-0.52876,151.09,0.50027,0.34616,-0.79366,137.46,0.17178,-0.93807,-0.30086,162.79

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.84866,0.014175,-0.52876,143.91,0.50027,0.34616,-0.79366,143.32,0.17178,-0.93807,-0.30086,140.56

> fitmap #3 inMap #1

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) to map cryosparc_P104_J3840_class_00_00014_volume.mrc (#1) using 4737
atoms  
average map value = 0.2715, steps = 128  
shifted from previous position = 4.03  
rotated from previous position = 24.4 degrees  
atoms outside contour = 1635, contour level = 0.17928  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) relative to cryosparc_P104_J3840_class_00_00014_volume.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.80367765 0.20930131 -0.55704142 139.20195012  
-0.56151103 -0.57663386 0.59346331 137.70755920  
-0.19699630 0.78973812 0.58095276 140.63323724  
Axis 0.22480157 -0.41237440 -0.88284291  
Axis point 97.39666990 13.51352648 0.00000000  
Rotation angle (degrees) 154.11595677  
Shift along axis -149.65131159  
  

> fitmap #4 inMap #1

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#4) to map cryosparc_P104_J3840_class_00_00014_volume.mrc (#1) using 4737
atoms  
average map value = 0.2727, steps = 156  
shifted from previous position = 6.21  
rotated from previous position = 12.7 degrees  
atoms outside contour = 1648, contour level = 0.17928  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#4) relative to cryosparc_P104_J3840_class_00_00014_volume.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.72465165 0.11784257 -0.67896473 139.13357974  
0.67018689 0.34985529 -0.65456153 139.46728049  
0.16040419 -0.92936236 -0.33249977 140.25765476  
Axis -0.26380023 -0.80576799 0.53023333  
Axis point 15.37419665 -0.00000000 136.83963007  
Rotation angle (degrees) 148.61069825  
Shift along axis -74.71245831  
  

> select clear

> select #4/C:1344

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.019792,0.61825,-0.78573,135.09,0.93872,0.259,0.22744,138.85,0.34412,-0.74208,-0.57524,139.06

> fitmap #4 inMap #1

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#4) to map cryosparc_P104_J3840_class_00_00014_volume.mrc (#1) using 4737
atoms  
average map value = 0.274, steps = 364  
shifted from previous position = 5.89  
rotated from previous position = 22.2 degrees  
atoms outside contour = 1693, contour level = 0.17928  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#4) relative to cryosparc_P104_J3840_class_00_00014_volume.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.00403472 0.32547376 -0.94554246 139.28256451  
0.98794031 0.14765329 0.04660945 138.66762524  
0.15478261 -0.93395145 -0.32214439 141.81145818  
Axis -0.60682679 -0.68094366 0.40997193  
Axis point -63.57020772 0.00000000 137.27636390  
Rotation angle (degrees) 126.10471944  
Shift along axis -120.80651422  
  

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> open C:/Users/lilyh/Downloads/cryosparc_P104_J3841_class_00_00015_volume.mrc

Opened cryosparc_P104_J3841_class_00_00015_volume.mrc as #5, grid size
100,100,100, pixel 2.78, shown at level 0.0751, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P104_J3841_class_02_00015_volume.mrc

Opened cryosparc_P104_J3841_class_02_00015_volume.mrc as #6, grid size
100,100,100, pixel 2.78, shown at level 0.115, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P104_J3841_class_01_00015_volume.mrc

Opened cryosparc_P104_J3841_class_01_00015_volume.mrc as #7, grid size
100,100,100, pixel 2.78, shown at level 0.104, step 1, values float32  

> volume level 0.1

> volume level 0.15

> hide #4 models

> hide #3 models

> hide #!2 models

> hide #!1 models

> hide #!7 models

> hide #!6 models

> volume #5 level 0.1727

[Repeated 1 time(s)]

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #3 models

> show #4 models

> hide #3 models

> show #3 models

> hide #4 models

> hide #3 models

> hide #!5 models

> show #!7 models

> show #!6 models

> volume level 0.16

> tile

2 models tiled  

> hide #!6 models

> hide #!7 models

> show #!5 models

> show #4 models

Drag select of 6 residues  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.44181,0.28757,-0.84977,136.71,0.87872,-0.32953,0.34535,139.19,-0.18072,-0.89928,-0.39828,143.75

> fitmap #4 inMap #5

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#4) to map cryosparc_P104_J3841_class_00_00015_volume.mrc (#5) using 4737
atoms  
average map value = 0.2677, steps = 108  
shifted from previous position = 4.19  
rotated from previous position = 29.2 degrees  
atoms outside contour = 1496, contour level = 0.16  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#4) relative to cryosparc_P104_J3841_class_00_00015_volume.mrc (#5)
coordinates:  
Matrix rotation and translation  
0.40458000 0.45199490 -0.79499420 137.51699231  
0.89851553 -0.03463048 0.43757376 139.00030117  
0.17025005 -0.89134812 -0.42013520 139.78403552  
Axis -0.78075886 -0.56709353 0.26233667  
Axis point 0.00000000 83.52968226 73.62359898  
Rotation angle (degrees) 121.67449137  
Shift along axis -149.52330366  
  

> show #3 models

> fitmap #3 inMap #5

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) to map cryosparc_P104_J3841_class_00_00015_volume.mrc (#5) using 4737
atoms  
average map value = 0.2672, steps = 252  
shifted from previous position = 2.19  
rotated from previous position = 32.3 degrees  
atoms outside contour = 1568, contour level = 0.16  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) relative to cryosparc_P104_J3841_class_00_00015_volume.mrc (#5)
coordinates:  
Matrix rotation and translation  
-0.82334954 0.19085833 -0.53447977 139.38346698  
-0.53284129 -0.58418121 0.61221922 137.66377373  
-0.19538591 0.78886335 0.58268255 139.87094027  
Axis 0.21581660 -0.41429106 -0.88418670  
Axis point 95.86945170 15.26248499 0.00000000  
Rotation angle (degrees) 155.84252521  
Shift along axis -150.62362998  
  

> ~tile

> hide #3 models

> hide #4 models

> show #!7 models

> hide #!7 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> show #!7 models

> tile

2 models tiled  

> select #7

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #7,-0.89191,0.41363,-0.18277,353.27,-0.08103,-0.54381,-0.83529,447.96,-0.44489,-0.73019,0.51855,-143.07

> view matrix models
> #7,0.96609,0.1062,-0.23537,69.625,0.23741,-0.72375,0.64794,161.46,-0.10154,-0.68184,-0.72442,1.1122

> select clear

> ~tile

> select #7

2 models selected  

> transparency #7.1 50

> select clear

> open C:/Users/lilyh/Downloads/cryosparc_P104_J2660_class_00_final_volume.mrc

Opened cryosparc_P104_J2660_class_00_final_volume.mrc as #8, grid size
128,128,128, pixel 2.02, shown at level 0.0239, step 1, values float32  

> ui mousemode right "rotate selected models"

Drag select of 8 cryosparc_P104_J2660_class_00_final_volume.mrc  

> ui mousemode right "translate selected models"

> view matrix models #8,1,0,0,212.72,0,1,0,59.179,0,0,1,-71.919

> volume #8 level 0.2662

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.37423,-0.69971,0.60858,404.61,-0.029598,0.66494,0.74631,12.347,-0.92687,0.26128,-0.26955,174.28

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.37423,-0.69971,0.60858,432.15,-0.029598,0.66494,0.74631,-1.6278,-0.92687,0.26128,-0.26955,74.045

> view matrix models
> #8,-0.37423,-0.69971,0.60858,380.54,-0.029598,0.66494,0.74631,-31.393,-0.92687,0.26128,-0.26955,52.549

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.1292,0.21741,-0.96749,395.59,0.26679,-0.94732,-0.17725,243.59,-0.95506,-0.23522,-0.1804,106.75

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.56913,-0.77999,0.2602,309.7,-0.76562,-0.6181,-0.17825,338.46,0.29986,-0.097772,-0.94896,19.951

> fitmap #8 inMap #7

Fit map cryosparc_P104_J2660_class_00_final_volume.mrc in map
cryosparc_P104_J3841_class_01_00015_volume.mrc using 3029 points  
correlation = 0.8162, correlation about mean = 0.204, overlap = 182.1  
steps = 108, shift = 23.8, angle = 36.1 degrees  
  
Position of cryosparc_P104_J2660_class_00_final_volume.mrc (#8) relative to
cryosparc_P104_J3841_class_01_00015_volume.mrc (#7) coordinates:  
Matrix rotation and translation  
0.64857666 -0.61909464 0.44279798 88.24673902  
0.50645738 0.78528765 0.35612380 -96.79789458  
-0.56819814 -0.00671530 0.82286438 173.90885359  
Axis -0.23321133 0.64980798 0.72343768  
Axis point 251.99048310 15.44791935 0.00000000  
Rotation angle (degrees) 51.07044851  
Shift along axis 42.33203390  
  

> ui mousemode right "rotate selected models"

[Repeated 1 time(s)]

> view matrix models
> #8,0.75259,0.23069,0.61676,113.86,0.34933,-0.93383,-0.076973,227.32,0.55819,0.27338,-0.78338,-62.498

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.61284,-0.71456,0.3374,444.76,-0.52427,0.68713,0.50299,69.501,-0.59125,0.13136,-0.79572,107.52

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.61284,-0.71456,0.3374,454.85,-0.52427,0.68713,0.50299,54.133,-0.59125,0.13136,-0.79572,102.79

> fitmap #8 inMap #7

Fit map cryosparc_P104_J2660_class_00_final_volume.mrc in map
cryosparc_P104_J3841_class_01_00015_volume.mrc using 3029 points  
correlation = 0.8442, correlation about mean = 0.1124, overlap = 211.3  
steps = 84, shift = 16.1, angle = 22.9 degrees  
  
Position of cryosparc_P104_J2660_class_00_final_volume.mrc (#8) relative to
cryosparc_P104_J3841_class_01_00015_volume.mrc (#7) coordinates:  
Matrix rotation and translation  
-0.33843644 -0.90901010 0.24323095 279.54240726  
0.94031514 -0.33648246 0.05086088 38.54103562  
0.03560988 0.24592693 0.96863399 47.18137507  
Axis 0.10424990 0.11095973 0.98834199  
Axis point 126.90884054 111.48145220 0.00000000  
Rotation angle (degrees) 110.67964412  
Shift along axis 80.05010425  
  

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.34366,-0.91896,0.19343,471.74,-0.59493,0.37242,0.71229,118.3,-0.7266,0.12971,-0.6747,52.323

> volume #7 level 0.199

> hide #!8 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
#9  
---  
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
#10  
---  
Chain | Description  
B | No description available  
C | No description available  
  
Drag select of 18 residues  

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.98433,0.022143,-0.17496,-0.66808,-0.059044,-0.89345,-0.44526,6.1219,-0.16618,0.44861,-0.87814,-8.0178

> view matrix models
> #9,0.99895,-0.045366,-0.0066739,0.1599,0.04289,0.87293,0.48596,2.1187,-0.016221,-0.48574,0.87395,1.5313

> view matrix models
> #9,0.66822,0.20542,-0.71504,-4.0514,0.50778,0.5765,0.64016,5.2699,0.54373,-0.79085,0.28092,2.7649

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.66822,0.20542,-0.71504,-4.0081,0.50778,0.5765,0.64016,102.34,0.54373,-0.79085,0.28092,-7.2576

Drag select of 7 residues  

> view matrix models #10,1,0,0,0.99151,0,1,0,112.48,0,0,1,-1.2505

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #10,0.68788,0.55306,-0.47004,2.8404,-0.13975,-0.53456,-0.8335,110.73,-0.71224,0.63903,-0.29042,2.0665

> ui mousemode right "translate selected models"

Drag select of 203 residues  

> view matrix models
> #9,0.66822,0.20542,-0.71504,30.898,0.50778,0.5765,0.64016,168.94,0.54373,-0.79085,0.28092,-30.565,#10,0.68788,0.55306,-0.47004,37.747,-0.13975,-0.53456,-0.8335,177.33,-0.71224,0.63903,-0.29042,-21.241

> view matrix models
> #9,0.66822,0.20542,-0.71504,245.22,0.50778,0.5765,0.64016,222.28,0.54373,-0.79085,0.28092,-76.139,#10,0.68788,0.55306,-0.47004,252.07,-0.13975,-0.53456,-0.8335,230.68,-0.71224,0.63903,-0.29042,-66.815

> view matrix models
> #9,0.66822,0.20542,-0.71504,246.23,0.50778,0.5765,0.64016,104.39,0.54373,-0.79085,0.28092,-32.852,#10,0.68788,0.55306,-0.47004,253.07,-0.13975,-0.53456,-0.8335,112.78,-0.71224,0.63903,-0.29042,-23.528

> view matrix models
> #9,0.66822,0.20542,-0.71504,271.91,0.50778,0.5765,0.64016,119.63,0.54373,-0.79085,0.28092,-37.1,#10,0.68788,0.55306,-0.47004,278.75,-0.13975,-0.53456,-0.8335,128.02,-0.71224,0.63903,-0.29042,-27.776

> view matrix models
> #9,0.66822,0.20542,-0.71504,288.57,0.50778,0.5765,0.64016,70.846,0.54373,-0.79085,0.28092,-26.604,#10,0.68788,0.55306,-0.47004,295.42,-0.13975,-0.53456,-0.8335,79.238,-0.71224,0.63903,-0.29042,-17.28

> view matrix models
> #9,0.66822,0.20542,-0.71504,295.91,0.50778,0.5765,0.64016,80.527,0.54373,-0.79085,0.28092,-32.517,#10,0.68788,0.55306,-0.47004,302.75,-0.13975,-0.53456,-0.8335,88.919,-0.71224,0.63903,-0.29042,-23.193

> fitmap #9 inMap #5

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#9) to map cryosparc_P104_J3841_class_00_00015_volume.mrc (#5) using 4737
atoms  
average map value = 0.2531, steps = 112  
shifted from previous position = 13  
rotated from previous position = 26.1 degrees  
atoms outside contour = 1672, contour level = 0.16  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#9) relative to cryosparc_P104_J3841_class_00_00015_volume.mrc (#5)
coordinates:  
Matrix rotation and translation  
0.78919791 0.48026688 -0.38276687 138.57310128  
-0.60009732 0.47054039 -0.64689642 140.90193819  
-0.13057568 0.74022663 0.65955632 142.30666846  
Axis 0.78094843 -0.14198330 -0.60824361  
Axis point 0.00000000 -67.75881031 273.63354210  
Rotation angle (degrees) 62.63564907  
Shift along axis 1.65560238  
  

> fitmap #10 inMap #5

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#10) to map cryosparc_P104_J3841_class_00_00015_volume.mrc (#5) using 4737
atoms  
average map value = 0.2677, steps = 116  
shifted from previous position = 13.7  
rotated from previous position = 25.9 degrees  
atoms outside contour = 1501, contour level = 0.16  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#10) relative to cryosparc_P104_J3841_class_00_00015_volume.mrc (#5)
coordinates:  
Matrix rotation and translation  
0.40431650 0.45195684 -0.79514980 137.52728504  
0.89853275 -0.03394204 0.43759211 138.96002973  
0.17078376 -0.89139384 -0.41982134 139.78924768  
Axis -0.78058761 -0.56734668 0.26229895  
Axis point 0.00000000 83.51913258 73.64363572  
Rotation angle (degrees) 121.64962689  
Shift along axis -149.52403183  
  

> select #9/B:44

6 atoms, 5 bonds, 1 residue, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.52546,0.090663,-0.84598,306.7,0.64148,0.61097,0.46392,82.451,0.55893,-0.78644,0.26288,-36.561

> fitmap #9 inMap #5

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#9) to map cryosparc_P104_J3841_class_00_00015_volume.mrc (#5) using 4737
atoms  
average map value = 0.2531, steps = 116  
shifted from previous position = 1.54  
rotated from previous position = 37.7 degrees  
atoms outside contour = 1675, contour level = 0.16  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#9) relative to cryosparc_P104_J3841_class_00_00015_volume.mrc (#5)
coordinates:  
Matrix rotation and translation  
0.78795938 0.48179115 -0.38340242 138.62887360  
-0.60153478 0.46942351 -0.64637258 140.89905027  
-0.13143850 0.73994518 0.65970075 142.30122984  
Axis 0.77999330 -0.14176416 -0.60951897  
Axis point -0.00000000 -67.57787002 273.76712820  
Rotation angle (degrees) 62.70694705  
Shift along axis 1.41985915  
  

> hide #!7 models

> select #5

2 models selected  

> transparency #5.1 40

> select clear

Drag select of 3 residues  

> ui mousemode right "rotate selected models"

> view matrix models
> #10,-0.54115,0.39838,-0.74057,312.04,-0.59235,-0.80568,-0.0005531,84.935,-0.59688,0.43838,0.67198,-34.397

> fitmap #10 inMap #5

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#10) to map cryosparc_P104_J3841_class_00_00015_volume.mrc (#5) using 4737
atoms  
average map value = 0.2695, steps = 164  
shifted from previous position = 3.51  
rotated from previous position = 15.2 degrees  
atoms outside contour = 1666, contour level = 0.16  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#10) relative to cryosparc_P104_J3841_class_00_00015_volume.mrc (#5)
coordinates:  
Matrix rotation and translation  
-0.63474801 0.13654917 -0.76055855 139.48720426  
0.75291691 0.33069089 -0.56899885 139.50146415  
0.17381348 -0.93380827 -0.31271557 139.92147679  
Axis -0.30986833 -0.79365358 0.52354142  
Axis point 5.15411940 0.00000000 139.45035548  
Rotation angle (degrees) 143.93856981  
Shift along axis -80.68381346  
  
Drag select of 3 residues  

> ui mousemode right "rotate selected models"

> view matrix models
> #9,-0.87633,0.25645,-0.40777,302.94,0.30826,0.94904,-0.06562,78.421,0.37016,-0.1832,-0.91072,-43.145

> ui mousemode right "translate selected models"

> view matrix models
> #9,-0.87633,0.25645,-0.40777,303.84,0.30826,0.94904,-0.06562,81.783,0.37016,-0.1832,-0.91072,-32.446

Drag select of 3 residues  

> view matrix models
> #10,-0.64585,0.18251,-0.74133,308.6,-0.37901,-0.91955,0.1038,84.536,-0.66275,0.34801,0.66307,-35.641

> ui mousemode right "rotate selected models"

> view matrix models
> #10,-0.033075,0.54731,-0.83628,305.22,-0.54907,-0.70911,-0.44236,85.098,-0.83512,0.44454,0.32396,-34.93

> fitmap #10 inMap #5

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#10) to map cryosparc_P104_J3841_class_00_00015_volume.mrc (#5) using 4737
atoms  
average map value = 0.2676, steps = 336  
shifted from previous position = 4.58  
rotated from previous position = 16 degrees  
atoms outside contour = 1629, contour level = 0.16  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#10) relative to cryosparc_P104_J3841_class_00_00015_volume.mrc (#5)
coordinates:  
Matrix rotation and translation  
-0.15805239 0.27883243 -0.94724439 139.68901397  
0.97228215 0.21133702 -0.10002054 138.86978828  
0.17229885 -0.93679729 -0.30450612 140.36999314  
Axis -0.53630226 -0.71753138 0.44444191  
Axis point -45.66636184 0.00000000 139.78927356  
Rotation angle (degrees) 128.72702769  
Shift along axis -112.17265703  
  

> fitmap #9 inMap #5

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#9) to map cryosparc_P104_J3841_class_00_00015_volume.mrc (#5) using 4737
atoms  
average map value = 0.2672, steps = 144  
shifted from previous position = 5.15  
rotated from previous position = 14.4 degrees  
atoms outside contour = 1567, contour level = 0.16  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#9) relative to cryosparc_P104_J3841_class_00_00015_volume.mrc (#5)
coordinates:  
Matrix rotation and translation  
-0.82457962 0.18916644 -0.53318343 139.37676089  
-0.53090671 -0.58434705 0.61373987 137.66693836  
-0.19546521 0.78914800 0.58227037 139.87069367  
Axis 0.21537034 -0.41465860 -0.88412322  
Axis point 95.77178000 15.34987923 0.00000000  
Rotation angle (degrees) 155.96940382  
Shift along axis -150.73008630  
  

> volume #5 level 0.1827

> volume #5 level 0.2219

> show #4 models

> hide #4 models

> hide #!5 models

> show #!5 models

> show #!8 models

> hide #!8 models

> show #!7 models

> volume #7 level 0.2154

> volume #7 level 0.2298

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

Opened run_it025_class002.mrc as #11, grid size 256,256,256, pixel 1.09, shown
at level 0.000939, step 1, values float32  

> volume #11 level 0.002252

> close #11

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

Opened run_it025_class003.mrc as #11, grid size 256,256,256, pixel 1.09, shown
at level 0.00128, step 1, values float32  

> volume #11 level 0.002547

> close #11

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

Opened run_it025_class004.mrc as #11, 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_class001.mrc

Opened run_it025_class001.mrc as #12, grid size 256,256,256, pixel 1.09, shown
at level 0.000951, step 1, values float32  

> volume #12 level 0.001977

> volume #11 level 0.001253

> close #11

> volume #12 level 0.002814

> volume #12 level 0.002205

> close #12

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

Opened run_it025_class005.mrc as #11, grid size 256,256,256, pixel 1.09, shown
at level 0.00106, step 1, values float32  

> volume #11 level 0.006096

> close #11

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

Opened run_it025_class002.mrc as #11, grid size 256,256,256, pixel 1.09, shown
at level 0.00137, step 1, values float32  

> volume #11 level 0.003523

> close #11

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

Opened run_it025_class001.mrc as #11, grid size 256,256,256, pixel 1.09, shown
at level 0.00129, step 1, values float32  

> volume #11 level 0.002185

> close #11

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

Opened run_it025_class006.mrc as #11, 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_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  

> volume #11 level 0.001803

> close #11

> volume #12 level 0.005643

> ui mousemode right "rotate selected models"

> select #12

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #12,-0.82607,-0.47214,-0.30772,362.05,0.54116,-0.51209,-0.66702,240.73,0.15735,-0.71753,0.67852,128.53

> close #12

> open C:/Users/lilyh/Downloads/Refine3D_Job216/run_class001.mrc

Opened run_class001.mrc as #11, grid size 256,256,256, pixel 1.09, shown at
level 0.00114, step 1, values float32  

> volume #11 level 0.003242

> close #11

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

Opened run_it025_class004.mrc as #11, grid size 256,256,256, pixel 1.09, shown
at level 0.00158, step 1, values float32  

> volume #11 level 0.00575

> close #11

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

Opened run_it025_class003.mrc as #11, 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 #12, 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 #13, grid size 256,256,256, pixel 1.09, shown
at level 0.00158, step 1, values float32  

> volume #11 level 0.004518

> ui mousemode right "rotate selected models"

> select #11

2 models selected  

> view matrix models
> #11,0.8962,-0.41114,-0.16668,96.395,-0.18162,0.0027544,-0.98336,306.73,0.40476,0.91157,-0.072204,-32.187

> view matrix models
> #11,-0.75473,-0.6337,-0.16971,370.42,0.2408,-0.026953,-0.9702,246.89,0.61024,-0.77311,0.17293,136.71

> view matrix models
> #11,-0.92814,0.31919,-0.19149,266.49,0.029443,-0.44989,-0.8926,325.62,-0.37106,-0.8341,0.40816,255.61

> view matrix models
> #11,-0.91741,-0.18544,-0.35209,358.19,0.35934,-0.7662,-0.53274,269.42,-0.17098,-0.61526,0.76956,143.83

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #11,-0.91741,-0.18544,-0.35209,383.47,0.35934,-0.7662,-0.53274,275.23,-0.17098,-0.61526,0.76956,-50.42

> ui mousemode right "rotate selected models"

> view matrix models
> #11,0.99334,-0.11503,0.0063032,41.353,-0.096633,-0.80217,0.58923,186,-0.062724,-0.58591,-0.80794,156.3

> ui mousemode right "translate selected models"

> view matrix models
> #11,0.99334,-0.11503,0.0063032,167.63,-0.096633,-0.80217,0.58923,170.5,-0.062724,-0.58591,-0.80794,140.95

> view matrix models
> #11,0.99334,-0.11503,0.0063032,148.87,-0.096633,-0.80217,0.58923,126.02,-0.062724,-0.58591,-0.80794,156.8

> view matrix models
> #11,0.99334,-0.11503,0.0063032,182.21,-0.096633,-0.80217,0.58923,123.81,-0.062724,-0.58591,-0.80794,170.65

> fitmap #11 inMap #5

Fit map run_it025_class003.mrc in map
cryosparc_P104_J3841_class_00_00015_volume.mrc using 36877 points  
correlation = 0.951, correlation about mean = 0.4103, overlap = 96.2  
steps = 96, shift = 3.76, angle = 18.4 degrees  
  
Position of run_it025_class003.mrc (#11) relative to
cryosparc_P104_J3841_class_00_00015_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
0.92672300 -0.37387705 -0.03742304 66.38262387  
0.37568856 0.92370680 0.07499282 -49.74916531  
0.00652983 -0.08355696 0.99648165 7.70962580  
Axis -0.20660367 -0.05727428 0.97674694  
Axis point 162.15789928 143.92730321 0.00000000  
Rotation angle (degrees) 22.56337518  
Shift along axis -3.33519283  
  

> volume #11 level 0.004225

> open C:/Users/lilyh/Downloads/cryosparc_P104_J3849_class_01_00019_volume.mrc

Opened cryosparc_P104_J3849_class_01_00019_volume.mrc as #14, grid size
100,100,100, pixel 2.78, shown at level 0.077, step 1, values float32  

> select #14

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.9718,0.22627,0.066405,-36.907,0.11593,-0.70364,0.70103,125.5,0.20535,-0.67356,-0.71003,301.76

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.9718,0.22627,0.066405,-14.704,0.11593,-0.70364,0.70103,46.697,0.20535,-0.67356,-0.71003,124.38

> view matrix models
> #14,0.9718,0.22627,0.066405,64.968,0.11593,-0.70364,0.70103,55.41,0.20535,-0.67356,-0.71003,144.69

> view matrix models
> #14,0.9718,0.22627,0.066405,136.8,0.11593,-0.70364,0.70103,63.185,0.20535,-0.67356,-0.71003,135.07

> volume #14 level 0.1526

> fitmap #14 inMap #5

Fit map cryosparc_P104_J3849_class_01_00019_volume.mrc in map
cryosparc_P104_J3841_class_00_00015_volume.mrc using 4897 points  
correlation = 0.9978, correlation about mean = 0.986, overlap = 599.5  
steps = 84, shift = 7.4, angle = 15.9 degrees  
  
Position of cryosparc_P104_J3849_class_01_00019_volume.mrc (#14) relative to
cryosparc_P104_J3841_class_00_00015_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99999757 -0.00220530 -0.00028950 0.34498766  
0.00220542 0.99999752 0.00040847 -0.28661408  
0.00028860 -0.00040910 0.99999991 -0.16714422  
Axis -0.18076164 -0.12781697 0.97518616  
Axis point 141.05738771 140.80854643 0.00000000  
Rotation angle (degrees) 0.12957298  
Shift along axis -0.18872312  
  

> hide #!11 models

> hide #10 models

> hide #9 models

> hide #!7 models

> hide #!14 models

> show #!14 models

> select #14

2 models selected  

> transparency #14.1 50

> select clear

> select add #5

2 models selected  

> transparency #5.1 0

> select clear

[Repeated 1 time(s)]

> hide #!5 models

> show #!5 models

> hide #!14 models

> show #!14 models

> show #!6 models

> hide #!6 models

> show #!8 models

> hide #!8 models

> show #!7 models

> hide #!7 models

> show #!7 models

> volume #5 level 0.153

> hide #!7 models

> show #!7 models

> volume #14 level 0.1545

> hide #!7 models

> hide #!5 models

> volume #14 level 0.2075

> volume #5 level 0.207

> ~tile

[Repeated 1 time(s)]

> select #14

2 models selected  

> transparency #14.1 0

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.9987,-0.0040992,-0.050866,147.89,0.036065,-0.64851,0.76035,149.04,-0.036104,-0.76119,-0.64752,88.288

> select clear

> show #!7 models

> hide #!5 models

> hide #!14 models

> volume #7 level 0.1887

> show #!8 models

> select #7

2 models selected  

> transparency #7.1 0

> select #8

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.34366,-0.91896,0.19343,514.32,-0.59493,0.37242,0.71229,45.093,-0.7266,0.12971,-0.6747,63.542

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.5098,-0.7872,0.34702,500.82,-0.53663,0.60626,0.58692,23.959,-0.67241,0.11299,-0.73151,65.518

> select clear

> select #8

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.21274,0.61919,0.75587,237.05,-0.88323,-0.45272,0.12227,258.09,0.4179,-0.6416,0.6432,-154.02

> volume #8 level 0.2313

> view matrix models
> #8,0.61822,-0.78599,0.004733,393.96,0.71276,0.56314,0.41815,-113.7,-0.33133,-0.25514,0.90836,-135.93

> view matrix models
> #8,0.93832,0.34137,-0.05506,219.37,0.020064,-0.21272,-0.97691,243.93,-0.3452,0.91554,-0.20644,-143.17

> view matrix models
> #8,0.43219,-0.49225,0.75558,290.24,0.80544,-0.16609,-0.56892,85.153,0.40555,0.85446,0.32469,-299.08

> view matrix models
> #8,0.95951,-0.10645,0.26077,233.56,-0.27339,-0.12922,0.95318,36.366,-0.067772,-0.98589,-0.15309,49.749

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.95951,-0.10645,0.26077,270.65,-0.27339,-0.12922,0.95318,67.45,-0.067772,-0.98589,-0.15309,101.38

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.95951,-0.10645,0.26077,237.28,-0.27339,-0.12922,0.95318,41.515,-0.067772,-0.98589,-0.15309,55.27

> view matrix models
> #8,0.95951,-0.10645,0.26077,168.92,-0.27339,-0.12922,0.95318,69.864,-0.067772,-0.98589,-0.15309,46.926

> view matrix models
> #8,0.95951,-0.10645,0.26077,158.19,-0.27339,-0.12922,0.95318,75.927,-0.067772,-0.98589,-0.15309,79.931

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.92751,0.11756,0.35483,366.78,0.32522,0.72177,0.61097,-66.466,-0.18428,0.68208,-0.70768,-43.935

> fitmap #8 inMap #7

Fit map cryosparc_P104_J2660_class_00_final_volume.mrc in map
cryosparc_P104_J3841_class_01_00015_volume.mrc using 3905 points  
correlation = 0.8418, correlation about mean = 0.1304, overlap = 246  
steps = 128, shift = 7.24, angle = 74.8 degrees  
  
Position of cryosparc_P104_J2660_class_00_final_volume.mrc (#8) relative to
cryosparc_P104_J3841_class_01_00015_volume.mrc (#7) coordinates:  
Matrix rotation and translation  
-0.35794962 -0.89860469 0.25373505 279.32584170  
0.93341762 -0.35150982 0.07191796 38.28272836  
0.02456447 0.26258389 0.96459646 46.98423914  
Axis 0.10272289 0.12346760 0.98701761  
Axis point 127.47890854 109.07934950 0.00000000  
Rotation angle (degrees) 111.86565401  
Shift along axis 79.79410559  
  

> ui mousemode right "rotate selected models"

[Repeated 1 time(s)]

> view matrix models
> #8,-0.33649,-0.93498,0.11221,464.28,-0.65644,0.31833,0.68392,101.74,-0.67517,0.15648,-0.72087,93.401

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.523,0.0458,0.8511,276.86,-0.67344,0.58987,-0.44557,208.25,-0.52245,-0.8062,-0.27766,138.62

> view matrix models
> #8,0.41062,0.24389,0.87858,126.3,0.90783,-0.19927,-0.36897,89.083,0.085085,0.94911,-0.30324,-155.8

> view matrix models
> #8,-0.33176,-0.93784,0.10194,465.27,-0.74618,0.327,0.5799,125.16,-0.57719,0.11632,-0.80828,96.19

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.33176,-0.93784,0.10194,432.23,-0.74618,0.327,0.5799,167.99,-0.57719,0.11632,-0.80828,83.083

> show #9 models

> close session

> open C:/Users/lilyh/Downloads/cryosparc_P104_J3854_class_00_00019_volume.mrc

Opened cryosparc_P104_J3854_class_00_00019_volume.mrc as #1, grid size
100,100,100, pixel 2.78, shown at level 0.0777, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P104_J3854_class_01_00019_volume.mrc

Opened cryosparc_P104_J3854_class_01_00019_volume.mrc as #2, grid size
100,100,100, pixel 2.78, shown at level 0.157, step 1, values float32  

> volume level 0.06

> volume level 0.1

> volume level 0.3

> volume #1 level 0.1684

> volume level 0.168

> select #2

2 models selected  

> transparency #2.1 50

> select clear

> volume #2 level 0.2507

> volume level 0.251

> open C:/Users/lilyh/Downloads/cryosparc_P104_J3849_class_01_00019_volume.mrc

Opened cryosparc_P104_J3849_class_01_00019_volume.mrc as #3, grid size
100,100,100, pixel 2.78, shown at level 0.077, step 1, values float32  

> volume #3 level 0.251

> volume #3 level 0.2037

> volume #2 level 0.204

> volume #1 level 0.204

> open C:/Users/lilyh/Downloads/cryosparc_P104_J3849_class_02_00019_volume.mrc

Opened cryosparc_P104_J3849_class_02_00019_volume.mrc as #4, grid size
100,100,100, pixel 2.78, shown at level 0.155, step 1, values float32  

> volume #4 level 0.251

> volume #4 level 0.2322

> open C:/Users/lilyh/Downloads/cryosparc_P122_J577_class_00_final_volume.mrc

Opened cryosparc_P122_J577_class_00_final_volume.mrc as #5, grid size
128,128,128, pixel 2.17, shown at level 0.0161, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J578_class_02_final_volume.mrc

Opened cryosparc_P122_J578_class_02_final_volume.mrc as #6, grid size
128,128,128, pixel 2.17, shown at level 0.0433, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J578_class_01_final_volume.mrc

Opened cryosparc_P122_J578_class_01_final_volume.mrc as #7, grid size
128,128,128, pixel 2.17, shown at level 0.0228, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J578_class_00_final_volume.mrc

Opened cryosparc_P122_J578_class_00_final_volume.mrc as #8, grid size
128,128,128, pixel 2.17, shown at level 0.0381, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J577_class_01_final_volume.mrc

Opened cryosparc_P122_J577_class_01_final_volume.mrc as #9, grid size
128,128,128, pixel 2.17, shown at level 0.0243, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J577_class_02_final_volume.mrc

Opened cryosparc_P122_J577_class_02_final_volume.mrc as #10, grid size
128,128,128, pixel 2.17, shown at level 0.0142, step 1, values float32  

> volume level 0.251

> hide #!10 models

> hide #!9 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> close session

> open C:/Users/lilyh/Downloads/cryosparc_P122_J577_class_00_final_volume.mrc

Opened cryosparc_P122_J577_class_00_final_volume.mrc as #1, grid size
128,128,128, pixel 2.17, shown at level 0.0161, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J578_class_02_final_volume.mrc

Opened cryosparc_P122_J578_class_02_final_volume.mrc as #2, grid size
128,128,128, pixel 2.17, shown at level 0.0433, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J578_class_01_final_volume.mrc

Opened cryosparc_P122_J578_class_01_final_volume.mrc as #3, grid size
128,128,128, pixel 2.17, shown at level 0.0228, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J578_class_00_final_volume.mrc

Opened cryosparc_P122_J578_class_00_final_volume.mrc as #4, grid size
128,128,128, pixel 2.17, shown at level 0.0381, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J577_class_01_final_volume.mrc

Opened cryosparc_P122_J577_class_01_final_volume.mrc as #5, grid size
128,128,128, pixel 2.17, shown at level 0.0243, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J577_class_02_final_volume.mrc

Opened cryosparc_P122_J577_class_02_final_volume.mrc as #6, grid size
128,128,128, pixel 2.17, shown at level 0.0142, step 1, values float32  

> volume level 0.251

> tile

6 models tiled  

> hide #!1 models

> show #!1 models

Drag select of 5 cryosparc_P122_J577_class_01_final_volume.mrc , 6
cryosparc_P122_J577_class_02_final_volume.mrc  

> color #5.1#6.1 dark gray

> select clear

> volume #1 level 0.1001

> ui mousemode right "rotate selected models"

> select #1

2 models selected  

> view matrix models
> #1,-0.17616,-0.39778,-0.90041,347.09,0.78554,-0.60804,0.11494,117.04,-0.59321,-0.68706,0.41959,254.94

> view matrix models
> #1,-0.82247,-0.18641,-0.53739,351.91,0.23322,-0.97222,-0.019702,263.76,-0.51879,-0.14153,0.8431,105.23

> view matrix models
> #1,0.0079879,-0.026827,0.99961,6.0704,0.21935,-0.97525,-0.027926,267.19,0.97561,0.21949,-0.0019056,-32.258

> volume #1 level 0.3873

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.84596,-0.27576,0.4564,238.86,0.019045,-0.87098,-0.49094,344.59,0.5329,-0.40663,0.74207,18.775

Drag select of 2 cryosparc_P122_J578_class_02_final_volume.mrc  

> select #2

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.08381,-0.71697,0.69204,250.28,0.95236,0.14672,0.26734,-39.145,-0.29322,0.68148,0.67052,-17.307

> volume #2 level 0.1605

> volume #2 level 0.1242

> view matrix models
> #2,-0.22735,0.96053,0.16029,97.974,0.44963,-0.042463,0.89221,-31.5,0.8638,0.27491,-0.42223,40.225

> select #3

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.20471,0.71567,-0.66777,342.66,-0.11569,0.65974,0.74253,-34.841,0.97196,0.22926,-0.052255,-24.902

> volume #3 level 0.1706

> view matrix models
> #3,0.86882,-0.4906,-0.066818,274.59,-0.15688,-0.40077,0.90265,101.41,-0.46962,-0.77376,-0.42516,383.2

> select #4

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.25412,0.18404,0.9495,20.74,-0.0049442,-0.98196,0.18901,175.51,0.96716,0.043337,0.25045,-33.074

> volume #4 level 0.3193

> view matrix models
> #4,-0.42473,-0.35812,0.83148,138.34,-0.54636,-0.63093,-0.55084,296.66,0.72187,-0.68824,0.07231,130.18

> view matrix models
> #4,-0.12584,-0.25431,0.9589,65.83,-0.28566,-0.91636,-0.28051,266.73,0.95003,-0.30922,0.042668,48.259

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.12584,-0.25431,0.9589,35.333,-0.28566,-0.91636,-0.28051,259.39,0.95003,-0.30922,0.042668,48.259

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.0045928,-0.22442,0.97448,11.285,-0.4067,-0.89067,-0.2032,261.67,0.91355,-0.39539,-0.095363,84.178

> volume #4 level 0.2805

> view matrix models
> #4,-0.2976,0.70521,-0.64352,133.16,-0.83644,-0.51754,-0.18033,262.37,-0.46022,0.4846,0.74388,29.503

> volume #5 level 0.2636

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.31726,0.82371,-0.46994,95.28,-0.90368,-0.11231,0.41322,132.85,0.28759,0.55577,0.78001,-87.059

> select #5

2 models selected  

> view matrix models
> #5,-0.13106,0.13096,-0.98269,363.95,0.38525,0.92006,0.071229,-133.3,0.91346,-0.36924,-0.17104,87.836

> volume #6 level 0.397

> select #6

2 models selected  

> view matrix models
> #6,-0.45924,-0.38566,0.80023,333.1,-0.83047,-0.13334,-0.54086,261.91,0.31529,-0.91296,-0.25905,255.17

> select clear

> hide #!4 models

> show #!4 models

> close session

> open C:/Users/lilyh/Downloads/cryosparc_P104_J2660_class_00_final_volume.mrc

Opened cryosparc_P104_J2660_class_00_final_volume.mrc as #1, grid size
128,128,128, pixel 2.02, shown at level 0.0239, step 1, values float32  

> volume #1 level 0.09419

> volume #1 level 0.232

> volume #1 level 0.1167

> volume #1 level 0.1012

> 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  

> tile

6 models tiled  

> volume 0.004

Expected a density maps specifier or a keyword  

> volume level0.004

Expected a density maps specifier or a keyword  

> volume level 0.004

> volume level 0.003

> volume level 0.002

> hide #!4 models

> show #!4 models

> close session

> ~tile

No models found for tiling.  

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

Opened run_it025_class002.mrc as #1, grid size 256,256,256, pixel 1.09, shown
at level 0.00113, 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
#2  
---  
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
#3  
---  
Chain | Description  
B | No description available  
C | No description available  
  
Drag select of 496 residues  

> ui mousemode right "translate selected models"

> view matrix models
> #2,1,0,0,116.83,0,1,0,136.92,0,0,1,0,#3,1,0,0,116.83,0,1,0,136.92,0,0,1,0

> view matrix models
> #2,1,0,0,175.39,0,1,0,151.12,0,0,1,143.42,#3,1,0,0,175.39,0,1,0,151.12,0,0,1,143.42

> view matrix models
> #2,1,0,0,169.46,0,1,0,151.58,0,0,1,154.07,#3,1,0,0,169.46,0,1,0,151.58,0,0,1,154.07

> volume #1 level 0.002369

Drag select of 3 residues  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.87121,0.48795,-0.053756,161.34,-0.24368,-0.33479,0.91024,158.95,0.42616,0.80611,0.41058,150.4

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.87121,0.48795,-0.053756,155.75,-0.24368,-0.33479,0.91024,134.02,0.42616,0.80611,0.41058,146.12

Drag select of 1 run_it025_class002.mrc , 13 residues  
Drag select of 4 residues  

> view matrix models #3,1,0,0,161.41,0,1,0,120.33,0,0,1,140.77

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.30497,0.41351,-0.85791,168.55,0.95236,0.13377,-0.27407,113.45,0.0014333,-0.90062,-0.4346,138.1

> ui mousemode right "translate selected models"

Drag select of 9 residues  

> view matrix models
> #3,-0.30497,0.41351,-0.85791,133.95,0.95236,0.13377,-0.27407,135.36,0.0014333,-0.90062,-0.4346,144.65

Drag select of 8 residues  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.83018,0.13244,-0.54154,155.84,-0.50626,-0.58589,0.6328,133.36,-0.23348,0.79949,0.55344,144.46

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.83018,0.13244,-0.54154,138.53,-0.50626,-0.58589,0.6328,140.66,-0.23348,0.79949,0.55344,148.39

> fitmap #2 inMap #1

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#2) to map run_it025_class002.mrc (#1) using 4737 atoms  
average map value = 0.003807, steps = 168  
shifted from previous position = 8.75  
rotated from previous position = 11.1 degrees  
atoms outside contour = 1494, contour level = 0.0023689  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#2) relative to run_it025_class002.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.75937635 0.28001334 -0.58731599 140.81258219  
-0.60889975 -0.62397495 0.48979213 135.34798763  
-0.22932214 0.72955314 0.64433187 142.34319149  
Axis 0.24271444 -0.36240369 -0.89986292  
Axis point 101.86610532 13.24621529 0.00000000  
Rotation angle (degrees) 150.40171516  
Shift along axis -142.96272337  
  

> fitmap #3 inMap #1

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#3) to map run_it025_class002.mrc (#1) using 4737 atoms  
average map value = 0.003757, steps = 216  
shifted from previous position = 6.57  
rotated from previous position = 31 degrees  
atoms outside contour = 1469, contour level = 0.0023689  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#3) relative to run_it025_class002.mrc (#1) coordinates:  
Matrix rotation and translation  
0.16861729 0.36118350 -0.91712308 139.70264159  
0.95540655 0.16894469 0.24219006 136.18049483  
0.24241813 -0.91706281 -0.31659005 142.84727065  
Axis -0.66471271 -0.66487803 0.34072601  
Axis point -81.32086041 0.00000000 128.39297460  
Rotation angle (degrees) 119.30864552  
Shift along axis -134.73375957  
  

> select clear

> select #1

2 models selected  

> transparency #1.1 50

> select clear

> volume #1 level 0.003368

> close session

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

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

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

Opened run_it025_class005.mrc as #2, 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 #3, 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 #4, 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 #5, 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 #6, grid size 256,256,256, pixel 1.09, shown
at level 0.000747, step 1, values float32  

> tile

6 models tiled  

> volume level 0.003

> close session

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

Opened run_it025_class003.mrc as #1, 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 #2, 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 #3, 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 #4, 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  
Drag select of 1 run_it025_class003.mrc , 2 run_it025_class002.mrc , 3
run_it025_class001.mrc , 4 run_it025_class004.mrc  

> color #1.1#2.1#3.1#4.1 orange

> select clear

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

Opened run_it025_class001.mrc as #5, 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 #6, 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 #7, 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 #8, 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 #9, grid size 256,256,256, pixel 1.09, shown
at level 0.00117, step 1, values float32  

> tile

9 models tiled  

> volume level 0.003

Drag select of 5 run_it025_class001.mrc , 6 run_it025_class005.mrc , 8
run_it025_class003.mrc , 9 run_it025_class002.mrc  

> select clear

> select #7

2 models selected  
Drag select of 7 run_it025_class004.mrc , 8 run_it025_class003.mrc , 9
run_it025_class002.mrc  

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.92803,0.075234,0.36484,-33.016,0.24446,-0.862,-0.44407,-124.01,0.28108,0.5013,-0.81835,100.71,#8,0.92803,0.075234,0.36484,135.73,0.24446,-0.862,-0.44407,-79.793,0.28108,0.5013,-0.81835,152.68,#9,0.92803,0.075234,0.36484,304.3,0.24446,-0.862,-0.44407,-35.115,0.28108,0.5013,-0.81835,205.29

Drag select of 5 run_it025_class001.mrc , 6 run_it025_class005.mrc  
Drag select of 5 run_it025_class001.mrc  

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.11241,0.020331,-0.99345,439.78,0.051347,-0.99857,-0.014626,83.128,-0.99233,-0.049367,-0.11329,302.1

> select #6

2 models selected  

> view matrix models
> #6,0.14293,-0.1056,-0.98408,645.1,-0.26054,-0.96324,0.06552,122.73,-0.95482,0.24703,-0.16519,273.18

Drag select of 7 run_it025_class004.mrc  

> view matrix models
> #7,0.068303,-0.088093,-0.99377,292.88,-0.47246,-0.88017,0.04555,-95.731,-0.8787,0.46641,-0.10174,157.79

> select #8

2 models selected  

> view matrix models
> #8,-0.091781,-0.043884,-0.99481,485.95,-0.23436,-0.97001,0.064412,-68.059,-0.96781,0.23905,0.078744,240.43

> select #9

2 models selected  

> view matrix models
> #9,0.074899,0.055928,-0.99562,621.2,-0.21459,-0.97413,-0.070864,-5.7458,-0.97383,0.21896,-0.06096,319.14

Drag select of 7 run_it025_class004.mrc  

> ui mousemode right "translate selected models"

> view matrix models
> #7,0.068303,-0.088093,-0.99377,284.63,-0.47246,-0.88017,0.04555,-5.874,-0.8787,0.46641,-0.10174,157.79

Drag select of 8 run_it025_class003.mrc  

> view matrix models
> #8,-0.091781,-0.043884,-0.99481,484.98,-0.23436,-0.97001,0.064412,-30.174,-0.96781,0.23905,0.078744,240.43

> select clear

> 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_Job215/run_it025_class003.mrc

Opened run_it025_class003.mrc as #1, 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 #2, 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 #3, 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_class004.mrc

Opened run_it025_class004.mrc as #4, grid size 256,256,256, pixel 1.09, shown
at level 0.00158, step 1, values float32  

> tile

4 models tiled  

> volume level 0.003

> open C:/Users/lilyh/Downloads/Refine3D_Job216/run_class001.mrc

Opened run_class001.mrc as #5, grid size 256,256,256, pixel 1.09, shown at
level 0.00114, step 1, values float32  

> close session

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

Opened run_it025_class003.mrc as #1, 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 #2, 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 #3, 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 #4, 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  

> 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  

> tile

6 models tiled  

> volume level 0.003

> 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  

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

Opened run_it025_class005.mrc as #6, grid size 256,256,256, pixel 1.09, shown
at level 0.00106, step 1, values float32  

> volume level 0.003

> 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  

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

Opened run_it025_class004.mrc as #6, 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 #7, 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 #8, 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 #9, grid size 256,256,256, pixel 1.09, shown
at level 0.000951, step 1, values float32  

> tile

9 models tiled  

> volume level 0.003

> 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  
Drag select of 1 run_it025_class005.mrc , 2 run_it025_class004.mrc , 3
run_it025_class003.mrc , 4 run_it025_class002.mrc , 5 run_it025_class001.mrc ,
6 run_it025_class006.mrc  

> color #1.1#2.1#3.1#4.1#5.1#6.1 dark gray

> select clear

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

Opened run_it025_class001.mrc as #7, 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 #8, 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 #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  

> tile

12 models tiled  

> volume level 0.003

> volume level 0.002

> volume level 0.0015

> close session

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

Opened run_it025_class005.mrc as #1, 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 #2, 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 #3, 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 #4, 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 #5, grid size 256,256,256, pixel 1.09, shown
at level 0.000995, step 1, values float32  

> volume level 0.0015

> tile

5 models tiled  

> volume level 0.002

> close session

> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J579_class_00_00124_volume_sharp.mrc

Opened cryosparc_P122_J579_class_00_00124_volume_sharp.mrc as #1, grid size
128,128,128, pixel 2.17, shown at level 0.0717, step 1, values float32  

> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J579_class_02_00124_volume_sharp.mrc

Opened cryosparc_P122_J579_class_02_00124_volume_sharp.mrc as #2, grid size
128,128,128, pixel 2.17, shown at level 0.0743, step 1, values float32  

> volume level 0.02

> volume level 0.2

> tile

2 models tiled  

> ~tile

> ui mousemode right "rotate selected models"

> select #2

2 models selected  

> view matrix models
> #2,-0.82076,0.49498,-0.28521,213.75,-0.49668,-0.86496,-0.071823,349.79,-0.28224,0.082706,0.95577,28.08

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.82076,0.49498,-0.28521,242.1,-0.49668,-0.86496,-0.071823,287.56,-0.28224,0.082706,0.95577,21.525

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.60426,0.76104,-0.23599,166.93,-0.78805,-0.61457,0.035887,275.03,-0.11772,0.20766,0.97109,-21.167

> select #1

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.81076,0.33009,0.48343,108.17,-0.10199,0.73356,-0.67193,181.79,-0.57642,-0.59408,-0.56108,386.98

> select clear

> close session

> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J579_class_00_00124_volume_sharp.mrc

Opened cryosparc_P122_J579_class_00_00124_volume_sharp.mrc as #1, grid size
128,128,128, pixel 2.17, shown at level 0.0717, step 1, values float32  

> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J579_class_02_00124_volume_sharp.mrc

Opened cryosparc_P122_J579_class_02_00124_volume_sharp.mrc as #2, grid size
128,128,128, pixel 2.17, shown at level 0.0743, 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
#3  
---  
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
#4  
---  
Chain | Description  
B | No description available  
C | No description available  
  
Drag select of 260 residues  

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> view matrix models
> #3,1,0,0,121.01,0,1,0,116.62,0,0,1,0,#4,1,0,0,121.01,0,1,0,116.62,0,0,1,0

> view matrix models
> #3,1,0,0,118.88,0,1,0,140.35,0,0,1,131.07,#4,1,0,0,118.88,0,1,0,140.35,0,0,1,131.07

> volume level 0.2

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.99439,-0.01493,0.10467,119.11,0.051869,0.93155,-0.35989,139.49,-0.092133,0.3633,0.9271,131.09,#4,0.99439,-0.01493,0.10467,119.11,0.051869,0.93155,-0.35989,139.49,-0.092133,0.3633,0.9271,131.09

> ui mousemode right "rotate selected models"

Drag select of 6 residues  

> view matrix models
> #4,-0.38032,-0.18041,0.90709,128.09,-0.73751,-0.53266,-0.41516,142.61,0.55807,-0.82688,0.069528,124.96

> select #1

2 models selected  

> fitmap #3 inMap #1

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) to map cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) using
4737 atoms  
average map value = 0.2555, steps = 136  
shifted from previous position = 15.6  
rotated from previous position = 35.2 degrees  
atoms outside contour = 1739, contour level = 0.2  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) relative to cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.98556459 0.00194738 -0.16928863 133.30506575  
-0.13601960 0.60447552 -0.78492548 139.94249861  
0.10080228 0.79662133 0.59601455 123.84832233  
Axis 0.98210478 -0.16772034 -0.08567437  
Axis point 0.00000000 -51.75014692 225.05652621  
Rotation angle (degrees) 53.62786733  
Shift along axis 96.83771109  
  

> hide #!2 models

Drag select of 6 residues  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.031318,0.76274,-0.64594,124.72,0.99934,-0.035783,0.006198,133.31,-0.018386,-0.64571,-0.76336,127.56

> fitmap #4 inMap #1

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#4) to map cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) using
4737 atoms  
average map value = 0.2742, steps = 104  
shifted from previous position = 17  
rotated from previous position = 24 degrees  
atoms outside contour = 1545, contour level = 0.2  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#4) relative to cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.13533655 0.44155599 -0.88696805 137.99152580  
0.99063175 -0.07678487 0.11292838 141.93198995  
-0.01824152 -0.89394206 -0.44781117 128.33340948  
Axis -0.69983042 -0.60381280 0.38163790  
Axis point 0.00000000 65.78654861 83.15596640  
Rotation angle (degrees) 133.99771996  
Shift along axis -133.29412642  
  

> fitmap #3 inMap #1

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) to map cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) using
4737 atoms  
average map value = 0.2555, steps = 40  
shifted from previous position = 0.00486  
rotated from previous position = 0.0199 degrees  
atoms outside contour = 1740, contour level = 0.2  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) relative to cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.98552600 0.00208071 -0.16951152 133.30889725  
-0.13629950 0.60429427 -0.78501648 139.94459415  
0.10080144 0.79675850 0.59583132 123.84874121  
Axis 0.98206547 -0.16782730 -0.08591515  
Axis point 0.00000000 -51.72488393 225.03554041  
Rotation angle (degrees) 53.64220726  
Shift along axis 96.79105807  
  
Drag select of 2 residues  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.62373,0.018902,-0.78141,126.25,-0.77429,-0.15166,0.61439,145.19,-0.1069,0.98825,0.10923,120.94

> fitmap #3 inMap #1

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) to map cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) using
4737 atoms  
average map value = 0.2689, steps = 116  
shifted from previous position = 15.4  
rotated from previous position = 12.3 degrees  
atoms outside contour = 1605, contour level = 0.2  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) relative to cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.71040150 0.15495235 -0.68652708 138.47625368  
-0.69954593 -0.26250889 0.66462361 142.65718785  
-0.07723447 0.95240686 0.29488300 129.84315872  
Axis 0.26445305 -0.55989809 -0.78522526  
Axis point 102.66199128 -8.28660745 0.00000000  
Rotation angle (degrees) 147.03611534  
Shift along axis -145.20914845  
  

> select #1

2 models selected  

> transparency #1.1 40

> select clear

> volume #1 level 0.1836

Drag select of 5 residues  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.83225,0.065146,-0.55057,137.99,-0.53869,-0.3298,0.77527,142.68,-0.13107,0.9418,0.30957,128.36,#4,0.3305,0.44933,-0.82998,137.43,0.94315,-0.12452,0.30815,142.13,0.035113,-0.88464,-0.46494,126.8

> fitmap #3 inMap #1

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) to map cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) using
4737 atoms  
average map value = 0.2688, steps = 64  
shifted from previous position = 1.78  
rotated from previous position = 11.4 degrees  
atoms outside contour = 1465, contour level = 0.18355  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) relative to cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.71708570 0.14797209 -0.68109641 138.44697916  
-0.69213214 -0.26629377 0.67085073 142.61883019  
-0.08210455 0.95246620 0.29337169 129.79896388  
Axis 0.26331008 -0.56005657 -0.78549630  
Axis point 102.26986916 -7.56904057 0.00000000  
Rotation angle (degrees) 147.67235336  
Shift along axis -145.37673364  
  

> fitmap #4 inMap #1

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#4) to map cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) using
4737 atoms  
average map value = 0.2742, steps = 60  
shifted from previous position = 1.68  
rotated from previous position = 11.8 degrees  
atoms outside contour = 1444, contour level = 0.18355  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#4) relative to cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.13846539 0.44187094 -0.88632805 137.99583077  
0.99021338 -0.07754580 0.11603496 141.92403457  
-0.01745854 -0.89372073 -0.44828392 128.33220276  
Axis -0.70094544 -0.60314602 0.38064468  
Axis point 0.00000000 65.93479466 83.00386969  
Rotation angle (degrees) 133.92229560  
Shift along axis -133.47949403  
  

> hide #3 models

> hide #4 models

> show #!2 models

> hide #!1 models

> select #2

2 models selected  

> transparency #2.1 30

> show #3 models

> show #4 models

Drag select of 19 residues  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.50701,0.052533,-0.86034,137.09,0.30081,0.94617,-0.1195,147.58,0.80775,-0.31938,-0.49552,140.25,#4,-0.10252,0.58529,-0.80432,137.06,-0.54894,-0.7076,-0.44494,146.72,-0.82955,0.3959,0.39383,141.7

> fitmap #4 inMap #2

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#4) to map cryosparc_P122_J579_class_02_00124_volume_sharp.mrc (#2) using
4737 atoms  
average map value = 0.2256, steps = 96  
shifted from previous position = 16  
rotated from previous position = 11.4 degrees  
atoms outside contour = 2119, contour level = 0.2  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#4) relative to cryosparc_P122_J579_class_02_00124_volume_sharp.mrc (#2)
coordinates:  
Matrix rotation and translation  
-0.26691230 0.49881238 -0.82458724 135.25686697  
-0.57463650 -0.76926112 -0.27933905 145.17926819  
-0.77366065 0.39927888 0.49196104 157.75433495  
Axis 0.53392982 -0.04006853 -0.84457887  
Axis point 147.74647439 32.55639145 0.00000000  
Rotation angle (degrees) 140.54339965  
Shift along axis -66.83542338  
  

> fitmap #3 inMap #2

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) to map cryosparc_P122_J579_class_02_00124_volume_sharp.mrc (#2) using
4737 atoms  
average map value = 0.2187, steps = 76  
shifted from previous position = 13.2  
rotated from previous position = 11.5 degrees  
atoms outside contour = 2261, contour level = 0.2  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) relative to cryosparc_P122_J579_class_02_00124_volume_sharp.mrc (#2)
coordinates:  
Matrix rotation and translation  
-0.47059802 0.13194765 -0.87242614 133.11498143  
0.48403457 0.86530475 -0.13022396 145.00370756  
0.73773172 -0.48356754 -0.47107791 153.13314678  
Axis -0.20961825 -0.95521326 0.20887275  
Axis point -1.32659429 0.00000000 122.51744697  
Rotation angle (degrees) 122.56020872  
Shift along axis -134.42745161  
  

> hide #4 models

> hide #3 models

> show #!1 models

> hide #!2 models

> open C:/Users/lilyh/Downloads/cryosparc_P104_J3849_class_01_00019_volume.mrc

Opened cryosparc_P104_J3849_class_01_00019_volume.mrc as #5, grid size
100,100,100, pixel 2.78, shown at level 0.077, step 1, values float32  

> volume #5 level 0.1687

> fitmap #1 inMap #5

Fit map cryosparc_P122_J579_class_00_00124_volume_sharp.mrc in map
cryosparc_P104_J3849_class_01_00019_volume.mrc using 10424 points  
correlation = 0.8079, correlation about mean = 0.2155, overlap = 958.6  
steps = 236, shift = 15.7, angle = 41.6 degrees  
  
Position of cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) relative
to cryosparc_P104_J3849_class_01_00019_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
0.76523195 -0.59437069 0.24727220 87.70900441  
0.63192762 0.76683867 -0.11236516 -42.62192586  
-0.12283133 0.24224355 0.96240871 2.21063063  
Axis 0.26680177 0.27845982 0.92264671  
Axis point 109.64767691 98.16464158 0.00000000  
Rotation angle (degrees) 41.64816803  
Shift along axis 13.57205455  
  

> volume #5 level 0.2035

> hide #!5 models

> volume #1 level 0.1653

> show #!5 models

> hide #!5 models

> show #4 models

Drag select of 23 residues  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.09026,0.5094,-0.85579,133.11,0.99122,0.037447,0.12683,137.19,0.096655,-0.85972,-0.50154,150.09

> fitmap #4 inMap #1

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#4) to map cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) using
4737 atoms  
average map value = 0.2742, steps = 140  
shifted from previous position = 11.4  
rotated from previous position = 39.6 degrees  
atoms outside contour = 1320, contour level = 0.16533  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#4) relative to cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.13637045 0.44207814 -0.88654955 138.00552132  
0.99049224 -0.07721288 0.11385685 141.92033464  
-0.01811942 -0.89364713 -0.44840450 128.33544356  
Axis -0.70026483 -0.60360166 0.38117478  
Axis point -0.00000000 65.79183148 83.11487984  
Rotation angle (degrees) 133.99721845  
Shift along axis -133.38552807  
  

> volume #1 level 0.1858

> show #3 models

Drag select of 9 residues  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.32184,0.3742,-0.86971,132.62,-0.93442,-0.27357,0.22808,146.15,-0.15258,0.88608,0.43771,147.49

> fitmap #3 inMap #1

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) to map cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) using
4737 atoms  
average map value = 0.2688, steps = 92  
shifted from previous position = 11.2  
rotated from previous position = 12.4 degrees  
atoms outside contour = 1491, contour level = 0.18583  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) relative to cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.71613368 0.14940334 -0.68178534 138.45919970  
-0.69325450 -0.26553269 0.66999303 142.61665337  
-0.08093709 0.95245530 0.29373143 129.80825196  
Axis 0.26329719 -0.56008065 -0.78548345  
Axis point 102.31616735 -7.69697547 0.00000000  
Rotation angle (degrees) 147.56147530  
Shift along axis -145.38314455  
  

> volume #1 level 0.1767

Drag select of 9 residues  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.50674,0.34267,-0.79107,139.7,-0.82603,-0.45562,0.33177,138.69,-0.24674,0.82158,0.51394,142.36,#4,-0.13956,0.32165,-0.93652,139.26,0.95264,0.30167,-0.038355,138.32,0.27019,-0.89752,-0.34852,140.77

> fitmap #3 inMap #1

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) to map cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) using
4737 atoms  
average map value = 0.2688, steps = 108  
shifted from previous position = 3.66  
rotated from previous position = 23.1 degrees  
atoms outside contour = 1421, contour level = 0.17672  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) relative to cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.71574780 0.14957956 -0.68215180 138.43929202  
-0.69369701 -0.26495699 0.66976289 142.65725088  
-0.08055805 0.95258796 0.29340527 129.79726519  
Axis 0.26339007 -0.56025381 -0.78532881  
Axis point 102.33277642 -7.73811179 0.00000000  
Rotation angle (degrees) 147.52755502  
Shift along axis -145.39426500  
  

> hide #4 models

> hide #3 models

> show #!2 models

> hide #!2 models

> open "C:/Users/lilyh/Downloads/cryosparc_P104_J3854_class_00_00019_volume
> (1).mrc"

Opened cryosparc_P104_J3854_class_00_00019_volume (1).mrc as #6, grid size
100,100,100, pixel 2.78, shown at level 0.0777, step 1, values float32  

> open "C:/Users/lilyh/Downloads/cryosparc_P104_J3849_class_01_00019_volume
> (1).mrc"

Opened cryosparc_P104_J3849_class_01_00019_volume (1).mrc as #7, grid size
100,100,100, pixel 2.78, shown at level 0.077, step 1, values float32  

> volume #7 level 0.09781

> volume #6 level 0.1267

> volume #6 level 0.123

> volume #6 level 0.1475

> volume #7 level 0.1337

> volume #7 level 0.1489

> volume #6 level 0.149

> close #7

> fitmap #6 inMap #1

Fit map cryosparc_P104_J3854_class_00_00019_volume (1).mrc in map
cryosparc_P122_J579_class_00_00124_volume_sharp.mrc using 5052 points  
correlation = 0.8841, correlation about mean = 0.5569, overlap = 458.8  
steps = 92, shift = 0.816, angle = 5.08 degrees  
  
Position of cryosparc_P104_J3854_class_00_00019_volume (1).mrc (#6) relative
to cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.81555363 0.56673568 -0.11697413 -38.24119429  
-0.52459142 0.80939265 0.26398366 66.21842924  
0.24428696 -0.15392921 0.95740779 -21.22450642  
Axis -0.34166254 -0.29534717 -0.89220892  
Axis point 99.65908914 92.40817847 0.00000000  
Rotation angle (degrees) 37.70435627  
Shift along axis 12.44485188  
  

> fitmap #6 inMap #5

Fit map cryosparc_P104_J3854_class_00_00019_volume (1).mrc in map
cryosparc_P104_J3849_class_01_00019_volume.mrc using 5052 points  
correlation = 1, correlation about mean = 0.9999, overlap = 601.7  
steps = 60, shift = 0.818, angle = 5.12 degrees  
  
Position of cryosparc_P104_J3854_class_00_00019_volume (1).mrc (#6) relative
to cryosparc_P104_J3849_class_01_00019_volume.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99999969 0.00070324 0.00036556 -0.15984070  
-0.00070335 0.99999971 0.00030313 0.07555488  
-0.00036535 -0.00030338 0.99999989 0.07006065  
Axis -0.35735128 0.43064975 -0.82875862  
Axis point 87.98866178 211.27603754 0.00000000  
Rotation angle (degrees) 0.04862214  
Shift along axis 0.03159360  
  

> fitmap #5 inMap #1

Fit map cryosparc_P104_J3849_class_01_00019_volume.mrc in map
cryosparc_P122_J579_class_00_00124_volume_sharp.mrc using 3734 points  
correlation = 0.9083, correlation about mean = 0.4662, overlap = 430.2  
steps = 52, shift = 0.983, angle = 2.62 degrees  
  
Position of cryosparc_P104_J3849_class_01_00019_volume.mrc (#5) relative to
cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.78154503 0.61086849 -0.12659800 -38.46538511  
-0.56423810 0.77872567 0.27426573 74.83696355  
0.26612541 -0.14291960 0.95328446 -25.00206973  
Axis -0.31910885 -0.30039770 -0.89884969  
Axis point 102.59521868 93.24976900 0.00000000  
Rotation angle (degrees) 40.81906577  
Shift along axis 12.26689573  
  

> volume #5 level 0.149

> close #6

> fitmap #5 inMap #1

Fit map cryosparc_P104_J3849_class_01_00019_volume.mrc in map
cryosparc_P122_J579_class_00_00124_volume_sharp.mrc using 5016 points  
correlation = 0.8849, correlation about mean = 0.5542, overlap = 458.2  
steps = 80, shift = 0.341, angle = 3.19 degrees  
  
Position of cryosparc_P104_J3849_class_01_00019_volume.mrc (#5) relative to
cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.81494805 0.56731495 -0.11837831 -38.08192224  
-0.52490148 0.80913880 0.26414548 66.31218937  
0.24563816 -0.15312790 0.95719055 -21.48783322  
Axis -0.34075206 -0.29726162 -0.89192127  
Axis point 99.83712720 92.22649630 0.00000000  
Rotation angle (degrees) 37.75476089  
Shift along axis 12.42988002  
  

> show #3 models

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.96937,0.21384,-0.1208,141.73,-0.22179,-0.5509,0.80456,145.72,0.10549,0.80671,0.58145,145.79,#4,0.87271,0.14575,-0.46597,138.86,0.48676,-0.18553,0.85361,146.78,0.03796,-0.97177,-0.23286,142.53

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.96937,0.21384,-0.1208,140.12,-0.22179,-0.5509,0.80456,136.76,0.10549,0.80671,0.58145,143.16,#4,0.87271,0.14575,-0.46597,137.25,0.48676,-0.18553,0.85361,137.82,0.03796,-0.97177,-0.23286,139.9

> fitmap #3 inMap #5

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) to map cryosparc_P104_J3849_class_01_00019_volume.mrc (#5) using 4737
atoms  
average map value = 0.2668, steps = 208  
shifted from previous position = 2.92  
rotated from previous position = 31.4 degrees  
atoms outside contour = 1519, contour level = 0.149  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) relative to cryosparc_P104_J3849_class_01_00019_volume.mrc (#5)
coordinates:  
Matrix rotation and translation  
-0.81080467 0.20616304 -0.54780710 139.35960081  
-0.55233221 -0.57923773 0.59951051 137.59557427  
-0.19371363 0.78865741 0.58351913 140.28578361  
Axis 0.22040457 -0.41260955 -0.88384115  
Axis point 96.82418453 14.06069474 0.00000000  
Rotation angle (degrees) 154.59016123  
Shift along axis -150.04810474  
  

> show #4 models

Drag select of 2 residues  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.14863,0.80296,-0.57721,142.09,0.984,-0.06209,0.167,134.15,0.098258,-0.5928,-0.79934,139.24

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.14863,0.80296,-0.57721,142.69,0.984,-0.06209,0.167,140.01,0.098258,-0.5928,-0.79934,141.56

> fitmap #4 inMap #5

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#4) to map cryosparc_P104_J3849_class_01_00019_volume.mrc (#5) using 4737
atoms  
average map value = 0.2681, steps = 128  
shifted from previous position = 3.92  
rotated from previous position = 28.2 degrees  
atoms outside contour = 1432, contour level = 0.149  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#4) relative to cryosparc_P104_J3849_class_01_00019_volume.mrc (#5)
coordinates:  
Matrix rotation and translation  
0.39950150 0.44819153 -0.79970181 137.49352972  
0.90099617 -0.03102539 0.43271628 138.90692727  
0.16912871 -0.89339905 -0.41621353 140.30829554  
Axis -0.77842029 -0.56869664 0.26579311  
Axis point 0.00000000 83.79869954 74.12315287  
Rotation angle (degrees) 121.59211575  
Shift along axis -148.73067764  
  

> hide #4 models

> hide #3 models

> show #4 models

> show #3 models

> hide #!1 models

> select #5

2 models selected  

> transparency #5.1 40

> select clear

Drag select of 31 residues  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.78315,-0.20016,0.58874,148.18,0.51615,0.73727,-0.43593,135.95,-0.3468,0.64527,0.6807,140.6,#4,-0.36052,-0.47912,0.80029,150.09,-0.84976,-0.18509,-0.49361,134.73,0.38463,-0.85801,-0.3404,140.84

> fitmap #4 inMap #5

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#4) to map cryosparc_P104_J3849_class_01_00019_volume.mrc (#5) using 4737
atoms  
average map value = 0.2593, steps = 152  
shifted from previous position = 11.1  
rotated from previous position = 24.1 degrees  
atoms outside contour = 1623, contour level = 0.149  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#4) relative to cryosparc_P104_J3849_class_01_00019_volume.mrc (#5)
coordinates:  
Matrix rotation and translation  
-0.71780569 -0.39253813 0.57503815 138.86001325  
-0.68092381 0.22348703 -0.69742122 136.90328824  
0.14525085 -0.89217008 -0.42770881 140.57539436  
Axis -0.35216703 0.77719026 -0.52149178  
Axis point 112.45114541 0.00000000 104.12749990  
Rotation angle (degrees) 163.94853420  
Shift along axis -15.81092807  
  

> fitmap #3 inMap #5

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) to map cryosparc_P104_J3849_class_01_00019_volume.mrc (#5) using 4737
atoms  
average map value = 0.2558, steps = 84  
shifted from previous position = 9.18  
rotated from previous position = 23.6 degrees  
atoms outside contour = 1692, contour level = 0.149  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) relative to cryosparc_P104_J3849_class_01_00019_volume.mrc (#5)
coordinates:  
Matrix rotation and translation  
0.82601767 -0.11849555 0.55104777 138.85065549  
0.54580427 0.41218081 -0.72952364 135.66491262  
-0.14068601 0.90336362 0.40514400 140.95811018  
Axis 0.86227214 0.36528105 0.35079411  
Axis point 0.00000000 -13.56525628 87.37325479  
Rotation angle (degrees) 71.23597585  
Shift along axis 218.73014810  
  

> hide #3 models

> hide #4 models

> show #!1 models

> volume #1 level 0.4159

> volume #5 level 0.1343

> volume #2 level 0.2038

> hide #!2 models

> show #!1 models

> volume #1 level 0.1904

> hide #!1 models

> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J586_class_01_00144_volume_sharp.mrc

Opened cryosparc_P122_J586_class_01_00144_volume_sharp.mrc as #6, grid size
128,128,128, pixel 2.17, shown at level 0.0602, step 1, values float32  

> volume #6 level 0.2555

> volume #6 level 0.2117

> show #3 models

Drag select of 5 residues  

> select #6

2 models selected  

> transparency #6.1 50

Drag select of 6 residues  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.67813,0.33882,-0.65218,128.67,-0.69902,-0.57138,0.42999,139.5,-0.22696,0.74748,0.62431,142.53

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.67813,0.33882,-0.65218,128.31,-0.69902,-0.57138,0.42999,134.3,-0.22696,0.74748,0.62431,144.29

> view matrix models
> #3,-0.67813,0.33882,-0.65218,136.6,-0.69902,-0.57138,0.42999,129.07,-0.22696,0.74748,0.62431,145.24

> fitmap #3 inMap #6

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) to map cryosparc_P122_J586_class_01_00144_volume_sharp.mrc (#6) using
4737 atoms  
average map value = 0.354, steps = 84  
shifted from previous position = 6.63  
rotated from previous position = 12.8 degrees  
atoms outside contour = 1827, contour level = 0.21168  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) relative to cryosparc_P122_J586_class_01_00144_volume_sharp.mrc (#6)
coordinates:  
Matrix rotation and translation  
-0.81462726 0.20404364 -0.54290759 140.14001245  
-0.52658410 -0.65253920 0.54488699 135.03225157  
-0.24308776 0.72976629 0.63902234 143.44609953  
Axis 0.22793547 -0.36964427 -0.90078218  
Axis point 97.70125556 17.65667045 0.00000000  
Rotation angle (degrees) 156.07428711  
Shift along axis -147.18470905  
  

> volume #6 level 0.2595

> volume #6 level 0.2077

> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J586_class_00_00144_volume_sharp.mrc

Opened cryosparc_P122_J586_class_00_00144_volume_sharp.mrc as #7, grid size
128,128,128, pixel 2.17, shown at level 0.0711, step 1, values float32  

> volume #7 level 0.05556

> volume #7 level 0.1917

> select #7

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.60037,-0.77149,0.2106,129.13,-0.79701,-0.59888,0.07824,312.5,0.065759,-0.21482,-0.97444,290.71

> ui mousemode right "translate selected models"

> view matrix models
> #7,0.60037,-0.77149,0.2106,130.29,-0.79701,-0.59888,0.07824,320.1,0.065759,-0.21482,-0.97444,293.03

> fitmap #3 inMap #7

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) to map cryosparc_P122_J586_class_00_00144_volume_sharp.mrc (#7) using
4737 atoms  
average map value = 0.2552, steps = 164  
shifted from previous position = 6.96  
rotated from previous position = 14.9 degrees  
atoms outside contour = 2257, contour level = 0.1917  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) relative to cryosparc_P122_J586_class_00_00144_volume_sharp.mrc (#7)
coordinates:  
Matrix rotation and translation  
-0.24813858 0.56820600 -0.78458221 140.40470068  
0.95029673 0.29999978 -0.08328460 140.54712847  
0.18805168 -0.76625201 -0.61440581 132.39978626  
Axis -0.54708262 -0.77911638 0.30606907  
Axis point -18.95166982 0.00000000 107.44407402  
Rotation angle (degrees) 141.37721299  
Shift along axis -145.79206219  
  

> hide #!6 models

> select #7

2 models selected  

> transparency #7.1 50

> select clear

> volume #7 level 0.2812

> fitmap #3 inMap #7

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) to map cryosparc_P122_J586_class_00_00144_volume_sharp.mrc (#7) using
4737 atoms  
average map value = 0.2552, steps = 44  
shifted from previous position = 0.0269  
rotated from previous position = 0.429 degrees  
atoms outside contour = 2734, contour level = 0.28116  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) relative to cryosparc_P122_J586_class_00_00144_volume_sharp.mrc (#7)
coordinates:  
Matrix rotation and translation  
-0.25509729 0.56550088 -0.78430490 140.42174494  
0.94831869 0.30464485 -0.08878766 140.55147930  
0.18872495 -0.76642047 -0.61398912 132.41045159  
Axis -0.54384537 -0.78092113 0.30723673  
Axis point -18.36724619 0.00000000 107.57844873  
Rotation angle (degrees) 141.46435832  
Shift along axis -145.44598047  
  

> select clear

> select #3/B:100

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.91714,-0.176,-0.35761,134.82,-0.098454,-0.76939,0.63115,135.49,-0.38623,0.61406,0.6883,143.89

> fitmap #3 inMap #7

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) to map cryosparc_P122_J586_class_00_00144_volume_sharp.mrc (#7) using
4737 atoms  
average map value = 0.2621, steps = 160  
shifted from previous position = 2.36  
rotated from previous position = 12.9 degrees  
atoms outside contour = 2676, contour level = 0.28116  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) relative to cryosparc_P122_J586_class_00_00144_volume_sharp.mrc (#7)
coordinates:  
Matrix rotation and translation  
-0.61122751 0.36402006 -0.70277334 140.39505130  
0.76369176 0.50438723 -0.40294975 141.17512270  
0.20778810 -0.78299616 -0.58629446 132.33946309  
Axis -0.35699750 -0.85533805 0.37543256  
Axis point 10.76974698 0.00000000 113.51955199  
Rotation angle (degrees) 147.84025622  
Shift along axis -121.18859343  
  

> hide #3 models

> hide #!7 models

> show #!5 models

> hide #!5 models

> show #!6 models

> volume #2 level 0.2966

> close session

> open C:/Users/lilyh/Downloads/Class3D_Job219/run_it025_class003.mrc

Opened run_it025_class003.mrc as #1, grid size 256,256,256, pixel 1.09, shown
at level 0.000799, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job219/run_it025_class002.mrc

Opened run_it025_class002.mrc as #2, grid size 256,256,256, pixel 1.09, shown
at level 0.000869, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job219/run_it025_class001.mrc

Opened run_it025_class001.mrc as #3, grid size 256,256,256, pixel 1.09, shown
at level 0.000826, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job219/run_it025_class004.mrc

Opened run_it025_class004.mrc as #4, grid size 256,256,256, pixel 1.09, shown
at level 0.00106, step 1, values float32  

> volume level 0.2

> volume level 0.02

> volume level 0.01

> tile

4 models tiled  

> volume #1 level 0.003781

> volume level 0.003

> tile

4 models tiled  

> volume #2 level 0.003072

> volume #3 level 0.002963

> volume #3 level 0.00183

> volume #3 level 0.001684

> volume #3 level 0.0009525

> volume #3 level 0.0007696

> volume #3 level 0.0006234

> volume #3 level 0.00066

> volume #3 level 0.001172

> volume #3 level 0.001208

> volume #3 level 0.001647

> volume #3 level 0.001684

> volume #3 level 0.002159

> volume #3 level 0.002196

> volume #3 level 0.002452

> volume #3 level 0.002525

> volume #3 level 0.002707

> volume #3 level 0.002744

> volume #3 level 0.002781

> volume #3 level 0.002854

> volume #3 level 0.003219

> volume #3 level 0.003256

> volume #3 level 0.003329

> volume #3 level 0.005925

> volume level 0.006

> volume #4 level 0.00359

> volume #4 level 0.005905

> volume level 0.006

> volume #2 level 0.002526

> volume level 0.002

> volume #4 level 0.003205

> volume level 0.0032

> hide #!4 models

> ui hideFloating toggle

> tile

3 models tiled  

> ~tile

> volume #1 level 0.005461

> close session

> open C:/Users/lilyh/Downloads/Class3D_Job220/run_it025_class002.mrc

Opened run_it025_class002.mrc as #1, grid size 256,256,256, pixel 1.09, shown
at level 0.000898, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job220/run_it025_class001.mrc

Opened run_it025_class001.mrc as #2, grid size 256,256,256, pixel 1.09, shown
at level 0.000933, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job220/run_it025_class003.mrc

Opened run_it025_class003.mrc as #3, grid size 256,256,256, pixel 1.09, shown
at level 0.00118, step 1, values float32  

> tile

3 models tiled  

> volume level 0.0032

> volume #1 level 0.005225

> volume level 0.005

> volume #3 level 0.006761

> volume #2 level 0.005889

> volume level 0.00589

> volume #3 level 0.005749

> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J586_class_01_00144_volume_sharp.mrc

Opened cryosparc_P122_J586_class_01_00144_volume_sharp.mrc as #4, grid size
128,128,128, pixel 2.17, shown at level 0.0602, step 1, values float32  

> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J587_class_01_00163_volume_sharp.mrc

Opened cryosparc_P122_J587_class_01_00163_volume_sharp.mrc as #5, grid size
128,128,128, pixel 2.17, shown at level 0.056, step 1, values float32  

> volume #5 level 0.2687

> volume #4 level 0.2037

> ui mousemode right "rotate selected models"

> select #4

2 models selected  

> view matrix models
> #4,0.021877,-0.024926,-0.99945,276.72,0.17372,-0.98439,0.028353,257.1,-0.98455,-0.17425,-0.017206,301.51

> select #5

2 models selected  

> view matrix models
> #5,0.20848,0.28289,0.93622,-62.447,0.16421,-0.95379,0.25163,221.01,0.96414,0.10127,-0.2453,27.116

> view matrix models
> #5,0.32816,0.039176,-0.94381,218.11,0.0048989,-0.9992,-0.039771,289.96,-0.94461,0.0084276,-0.32809,313.46

> hide #!3 models

> hide #!2 models

> hide #!1 models

> close session

> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J586_class_01_00144_volume_sharp.mrc

Opened cryosparc_P122_J586_class_01_00144_volume_sharp.mrc as #1, grid size
128,128,128, pixel 2.17, shown at level 0.0602, step 1, values float32  

> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J587_class_01_00163_volume_sharp.mrc

Opened cryosparc_P122_J587_class_01_00163_volume_sharp.mrc as #2, grid size
128,128,128, pixel 2.17, shown at level 0.056, step 1, values float32  

> volume level 0.2

> open C:/Users/lilyh/Downloads/Class3D_Job219/run_it025_class003.mrc

Opened run_it025_class003.mrc as #3, grid size 256,256,256, pixel 1.09, shown
at level 0.000799, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job219/run_it025_class002.mrc

Opened run_it025_class002.mrc as #4, grid size 256,256,256, pixel 1.09, shown
at level 0.000869, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job219/run_it025_class001.mrc

Opened run_it025_class001.mrc as #5, grid size 256,256,256, pixel 1.09, shown
at level 0.000826, step 1, values float32  

> hide #!3 models

> hide #!2 models

> hide #!1 models

> hide #!4 models

> hide #!5 models

> show #!3 models

> volume #3 level 0.002495

> volume #4 level 0.003945

> volume #3 level 0.005145

> volume #4 level 0.005899

> volume #4 level 0.00561

> volume #5 level 0.005506

> volume #5 level 0.006128

> fitmap #3 inMap #2

Fit map run_it025_class003.mrc in map
cryosparc_P122_J587_class_01_00163_volume_sharp.mrc using 32143 points  
correlation = 0.949, correlation about mean = 0.6576, overlap = 133.9  
steps = 64, shift = 0.9, angle = 2.44 degrees  
  
Position of run_it025_class003.mrc (#3) relative to
cryosparc_P122_J587_class_01_00163_volume_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99913921 -0.03934563 -0.01314413 7.14587444  
0.03946968 0.99917734 0.00931547 -6.53061788  
0.01276680 -0.00982625 0.99987022 0.45256795  
Axis -0.22481375 -0.30431613 0.92566218  
Axis point 163.09879041 182.61971920 0.00000000  
Rotation angle (degrees) 2.43995581  
Shift along axis 0.79980652  
  

> select clear

> fitmap #3 inMap #1

Fit map run_it025_class003.mrc in map
cryosparc_P122_J586_class_01_00144_volume_sharp.mrc using 32143 points  
correlation = 0.956, correlation about mean = 0.6745, overlap = 129.2  
steps = 44, shift = 0.136, angle = 0.4 degrees  
  
Position of run_it025_class003.mrc (#3) relative to
cryosparc_P122_J586_class_01_00144_volume_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99885143 -0.04625382 -0.01250607 8.12141889  
0.04636230 0.99888829 0.00852814 -7.27175418  
0.01209771 -0.00909815 0.99988543 0.53410225  
Axis -0.18090112 -0.25251222 0.95053267  
Axis point 156.28140350 175.12403655 0.00000000  
Rotation angle (degrees) 2.79244185  
Shift along axis 0.87471463  
  

> hide #!1 models

> show #!1 models

> hide #!3 models

> volume #1 level 0.3754

> show #!2 models

> hide #!2 models

> show #!3 models

> select #1

2 models selected  

> surface style #1 mesh

> select clear

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

Drag select of 1 cryosparc_P122_J586_class_01_00144_volume_sharp.mrc  

> transparency #1.1 0

> surface style #1 solid

> select clear

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> open 2f6h

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 97, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\manager.py", line 198, in open_data  
return provider_open(self.session, [path], _return_status=True,  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 465, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 43, in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  

> open 2f6h

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 97, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\manager.py", line 198, in open_data  
return provider_open(self.session, [path], _return_status=True,  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 465, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 43, in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
  
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