ffmpeg: Permission denied

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.6.1-x86_64-i386-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Spin movie

Log:
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/geordanstukey/Desktop/AIP1 Cofilin Project/Data/NCCAT 082225/AF
> Structures/isoform_correct_aip1_cofilin_actin/fold_isoform_correct_aip1_cofilin_actin_model_0.cif"
> format mmcif

Chain information for fold_isoform_correct_aip1_cofilin_actin_model_0.cif #1  
---  
Chain | Description  
A B C D | .  
E F G H | .  
I | .  
  

> hide cartoons

> hide atoms

> show cartoons

Computing secondary structure  

> open /Users/geordanstukey/Downloads/cryosparc_P28_J755_004_volume_map.mrc

Opened cryosparc_P28_J755_004_volume_map.mrc as #2, grid size 600,600,600,
pixel 0.73, shown at level 0.0311, step 4, values float32  

> lighting simple

> volume #2 step 1

> volume #2 level 0.08

> volume #2 level 0.07

> volume #2 level 0.06

> volume #2 level 0.05

> select add #1

21172 atoms, 21597 bonds, 2727 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,82.75,0,1,0,90.971,0,0,1,188.8

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.11456,-0.0082424,0.99338,99.198,0.19912,-0.97986,0.014833,82.597,0.97326,0.1995,0.1139,174.96

> transparency 50

> view matrix models
> #1,0.03399,0.2913,-0.95603,85.491,-0.90604,0.41272,0.093546,97.435,0.42182,0.86302,0.27796,183.12

> view matrix models
> #1,0.59889,-0.041861,-0.79973,80.554,-0.66454,0.5313,-0.52546,91.485,0.44689,0.84615,0.29037,182.93

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.59889,-0.041861,-0.79973,223.84,-0.66454,0.5313,-0.52546,105.86,0.44689,0.84615,0.29037,218.46

> view matrix models
> #1,0.59889,-0.041861,-0.79973,181.32,-0.66454,0.5313,-0.52546,183.23,0.44689,0.84615,0.29037,234.47

> view matrix models
> #1,0.59889,-0.041861,-0.79973,213.06,-0.66454,0.5313,-0.52546,222.47,0.44689,0.84615,0.29037,228.81

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.95205,-0.29828,0.068005,215.13,0.17536,0.3499,-0.92023,211.87,0.25069,0.88803,0.38543,231.31

> view matrix models
> #1,0.9265,-0.37628,0.0010007,214.62,0.16565,0.40548,-0.89897,212.29,0.33786,0.83306,0.43801,230.73

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.9265,-0.37628,0.0010007,218.8,0.16565,0.40548,-0.89897,218.7,0.33786,0.83306,0.43801,225.88

> fitmap #1 inMap #2

Fit molecule fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) to map
cryosparc_P28_J755_004_volume_map.mrc (#2) using 21172 atoms  
average map value = 0.07595, steps = 260  
shifted from previous position = 4.3  
rotated from previous position = 25.6 degrees  
atoms outside contour = 8293, contour level = 0.05  
  
Position of fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) relative
to cryosparc_P28_J755_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.83796344 -0.38990697 -0.38182435 218.27546116  
-0.23861262 0.36746262 -0.89890780 216.69267937  
0.49079659 0.84435998 0.21488352 229.98152136  
Axis 0.89154373 -0.44627667 0.07737511  
Axis point 0.00000000 9.54084071 291.78566988  
Rotation angle (degrees) 77.86857663  
Shift along axis 115.69207804  
  

> select subtract #1

Nothing selected  

> hide #!2 models

> delete #1/A-C

> delete #1/E-I

> show #!2 models

> select add #1

2947 atoms, 3010 bonds, 377 residues, 1 model selected  

> molmap sel 6.5 onGrid #2

Opened fold_isoform_correct_aip1_cofilin_actin_model_0.cif map 6.5 as #3, grid
size 600,600,600, pixel 0.73, shown at level 0.0901, step 1, values float32  

> hide #!2 models

> hide #1 models

> select subtract #1

Nothing selected  

> save "/Users/geordanstukey/Desktop/AIP1 Cofilin
> Project/Data/100325_BE_Working/BE_ExtraActin_Mask_Redo.mrc" models #3

> close #1#2-3

> open
> /Users/geordanstukey/Downloads/cryosparc_P28_J742_class_00_00067_volume.mrc

Opened cryosparc_P28_J742_class_00_00067_volume.mrc as #1, grid size
120,120,120, pixel 3.65, shown at level 0.428, step 1, values float32  

> close #1

> open
> /Users/geordanstukey/Downloads/cryosparc_P28_J742_class_00_00067_volume.mrc
> format mrc

Opened cryosparc_P28_J742_class_00_00067_volume.mrc as #1, grid size
120,120,120, pixel 3.65, shown at level 0.428, step 1, values float32  

> open
> /Users/geordanstukey/Downloads/cryosparc_P28_J742_class_03_00067_volume.mrc

Opened cryosparc_P28_J742_class_03_00067_volume.mrc as #2, grid size
120,120,120, pixel 3.65, shown at level 0.431, step 1, values float32  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> close #1

> open /Users/geordanstukey/Downloads/cryosparc_P28_J765_map.mrc

Opened cryosparc_P28_J765_map.mrc as #1, grid size 120,120,120, pixel 3.65,
shown at level 0.427, step 1, values float32  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> close #1

> open /Users/geordanstukey/Downloads/cryosparc_P28_J765_map(1).mrc

Opened cryosparc_P28_J765_map(1).mrc as #1, grid size 120,120,120, pixel 3.65,
shown at level 0.402, step 1, values float32  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> close #1-2

> open "/Users/geordanstukey/Desktop/AIP1 Cofilin Project/Data/NCCAT 082225/AF
> Structures/isoform_correct_aip1_cofilin_actin/fold_isoform_correct_aip1_cofilin_actin_model_0.cif"
> format mmcif

Chain information for fold_isoform_correct_aip1_cofilin_actin_model_0.cif #1  
---  
Chain | Description  
A B C D | .  
E F G H | .  
I | .  
  

> hide atoms

> show cartoons

Computing secondary structure  

> open /Users/geordanstukey/Downloads/cryosparc_P28_J768_005_volume_map.mrc

Opened cryosparc_P28_J768_005_volume_map.mrc as #2, grid size 600,600,600,
pixel 0.73, shown at level 0.0317, step 4, values float32  

> volume #2 level 0.05

> volume #2 step 1

> volume #2 level 0.06

> volume #2 level 0.07

> select add #1

21172 atoms, 21597 bonds, 2727 residues, 1 model selected  

> view matrix models #1,1,0,0,167.84,0,1,0,92.596,0,0,1,237.99

> lighting soft

> volume #2 level 0.06

> select subtract #1

Nothing selected  

> select add #1

21172 atoms, 21597 bonds, 2727 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.93974,-0.27967,-0.19664,182.28,0.27858,-0.29297,-0.91464,79.469,0.19818,-0.91431,0.35323,228.7

> view matrix models
> #1,0.54517,0.40065,0.73639,178.22,-0.038602,-0.86548,0.49946,90.008,0.83744,-0.30072,-0.45637,219.69

> lighting simple

> transparency 50

> view matrix models
> #1,-0.010074,0.71786,0.69611,183.81,-0.87135,-0.34782,0.34608,97.907,0.49057,-0.60307,0.62901,229.14

> view matrix models
> #1,-0.59746,-0.6282,0.49841,182.93,0.72984,-0.68348,0.013414,80.641,0.33222,0.37177,0.86684,235.48

> view matrix models
> #1,-0.32805,0.24129,0.91332,186.43,0.61729,-0.6771,0.40061,84.305,0.71507,0.69521,0.073175,227.8

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.32805,0.24129,0.91332,127.6,0.61729,-0.6771,0.40061,165.34,0.71507,0.69521,0.073175,208.17

> view matrix models
> #1,-0.32805,0.24129,0.91332,187.15,0.61729,-0.6771,0.40061,257.98,0.71507,0.69521,0.073175,204.35

> view matrix models
> #1,-0.32805,0.24129,0.91332,205.94,0.61729,-0.6771,0.40061,221.35,0.71507,0.69521,0.073175,198.63

> view matrix models
> #1,-0.32805,0.24129,0.91332,219.6,0.61729,-0.6771,0.40061,230.45,0.71507,0.69521,0.073175,204.96

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.64222,0.21454,0.73588,220.99,0.48699,-0.62718,0.60786,233.18,0.59194,0.74875,0.29831,207.75

> view matrix models
> #1,-0.7392,0.33873,0.58211,221.2,0.42086,-0.44246,0.7919,235.65,0.5258,0.83036,0.18451,207.82

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.7392,0.33873,0.58211,226.55,0.42086,-0.44246,0.7919,225.24,0.5258,0.83036,0.18451,202.99

> fitmap #1 inMap #2

Fit molecule fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) to map
cryosparc_P28_J768_005_volume_map.mrc (#2) using 21172 atoms  
average map value = 0.08213, steps = 92  
shifted from previous position = 1.84  
rotated from previous position = 6.38 degrees  
atoms outside contour = 8854, contour level = 0.06  
  
Position of fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) relative
to cryosparc_P28_J768_005_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.69654049 0.27790870 0.66151197 225.62236157  
0.51046229 -0.45597318 0.72905192 223.77272269  
0.50424159 0.84549110 0.17574187 202.58646658  
Axis 0.38311230 0.51745654 0.76515600  
Axis point 60.15031963 47.81694365 0.00000000  
Rotation angle (degrees) 171.25919201  
Shift along axis 357.24160903  
  

> select subtract #1

Nothing selected  

> hide #!2 models

> delete #1/I

> delete #1/C,B,F,G

> show #!2 models

> molmap sel 6.5 onGrid #2

No atoms specified  

> select add #1

8280 atoms, 8438 bonds, 1058 residues, 1 model selected  

> molmap sel 6.5 onGrid #2

Opened fold_isoform_correct_aip1_cofilin_actin_model_0.cif map 6.5 as #3, grid
size 600,600,600, pixel 0.73, shown at level 0.0928, step 1, values float32  

> hide #!2 models

> hide #1 models

> select subtract #1

Nothing selected  

> save "/Users/geordanstukey/Desktop/AIP1 Cofilin
> Project/Data/100325_BE_Working/BE_2xActinCof_Mask_updated.mrc" models #3

> close #2

> show #1 models

> hide #!3 models

> close #3

> close

> open "/Users/geordanstukey/Desktop/AIP1 Cofilin Project/Data/NCCAT 082225/AF
> Structures/isoform_correct_aip1_cofilin_actin/fold_isoform_correct_aip1_cofilin_actin_model_0.cif"
> format mmcif

Chain information for fold_isoform_correct_aip1_cofilin_actin_model_0.cif #1  
---  
Chain | Description  
A B C D | .  
E F G H | .  
I | .  
  

> hide atoms

> show cartoons

Computing secondary structure  

> open /Users/geordanstukey/Downloads/cryosparc_P28_J769_004_volume_map.mrc

Opened cryosparc_P28_J769_004_volume_map.mrc as #2, grid size 600,600,600,
pixel 0.73, shown at level 0.0375, step 4, values float32  

> volume #2 step 1

> volume #2 level 0.06

> lighting soft

> select add #1

21172 atoms, 21597 bonds, 2727 residues, 1 model selected  

> view matrix models #1,1,0,0,137.29,0,1,0,1.1896,0,0,1,258.93

> lighting simple

> transparency 50

> view matrix models #1,1,0,0,219.47,0,1,0,-34.355,0,0,1,330.15

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.987,0.052148,0.15204,220.81,-0.026416,0.98567,-0.16659,-35.325,-0.15855,0.16041,0.97423,331.88

> view matrix models
> #1,0.93144,-0.32133,0.17078,220.14,0.22412,0.1368,-0.96491,-45.892,0.2867,0.93703,0.19944,325.35

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.93144,-0.32133,0.17078,318.22,0.22412,0.1368,-0.96491,67.359,0.2867,0.93703,0.19944,213.79

> view matrix models
> #1,0.93144,-0.32133,0.17078,193.24,0.22412,0.1368,-0.96491,134.42,0.2867,0.93703,0.19944,239.17

> view matrix models
> #1,0.93144,-0.32133,0.17078,232.84,0.22412,0.1368,-0.96491,206.29,0.2867,0.93703,0.19944,222.74

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.83378,-0.50332,0.22691,233.45,0.20743,-0.095312,-0.9736,205.58,0.51165,0.85883,0.024933,219.33

> view matrix models
> #1,0.86084,-0.46982,-0.1955,230.41,-0.15163,0.12992,-0.97986,209.4,0.48576,0.87315,0.040602,219.71

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.86084,-0.46982,-0.1955,214.03,-0.15163,0.12992,-0.97986,214.58,0.48576,0.87315,0.040602,233.21

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.8823,-0.27146,-0.38451,213.22,-0.26078,0.39815,-0.87947,217.13,0.39184,0.87623,0.2805,235.69

> fitmap #1 inMap #2

Fit molecule fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) to map
cryosparc_P28_J769_004_volume_map.mrc (#2) using 21172 atoms  
average map value = 0.07752, steps = 128  
shifted from previous position = 7.61  
rotated from previous position = 7.26 degrees  
atoms outside contour = 8601, contour level = 0.06  
  
Position of fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) relative
to cryosparc_P28_J769_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.83664221 -0.38741000 -0.38722514 217.79473247  
-0.24430540 0.36880282 -0.89682738 216.77827114  
0.49024962 0.84492483 0.21390965 229.77954914  
Axis 0.89067525 -0.44871196 0.07317902  
Axis point 0.00000000 9.43444712 291.87872695  
Rotation angle (degrees) 77.89655559  
Shift along axis 113.52841725  
  

> view matrix models
> #1,-0.43588,0.25146,0.86416,239.59,0.73726,-0.45094,0.50309,215.16,0.51619,0.8564,0.011169,228.2

> view matrix models
> #1,-0.74071,0.52515,0.41901,240.09,0.31843,-0.27476,0.90726,222.17,0.59157,0.80544,0.036292,227.54

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.74071,0.52515,0.41901,220.49,0.31843,-0.27476,0.90726,216,0.59157,0.80544,0.036292,258.29

> view matrix models
> #1,-0.74071,0.52515,0.41901,228.88,0.31843,-0.27476,0.90726,225.69,0.59157,0.80544,0.036292,262.31

> view matrix models
> #1,-0.74071,0.52515,0.41901,230.34,0.31843,-0.27476,0.90726,227.78,0.59157,0.80544,0.036292,259.59

> view matrix models
> #1,-0.74071,0.52515,0.41901,226.99,0.31843,-0.27476,0.90726,230.52,0.59157,0.80544,0.036292,261.6

> fitmap #1 inMap #2

Fit molecule fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) to map
cryosparc_P28_J769_004_volume_map.mrc (#2) using 21172 atoms  
average map value = 0.05844, steps = 312  
shifted from previous position = 6.55  
rotated from previous position = 21.2 degrees  
atoms outside contour = 13175, contour level = 0.06  
  
Position of fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) relative
to cryosparc_P28_J769_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.85357546 0.51357297 0.08747423 223.66089491  
-0.01641455 -0.19433575 0.98079773 226.87778849  
0.52071058 0.83574902 0.17431030 256.94540708  
Axis -0.20729291 -0.61914942 -0.75741907  
Axis point 75.56101345 -8.82248331 0.00000000  
Rotation angle (degrees) 159.52099524  
Shift along axis -381.44992047  
  

> select subtract #1

Nothing selected  

> hide #1 models

> show #1 models

> hide #!2 models

> delete #1/A-C

> delete #1/I

> delete #1/E-G

> show #!2 models

> select add #1

4140 atoms, 4219 bonds, 529 residues, 1 model selected  

> molmap sel 6.5 onGrid #2

Opened fold_isoform_correct_aip1_cofilin_actin_model_0.cif map 6.5 as #3, grid
size 600,600,600, pixel 0.73, shown at level 0.0914, step 1, values float32  

> hide #!2 models

> hide #1 models

> select subtract #1

Nothing selected  

> save "/Users/geordanstukey/Desktop/AIP1 Cofilin
> Project/Data/100325_BE_Working/BE_ExtraES_Mask.mrc" models #3

> close #1#2-3

> open "/Users/geordanstukey/Desktop/AIP1 Cofilin Project/Data/NCCAT 082225/AF
> Structures/isoform_correct_aip1_cofilin_actin/fold_isoform_correct_aip1_cofilin_actin_model_0.cif"
> format mmcif

Chain information for fold_isoform_correct_aip1_cofilin_actin_model_0.cif #1  
---  
Chain | Description  
A B C D | .  
E F G H | .  
I | .  
  

> hide atoms

> show cartoons

Computing secondary structure  

> open /Users/geordanstukey/Downloads/cryosparc_P28_J767_004_volume_map.mrc

Opened cryosparc_P28_J767_004_volume_map.mrc as #2, grid size 600,600,600,
pixel 0.73, shown at level 0.0321, step 4, values float32  

> volume #2 step 1

> volume #2 level 0.05

> volume #2 level 0.045

> lighting soft

> lighting simple

> transparency 50

> select add #1

21172 atoms, 21597 bonds, 2727 residues, 1 model selected  

> view matrix models #1,1,0,0,124.1,0,1,0,57.228,0,0,1,113.7

> view matrix models #1,1,0,0,130.08,0,1,0,69.881,0,0,1,137.88

> view matrix models #1,1,0,0,116.04,0,1,0,77.747,0,0,1,191.9

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.31489,-0.51275,0.79871,131.15,0.94231,-0.26955,0.19846,66.646,0.11354,0.81512,0.56805,190.73

> delete #1/I

> view matrix models
> #1,-0.49347,-0.40925,0.76747,132.56,0.86476,-0.32541,0.3825,70.016,0.093204,0.85242,0.51448,190.19

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.49347,-0.40925,0.76747,135.51,0.86476,-0.32541,0.3825,229.97,0.093204,0.85242,0.51448,129.04

> view matrix models
> #1,-0.49347,-0.40925,0.76747,222.7,0.86476,-0.32541,0.3825,248.27,0.093204,0.85242,0.51448,166.22

> view matrix models
> #1,-0.49347,-0.40925,0.76747,230.22,0.86476,-0.32541,0.3825,220.18,0.093204,0.85242,0.51448,169.74

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.52803,0.060688,0.84706,233.37,0.69806,-0.53701,0.47363,222.33,0.48362,0.84139,0.24119,162.04

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.52803,0.060688,0.84706,230.59,0.69806,-0.53701,0.47363,226.86,0.48362,0.84139,0.24119,147.81

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.32317,-0.039031,0.94554,230.03,0.83769,-0.47663,0.26664,222.61,0.44026,0.87824,0.18673,147.46

> fitmap #1 inMap #2

Fit molecule fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) to map
cryosparc_P28_J767_004_volume_map.mrc (#2) using 16560 atoms  
average map value = 0.05003, steps = 200  
shifted from previous position = 4.9  
rotated from previous position = 0.716 degrees  
atoms outside contour = 9659, contour level = 0.045  
  
Position of fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) relative
to cryosparc_P28_J767_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.31624079 -0.03032365 0.94819420 226.23367579  
0.83621481 -0.48094262 0.26351279 219.81427890  
0.44803633 0.87622753 0.17745076 148.69458089  
Axis 0.52224652 0.42630884 0.73859281  
Axis point 42.40615633 79.77251248 0.00000000  
Rotation angle (degrees) 144.08287283  
Shift along axis 321.68326950  
  

> select subtract #1

Nothing selected  

> hide #1 models

> show #1 models

> hide #!2 models

> delete #1/A-B

> delete #1/D-F

> delete #1/H

> show #!2 models

> hide #!2 models

> show #!2 models

> select add #1

4140 atoms, 4219 bonds, 529 residues, 1 model selected  

> molmap sel 6.5 onGrid #2

Opened fold_isoform_correct_aip1_cofilin_actin_model_0.cif map 6.5 as #3, grid
size 600,600,600, pixel 0.73, shown at level 0.0915, step 1, values float32  

> save "/Users/geordanstukey/Desktop/AIP1 Cofilin
> Project/Data/100325_BE_Working/PE_ExtraSubunit_Mask.mrc" models #3

> close #1#2-3

> open "/Users/geordanstukey/Desktop/AIP1 Cofilin Project/Data/NCCAT 082225/AF
> Structures/isoform_correct_aip1_cofilin_actin/fold_isoform_correct_aip1_cofilin_actin_model_0.cif"
> format mmcif

Chain information for fold_isoform_correct_aip1_cofilin_actin_model_0.cif #1  
---  
Chain | Description  
A B C D | .  
E F G H | .  
I | .  
  

> hide atoms

> show cartoons

Computing secondary structure  

> open /Users/geordanstukey/Downloads/cryosparc_P28_J769_004_volume_map.mrc

Opened cryosparc_P28_J769_004_volume_map.mrc as #2, grid size 600,600,600,
pixel 0.73, shown at level 0.0375, step 4, values float32  

> volume #2 step 1

> select add #1

21172 atoms, 21597 bonds, 2727 residues, 1 model selected  

> view matrix models
> #1,1,4.6308e-05,-0.0018125,-0.01233,-4.7815e-05,1,-0.00083149,-0.0053238,0.0018125,0.00083157,1,-0.012825

> volume #2 level 0.05

> view matrix models
> #1,0.8053,-0.35084,-0.47792,-2.8129,0.16975,-0.63592,0.75285,-1.8559,-0.56805,-0.6874,-0.45255,-7.4607

> lighting simple

> view matrix models
> #1,0.48306,-0.82709,-0.28735,-0.3414,0.59455,0.55076,-0.58581,-10.708,0.64278,0.11213,0.7578,-6.838

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.48306,-0.82709,-0.28735,78.797,0.59455,0.55076,-0.58581,4.5702,0.64278,0.11213,0.7578,294.65

> view matrix models
> #1,0.48306,-0.82709,-0.28735,166.35,0.59455,0.55076,-0.58581,107.36,0.64278,0.11213,0.7578,262.16

> transparency 50

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.73124,0.14407,-0.66673,177.53,-0.42183,-0.86364,0.27602,117.26,-0.53605,0.48308,0.6923,273.15

> view matrix models
> #1,-0.66497,0.72133,0.19364,184.86,-0.13306,-0.36953,0.91964,120.89,0.73492,0.58577,0.34171,260.11

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.66497,0.72133,0.19364,255.61,-0.13306,-0.36953,0.91964,202.7,0.73492,0.58577,0.34171,252.12

> view matrix models
> #1,-0.66497,0.72133,0.19364,221.02,-0.13306,-0.36953,0.91964,226.1,0.73492,0.58577,0.34171,256.54

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.79272,0.44292,0.41884,222.73,0.15612,-0.51665,0.84184,222.56,0.58926,0.73273,0.34041,258.29

> view matrix models
> #1,-0.81211,0.58345,0.0080231,220.54,-0.16659,-0.24502,0.9551,227.05,0.55922,0.77431,0.29618,258.39

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.81211,0.58345,0.0080231,217.23,-0.16659,-0.24502,0.9551,227.73,0.55922,0.77431,0.29618,261.88

> fitmap #1 inMap #2

Fit molecule fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) to map
cryosparc_P28_J769_004_volume_map.mrc (#2) using 21172 atoms  
average map value = 0.05844, steps = 164  
shifted from previous position = 8.22  
rotated from previous position = 9.84 degrees  
atoms outside contour = 11485, contour level = 0.05  
  
Position of fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) relative
to cryosparc_P28_J769_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.85358361 0.51356257 0.08745588 223.66442096  
-0.01643553 -0.19433957 0.98079662 226.87271517  
0.52069657 0.83575453 0.17432574 256.94905158  
Axis -0.20728070 -0.61914737 -0.75742408  
Axis point 75.56417706 -8.82661412 0.00000000  
Rotation angle (degrees) 159.52071011  
Shift along axis -381.44836296  
  

> select subtract #1

Nothing selected  

> hide #1 models

> show #1 models

> hide #!2 models

> delete #1/A-G

> delete #1/I

> show #!2 models

> select add #1

1193 atoms, 1209 bonds, 152 residues, 1 model selected  

> molmap sel 6.5 onGrid #2

Opened fold_isoform_correct_aip1_cofilin_actin_model_0.cif map 6.5 as #3, grid
size 600,600,600, pixel 0.73, shown at level 0.0726, step 1, values float32  

> hide #!2 models

> hide #!3 models

> select subtract #1

Nothing selected  

> show #!3 models

> hide #1 models

> save "/Users/geordanstukey/Desktop/AIP1 Cofilin
> Project/Data/100325_BE_Working/BE_ES_Cofilin mask.mrc" models #3

> close #1#2-3

> open "/Users/geordanstukey/Desktop/AIP1 Cofilin Project/Data/NCCAT 082225/AF
> Structures/isoform_correct_aip1_cofilin_actin/fold_isoform_correct_aip1_cofilin_actin_model_0.cif"
> format mmcif

Chain information for fold_isoform_correct_aip1_cofilin_actin_model_0.cif #1  
---  
Chain | Description  
A B C D | .  
E F G H | .  
I | .  
  

> hide atoms

> show cartoons

Computing secondary structure  

> open /Users/geordanstukey/Downloads/cryosparc_P28_J783_005_volume_map.mrc

Opened cryosparc_P28_J783_005_volume_map.mrc as #2, grid size 600,600,600,
pixel 0.73, shown at level 0.037, step 4, values float32  

> volume #2 step 1

> volume #2 level 0.05

> volume #2 level 0.06

> lighting simple

> transparency 50

> select add #1

21172 atoms, 21597 bonds, 2727 residues, 1 model selected  

> view matrix models #1,1,0,0,170.01,0,1,0,23.082,0,0,1,203.01

> view matrix models #1,1,0,0,193.31,0,1,0,143.68,0,0,1,242.83

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.84849,-0.27427,-0.45258,190.56,-0.26112,0.52688,-0.80884,138.74,0.4603,0.80447,0.37543,237.29

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.84849,-0.27427,-0.45258,240.09,-0.26112,0.52688,-0.80884,166.24,0.4603,0.80447,0.37543,219.1

> view matrix models
> #1,0.84849,-0.27427,-0.45258,216.4,-0.26112,0.52688,-0.80884,214.31,0.4603,0.80447,0.37543,231.01

> fitmap #1 inMap #2

Fit molecule fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) to map
cryosparc_P28_J783_005_volume_map.mrc (#2) using 21172 atoms  
average map value = 0.06892, steps = 152  
shifted from previous position = 3.11  
rotated from previous position = 11.4 degrees  
atoms outside contour = 9234, contour level = 0.06  
  
Position of fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) relative
to cryosparc_P28_J783_005_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.83634991 -0.38899154 -0.38626987 217.85218298  
-0.24279336 0.36890248 -0.89719694 216.68865363  
0.49149793 0.84415433 0.21408699 229.92055902  
Axis 0.89046873 -0.44886106 0.07476085  
Axis point 0.00000000 9.44758446 291.86345099  
Rotation angle (degrees) 77.89700404  
Shift along axis 113.91651500  
  

> select subtract #1

Nothing selected  

> hide #!2 models

> delete #1/A-F

> delete #1/I

> delete #1/G

> show #!2 models

> molmap sel 6.5 onGrid #2

No atoms specified  

> select add #1

1193 atoms, 1209 bonds, 152 residues, 1 model selected  

> molmap sel 6.5 onGrid #2

Opened fold_isoform_correct_aip1_cofilin_actin_model_0.cif map 6.5 as #3, grid
size 600,600,600, pixel 0.73, shown at level 0.0726, step 1, values float32  

> hide #!2 models

> hide #1 models

> select subtract #1

Nothing selected  
No map chosen to save  

> save "/Users/geordanstukey/Desktop/AIP1 Cofilin
> Project/Data/100325_BE_Working/BE_ES_Cofilin mask_updated.mrc" models #3

> hide #!3 models

> show #!2 models

> show #1 models

> select add #1

1193 atoms, 1209 bonds, 152 residues, 1 model selected  

> view matrix models
> #1,0.83635,-0.38899,-0.38627,206.64,-0.24279,0.3689,-0.8972,209.05,0.4915,0.84415,0.21409,174.63

> view matrix models
> #1,0.83635,-0.38899,-0.38627,218.95,-0.24279,0.3689,-0.8972,200.13,0.4915,0.84415,0.21409,177.5

> view matrix models
> #1,0.83635,-0.38899,-0.38627,212.15,-0.24279,0.3689,-0.8972,192.68,0.4915,0.84415,0.21409,175.45

> fitmap #1 inMap #2

Fit molecule fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) to map
cryosparc_P28_J783_005_volume_map.mrc (#2) using 1193 atoms  
average map value = 0.0802, steps = 140  
shifted from previous position = 3.41  
rotated from previous position = 31 degrees  
atoms outside contour = 358, contour level = 0.06  
  
Position of fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) relative
to cryosparc_P28_J783_005_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.62763091 -0.08855145 -0.77345852 212.00308365  
-0.66589618 0.45363239 -0.59228365 218.74926718  
0.40331341 0.88677860 0.22574764 178.61040185  
Axis 0.74840133 -0.59544328 -0.29213481  
Axis point 0.00000000 59.83025760 290.24544376  
Rotation angle (degrees) 81.16987115  
Shift along axis -23.76770634  
  

> select subtract #1

Nothing selected  

> close #1#2-3

> open "/Users/geordanstukey/Desktop/AIP1 Cofilin Project/Data/NCCAT 082225/AF
> Structures/isoform_correct_aip1_cofilin_actin/fold_isoform_correct_aip1_cofilin_actin_model_0.cif"
> format mmcif

Chain information for fold_isoform_correct_aip1_cofilin_actin_model_0.cif #1  
---  
Chain | Description  
A B C D | .  
E F G H | .  
I | .  
  

> hide atoms

> show cartoons

Computing secondary structure  

> open /Users/geordanstukey/Downloads/cryosparc_P28_J795_005_volume_map.mrc

Opened cryosparc_P28_J795_005_volume_map.mrc as #2, grid size 600,600,600,
pixel 0.73, shown at level 0.0318, step 4, values float32  

> delete #1/I

> volume #2 step 1

> volume #2 level 0.06

> select add #1

16560 atoms, 16876 bonds, 2116 residues, 1 model selected  

> view matrix models #1,1,0,0,100.84,0,1,0,199.19,0,0,1,177.11

> lighting simple

> transparency 50

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.37549,0.85317,-0.36209,109.94,0.74264,0.043216,-0.66829,179.01,-0.55452,-0.51983,-0.64983,154.22

> view matrix models
> #1,0.69747,-0.12637,-0.70538,91.942,0.56854,-0.50162,0.65203,199.39,-0.43623,-0.85581,-0.27802,157.89

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.69747,-0.12637,-0.70538,172.36,0.56854,-0.50162,0.65203,261.37,-0.43623,-0.85581,-0.27802,143.33

> view matrix models
> #1,0.69747,-0.12637,-0.70538,167.44,0.56854,-0.50162,0.65203,223.11,-0.43623,-0.85581,-0.27802,146.45

> view matrix models
> #1,0.69747,-0.12637,-0.70538,208.06,0.56854,-0.50162,0.65203,219.39,-0.43623,-0.85581,-0.27802,150.4

> view matrix models
> #1,0.69747,-0.12637,-0.70538,214.11,0.56854,-0.50162,0.65203,218.76,-0.43623,-0.85581,-0.27802,150.54

> view matrix models
> #1,0.69747,-0.12637,-0.70538,218.31,0.56854,-0.50162,0.65203,214.82,-0.43623,-0.85581,-0.27802,152.28

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.43525,0.0096218,-0.90026,217.98,0.6589,-0.68482,0.31124,208.06,-0.61352,-0.72865,-0.30441,153.83

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.43525,0.0096218,-0.90026,213.79,0.6589,-0.68482,0.31124,207.97,-0.61352,-0.72865,-0.30441,153.04

> fitmap #1 inMap #2

Fit molecule fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) to map
cryosparc_P28_J795_005_volume_map.mrc (#2) using 16560 atoms  
average map value = 0.03957, steps = 152  
shifted from previous position = 14.9  
rotated from previous position = 8.01 degrees  
atoms outside contour = 12875, contour level = 0.06  
  
Position of fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) relative
to cryosparc_P28_J795_005_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.50559680 -0.09167652 -0.85788536 214.25996169  
0.62837136 -0.64223110 0.43896315 220.98795226  
-0.59120327 -0.76100896 -0.26710309 162.32258577  
Axis -0.84231462 -0.18719621 0.50543413  
Axis point 0.00000000 144.56936559 97.04277863  
Rotation angle (degrees) 134.57712260  
Shift along axis -139.79902950  
  

> view matrix models
> #1,0.5056,-0.091677,-0.85789,214.11,0.62837,-0.64223,0.43896,221.34,-0.5912,-0.76101,-0.2671,157.11

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.39497,-0.048979,-0.91739,214.27,0.78288,-0.50459,0.364,219.3,-0.48073,-0.86197,-0.16095,157.47

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.39497,-0.048979,-0.91739,213.55,0.78288,-0.50459,0.364,219.59,-0.48073,-0.86197,-0.16095,152.2

> fitmap #1 inMap #2

Fit molecule fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) to map
cryosparc_P28_J795_005_volume_map.mrc (#2) using 16560 atoms  
average map value = 0.03999, steps = 144  
shifted from previous position = 11.9  
rotated from previous position = 7.84 degrees  
atoms outside contour = 12856, contour level = 0.06  
  
Position of fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) relative
to cryosparc_P28_J795_005_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.48753858 -0.10848423 -0.86633556 214.98622595  
0.69738752 -0.54861796 0.46116047 221.67703638  
-0.52531589 -0.82900513 -0.19181687 163.85738009  
Axis -0.82759888 -0.21875293 0.51694027  
Axis point 0.00000000 151.07893971 93.86338644  
Rotation angle (degrees) 128.78855523  
Shift along axis -141.71038179  
  

> view matrix models
> #1,0.48754,-0.10848,-0.86634,215.27,0.69739,-0.54862,0.46116,222.77,-0.52532,-0.82901,-0.19182,149.91

> view matrix models
> #1,0.48754,-0.10848,-0.86634,215.44,0.69739,-0.54862,0.46116,222.17,-0.52532,-0.82901,-0.19182,150.43

> view matrix models
> #1,0.48754,-0.10848,-0.86634,217.29,0.69739,-0.54862,0.46116,218.14,-0.52532,-0.82901,-0.19182,149.71

> view matrix models
> #1,0.48754,-0.10848,-0.86634,215.49,0.69739,-0.54862,0.46116,222.06,-0.52532,-0.82901,-0.19182,150.4

> select subtract #1

Nothing selected  

> select add #1

16560 atoms, 16876 bonds, 2116 residues, 1 model selected  

> view matrix models
> #1,0.48754,-0.10848,-0.86634,212.73,0.69739,-0.54862,0.46116,220.3,-0.52532,-0.82901,-0.19182,152.02

> view matrix models
> #1,0.48754,-0.10848,-0.86634,212.66,0.69739,-0.54862,0.46116,224.92,-0.52532,-0.82901,-0.19182,160.67

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.76201,-0.13169,-0.63404,213.85,-0.38569,0.69419,-0.60773,221.73,0.52018,0.70764,0.47819,167.41

> view matrix models
> #1,0.438,-0.15123,-0.88616,212.63,-0.65372,0.62307,-0.42945,226.6,0.61709,0.7674,0.17405,162.01

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.438,-0.15123,-0.88616,206.38,-0.65372,0.62307,-0.42945,217.76,0.61709,0.7674,0.17405,167.89

> view matrix models
> #1,0.438,-0.15123,-0.88616,208.61,-0.65372,0.62307,-0.42945,216.63,0.61709,0.7674,0.17405,177.47

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.55786,-0.25319,-0.79037,208.73,-0.57258,0.57198,-0.58737,213.28,0.60079,0.78022,0.17411,177.66

> view matrix models
> #1,0.41153,-0.081368,-0.90775,208.73,-0.73134,0.56486,-0.38219,217.85,0.54385,0.82117,0.17295,178.27

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.41153,-0.081368,-0.90775,214.13,-0.73134,0.56486,-0.38219,222.51,0.54385,0.82117,0.17295,176.68

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.42955,-0.0094487,-0.90299,214.29,-0.78423,0.49187,-0.37821,222.78,0.44773,0.87061,0.20388,178.16

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.42955,-0.0094487,-0.90299,214.17,-0.78423,0.49187,-0.37821,220.6,0.44773,0.87061,0.20388,175.09

> fitmap #1 inMap #2

Fit molecule fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) to map
cryosparc_P28_J795_005_volume_map.mrc (#2) using 16560 atoms  
average map value = 0.06782, steps = 104  
shifted from previous position = 0.97  
rotated from previous position = 8.54 degrees  
atoms outside contour = 8768, contour level = 0.06  
  
Position of fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) relative
to cryosparc_P28_J795_005_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.52906795 -0.08625008 -0.84418483 215.01220751  
-0.69207963 0.53179827 -0.48807416 218.91801386  
0.49103247 0.84246752 0.22166550 175.13777970  
Axis 0.67200996 -0.67437145 -0.30598327  
Axis point 81.72147305 0.00000000 254.26979921  
Rotation angle (degrees) 81.87889698  
Shift along axis -56.73094447  
  

> select subtract #1

Nothing selected  

> hide #1 models

> show #1 models

> hide #!2 models

> delete #1/A-B

> delete #1/D-F

> delete #1/H

> show #!2 models

> molmap sel 6.5 onGrid #2

No atoms specified  

> select add #1

4140 atoms, 4219 bonds, 529 residues, 1 model selected  

> molmap sel 6.5 onGrid #2

Opened fold_isoform_correct_aip1_cofilin_actin_model_0.cif map 6.5 as #3, grid
size 600,600,600, pixel 0.73, shown at level 0.0915, step 1, values float32  

> select subtract #1

Nothing selected  

> hide #1 models

> hide #!2 models

> save "/Users/geordanstukey/Desktop/AIP1 Cofilin
> Project/Data/100325_BE_Working/PE_terminal_subunit_mask.mrc" models #3

> close #1#2-3

> open /Users/geordanstukey/Downloads/cryosparc_P28_J650_004_volume_map.mrc
> format mrc

Opened cryosparc_P28_J650_004_volume_map.mrc as #1, grid size 450,450,450,
pixel 0.73, shown at level 0.057, step 2, values float32  

> open
> /Users/geordanstukey/Downloads/cryosparc_P28_J802_class_00_00042_volume.mrc

Opened cryosparc_P28_J802_class_00_00042_volume.mrc as #2, grid size
120,120,120, pixel 3.65, shown at level 0.396, step 1, values float32  

> close #1

> open /Users/geordanstukey/Downloads/cryosparc_P28_J809_map.mrc

Opened cryosparc_P28_J809_map.mrc as #1, grid size 120,120,120, pixel 3.65,
shown at level 0.388, step 1, values float32  

> hide #!2 models

> hide #!1 models

> show #!1 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> show #!2 models

> open /Users/geordanstukey/Downloads/cryosparc_P28_J810_map.mrc

Opened cryosparc_P28_J810_map.mrc as #3, grid size 120,120,120, pixel 3.65,
shown at level 0.381, step 1, values float32  

> open /Users/geordanstukey/Downloads/cryosparc_P28_J811_map.mrc

Opened cryosparc_P28_J811_map.mrc as #4, grid size 120,120,120, pixel 3.65,
shown at level 0.368, step 1, values float32  

> hide #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!2 models

> select add #2

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.83644,0.54781,-0.016334,-79.386,-0.54805,0.83593,-0.029262,164.68,-0.0023761,0.033428,0.99944,-6.6389

> select subtract #2

Nothing selected  

> show #!1 models

> close #1-4

> open "/Users/geordanstukey/Desktop/AIP1 Cofilin Project/Data/NCCAT 082225/AF
> Structures/isoform_correct_aip1_cofilin_actin/fold_isoform_correct_aip1_cofilin_actin_model_0.cif"
> format mmcif

Chain information for fold_isoform_correct_aip1_cofilin_actin_model_0.cif #1  
---  
Chain | Description  
A B C D | .  
E F G H | .  
I | .  
  

> hide atoms

> show cartoons

Computing secondary structure  

> delete #1/I

> open /Users/geordanstukey/Downloads/cryosparc_P28_J817_005_volume_map.mrc

Opened cryosparc_P28_J817_005_volume_map.mrc as #2, grid size 600,600,600,
pixel 0.73, shown at level 0.0305, step 4, values float32  

> volume #2 step 1

> volume #2 level 0.05

> select add #1

16560 atoms, 16876 bonds, 2116 residues, 1 model selected  

> view matrix models
> #1,0.24261,0.89874,-0.36525,3.8707,-0.95396,0.28946,0.078598,7.0462,0.17636,0.32937,0.92758,-1.536

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.24261,0.89874,-0.36525,45.447,-0.95396,0.28946,0.078598,369.65,0.17636,0.32937,0.92758,123.16

> view matrix models
> #1,0.24261,0.89874,-0.36525,130.33,-0.95396,0.28946,0.078598,235.99,0.17636,0.32937,0.92758,192.86

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.059085,-0.26844,-0.96148,118.57,-0.95903,-0.28259,0.019963,233.16,-0.27707,0.92091,-0.27413,179.92

> lighting simple

> transparency 50

> view matrix models
> #1,0.73481,-0.078925,-0.67366,117.9,-0.63617,0.26425,-0.72488,220.54,0.23523,0.96122,0.14397,182.2

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.73481,-0.078925,-0.67366,186.78,-0.63617,0.26425,-0.72488,183.13,0.23523,0.96122,0.14397,188.1

> view matrix models
> #1,0.73481,-0.078925,-0.67366,218.88,-0.63617,0.26425,-0.72488,227.04,0.23523,0.96122,0.14397,152.09

> view matrix models
> #1,0.73481,-0.078925,-0.67366,209.01,-0.63617,0.26425,-0.72488,213.72,0.23523,0.96122,0.14397,171.22

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.39254,0.083126,-0.91597,208.71,-0.83505,0.44963,-0.31706,222.48,0.38549,0.88934,0.24591,171.28

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.39254,0.083126,-0.91597,212.68,-0.83505,0.44963,-0.31706,217.33,0.38549,0.88934,0.24591,177.44

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.62457,-0.029797,-0.7804,212.42,-0.68113,0.4681,-0.56299,212.21,0.38208,0.88318,0.27206,177.86

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.62457,-0.029797,-0.7804,210.36,-0.68113,0.4681,-0.56299,217.82,0.38208,0.88318,0.27206,173.6

> fitmap #1 inMap #2

Fit molecule fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) to map
cryosparc_P28_J817_005_volume_map.mrc (#2) using 16560 atoms  
average map value = 0.06221, steps = 136  
shifted from previous position = 5.98  
rotated from previous position = 8.21 degrees  
atoms outside contour = 8220, contour level = 0.05  
  
Position of fold_isoform_correct_aip1_cofilin_actin_model_0.cif (#1) relative
to cryosparc_P28_J817_005_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.52827289 -0.08904253 -0.84439283 215.25863798  
-0.69584346 0.52447231 -0.49064317 219.24419108  
0.48654875 0.84675869 0.21510483 175.16069231  
Axis 0.67477968 -0.67152018 -0.30615850  
Axis point 0.00000000 82.65335985 290.64418405  
Rotation angle (degrees) 82.30353722  
Shift along axis -55.60167677  
  

> select subtract #1

Nothing selected  

> hide #!2 models

> delete #1/H

> delete #1/D-F

> delete #1/A-B

> show #!2 models

> molmap sel 6.5 onGrid #2

No atoms specified  

> select add #1

4140 atoms, 4219 bonds, 529 residues, 1 model selected  

> molmap sel 6.5 onGrid #2

Opened fold_isoform_correct_aip1_cofilin_actin_model_0.cif map 6.5 as #3, grid
size 600,600,600, pixel 0.73, shown at level 0.0914, step 1, values float32  

> hide #!2 models

> hide #1 models

> select subtract #1

Nothing selected  

> save "/Users/geordanstukey/Desktop/AIP1 Cofilin
> Project/Data/100325_BE_Working/PE_another_terminalActin_Mask.mrc" models #3

> close #1#2-3

> open "/Users/geordanstukey/Desktop/AIP1 Cofilin Project/Data/Completed
> Structures/092725/cryosparc_P28_J668_004_volume_map_sharp.mrc"

Opened cryosparc_P28_J668_004_volume_map_sharp.mrc as #1, grid size
450,450,450, pixel 0.73, shown at level 0.0892, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.15

> volume #1 level 0.14

> volume #1 level 0.13

> surface dust #1 size 7.3

> open "/Users/geordanstukey/Desktop/AIP1 Cofilin Project/Data/Completed
> Structures/092725/2xAIP1_model_HR_Refined.pdb"

Chain information for 2xAIP1_model_HR_Refined.pdb #2  
---  
Chain | Description  
A B C D K L M Q R | No description available  
E F G H N O P | No description available  
I J | No description available  
  

> hide atoms

> show cartoons

> transparency 50

> transparency 0

> transparency 50

> hide #2 models

> transparency 0

> lighting soft

> graphics silhouettes true

> set bgColor white

> set bgColor #ffffff00

> open "/Users/geordanstukey/Desktop/AIP1 Cofilin Project/Data/092225_Working
> Structures/1xAIP1 Mid filament
> 2.69/cryosparc_P28_J674_004_volume_map_sharp.mrc"

Opened cryosparc_P28_J674_004_volume_map_sharp.mrc as #3, grid size
450,450,450, pixel 0.73, shown at level 0.0947, step 2, values float32  

> hide #!1 models

> volume #3 step 1

> volume #3 level 0.013

> volume #3 level 0.13

> volume #3 level 0.14

> surface dust #3 size 7.3

> volume #3 level 0.13

> surface dust #3 size 7.3

> lighting simple

> lighting soft

> lighting full

> lighting soft

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #2 models

> show #!1 models

> hide #!1 models

> color #2/E,F,G,H,N,O,P #FF6F00

> color #2/A,B,C,D,K,L,M,Q,R #C0C0C0

> color #2/I #12C14D

> color #2/J #7A13E1

> show #!1 models

> select add #2

44098 atoms, 44995 bonds, 5679 residues, 1 model selected  

> color zone #1 near sel distance 4

> select subtract #2

Nothing selected  

> hide #2 models

> hide #!1 models

> show #2 models

> hide #2 models

> show #!1 models

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

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/geordanstukey/Desktop/movie1.mp4

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 185, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider  
shortcuts.run_provider(session, name)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1394, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 403, in try_shortcut  
self.run_shortcut(keys)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 421, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 340, in run  
f(s)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1312, in save_spin_movie  
run(session, cmd)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 202, in movie_encode  
encode_op(session, output[-1], format, quality, qscale, bitrate,  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 260, in encode_op  
movie.start_encoding(output, f['ffmpeg_name'], output_size, f['ffmpeg_codec'],
"yuv420p", f['size_restriction'],  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/movie.py", line 324, in start_encoding  
self.encoder.run(Status_Reporter())  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/encode.py", line 232, in run  
p = Popen(self.arg_list, stdin=DEVNULL, stdout=PIPE, stderr=PIPE)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1026, in __init__  
self._execute_child(args, executable, preexec_fn, close_fds,  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child  
raise child_exception_type(errno_num, err_msg, err_filename)  
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'  
  
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'  
  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child  
raise child_exception_type(errno_num, err_msg, err_filename)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-7.0.23
OpenGL renderer: AMD Radeon Pro 555X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,2
      Processor Name: Quad-Core Intel Core i3
      Processor Speed: 3.6 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 16 GB
      System Firmware Version: 2075.100.3.0.3
      OS Loader Version: 583~2210
      SMC Version (system): 2.47f3

Software:

    System Software Overview:

      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
      Time since boot: 17 days, 20 hours, 59 minutes

Graphics/Displays:

    Radeon Pro 555X:

      Chipset Model: Radeon Pro 555X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 2 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00e3
      ROM Revision: 113-C981AA-042
      VBIOS Version: 113-C9819A148P-003
      EFI Driver Version: 01.B1.042
      Metal Support: Metal 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 4096 x 2304 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.5.0
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 2.5.1
    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: 1.6.2
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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: 1.19.1
    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: 2.5.2
    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: 1.45.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.9.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.4
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.0
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14