ffmpeg: Permission denied

[abdel104@…]

The following bug report has been submitted:
Platform:        macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Gave ChimeraX permission to read desktop/documents/downloads upon opening. Clicked "Spin movie" button. Error appeared. This happens when using a command like "movie record; rock x 1 136; wait; movie encode" as well.

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

> open "/Users/abdel104/Documents/Aihara Lab/Model
> Building/Borf2-A3B-B10-B1/model_interpretation2.cxs" format session

Opened cryosparc_P1065_J83_004_volume_map.mrc as #1, grid size 480,480,480,
pixel 0.825, shown at level 0.0291, step 1, values float32  
Opened cryosparc_P1065_J83_004_volume_map_half.mrc as #3, grid size
480,480,480, pixel 0.825, shown at level 0.0291, step 1, values float32  
Opened cryosparc_P1065_J91_004_volume_map.mrc as #4, grid size 480,480,480,
pixel 0.825, shown at level 0.043, step 1, values float32  
Opened cryosparc_P1065_J91_004_volume_map_A3Bctd_nbB01_nbB10.mrc as #5, grid
size 480,480,480, pixel 0.825, shown at level 0.043, step 1, values float32  
Opened cryosparc_P1065_J91_004_volume_map_A3Bctd_nbB10.mrc as #6, grid size
480,480,480, pixel 0.825, shown at level 0.043, step 1, values float32  
Opened cryosparc_P1065_J91_004_volume_map_A3Bctd_nbB01.mrc as #7, grid size
480,480,480, pixel 0.825, shown at level 0.043, step 1, values float32  
Opened cryosparc_P1065_J91_004_volume_map_A3Bctd.mrc as #8, grid size
480,480,480, pixel 0.825, shown at level 0.043, step 1, values float32  
Opened cryosparc_P1065_J124_004_volume_map_sharp.mrc as #11, grid size
480,480,480, pixel 0.825, shown at level 0.113, step 1, values float32  
Opened cryosparc_P1065_J128_005_volume_map_sharp.mrc as #9, grid size
480,480,480, pixel 0.825, shown at level 0.152, step 1, values float32  
Log from Tue Aug 26 06:37:41 2025You can double click a model's Name or ID in
the model panel to edit those fields  
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/abdel104/Downloads/cryosparc_P1065_J83_004_volume_map.mrc

Opened cryosparc_P1065_J83_004_volume_map.mrc as #1, grid size 480,480,480,
pixel 0.825, shown at level 0.00605, step 2, values float32  

> set bgColor white

> volume #1 step 1

> volume #1 level 0.02907

> ui tool show "Segment Map"

Segmenting cryosparc_P1065_J83_004_volume_map.mrc, density threshold 0.029067  
Showing 92 region surfaces  
1180 watershed regions, grouped to 92 regions  
Showing cryosparc_P1065_J83_004_volume_map.seg - 92 regions, 92 surfaces  
Drag select of 1767, 1754, 1779, 13784 of 22244 triangles, 1789, 15033 of
15708 triangles, 1785, 14821 of 15044 triangles, 1725, 1783, 12838 of 14588
triangles, 1764, 1618, 1790, 9004 of 10968 triangles, 1566, 1739, 94 of 8772
triangles, 1740, 1677, 1737, 3546 of 5912 triangles, 1748, 4697 of 5228
triangles, 1524, 377 of 5108 triangles, 1
cryosparc_P1065_J83_004_volume_map.mrc  
Grouped 17 regions  

> select add #2.52

4 models selected  

> select add #2.70

5 models selected  

> select add #2.13

6 models selected  

> select add #2.47

7 models selected  

> select add #2.11

8 models selected  

> select add #2.82

9 models selected  

> select add #2.85

10 models selected  

> select add #2.92

11 models selected  

> select add #2.45

12 models selected  

> select add #2.38

13 models selected  
Grouped 11 regions  

> select add #2.44

4 models selected  

> select add #2.27

5 models selected  

> select add #2.6

6 models selected  
Grouped 4 regions  

> select add #2.63

4 models selected  

> select add #2.83

5 models selected  
Grouped 3 regions  

> select add #2.1

4 models selected  

> select add #2.41

5 models selected  
Grouped 3 regions  

> select add #2.26

4 models selected  

> select add #2.54

5 models selected  
Grouped 3 regions  

> select add #2.22

4 models selected  

> select add #2.72

5 models selected  
Grouped 3 regions  

> select add #2.23

4 models selected  
Grouped 2 regions  

> select add #2.79

4 models selected  

> select add #2.61

5 models selected  
Grouped 3 regions  

> select add #2.20

4 models selected  

> select add #2.87

5 models selected  
Grouped 3 regions  

> hide #!1 models

> select #2.65

1 model selected  

> select add #2.67

2 models selected  
Grouped 2 regions  
Drag select of 1810, 85864 of 392636 triangles, 1811, 7369 of 15056 triangles  
Grouped 2 regions  

> volume mask #1 surfaces #2.1 fullMap true

Opened cryosparc_P1065_J83_004_volume_map.mrc masked as #3, grid size
480,480,480, pixel 0.825, shown at step 1, values float32  

> save /Users/abdel104/Downloads/cryosparc_P1065_J83_004_volume_map_half.mrc
> models #3

> hide #!3 models

> select add #2

49 models selected  

> select subtract #2

Nothing selected  

> open /Users/abdel104/Downloads/cryosparc_P1065_J91_004_volume_map.mrc

Opened cryosparc_P1065_J91_004_volume_map.mrc as #4, grid size 480,480,480,
pixel 0.825, shown at level 0.00725, step 2, values float32  

> hide #!2 models

> volume #4 step 1

> volume #4 level 0.04279

> volume #4 level 0.043

Segmenting cryosparc_P1065_J91_004_volume_map.mrc, density threshold 0.043000  
Showing 82 region surfaces  
1346 watershed regions, grouped to 82 regions  
Showing cryosparc_P1065_J91_004_volume_map.seg - 82 regions, 82 surfaces  
Drag select of 1991, 1985, 22204 of 23156 triangles, 1987, 388 of 25960
triangles, 1996, 1964, 2008, 13815 of 16316 triangles, 1986, 14718 of 15348
triangles, 1927, 1982, 3292 of 11552 triangles, 1990, 8230 of 10504 triangles,
1994, 1945, 1999, 1953, 524 of 6072 triangles, 1995, 1997, 6048 of 6216
triangles, 1673, 3703 of 5328 triangles, 1929, 4586 of 5824 triangles, 1637,
1946, 1899, 1924, 1896, 2632 of 2668 triangles, 1449, 4
cryosparc_P1065_J91_004_volume_map.mrc  

> select subtract #2.4

25 models selected  
Grouped 23 regions  

> volume mask #4 surfaces #2.1 fullMap true

Opened cryosparc_P1065_J91_004_volume_map.mrc masked as #5, grid size
480,480,480, pixel 0.825, shown at step 1, values float32  

> save
> /Users/abdel104/Downloads/cryosparc_P1065_J91_004_volume_map_A3Bctd_nbB01_nbB10.mrc
> models #5

Ungrouped to 23 regions  

> select #2.31

1 model selected  
Ungrouped to 8 regions  
Drag select of 1927, 10236 of 10476 triangles, 1964, 9926 of 14000 triangles,
1994, 1995, 1449, 510 of 2416 triangles, 1637, 2624 of 4108 triangles, 1711,
2737 of 3556 triangles, 1839, 383 of 1860 triangles, 1666, 1989 of 3996
triangles, 1901, 1162 of 17804 triangles, 5
cryosparc_P1065_J91_004_volume_map_A3Bctd_nbB01_nbB10.mrc  

> select #2.88

1 model selected  
Ungrouped to 13 regions  
Drag select of 1927, 10409 of 10476 triangles, 1964, 10847 of 14000 triangles,
1994, 1995, 5419 of 5432 triangles, 1449, 1142 of 2416 triangles, 1637, 2162
of 4108 triangles, 1711, 2558 of 3556 triangles, 1839, 574 of 1860 triangles,
1666, 2575 of 3996 triangles, 1931, 163 of 5856 triangles, 1364, 96 of 2408
triangles, 71, 595 of 1520 triangles, 84, 757 of 1480 triangles, 5
cryosparc_P1065_J91_004_volume_map_A3Bctd_nbB01_nbB10.mrc  
Grouped 13 regions  

> select add #2.91

4 models selected  

> select add #2.93

5 models selected  
Grouped 3 regions  

> select add #2.97

4 models selected  
Grouped 2 regions  

> select add #2.95

4 models selected  
Grouped 2 regions  

> select add #2.96

4 models selected  

> select add #2.100

5 models selected  
Grouped 3 regions  

> select add #2.101

4 models selected  
Grouped 2 regions  

> select add #2.99

4 models selected  
Grouped 2 regions  

> select #2.14

1 model selected  
Ungrouped to 2 regions  

> select #2.31

1 model selected  
Ungrouped to 5 regions  

> select #2.83

1 model selected  

> select add #2.57

2 models selected  

> select add #2.7

3 models selected  

> select add #2.72

4 models selected  
Grouped 4 regions  

> select add #2.24

2 models selected  
Grouped 2 regions  

> select add #2.42

2 models selected  
Grouped 2 regions  

> select add #2.46

2 models selected  
Grouped 2 regions  

> select add #2.14

2 models selected  
Grouped 2 regions  

> select #2.59

1 model selected  

> select add #2.90

2 models selected  

> select add #2.74

3 models selected  

> select add #2.85

4 models selected  

> select add #2.21

5 models selected  

> select add #2.98

6 models selected  

> select add #2.49

7 models selected  

> select add #2.73

8 models selected  

> select add #2.54

9 models selected  

> select add #2.3

10 models selected  

> select add #2.5

11 models selected  
Grouped 11 regions  

> select add #2.80

2 models selected  

> select add #2.10

3 models selected  

> select add #2.8

4 models selected  

> select add #2.70

5 models selected  
Grouped 5 regions  

> select add #2.94

2 models selected  
Grouped 2 regions  

> select #2.86

1 model selected  

> select add #2.3

2 models selected  
Grouped 2 regions  

> select add #2.38

2 models selected  
Grouped 2 regions  

> select #2.1

1 model selected  

> select add #2.3

2 models selected  

> select add #2.7

3 models selected  

> select #2.3

1 model selected  

> select #2.3

1 model selected  

> select #2.3

1 model selected  

> select clear

[Repeated 3 time(s)]

> select add #2

63 models selected  

> select subtract #2

Nothing selected  

> select subtract #2.1

Nothing selected  

> select subtract #2.3

Nothing selected  

> select subtract #2.7

Nothing selected  

> select #2.1

1 model selected  

> select #2.3

1 model selected  

> select clear

> select add #2

63 models selected  

> select subtract #2

Nothing selected  

> select add #2.1

1 model selected  

> select add #2.3

2 models selected  
Grouped 2 regions  

> volume mask #4 surfaces #2.1 fullMap true

Opened cryosparc_P1065_J91_004_volume_map.mrc masked as #6, grid size
480,480,480, pixel 0.825, shown at step 1, values float32  
Ungrouped to 2 regions  

> select #2.5

1 model selected  

> select add #2.7

2 models selected  
Grouped 2 regions  

> volume mask #4 surfaces #2.1 fullMap true

Opened cryosparc_P1065_J91_004_volume_map.mrc masked as #7, grid size
480,480,480, pixel 0.825, shown at step 1, values float32  
Ungrouped to 2 regions  

> select #2.7

1 model selected  

> select #2.7

1 model selected  

> select clear

> select subtract #2.5

Nothing selected  

> volume mask #4 surfaces #2.7 fullMap true

Opened cryosparc_P1065_J91_004_volume_map.mrc masked as #8, grid size
480,480,480, pixel 0.825, shown at step 1, values float32  

> hide #!2 models

> save
> /Users/abdel104/Downloads/cryosparc_P1065_J91_004_volume_map_A3Bctd_nbB10.mrc
> models #6

> save
> /Users/abdel104/Downloads/cryosparc_P1065_J91_004_volume_map_A3Bctd_nbB01.mrc
> models #7

> save /Users/abdel104/Downloads/cryosparc_P1065_J91_004_volume_map_A3Bctd.mrc
> models #8

Desktop color scheme is dark  
Desktop color scheme is light  

> open "/Users/abdel104/Documents/Aihara Lab/Model Building/KSHV-
> Orf61_A3BctdWT/4strand_monomer_nodimerclashes2-coot-0_544aligned-coot-0.pdb"

Chain information for 4strand_monomer_nodimerclashes2-coot-0_544aligned-
coot-0.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #!8 models

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 9/A  

> sequence chain /B

Alignment identifier is 9/B  

> select /B:308

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select /B:308

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel atoms

> select /B:230

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

> select /B:230

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

> show sel atoms

> open "/Users/abdel104/Documents/Aihara Lab/Model Building/KSHV-
> Orf61_A3BctdWT/4strand_monomer_nodimerclashes2-coot-0_544aligned-
> coot-0_real_space_refined_016-combined.pdb"

Summary of feedback from opening /Users/abdel104/Documents/Aihara Lab/Model
Building/KSHV-
Orf61_A3BctdWT/4strand_monomer_nodimerclashes2-coot-0_544aligned-
coot-0_real_space_refined_016-combined.pdb  
---  
warnings | Cannot find LINK/SSBOND residue ZN (401 )  
Cannot find LINK/SSBOND residue ZN (401 )  
Cannot find LINK/SSBOND residue ZN (401 )  
Cannot find LINK/SSBOND residue ZN (401 )  
Cannot find LINK/SSBOND residue ZN (401 )  
88 messages similar to the above omitted  
  
Chain information for 4strand_monomer_nodimerclashes2-coot-0_544aligned-
coot-0_real_space_refined_016-combined.pdb #10  
---  
Chain | Description  
0 1 4 7 A2 A5 A8 AC AF AI AL AO AR AU AX Aa Ad Ag Aj Am Ap As Av Ay B BA BD BG BJ BM BP BS BV BY Bb Be E H K N Q T W Z c f i l o r u x | No description available  
3 6 9 A A0 A1 A4 A7 AB AE AH AK AN AQ AT AW AZ Ac Af Ai Al Ao Ar Au Ax BC BF BI BL BO BR BU BX Ba Bd D G J M P S V Y b e h k n q t w z | No description available  
  

> select add #9

7441 atoms, 7337 bonds, 4 pseudobonds, 1180 residues, 3 models selected  

> select subtract #9

Nothing selected  

> select add #10

386932 atoms, 381524 bonds, 208 pseudobonds, 61360 residues, 3 models selected  

> show sel atoms

> show sel cartoons

> style sel stick

Changed 386932 atom styles  

> hide sel atoms

> hide #!9 models

> select #10/AX:275

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

> select up

70 atoms, 73 bonds, 7 residues, 1 model selected  

> select up

1559 atoms, 1605 bonds, 187 residues, 1 model selected  

> select up

386932 atoms, 381524 bonds, 61360 residues, 1 model selected  

> select down

1559 atoms, 1605 bonds, 187 residues, 1 model selected  

> show sel atoms

> color sel byhetero

Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  

> open /Users/abdel104/Downloads/cryosparc_P1065_J124_004_volume_map_sharp.mrc

Opened cryosparc_P1065_J124_004_volume_map_sharp.mrc as #11, grid size
480,480,480, pixel 0.825, shown at level 0.0349, step 2, values float32  

> close #9-10

> volume #11 step 1

> volume #11 level 0.1127

Desktop color scheme is dark  
Desktop color scheme is light  

> open /Users/abdel104/Downloads/cryosparc_P1065_J128_005_volume_map_sharp.mrc

Opened cryosparc_P1065_J128_005_volume_map_sharp.mrc as #9, grid size
480,480,480, pixel 0.825, shown at level 0.0423, step 2, values float32  

> volume #9 step 1

> volume #9 level 0.113

> volume #9 level 0.1517

> open "/Users/abdel104/Documents/Aihara Lab/Model
> Building/Borf2-A3B-B10-B1/RealSpaceRefine_11/A3B-B1-B10_aligned_real_space_refined_003_aligned_borf2_real_space_refined_004-coot-1_real_space_refined_009-coot-0_real_space_refined_010-coot-0_real_space_refined_011_noSS_coot-0.pdb"

Chain information for
A3B-B1-B10_aligned_real_space_refined_003_aligned_borf2_real_space_refined_004-coot-1_real_space_refined_009-coot-0_real_space_refined_010-coot-0_real_space_refined_011_noSS_coot-0.pdb
#10  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select add #10

8747 atoms, 8955 bonds, 8 pseudobonds, 1099 residues, 3 models selected  

> ui mousemode right "translate selected models"

> view matrix models #10,1,0,0,-3.2329,0,1,0,54.574,0,0,1,46.845

> view matrix models #10,1,0,0,49.734,0,1,0,64.675,0,0,1,50.268

> ui tool show "Fit in Map"

> fitmap #10 inMap #9

Fit molecule
A3B-B1-B10_aligned_real_space_refined_003_aligned_borf2_real_space_refined_004-coot-1_real_space_refined_009-coot-0_real_space_refined_010-coot-0_real_space_refined_011_noSS_coot-0.pdb
(#10) to map cryosparc_P1065_J128_005_volume_map_sharp.mrc (#9) using 8747
atoms  
average map value = 0.03391, steps = 148  
shifted from previous position = 4.19  
rotated from previous position = 1.7 degrees  
atoms outside contour = 7879, contour level = 0.15167  
  
Position of
A3B-B1-B10_aligned_real_space_refined_003_aligned_borf2_real_space_refined_004-coot-1_real_space_refined_009-coot-0_real_space_refined_010-coot-0_real_space_refined_011_noSS_coot-0.pdb
(#10) relative to cryosparc_P1065_J128_005_volume_map_sharp.mrc (#9)
coordinates:  
Matrix rotation and translation  
0.99957841 0.02381053 -0.01661491 46.89039385  
-0.02370890 0.99969913 0.00628729 65.95493159  
0.01675961 -0.00589072 0.99984219 45.14517565  
Axis -0.20525268 -0.56250673 -0.80091043  
Axis point 831.18672587 -1240.13528631 -0.00000000  
Rotation angle (degrees) 1.69997949  
Shift along axis -82.88171380  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #10,0.9995,-0.0007896,0.031641,43.861,0.0086846,0.96816,-0.25017,100.4,-0.030436,0.25032,0.96768,20.046

> view matrix models
> #10,0.98807,-0.11294,-0.10469,80.078,0.083922,0.96489,-0.24889,89.41,0.12913,0.23713,0.96286,-1.3548

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.98807,-0.11294,-0.10469,81.846,0.083922,0.96489,-0.24889,82.159,0.12913,0.23713,0.96286,-5.7045

> fitmap sel inMap #9

Fit molecule
A3B-B1-B10_aligned_real_space_refined_003_aligned_borf2_real_space_refined_004-coot-1_real_space_refined_009-coot-0_real_space_refined_010-coot-0_real_space_refined_011_noSS_coot-0.pdb
(#10) to map cryosparc_P1065_J128_005_volume_map_sharp.mrc (#9) using 8747
atoms  
average map value = 0.1817, steps = 144  
shifted from previous position = 2.19  
rotated from previous position = 6.78 degrees  
atoms outside contour = 5261, contour level = 0.15167  
  
Position of
A3B-B1-B10_aligned_real_space_refined_003_aligned_borf2_real_space_refined_004-coot-1_real_space_refined_009-coot-0_real_space_refined_010-coot-0_real_space_refined_011_noSS_coot-0.pdb
(#10) relative to cryosparc_P1065_J128_005_volume_map_sharp.mrc (#9)
coordinates:  
Matrix rotation and translation  
0.98989179 -0.14149843 0.00961404 71.47010885  
0.13909094 0.95533269 -0.26075497 75.61893287  
0.02771181 0.25945643 0.96535715 5.63192046  
Axis 0.87972274 -0.03060492 0.47450105  
Axis point 0.00000000 130.65724294 275.03995392  
Rotation angle (degrees) 17.19758653  
Shift along axis 63.23192072  
  

> volume all transparency 0.5

> save "/Users/abdel104/Documents/Aihara Lab/Model
> Building/Borf2-A3B-B10-B1/RealSpaceRefine_11/A3B-B1-B10_P1065_J128_starting.pdb"
> relModel #9

Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  

Unsupported scale factor (0.000000) detected on Display1  

[Repeated 2 time(s)]Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  
Desktop color scheme is light  
Desktop color scheme is dark  

> save "/Users/abdel104/Documents/Aihara Lab/Model
> Building/Borf2-A3B-B10-B1/model_interpretation2.cxs"

——— End of log from Tue Aug 26 06:37:41 2025 ———

> view name session-start

opened ChimeraX session  
Showing cryosparc_P1065_J91_004_volume_map.seg - 62 regions, 62 surfaces  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/abdel104/Desktop/movie11.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 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

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: MacBook Pro
      Model Identifier: MacBookPro18,1
      Model Number: Z14V0016ELL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 63 days, 22 hours, 20 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          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
    biopython: 1.85
    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-MIC: 0.2
    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
    fsspec: 2025.5.1
    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
    joblib: 1.5.1
    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
    mmh3: 2.5.1
    mpmath: 1.3.0
    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
    pandas: 2.3.0
    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
    scikit-learn: 1.7.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    simplejson: 3.20.1
    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
    sympy: 1.14.0
    tables: 3.10.2
    tcia_utils: 1.5.1
    threadpoolctl: 3.6.0
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    torch: 2.7.1
    tornado: 6.5.1
    tqdm: 4.67.1
    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
File attachment: Screenshot 2025-08-26 at 6.41.19 AM.png

Screenshot 2025-08-26 at 6.41.19 AM.png​

[abdel104@…]

Added by email2trac

[abdel104@…]

      
I misunderstood, the issue was my user did not have permission to execute ffmpeg. A delete and reinstall fixed the problem.
  
​
  
  
  
—   
  
Ryan Abdella, Ph.D.
  
CryoEM Facility Manager |   Characterization Facility   |   cse.umn.edu/charfac (http://cse.umn.edu/charfac)   
  
Research Assistant Professor |   Department of Biochemistry, Molecular   Biology, and Biophysics   |   cbs.umn.edu/bmbb (http://cbs.umn.edu/bmbb)
  
1-234 Nils Hasselmo Hall
  
University of Minnesota |   umn.edu (http://umn.edu/)   | o. 612.626.5315   | c. 507.581.2651
  
he, him, his
  
  
     

[pett]

Hi Ryan,

This was a problem in 1.10, so if you de-installed that and then installed 1.10.1, then that's what fixed it. Glad it's working for you now.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab