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Opened 10 days ago
Closed 10 days ago
#19068 closed defect (duplicate)
ffmpeg: Permission denied
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Build System | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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
Change History (2)
comment:1 by , 10 days ago
| Component: | Unassigned → Build System |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ffmpeg: Permission denied |
comment:2 by , 10 days ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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