Scalebar: invalid literal for int() with base 10

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\\\Users\\\MX-
> User\\\Desktop\\\GIMM_REPORT\\\cryosparc_P64_J100_class_00_final_volume.mrc

Opened cryosparc_P64_J100_class_00_final_volume.mrc as #1, grid size
150,150,150, pixel 4.68, shown at level 0.333, step 1, values float32  

> volume #1 level 0.6897

> surface dust #1 size 46.8

> volume #1 level 0.486

> volume #1 level 0.5951

> volume #1 level 0.806

> volume #1 level 0.8642

> volume #1 level 0.8933

> open C:/Users/MX-User/Downloads/emd_36021.map/emd_36021.map

Opened emd_36021.map as #2, grid size 336,336,336, pixel 1.09, shown at level
3.59, step 2, values float32  

> volume #2 level 1.465

> surface dust #1 size 46.8

> surface dust #2 size 10.9

> volume #2 step 1

> volume #2 step 4

> volume #2 step 1

> volume #2 level 1.788

> volume #2 level 2.218

> volume #2 level 3.617

> select add #1

2 models selected  

> volume #2 level 4.262

> volume #2 step 8

> volume #2 step 1

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.72367,-0.62998,-0.28183,418.88,0.69012,0.66403,0.28775,-232.65,0.0058638,-0.40273,0.9153,168.39

> view matrix models
> #1,0.51331,-0.80246,0.30425,344.59,0.73895,0.59356,0.31882,-236.68,-0.43643,0.061176,0.89766,171.33

> view matrix models
> #1,-0.052753,-0.98702,-0.15171,774.24,0.80723,-0.13158,0.57538,-100.38,-0.58787,-0.092111,0.8037,312.43

> view matrix models
> #1,-0.42741,-0.72225,-0.54377,956.19,0.59836,-0.67688,0.42872,216.57,-0.6777,-0.14213,0.72147,391.36

> view matrix models
> #1,-0.53102,-0.3404,-0.77598,943.33,0.14433,-0.93872,0.31302,511.42,-0.83497,0.054221,0.54761,441.39

> view matrix models
> #1,-0.49997,-0.070139,-0.8632,869.32,-0.10238,-0.98494,0.13933,677.82,-0.85997,0.15803,0.48526,436.49

> view matrix models
> #1,-0.95997,0.19127,-0.2046,707.3,-0.21606,-0.97057,0.10637,725.24,-0.17824,0.14632,0.97305,22.422

> view matrix models
> #1,-0.98163,0.080061,-0.17316,742.52,-0.10057,-0.98848,0.11311,687.78,-0.16211,0.12845,0.97838,20.971

> volume #1 level 1.068

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.98163,0.080061,-0.17316,563.89,-0.10057,-0.98848,0.11311,652.72,-0.16211,0.12845,0.97838,-105.47

> view matrix models
> #1,-0.98163,0.080061,-0.17316,578.35,-0.10057,-0.98848,0.11311,546.35,-0.16211,0.12845,0.97838,-128.29

> view matrix models
> #1,-0.98163,0.080061,-0.17316,572.84,-0.10057,-0.98848,0.11311,537.7,-0.16211,0.12845,0.97838,-119.37

> view matrix models
> #1,-0.98163,0.080061,-0.17316,571.02,-0.10057,-0.98848,0.11311,539.91,-0.16211,0.12845,0.97838,-113.15

> view matrix models
> #1,-0.98163,0.080061,-0.17316,569.25,-0.10057,-0.98848,0.11311,548.75,-0.16211,0.12845,0.97838,-116.08

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.99628,0.0536,0.067528,497.51,-0.037346,-0.97426,0.22233,482.13,0.077707,0.21898,0.97263,-231.1

> view matrix models
> #1,-0.99787,0.060905,-0.023222,528.03,-0.06414,-0.98093,0.18347,507.93,-0.011605,0.18457,0.98275,-190.88

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.99787,0.060905,-0.023222,519.02,-0.06414,-0.98093,0.18347,508.79,-0.011605,0.18457,0.98275,-193.65

> view matrix models
> #1,-0.99787,0.060905,-0.023222,516.03,-0.06414,-0.98093,0.18347,509.83,-0.011605,0.18457,0.98275,-198.32

> view matrix models
> #1,-0.99787,0.060905,-0.023222,515.52,-0.06414,-0.98093,0.18347,503.45,-0.011605,0.18457,0.98275,-194.29

> open C:/Users/MX-
> User/Desktop/GIMM_REPORT/cryosparc_P64_J86_class_00_final_volume.mrc

Opened cryosparc_P64_J86_class_00_final_volume.mrc as #3, grid size
150,150,150, pixel 4.68, shown at level 0.351, step 1, values float32  

Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 3 maps.  

> surface dust #1 size 46.8

[Repeated 1 time(s)]

> select add #3

4 models selected  

> select add #2

6 models selected  

> surface dust #1 size 46.8

> surface dust #2 size 10.9

> surface dust #3 size 46.8

> select subtract #2

4 models selected  

> select subtract #3

2 models selected  

> select subtract #1

Nothing selected  

> volume #3 level 0.7176

> volume #3 level 1.216

> select add #3

2 models selected  

> ui mousemode right "move picked models"

> view matrix models #3,1,0,0,15.699,0,1,0,-133.72,0,0,1,-26.242

> view matrix models #3,1,0,0,-186.32,0,1,0,-149.78,0,0,1,-92.576

> view matrix models #3,1,0,0,-188.47,0,1,0,-145.51,0,0,1,-132.64

> view matrix models #3,1,0,0,-184.82,0,1,0,-146.42,0,0,1,-128.38

> view matrix models #3,1,0,0,-174.01,0,1,0,-144.54,0,0,1,-131.34

> view matrix models
> #1,-0.99787,0.060905,-0.023222,515.25,-0.06414,-0.98093,0.18347,509.34,-0.011605,0.18457,0.98275,-198.55

> view matrix models
> #1,-0.99787,0.060905,-0.023222,515.5,-0.06414,-0.98093,0.18347,504.97,-0.011605,0.18457,0.98275,-200.23

> view matrix models
> #1,-0.99787,0.060905,-0.023222,515.11,-0.06414,-0.98093,0.18347,505.44,-0.011605,0.18457,0.98275,-196.69

> open C:/Users/MX-
> User/Desktop/GIMM_REPORT/cryosparc_P64_J101_class_00_final_volume.mrc

Opened cryosparc_P64_J101_class_00_final_volume.mrc as #4, grid size
150,150,150, pixel 4.68, shown at level 0.311, step 1, values float32  

> open C:/Users/MX-
> User/Desktop/GIMM_REPORT/cryosparc_P64_J102_001_volume_map_sharp.mrc

Opened cryosparc_P64_J102_001_volume_map_sharp.mrc as #5, grid size
150,150,150, pixel 4.68, shown at level 0.226, step 1, values float32  

> open C:/Users/MX-
> User/Desktop/GIMM_REPORT/cryosparc_P64_J103_001_volume_map_sharp.mrc

Opened cryosparc_P64_J103_001_volume_map_sharp.mrc as #6, grid size
150,150,150, pixel 4.68, shown at level 0.247, step 1, values float32  

> surface dust #3 size 46.8

> select add #4

4 models selected  

> select add #5

6 models selected  

> select add #6

8 models selected  

> surface dust #3 size 46.8

> surface dust #4 size 46.8

> surface dust #5 size 46.8

> surface dust #6 size 46.8

> select subtract #5

6 models selected  

> select subtract #6

4 models selected  

> select subtract #4

2 models selected  

> rename #3 A

> rename #4 B

> rename #6 B1

> rename #1 c

> rename #1 C

> rename #5 C1

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> select subtract #3

Nothing selected  

> hide #!1 models

> show #!1 models

> show #!5 models

> volume #5 level 1.047

> color #1 white models

> color #1 #e6a2deff models

[Repeated 1 time(s)]

> color #5 #f0f0f0ff models

> color #5 springgreen models

> color #5 #d86eccff models

> color #1 #f5daf2ff models

> color #1 white models

> color #1 #d86eccff models

> color #3 #6a6a6aff models

> color #3 #00b050ff models

[Repeated 1 time(s)]

> color #6 white models

> color #6 #ffc000ff models

> color #4 #ffc000ff models

> select add #5

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #5,1,0,0,-153.04,0,1,0,-135.68,0,0,1,-135.98

> view matrix models #5,1,0,0,-174.19,0,1,0,-135.48,0,0,1,-142.69

> view matrix models #5,1,0,0,-170.07,0,1,0,-135.52,0,0,1,-141.07

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.99999,3.2867e-05,-0.0036145,-168.79,-3.2784e-05,1,2.2927e-05,-135.52,0.0036145,-2.2808e-05,0.99999,-142.33

> view matrix models
> #5,-0.94591,0.084496,-0.31323,599.3,-0.052129,-0.99253,-0.11032,613.49,-0.32021,-0.088026,0.94325,22.754

> view matrix models
> #5,-0.99849,0.053828,0.011199,512.69,-0.05475,-0.9921,-0.11283,615.16,0.0050372,-0.11327,0.99355,-101.25

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> view matrix models
> #5,-0.99849,0.053828,0.011199,504.97,-0.05475,-0.9921,-0.11283,615.21,0.0050372,-0.11327,0.99355,-101.95

> view matrix models
> #1,-0.99787,0.060905,-0.023222,510.15,-0.06414,-0.98093,0.18347,504.63,-0.011605,0.18457,0.98275,-197.03

> undo

[Repeated 1 time(s)]

> view matrix models
> #1,-0.99787,0.060905,-0.023222,496.67,-0.06414,-0.98093,0.18347,502.44,-0.011605,0.18457,0.98275,-195.46

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.99849,0.053828,0.011199,501.04,-0.05475,-0.9921,-0.11283,613.27,0.0050372,-0.11327,0.99355,-99.485

> view matrix models
> #5,-0.99849,0.053828,0.011199,502.47,-0.05475,-0.9921,-0.11283,609.02,0.0050372,-0.11327,0.99355,-99.526

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!4 models

> volume #4 level 1.13

> select subtract #5

Nothing selected  

> select add #4

2 models selected  

> ui mousemode right zoom

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,-178.37,0,1,0,-10.306,0,0,1,-153.08

> view matrix models #4,1,0,0,-219.5,0,1,0,-133.78,0,0,1,-153.28

> view matrix models #4,1,0,0,-170.98,0,1,0,-143.56,0,0,1,-141.34

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.0076976,-0.99232,0.12345,478.96,0.95674,0.043215,0.28772,-250.17,-0.29085,0.11589,0.94972,-61.382

> view matrix models
> #4,-0.93075,-0.29734,-0.21284,687.42,0.16298,-0.85837,0.48646,271.56,-0.32734,0.41808,0.84738,-117.09

> view matrix models
> #4,-0.96969,-0.24235,-0.031205,617.29,0.20104,-0.86385,0.4619,268.83,-0.1389,0.44162,0.88639,-205.46

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.96969,-0.24235,-0.031205,616.53,0.20104,-0.86385,0.4619,271.34,-0.1389,0.44162,0.88639,-206.44

> view matrix models
> #4,-0.96969,-0.24235,-0.031205,614.1,0.20104,-0.86385,0.4619,274.7,-0.1389,0.44162,0.88639,-209.05

> view matrix models
> #4,-0.96969,-0.24235,-0.031205,615.34,0.20104,-0.86385,0.4619,269.87,-0.1389,0.44162,0.88639,-207.97

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.96933,-0.24481,-0.021758,612.7,0.20582,-0.85695,0.47252,262.01,-0.13432,0.45355,0.88105,-211.83

> view matrix models
> #4,-0.94943,-0.31377,0.011243,617.9,0.28824,-0.85689,0.42738,249.08,-0.12446,0.40901,0.904,-208

> view matrix models
> #4,-0.99679,-0.074542,0.029346,544.98,0.080017,-0.90878,0.40954,346.72,-0.0038588,0.41057,0.91182,-253.75

> view matrix models
> #4,-0.99877,-0.041413,0.027253,534.91,0.049035,-0.90617,0.42006,352.96,0.0072998,0.42088,0.90709,-259.57

> hide #!4 models

> select subtract #4

Nothing selected  

> show #!6 models

> select add #6

2 models selected  

> volume #6 level 0.7413

> ui mousemode right "translate selected models"

> view matrix models #6,1,0,0,-139.98,0,1,0,-160.11,0,0,1,-133.49

> view matrix models #6,1,0,0,-170.57,0,1,0,-139.3,0,0,1,-135.63

> view matrix models #6,1,0,0,-169.29,0,1,0,-149.77,0,0,1,-145.08

> view matrix models #6,1,0,0,-168.32,0,1,0,-147.88,0,0,1,-144.05

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.71273,0.70143,0.0028707,-310.2,-0.701,0.71242,-0.03248,213.79,-0.024828,0.021137,0.99947,-142.33

> view matrix models
> #6,0.22528,0.97409,0.019811,-236.88,-0.97416,0.22487,0.020961,461.33,0.015963,-0.024021,0.99958,-141.27

> view matrix models
> #6,-0.29893,0.95277,0.05364,-54.471,-0.95336,-0.30063,0.026996,634.09,0.041847,-0.043068,0.9982,-143.4

> view matrix models
> #6,-0.72742,0.68327,0.063325,188.54,-0.68549,-0.72775,-0.022028,704.25,0.031033,-0.059432,0.99775,-133.7

> view matrix models
> #6,-0.93112,0.3562,0.078352,369.36,-0.35836,-0.93346,-0.015085,656.37,0.067766,-0.042125,0.99681,-152.48

> view matrix models
> #6,-0.9624,-0.27157,0.0055482,624.46,0.27023,-0.95933,-0.081573,464.78,0.027475,-0.077007,0.99665,-125.94

> view matrix models
> #6,-0.98744,-0.10691,0.11636,536.54,0.086089,-0.98147,-0.17118,570.31,0.13251,-0.15901,0.97834,-128.42

> view matrix models
> #6,-0.96947,0.20336,0.13703,415.06,-0.22168,-0.9657,-0.1352,661.81,0.10484,-0.16145,0.9813,-118.75

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.96947,0.20336,0.13703,396.97,-0.22168,-0.9657,-0.1352,656.8,0.10484,-0.16145,0.9813,-116.26

> view matrix models
> #6,-0.96947,0.20336,0.13703,400.89,-0.22168,-0.9657,-0.1352,668.79,0.10484,-0.16145,0.9813,-115.11

> ui mousemode right "rotate selected models"

> view matrix models
> #6,-0.95083,0.29832,0.083256,380.56,-0.29729,-0.95447,0.024778,634.54,0.086856,-0.0011909,0.99622,-169.66

> view matrix models
> #6,-0.95743,0.2839,0.052216,399.04,-0.28312,-0.95883,0.021909,632.03,0.056286,0.0061933,0.9984,-162.09

> view matrix models
> #6,-0.98732,0.15063,0.050134,456.7,-0.15289,-0.98724,-0.044627,619.24,0.042772,-0.051726,0.99774,-136.93

> hide #!6 models

> select subtract #6

Nothing selected  

> show #!4 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #!1 models

> show #!3 models

> show #!2 models

> select add #3

2 models selected  

> transparency #3.1 40

> select subtract #3

Nothing selected  

> select add #2

2 models selected  

> show #!1 models

> hide #!1 models

> select subtract #2

Nothing selected  

> select add #3

2 models selected  

> select add #1

4 models selected  

> select add #4

6 models selected  

> select add #5

8 models selected  

> select add #6

10 models selected  

> transparency #3.1 40

> transparency #3.1 60

> transparency #3.1 50

> select up

12 models selected  

> select up

12 models selected  

> select down

10 models selected  

> select down

10 models selected  

> select down

10 models selected  

> fitmap #3 inMap #2

Fit map A in map emd_36021.map using 14684 points  
correlation = 0.4012, correlation about mean = 0.004826, overlap = 4.375e+04  
steps = 92, shift = 2.03, angle = 1.57 degrees  
  
Position of A (#3) relative to emd_36021.map (#2) coordinates:  
Matrix rotation and translation  
0.99965950 -0.02032379 0.01636566 -170.59473973  
0.02018699 0.99976025 0.00848118 -154.28061145  
-0.01653410 -0.00814792 0.99983010 -121.89490508  
Axis -0.30360216 0.60066018 0.73961684  
Axis point 3620.06127439 -10411.89699103 0.00000000  
Rotation angle (degrees) 1.56931746  
Shift along axis -131.03281403  
  

> hide #!3 models

> show #!4 models

> show #!1 models

> show #!5 models

> show #!6 models

> transparency #1.1#4.1#5.1#6.1 50

> hide #!5 models

> show #!5 models

> hide #!6 models

> hide #!5 models

> hide #!1 models

> fitmap #4 inMap #2

Fit map B in map emd_36021.map using 12100 points  
correlation = 0.4025, correlation about mean = 0.001208, overlap = 3.93e+04  
steps = 60, shift = 0.798, angle = 2.22 degrees  
  
Position of B (#4) relative to emd_36021.map (#2) coordinates:  
Matrix rotation and translation  
-0.99983556 -0.01781761 -0.00337544 538.36196996  
0.01473827 -0.90683673 0.42122432 364.19633832  
-0.01056619 0.42110531 0.90695021 -253.23094527  
Axis -0.00356968 0.21567427 0.97645884  
Axis point 267.00649753 212.35954749 0.00000000  
Rotation angle (degrees) 179.04481347  
Shift along axis -170.64359876  
  

> volume #6 level 0.9313

> fitmap #4 inMap #2

Fit map B in map emd_36021.map using 12100 points  
correlation = 0.4024, correlation about mean = 0.001251, overlap = 3.93e+04  
steps = 60, shift = 0.0234, angle = 0.00974 degrees  
  
Position of B (#4) relative to emd_36021.map (#2) coordinates:  
Matrix rotation and translation  
-0.99983553 -0.01781058 -0.00341925 538.37285725  
0.01471170 -0.90676805 0.42137308 364.14326531  
-0.01060537 0.42125348 0.90688094 -253.22623823  
Axis -0.00359099 0.21575418 0.97644111  
Axis point 267.01106453 212.34110667 0.00000000  
Rotation angle (degrees) 179.04578199  
Shift along axis -170.62837132  
  

> hide #!4 models

> show #!5 models

> hide #!6 models

> fitmap #5 inMap #2

Fit map C1 in map emd_36021.map using 12328 points  
correlation = 0.4161, correlation about mean = 0.01488, overlap = 3.544e+04  
steps = 84, shift = 4.65, angle = 1.49 degrees  
  
Position of C1 (#5) relative to emd_36021.map (#2) coordinates:  
Matrix rotation and translation  
-0.99921654 0.03382131 0.02055291 510.92523022  
-0.03570695 -0.99438411 -0.09962556 598.31300937  
0.01706802 -0.10028139 0.99481271 -107.52144785  
Axis -0.00942031 0.05005686 -0.99870194  
Axis point 261.12696090 291.99766516 0.00000000  
Rotation angle (degrees) 178.00517028  
Shift along axis 132.51847631  
  

> fitmap #6 inMap #2

Fit map B1 in map emd_36021.map using 14784 points  
correlation = 0.3819, correlation about mean = 0.03605, overlap = 3.406e+04  
steps = 104, shift = 1.57, angle = 3.65 degrees  
  
Position of B1 (#6) relative to emd_36021.map (#2) coordinates:  
Matrix rotation and translation  
-0.99451990 0.10295774 0.01816213 486.87541485  
-0.10330955 -0.99445555 -0.01962881 594.01642679  
0.01604049 -0.02139757 0.99964236 -138.51021640  
Axis -0.00857429 0.01028494 -0.99991035  
Axis point 259.35370351 283.67559814 0.00000000  
Rotation angle (degrees) 174.07981886  
Shift along axis 140.43261269  
  

> fitmap #1 inMap #2

Fit map C in map emd_36021.map using 12795 points  
correlation = 0.3974, correlation about mean = 0.01352, overlap = 3.699e+04  
steps = 100, shift = 1.22, angle = 1.26 degrees  
  
Position of C (#1) relative to emd_36021.map (#2) coordinates:  
Matrix rotation and translation  
-0.99863829 0.04135796 -0.03179765 524.07751873  
-0.04639130 -0.98281756 0.17865469 501.55437990  
-0.02386250 0.17988655 0.98339789 -191.41940773  
Axis 0.01397997 -0.09005358 -0.99583880  
Axis point 266.39754572 253.65645937 0.00000000  
Rotation angle (degrees) 177.47484734  
Shift along axis 152.78269173  
  

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> color #2 black models

> color #2 #0055ffff models

> color #2 #00557fff models

> color #2 blue models

> color #2 #aaaa7fff models

> color #2 #ff007fff models

> color #2 yellow models

> color #2 #ebf3ffff models

> color #2 #a2a7b0ff models

> show #!3 models

> select subtract #3

8 models selected  

> select subtract #1

6 models selected  

> select subtract #4

4 models selected  

> select subtract #5

2 models selected  

> select subtract #6

Nothing selected  

> select add #3

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.99966,-0.020324,0.016366,-183.89,0.020187,0.99976,0.0084812,-175.03,-0.016534,-0.0081479,0.99983,-130.51

> fitmap #3 inMap #2

Fit map A in map emd_36021.map using 14684 points  
correlation = 0.4197, correlation about mean = 0.05383, overlap = 4.831e+04  
steps = 132, shift = 13.2, angle = 5.35 degrees  
  
Position of A (#3) relative to emd_36021.map (#2) coordinates:  
Matrix rotation and translation  
0.99721188 0.06865790 0.02923294 -205.80673511  
-0.06957385 0.99707741 0.03156143 -150.88738395  
-0.02698057 -0.03350728 0.99907423 -120.16300351  
Axis -0.39969946 0.34530440 -0.84912025  
Axis point -2913.44349953 2109.68859924 0.00000000  
Rotation angle (degrees) 4.66887213  
Shift along axis 132.19160344  
  

> view matrix models
> #3,0.99721,0.068658,0.029233,-197.34,-0.069574,0.99708,0.031561,-127.74,-0.026981,-0.033507,0.99907,-113.63

> fitmap #3 inMap #2

Fit map A in map emd_36021.map using 14684 points  
correlation = 0.4052, correlation about mean = 0.02393, overlap = 4.463e+04  
steps = 144, shift = 2.97, angle = 2.4 degrees  
  
Position of A (#3) relative to emd_36021.map (#2) coordinates:  
Matrix rotation and translation  
0.99378050 0.10837984 0.02557609 -211.47840798  
-0.10885556 0.99389458 0.01800084 -108.05054836  
-0.02346901 -0.02067298 0.99951080 -120.76658445  
Axis -0.17109580 0.21697912 -0.96106519  
Axis point -1343.05861140 1670.86058755 0.00000000  
Rotation angle (degrees) 6.48932170  
Shift along axis 128.80291437  
  

> view matrix models
> #3,0.99378,0.10838,0.025576,-222.45,-0.10886,0.99389,0.018001,-113.37,-0.023469,-0.020673,0.99951,-127.35

> view matrix models
> #3,0.99378,0.10838,0.025576,-218.06,-0.10886,0.99389,0.018001,-119.81,-0.023469,-0.020673,0.99951,-130.94

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.99194,-0.047263,-0.11758,-112.43,0.045167,0.99877,-0.020428,-162.14,0.1184,0.014953,0.99285,-190.96

> view matrix models
> #3,0.95888,0.091432,-0.26869,-97.782,0.0052484,0.94081,0.33888,-252.15,0.28377,-0.32636,0.90165,-95.861

> view matrix models
> #3,0.9538,0.11633,-0.277,-101.97,-0.051497,0.97165,0.23074,-205.75,0.29599,-0.20581,0.93275,-153.79

> view matrix models
> #3,0.955,0.11113,-0.275,-101.24,-0.0393,0.96639,0.25407,-216.24,0.29399,-0.23183,0.92727,-141.94

> view matrix models
> #3,0.94883,0.13495,-0.2855,-103.91,-0.096895,0.98489,0.14352,-164.32,0.30055,-0.10851,0.94757,-195.12

> view matrix models
> #3,0.95873,0.092302,-0.26892,-97.956,0.0033347,0.94212,0.33525,-250.68,0.2843,-0.32231,0.90293,-97.932

> view matrix models
> #3,0.95781,0.25848,-0.12564,-206.41,-0.27173,0.95685,-0.10296,-7.6842,0.093603,0.13275,0.98672,-222.04

> view matrix models
> #3,0.91596,0.28887,-0.27852,-149.56,-0.32447,0.94156,-0.090505,11.898,0.23609,0.17327,0.95616,-275.73

> view matrix models
> #3,0.95771,0.2586,-0.12619,-206.23,-0.27192,0.9568,-0.10293,-7.6094,0.094117,0.13289,0.98665,-222.25

> view matrix models
> #3,0.98199,0.04977,-0.18227,-121.02,-0.058374,0.9974,-0.042143,-117.88,0.1797,0.052024,0.98234,-221.96

> view matrix models
> #3,0.89411,0.44784,-0.0020804,-294.29,-0.44284,0.8848,0.14499,-8.144,0.066772,-0.12871,0.98943,-120.62

> view matrix models
> #3,0.89019,0.45526,-0.01738,-290.25,-0.44826,0.88204,0.14516,-5.3231,0.081416,-0.12143,0.98926,-128.27

> fitmap #3 inMap #2

Fit map A in map emd_36021.map using 14684 points  
correlation = 0.4008, correlation about mean = 0.05938, overlap = 4.635e+04  
steps = 176, shift = 5.23, angle = 8.26 degrees  
  
Position of A (#3) relative to emd_36021.map (#2) coordinates:  
Matrix rotation and translation  
0.94386876 0.33001674 -0.01416715 -261.61236967  
-0.32154933 0.92777780 0.18929973 -83.31153624  
0.07561605 -0.17411866 0.98181714 -104.07853423  
Axis -0.48362491 -0.11948044 -0.86708210  
Axis point -268.03594622 414.88581104 0.00000000  
Rotation angle (degrees) 22.06903017  
Shift along axis 226.72099190  
  

> open C:/Users/MX-User/Downloads/emd_13078.map/emd_13078.map

Opened emd_13078.map as #7, grid size 500,500,500, pixel 0.82, shown at level
3.04, step 2, values float32  

> rename #7 PSII

> rename #2 PSI

> select subtract #3

Nothing selected  

> hide #!2 models

> hide #!3 models

> select add #7

2 models selected  

> surface dust #7 size 8.2

> open C:/Users/MX-User/Downloads/emd_16389.map/emd_16389.map

Opened emd_16389.map as #8, grid size 448,448,448, pixel 0.961, shown at level
0.574, step 2, values float32  

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!7 models

> select add #8

4 models selected  

> surface dust #8 size 9.61

> hide #!8 models

> show #!7 models

> hide #!7 models

> show #!8 models

> rename #8 "PSII C2S2"

> rename #7 "PSII C2S2M2"

> open C:/Users/MX-User/Downloads/emd_30536.map/emd_30536.map

Opened emd_30536.map as #9, grid size 360,360,360, pixel 1.31, shown at level
0.242, step 2, values float32  

> open C:/Users/MX-User/Downloads/emd_31605.map/emd_31605.map

Opened emd_31605.map as #10, grid size 400,400,400, pixel 0.806, shown at
level 0.0113, step 2, values float32  

> open C:/Users/MX-User/Downloads/emd_23040.map/emd_23040.map

Opened emd_23040.map as #11, grid size 280,280,280, pixel 1.04, shown at level
0.326, step 2, values float32  

> rename #9 "PSI Algae"

> rename #10 "PSI Cyanobacteria"

> rename #11 "PSI Moss"

> select add #9

6 models selected  

> select add #10

8 models selected  

> select add #11

10 models selected  

> surface dust #8 size 9.61

> surface dust #9 size 13.1

> surface dust #10 size 8.06

> surface dust #11 size 10.4

> select subtract #7

8 models selected  

> select subtract #8

6 models selected  

> select subtract #9

4 models selected  

> select subtract #11

2 models selected  

> select subtract #10

Nothing selected  

> select add #11

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #11,1,0,0,28.93,0,1,0,81.95,0,0,1,-177.42

> view matrix models #11,1,0,0,48.783,0,1,0,52.691,0,0,1,-204.32

> view matrix models #11,1,0,0,45.127,0,1,0,76.627,0,0,1,-163.2

> hide #!8 models

> hide #!9 models

> hide #!10 models

> show #!1 models

> view matrix models #11,1,0,0,74.075,0,1,0,60.746,0,0,1,73.301

> view matrix models #11,1,0,0,58.348,0,1,0,54.902,0,0,1,55.356

> view matrix models #11,1,0,0,42.391,0,1,0,75.811,0,0,1,65.109

> ui mousemode right "translate selected models"

> view matrix models #11,1,0,0,28.973,0,1,0,60.686,0,0,1,80.734

> ui mousemode right "rotate selected models"

> view matrix models
> #11,0.393,-0.24348,0.88672,19.528,0.6741,0.73214,-0.097729,15.282,-0.62541,0.63615,0.45186,163.11

> view matrix models
> #11,-0.11277,-0.31553,0.94219,95.595,0.5493,0.77037,0.32373,-35.342,-0.82798,0.55405,0.086448,259.55

> view matrix models
> #11,0.05394,-0.34849,0.93576,76.906,0.5742,0.77751,0.25646,-29.897,-0.81694,0.52348,0.24204,238.93

> ui mousemode right "translate selected models"

> view matrix models
> #11,0.05394,-0.34849,0.93576,77.993,0.5742,0.77751,0.25646,-29.054,-0.81694,0.52348,0.24204,225.17

> view matrix models
> #11,0.05394,-0.34849,0.93576,89.374,0.5742,0.77751,0.25646,-26.801,-0.81694,0.52348,0.24204,227.01

> ui mousemode right "rotate selected models"

> view matrix models
> #11,0.38571,-0.67338,-0.6307,323.19,0.88752,0.084044,0.45304,-2.367,-0.25206,-0.7345,0.63005,267.12

> view matrix models
> #11,0.21696,-0.18908,-0.95769,327.33,0.97559,0.0079868,0.21944,30.828,-0.033842,-0.98193,0.1862,337.57

> view matrix models
> #11,0.31708,-0.46361,-0.82736,332.61,0.94832,0.16608,0.27038,4.3919,0.012058,-0.87034,0.49231,268.74

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!1 models

> view matrix models
> #11,0.16201,-0.17955,-0.97032,335.9,0.88592,0.45956,0.062873,2.4713,0.43463,-0.86981,0.23352,245.73

> view matrix models
> #11,0.042591,-0.007343,-0.99907,332.91,0.94749,0.31752,0.038058,17.646,0.31694,-0.94822,0.020481,306.29

> view matrix models
> #11,-0.28928,0.31502,-0.90392,320.75,0.25988,0.93468,0.24257,-1.3349,0.92129,-0.16474,-0.35225,161.05

> view matrix models
> #11,-0.24307,0.17845,-0.95345,341.11,0.24926,0.96142,0.1164,15.346,0.93744,-0.20936,-0.27817,153.97

> ui mousemode right "translate selected models"

> view matrix models
> #11,-0.24307,0.17845,-0.95345,327.2,0.24926,0.96142,0.1164,17.821,0.93744,-0.20936,-0.27817,150.78

> view matrix models
> #11,-0.24307,0.17845,-0.95345,326.88,0.24926,0.96142,0.1164,15.81,0.93744,-0.20936,-0.27817,152.22

> view matrix models
> #11,-0.24307,0.17845,-0.95345,326.67,0.24926,0.96142,0.1164,20.036,0.93744,-0.20936,-0.27817,152.48

> hide #!11 models

> show #!10 models

> hide #!10 models

> select subtract #11

Nothing selected  

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!9 models

> hide #!9 models

> hide #!1 models

> show #!10 models

> hide #!10 models

> show #!9 models

> ui mousemode right select

> select #9

2 models selected  

> select #9

2 models selected  

> select #9

2 models selected  

> ui mousemode right select

> ui mousemode right rotate

> ui mousemode right select

> select #9

2 models selected  

> select #9

2 models selected  
Drag select of 9 PSI Algae  
[Repeated 2 time(s)]

> select clear

[Repeated 1 time(s)]Drag select of 9 PSI Algae  

> select clear

> ui mousemode right rotate

> ui mousemode right select

> open C:/Users/MX-User/Downloads/rcsb_pdb_7D0J.fasta

Sequence '7D0J_2|Chain B|Photosystem I P700 chlorophyll a apoprotein
A2|Chlamydomonas reinhardtii (3055)' differs in length from preceding
sequences, and it is therefore impossible to open these sequences as an
alignment. If you want to open the sequences individually, specify 'false' as
the value of the 'alignment' keyword in the 'open' command.  

> open C:/Users/MX-User/Downloads/rcsb_pdb_7D0J.fasta

Sequence '7D0J_2|Chain B|Photosystem I P700 chlorophyll a apoprotein
A2|Chlamydomonas reinhardtii (3055)' differs in length from preceding
sequences, and it is therefore impossible to open these sequences as an
alignment. If you want to open the sequences individually, specify 'false' as
the value of the 'alignment' keyword in the 'open' command.  

> open C:/Users/MX-User/Downloads/7D0J.cif

Summary of feedback from opening C:/Users/MX-User/Downloads/7D0J.cif  
---  
notes | Fetching CCD PQN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/PQN/PQN.cif  
Fetching CCD SF4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SF4/SF4.cif  
  
7D0J.cif title:  
Photosystem I-LHCI-LHCII of Chlamydomonas reinhardtii [more info...]  
  
Chain information for 7D0J.cif #12  
---  
Chain | Description | UniProt  
1 a | Chlorophyll a-b binding protein, chloroplastic | Q7DM26_CHLRE 35-228  
2 | Chlorophyll a-b binding protein, chloroplastic | A8IKC8_CHLRE 28-228  
3 | Chlorophyll a-b binding protein, chloroplastic | A8JF10_CHLRE 61-263  
4 | Chlorophyll a-b binding protein, chloroplastic | Q75VZ0_CHLRE 58-262  
5 | Chlorophyll a-b binding protein, chloroplastic | Q75VY8_CHLRE 32-256  
6 | Chlorophyll a-b binding protein, chloroplastic | Q75VY6_CHLRE 28-257  
7 | Chlorophyll a-b binding protein, chloroplastic | Q75VY4_CHLRE 29-241  
8 | Chlorophyll a-b binding protein, chloroplastic | Q75VY7_CHLRE 27-243  
9 | Chlorophyll a-b binding protein, chloroplastic | Q8S567_CHLRE 29-210  
A | Photosystem I P700 chlorophyll a apoprotein A1 | PSAA_CHLRE 12-751  
B | Photosystem I P700 chlorophyll a apoprotein A2 | PSAB_CHLRE 2-735  
C | Photosystem I iron-sulfur center | PSAC_CHLRE 2-81  
D | Photosystem I reaction center subunit II, chloroplastic | PSAD_CHLRE 53-196  
E | Photosystem I reaction center subunit IV, chloroplastic | PSAE_CHLRE 34-96  
F | Photosystem I reaction center subunit F, Photosystem I reaction center subunit III, chloroplastic | PSAF_CHLRE 63-227  
G | Photosystem I reaction center subunit V, chloroplastic | PSAG_CHLRE 32-122  
H | Photosystem I reaction center subunit VI, chloroplastic | PSAH_CHLRE 31-130  
I | Photosystem I reaction center subunit VIII | A8IFG7_CHLRE 68-104  
J | Photosystem I reaction center subunit IX | PSAJ_CHLRE 1-41  
K | Photosystem I reaction center subunit psaK, chloroplastic | PSAK_CHLRE 29-113  
L | PSI subunit V | A8IL32_CHLRE 38-196  
O | Photosystem I subunit O | A8JCL6_CHLRE 31-123  
P Q R T U | Chlorophyll a-b binding protein, chloroplastic | Q93WL4_CHLRE 30-248  
S | Chlorophyll a-b binding protein, chloroplastic | A8J264_CHLRE 21-254  
  
Non-standard residues in 7D0J.cif #12  
---  
BCR — β-carotene  
CHL — chlorophyll B  
CLA — chlorophyll A  
DGD — digalactosyl diacyl glycerol (DGDG)  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol; lutein)  
NEX —
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol
((3S,5R,6R,3'S,5'R,6'S)-5',6'-epoxy-6,7-didehydro-
5,6,5',6'-tetrahydro-β,β-carotene-3,5,3'-triol; 9'-cis-neoxanthin)  
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)  
SF4 — iron/sulfur cluster  
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)  
XAT — (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-
tetrahydro-β,β-carotene-3,3'-diol (violaxanthin)  
  

> hide #!9 models

> select /9:160@CE

1 atom, 1 residue, 1 model selected  

> select /9:65@CE3

1 atom, 1 residue, 1 model selected  

> select /P:48@CA

1 atom, 1 residue, 1 model selected  

> select /S:59@OG1

1 atom, 1 residue, 1 model selected  

> select /U:191@CB

1 atom, 1 residue, 1 model selected  
Drag select of 6218 atoms, 135 pseudobonds, 2448 bonds  

> select clear

[Repeated 2 time(s)]Drag select of 13111 atoms, 220 pseudobonds, 4229 bonds  

> ui mousemode right translate

Drag select of 4950 atoms, 101 pseudobonds, 2010 bonds  
Drag select of 5049 atoms, 104 pseudobonds, 1961 bonds  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

Drag select of 5181 atoms, 141 pseudobonds, 2040 bonds  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

Drag select of 3866 atoms, 94 pseudobonds, 1473 bonds  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

Drag select of 219 atoms, 8 pseudobonds, 84 bonds  

> select /P:130@CD1

1 atom, 1 residue, 1 model selected  
Drag select of 240 atoms, 9 pseudobonds, 91 bonds  
Drag select of 112 atoms, 11 pseudobonds, 66 bonds  
Drag select of 56 atoms, 7 pseudobonds, 37 bonds  
Drag select of 58 atoms, 7 pseudobonds, 36 bonds  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

Drag select of 460 atoms, 18 pseudobonds, 185 bonds  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

Drag select of 43 atoms, 6 pseudobonds, 25 bonds  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

Drag select of 7 atoms, 3 bonds  
Drag select of 341 atoms, 26 pseudobonds, 124 bonds  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

Drag select of 484 atoms, 26 pseudobonds, 160 bonds  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

Drag select of 104 atoms, 10 pseudobonds, 57 bonds  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

Drag select of 8 atoms, 4 bonds  

> delete atoms sel

> delete bonds sel

> select clear

Drag select of 116 atoms, 2 pseudobonds, 58 bonds  

> select clear

> select /S:240@C

1 atom, 1 residue, 1 model selected  

> select /S:241@OD1

1 atom, 1 residue, 1 model selected  

> select /S:241@N

1 atom, 1 residue, 1 model selected  

> select /S:237@ND2

1 atom, 1 residue, 1 model selected  
Drag select of 33 atoms, 2 pseudobonds, 14 bonds  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

Drag select of 7 atoms, 1 pseudobonds  
Drag select of 16 atoms, 1 pseudobonds  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

Drag select of 13 atoms, 6 pseudobonds  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

Drag select of 4 atoms, 3 pseudobonds  
Drag select of 5 atoms, 3 pseudobonds  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

> select /P:105@O

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

Drag select of 20 atoms, 12 bonds, 1 pseudobonds  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

Drag select of 2 atoms, 2 pseudobonds  
Drag select of 11 atoms, 4 bonds, 2 pseudobonds  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

Drag select of 3 atoms  

> delete atoms sel

> delete bonds sel

Drag select of 20 atoms, 3 pseudobonds  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

> select /P:181@CD2

1 atom, 1 residue, 1 model selected  
Drag select of 12 atoms  

> delete atoms sel

> delete bonds sel

> select /P:180@CB

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /P:180@C

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /P:180@O

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

Drag select of 11 atoms, 4 bonds, 1 pseudobonds  
Drag select of 15 atoms, 2 pseudobonds  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

Drag select of 2 atoms  

> delete atoms sel

> delete bonds sel

> select /S:106@CD1

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

Drag select of 9 atoms, 1 bonds, 1 pseudobonds  
Drag select of 4 atoms, 1 bonds  
Drag select of 37 atoms, 20 bonds  
Drag select of 68 atoms, 3 pseudobonds, 39 bonds  
Drag select of 12 atoms, 6 bonds  

> select /S:235@CD1

1 atom, 1 residue, 1 model selected  
Drag select of 29 atoms, 3 bonds  
Drag select of 75 atoms, 9 bonds, 2 pseudobonds  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

Drag select of 3 atoms, 2 bonds, 1 pseudobonds  
Drag select of 16 atoms, 1 pseudobonds, 6 bonds  
Drag select of 25 atoms, 16 bonds, 3 pseudobonds  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

Drag select of 16 atoms, 1 pseudobonds, 8 bonds  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

> select #12 chain A

Expected a keyword  

> select #12

52995 atoms, 55090 bonds, 1049 pseudobonds, 4956 residues, 3 models selected  

> split #12

Split 7D0J.cif (#12) into 25 models  
Chain information for 7D0J.cif 1 #12.1  
---  
Chain | Description  
1 | No description available  
  
Chain information for 7D0J.cif 2 #12.2  
---  
Chain | Description  
2 | No description available  
  
Chain information for 7D0J.cif 3 #12.3  
---  
Chain | Description  
3 | No description available  
  
Chain information for 7D0J.cif 4 #12.4  
---  
Chain | Description  
4 | No description available  
  
Chain information for 7D0J.cif 5 #12.5  
---  
Chain | Description  
5 | No description available  
  
Chain information for 7D0J.cif 6 #12.6  
---  
Chain | Description  
6 | No description available  
  
Chain information for 7D0J.cif 7 #12.7  
---  
Chain | Description  
7 | No description available  
  
Chain information for 7D0J.cif 8 #12.8  
---  
Chain | Description  
8 | No description available  
  
Chain information for 7D0J.cif 9 #12.9  
---  
Chain | Description  
9 | No description available  
  
Chain information for 7D0J.cif A #12.10  
---  
Chain | Description  
A | No description available  
  
Chain information for 7D0J.cif B #12.11  
---  
Chain | Description  
B | No description available  
  
Chain information for 7D0J.cif C #12.12  
---  
Chain | Description  
C | No description available  
  
Chain information for 7D0J.cif D #12.13  
---  
Chain | Description  
D | No description available  
  
Chain information for 7D0J.cif E #12.14  
---  
Chain | Description  
E | No description available  
  
Chain information for 7D0J.cif F #12.15  
---  
Chain | Description  
F | No description available  
  
Chain information for 7D0J.cif G #12.16  
---  
Chain | Description  
G | No description available  
  
Chain information for 7D0J.cif H #12.17  
---  
Chain | Description  
H | No description available  
  
Chain information for 7D0J.cif I #12.18  
---  
Chain | Description  
I | No description available  
  
Chain information for 7D0J.cif J #12.19  
---  
Chain | Description  
J | No description available  
  
Chain information for 7D0J.cif K #12.20  
---  
Chain | Description  
K | No description available  
  
Chain information for 7D0J.cif L #12.21  
---  
Chain | Description  
L | No description available  
  
Chain information for 7D0J.cif O #12.22  
---  
Chain | Description  
O | No description available  
  
Chain information for 7D0J.cif S #12.24  
---  
Chain | Description  
S | No description available  
  
Chain information for 7D0J.cif a #12.25  
---  
Chain | Description  
a | No description available  
  

> hide #!12 models

> show #!12 models

> select add #12.25

2375 atoms, 2475 bonds, 54 pseudobonds, 211 residues, 2 models selected  

> select subtract #12.25

Nothing selected  

> select add #12.24

123 atoms, 95 bonds, 11 pseudobonds, 20 residues, 2 models selected  

> delete atoms (#!12.24 & sel)

> delete bonds (#!12.24 & sel)

> select add #12.22

917 atoms, 954 bonds, 12 pseudobonds, 98 residues, 2 models selected  

> select subtract #12.22

Nothing selected  

> select add #12.21

1592 atoms, 1641 bonds, 21 pseudobonds, 168 residues, 3 models selected  

> select subtract #12.21

Nothing selected  

> select add #12.20

850 atoms, 876 bonds, 20 pseudobonds, 91 residues, 2 models selected  

> select subtract #12.20

Nothing selected  

> select add #12.19

647 atoms, 669 bonds, 8 pseudobonds, 48 residues, 2 models selected  

> select subtract #12.19

Nothing selected  

> select add #12.18

321 atoms, 334 bonds, 38 residues, 1 model selected  

> select subtract #12.18

Nothing selected  

> select add #12.18

321 atoms, 334 bonds, 38 residues, 1 model selected  

> select subtract #12.18

Nothing selected  

> rename #12 "PSI Cyano 7D0J.cif"

> molmap #12 3

Opened map 3 as #13, grid size 122,200,233, pixel 1, shown at level 0.109,
step 1, values float32  

> hide #!12 models

> rename #13 "PSI Cyano 7D0J.cif"

> show #!11 models

> hide #!11 models

> hide #!13 models

> show #!11 models

> hide #!11 models

> show #!13 models

> show #!10 models

> hide #!10 models

> show #!9 models

> hide #!9 models

> rename #12 "PSI Algae 7D0J.cif"

> rename #13 "PSI Algae 7D0J.cif"

> rename #9 "PSI-LHCII Algae"

> close #9

> show #!12 models

> hide #!12 models

> close #12

> hide #!13 models

> show #!13 models

> rename #13 "LHCI-PSI Algae 7D0J.cif"

> show #!11 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> hide #!11 models

> show #!10 models

> hide #!10 models

> show #!8 models

> hide #!8 models

> show #!7 models

> hide #!7 models

> show #!8 models

> hide #!8 models

> show #!6 models

> hide #!6 models

> show #!6 models

> show #!8 models

> hide #!6 models

> hide #!8 models

> show #!11 models

> show #!13 models

> show #!1 models

> hide #!1 models

> show #!4 models

> hide #!13 models

> fitmap #11 inMap #4

Fit map PSI Moss in map B using 27346 points  
correlation = 0.8218, correlation about mean = 0.3069, overlap = 3.851e+04  
steps = 220, shift = 50.4, angle = 48.9 degrees  
  
Position of PSI Moss (#11) relative to B (#4) coordinates:  
Matrix rotation and translation  
0.22124639 -0.35249798 0.90928280 237.21599276  
0.80094356 -0.46624919 -0.37563426 367.28287225  
0.55636269 0.81139193 0.17917504 97.12219776  
Axis 0.70141161 0.20853985 0.68156650  
Axis point 0.00000000 193.07860821 52.46149999  
Rotation angle (degrees) 122.20254631  
Shift along axis 309.17440034  
  

> volume #4 level 0.8208

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!13 models

> hide #!11 models

> show #!4 models

> select add #13

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #13,1,0,0,-51.815,0,1,0,-8.6082,0,0,1,-10.97

> fitmap #13 inMap #4

Fit map LHCI-PSI Algae 7D0J.cif in map B using 554261 points  
correlation = 0.733, correlation about mean = 0.001546, overlap = 4.532e+05  
steps = 76, shift = 13.4, angle = 16.2 degrees  
  
Position of LHCI-PSI Algae 7D0J.cif (#13) relative to B (#4) coordinates:  
Matrix rotation and translation  
-0.99866964 0.04904968 0.01590818 571.64294796  
-0.04602166 -0.98698745 0.15407070 544.80918833  
0.02325829 0.15313361 0.98793175 106.78488581  
Axis -0.00982690 -0.07707781 -0.99697665  
Axis point 291.67063561 261.45634362 0.00000000  
Rotation angle (degrees) 177.26711139  
Shift along axis -154.07221262  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #13,-0.61753,-0.25484,-0.74412,559.88,0.50266,-0.85553,-0.12415,295.73,-0.60498,-0.4507,0.65641,322.94

> view matrix models
> #13,-0.94503,0.25901,-0.19958,407.71,-0.21779,-0.95387,-0.20665,511.71,-0.24389,-0.15182,0.95784,102.83

> ui mousemode right "translate selected models"

> view matrix models
> #13,-0.94503,0.25901,-0.19958,526.74,-0.21779,-0.95387,-0.20665,554.67,-0.24389,-0.15182,0.95784,102.13

> view matrix models
> #13,-0.94503,0.25901,-0.19958,419.13,-0.21779,-0.95387,-0.20665,565.57,-0.24389,-0.15182,0.95784,78.889

> view matrix models
> #13,-0.94503,0.25901,-0.19958,395.02,-0.21779,-0.95387,-0.20665,564.93,-0.24389,-0.15182,0.95784,67.803

> view matrix models
> #13,-0.94503,0.25901,-0.19958,376.2,-0.21779,-0.95387,-0.20665,515.54,-0.24389,-0.15182,0.95784,93.595

> view matrix models
> #13,-0.94503,0.25901,-0.19958,381.17,-0.21779,-0.95387,-0.20665,516.38,-0.24389,-0.15182,0.95784,94.581

> fitmap #13 inMap #4

Fit map LHCI-PSI Algae 7D0J.cif in map B using 554261 points  
correlation = 0.7357, correlation about mean = 0.000194, overlap = 4.796e+05  
steps = 72, shift = 9.47, angle = 17.6 degrees  
  
Position of LHCI-PSI Algae 7D0J.cif (#13) relative to B (#4) coordinates:  
Matrix rotation and translation  
0.99295606 -0.10025343 -0.06314670 152.81914879  
0.11814937 0.79783774 0.59118158 16.22282658  
-0.00888716 -0.59447808 0.80406270 316.27717472  
Axis -0.98245990 -0.04496047 0.18097267  
Axis point 0.00000000 509.76989856 154.00188903  
Rotation angle (degrees) 37.11478426  
Shift along axis -93.63054693  
  

> show #!2 models

> hide #!13 models

> hide #!4 models

> show #!13 models

> hide #!13 models

> fitmap #12 inMap #4

No atoms or maps for #12  

> fitmap #2 inMap #4

Fit map PSI in map B using 286790 points  
correlation = 0.8217, correlation about mean = 0.1785, overlap = 3.72e+06  
steps = 112, shift = 30.9, angle = 20.5 degrees  
  
Position of PSI (#2) relative to B (#4) coordinates:  
Matrix rotation and translation  
-0.98666372 -0.15679987 0.04368653 547.63800036  
0.16105723 -0.97930518 0.12256403 477.19484277  
0.02356442 0.12796551 0.99149864 140.60142154  
Axis 0.01695705 0.06316997 0.99785871  
Axis point 253.91655984 256.01728363 0.00000000  
Rotation angle (degrees) 170.83549691  
Shift along axis 179.73105768  
  

> show #!4 models

> show #!13 models

> hide #!2 models

> hide #!4 models

> hide #!13 models

> show #!1 models

> lighting flat

> lighting soft

> graphics silhouettes false

> transparency #1 0

> set bgColor white

> set bgColor #ffffff00

> show #!5 models

> show #!4 models

> show #!3 models

> show #!6 models

> select add #6

4 models selected  

> select add #5

6 models selected  

> select add #3

8 models selected  

> select add #4

10 models selected  

> select add #1

12 models selected  

> transparency #1.1#3.1#4.1#5.1#6.1 0

> hide #!1 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> volume #3 level 1.059

> volume #3 level 0.8446

> volume #3 level 1.294

> center #3

Unknown command: center #3  

> turn #3 180

Expected an axis vector or a keyword  

> turn y 180 #3

Expected 'forever' or an integer >= 1 or a keyword  

> turn y 1 180 #3

Expected a keyword  

> turn y 1 180 model#3

Expected a keyword  

> turn y 1 180 model#3 center1

Expected a keyword  

> turn £3

Expected an axis vector or a keyword  

> turn #3

Expected an axis vector or a keyword  

> turn #3

Expected an axis vector or a keyword  

> turn y #3

Expected a number or a keyword  

> turn y models #3

[Repeated 31 time(s)]

> toolshed show

> ui tool show "Scale Bar"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\label\scalebar_gui.py", line 65, in _update_scalebar  
self._show_scalebar()  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\label\scalebar_gui.py", line 70, in _show_scalebar  
options = self._changed_options()  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\label\scalebar_gui.py", line 93, in _changed_options  
thickness = self._thickness.value  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\composite.py", line 185, in _get_value  
return self.string_to_value(self._line_edit.text())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: invalid literal for int() with base 10: '10.69'  
  
ValueError: invalid literal for int() with base 10: '10.69'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\composite.py", line 185, in _get_value  
return self.string_to_value(self._line_edit.text())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\label\scalebar_gui.py", line 65, in _update_scalebar  
self._show_scalebar()  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\label\scalebar_gui.py", line 70, in _show_scalebar  
options = self._changed_options()  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\label\scalebar_gui.py", line 93, in _changed_options  
thickness = self._thickness.value  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\composite.py", line 185, in _get_value  
return self.string_to_value(self._line_edit.text())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: invalid literal for int() with base 10: '10.69'  
  
ValueError: invalid literal for int() with base 10: '10.69'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\composite.py", line 185, in _get_value  
return self.string_to_value(self._line_edit.text())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\label\scalebar_gui.py", line 65, in _update_scalebar  
self._show_scalebar()  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\label\scalebar_gui.py", line 70, in _show_scalebar  
options = self._changed_options()  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\label\scalebar_gui.py", line 93, in _changed_options  
thickness = self._thickness.value  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\composite.py", line 185, in _get_value  
return self.string_to_value(self._line_edit.text())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: invalid literal for int() with base 10: '10.6'  
  
ValueError: invalid literal for int() with base 10: '10.6'  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\composite.py", line 185, in _get_value  
return self.string_to_value(self._line_edit.text())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 461.92
OpenGL renderer: Quadro K420/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: Hewlett-Packard
Model: HP Compaq 8200 Elite CMT PC
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 8,545,939,456
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-2400 CPU @ 3.10GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1

[Eric Pettersen]

Duplicate of #16649