ffmpeg: Permission Denied

[kstachowski@…]

The following bug report has been submitted:
Platform:        macOS-14.7.1-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Replace this text with list of actions that caused this problem to occur

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

> open "/Users/kyestachowski/Library/CloudStorage/GoogleDrive-
> kstachowski@structura.bio/.shortcut-targets-by-
> id/0B59fKuKLIntUUU1jOU9GdVk2ck0/SBI Cryo-EM Landscape/Drafts (2025)/GPCR
> Automation/Figures/modeling_improvements/10288_modeling_improvements.cxs"

Opened 10288_workflow_local.mrc as #1, grid size 300,300,300, pixel 1.03,
shown at level 0.495, step 1, values float32  
Opened 10288_workflow_local.mrc 0 as #4.1, grid size 300,300,300, pixel 1.03,
shown at level 0.804, step 1, values float32  
Opened 10288_workflow_local.mrc 1 as #4.2, grid size 300,300,300, pixel 1.03,
shown at level 0.367, step 1, values float32  
Opened 10288_deposited_global.map as #5, grid size 240,240,240, pixel 0.86,
shown at level 0.158, step 1, values float32  
Opened 10288_workflow_local_11119-mask.mrc as #6, grid size 300,300,300, pixel
1.03, shown at level 0.367, step 1, values float32  
Log from Thu Jun 5 11:59:25 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/kyestachowski/Desktop/GPCR_Automation_Final_run/figures/modeling_improvements/10288_modeling_improvements.cxs

Opened 10288_workflow_local.mrc as #1, grid size 300,300,300, pixel 1.03,
shown at level 0.495, step 1, values float32  
Opened 10288_workflow_local.mrc 0 as #4.1, grid size 300,300,300, pixel 1.03,
shown at level 0.804, step 1, values float32  
Opened 10288_workflow_local.mrc 1 as #4.2, grid size 300,300,300, pixel 1.03,
shown at level 0.367, step 1, values float32  
Opened 10288_deposited_global.map as #5, grid size 240,240,240, pixel 0.86,
shown at level 0.158, step 1, values float32  
Opened 10288_workflow_local_11119-mask.mrc as #6, grid size 300,300,300, pixel
1.03, shown at level 0.367, step 1, values float32  
Log from Thu Jun 5 10:58:06 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/kyestachowski/Desktop/GPCR_Automation_Final_run/figures/modeling_improvements/10288_modeling_improvements.cxs

Opened 10288_workflow_local.mrc as #1, grid size 300,300,300, pixel 1.03,
shown at level 0.495, step 1, values float32  
Opened 10288_workflow_local.mrc 0 as #4.1, grid size 300,300,300, pixel 1.03,
shown at level 0.804, step 1, values float32  
Opened 10288_workflow_local.mrc 1 as #4.2, grid size 300,300,300, pixel 1.03,
shown at level 0.367, step 1, values float32  
Opened 10288_deposited_global.map as #5, grid size 240,240,240, pixel 0.86,
shown at level 0.158, step 1, values float32  
Log from Fri May 23 11:23:34 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/kyestachowski/Desktop/GPCR_Automation_Final_run/figures/modeling_improvements/10288/10288_modeling_improvements.cxs

Opened 10288_workflow_local.mrc as #1, grid size 300,300,300, pixel 1.03,
shown at level 0.495, step 1, values float32  
Opened 10288_workflow_local.mrc 0 as #4.1, grid size 300,300,300, pixel 1.03,
shown at level 0.804, step 1, values float32  
Opened 10288_workflow_local.mrc 1 as #4.2, grid size 300,300,300, pixel 1.03,
shown at level 0.367, step 1, values float32  
Opened 10288_deposited_global.map as #5, grid size 240,240,240, pixel 0.86,
shown at level 0.158, step 1, values float32  
Log from Fri May 23 10:43:32 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/kyestachowski/Desktop/GPCR_Automation_Final_run/figures/modeling_improvements/10288/10288_modeling_improvements.cxs

Opened 10288_workflow_local.mrc as #1, grid size 300,300,300, pixel 1.03,
shown at level 0.495, step 1, values float32  
Opened 10288_workflow_local.mrc 0 as #4.1, grid size 300,300,300, pixel 1.03,
shown at level 0.804, step 1, values float32  
Opened 10288_workflow_local.mrc 1 as #4.2, grid size 300,300,300, pixel 1.03,
shown at level 0.367, step 1, values float32  
Opened 10288_deposited_global.map as #5, grid size 240,240,240, pixel 0.86,
shown at level 0.114, step 1, values float32  
Log from Wed May 21 16:48:09 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/kyestachowski/Desktop/GPCR_Automation_Final_run/figures/modeling_improvements/10288/10288_modeling_improvements.cxs

Opened 10288_workflow_local.mrc as #1, grid size 300,300,300, pixel 1.03,
shown at level 0.395, step 1, values float32  
Opened 10288_workflow_local.mrc 0 as #4.1, grid size 300,300,300, pixel 1.03,
shown at level 0.395, step 1, values float32  
Opened 10288_workflow_local.mrc 1 as #4.2, grid size 300,300,300, pixel 1.03,
shown at level 0.395, step 1, values float32  
Log from Tue May 20 16:40:26 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> graphics selection color blue width 6

> volume defaultvalues initialColors #c0c0c0,
> #0096ffff,#00a4c2,#fbbd00,#D3D3D3,#ea7100,#007d31

> alias hidedust ui tool show "Hide Dust"

> graphics silhouettes true

> lighting soft

> set bgColor white

> open /Users/kyestachowski/Documents/scripts/atom-mass.py

executed atom-mass.py  

> functionkey F1 "ui mousemode right 'translate selected models'"

> color name gpcr-mask #CDCDCD

Color 'gpcr-mask' is opaque: gray(80.4%) hex: #cdcdcd

  

> color name gpcr-alpha #5f7fd7

Color 'gpcr-alpha' is opaque: rgb(37.3%, 49.8%, 84.3%) hex: #5f7fd7

  

> color name gpcr-beta #BF547F

Color 'gpcr-beta' is opaque: rgb(74.9%, 32.9%, 49.8%) hex: #bf547f

  

> color name gpcr-gamma #86e8ba

Color 'gpcr-gamma' is opaque: rgb(52.5%, 91%, 72.9%) hex: #86e8ba

  

> color name gpcr-ab #F4b171

Color 'gpcr-ab' is opaque: rgb(95.7%, 69.4%, 44.3%) hex: #f4b171

  

> color name gpcr-ligand #009051

Color 'gpcr-ligand' is opaque: rgb(0%, 56.5%, 31.8%) hex: #009051

  

> color name gpcr-rec #7ec6db

Color 'gpcr-rec' is opaque: rgb(49.4%, 77.6%, 85.9%) hex: #7ec6db

  

> runscript /Users/kyestachowski/Documents/scripts/viridis_colormaps.py

New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`  
Default colormap for `rainbow` set to 'turbo'  
To unpatch, run `runscript viridis_colormaps.py --reset_defaults`  

> alias locres color sample $1 map $2 palette viridis range $3 $*

> alias imsave save ~/Desktop/$1.png super 3 trans true height 2800 width 2800
> $*

UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/kyestachowski/Desktop/GPCR_Automation_Final_run/final_maps_models/10288/10288_workflow_local.mrc

Opened 10288_workflow_local.mrc as #1, grid size 300,300,300, pixel 1.03,
shown at level 0.0552, step 2, values float32  

> open
> /Users/kyestachowski/Desktop/GPCR_Automation_Final_run/final_maps_models/10288/10288_receptor_remodeled_full.pdb

Chain information for 10288_receptor_remodeled_full.pdb #2  
---  
Chain | Description  
R | No description available  
  

> open
> /Users/kyestachowski/Desktop/GPCR_Automation_Final_run/final_maps_models/10288/10288_deposited_model.pdb

10288_deposited_model.pdb title:  
Cannabinoid receptor 1-G protein complex [more info...]  
  
Chain information for 10288_deposited_model.pdb #3  
---  
Chain | Description | UniProt  
A | adenylate cyclase-inhibiting G α protein | GNAI1_HUMAN 1-354  
B | transducin β chain 1 | GBB1_HUMAN 2-340  
C | G γ-I | GBG2_HUMAN 1-71  
R | cannabinoid receptor 1 | CNR1_HUMAN -6-472  
S | SCFV16 |   
  
Non-standard residues in 10288_deposited_model.pdb #3  
---  
CLR — cholesterol  
KCA — methyl N-{1-[(4-fluorophenyl)methyl]-1H-indazole-3-carbonyl}-3-methyl-L-
valinate  
  

> mmaker #3/R to #2

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 10288_receptor_remodeled_full.pdb, chain R (#2) with
10288_deposited_model.pdb, chain R (#3), sequence alignment score = 1307.8  
RMSD between 260 pruned atom pairs is 0.766 angstroms; (across all 276 pairs:
1.478)  
  

> show cartoons

> style stick

Changed 13359 atom styles  

> color byhetero

> color #3 #ff2600ff

> color #2 #442a7dff

> transparency 50

> color byhetero

> hide H

> split #3

Split 10288_deposited_model.pdb (#3) into 5 models  
Chain information for 10288_deposited_model.pdb A #3.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 10288_deposited_model.pdb B #3.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 10288_deposited_model.pdb C #3.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 10288_deposited_model.pdb R #3.4  
---  
Chain | Description  
R | No description available  
  
Chain information for 10288_deposited_model.pdb S #3.5  
---  
Chain | Description  
S | No description available  
  

> hide #!3.1 models

> hide #3.2 models

> hide #3.3 models

> hide #!3.5 models

> volume #1 step 1

> volume #1 level 0.3946

> fitmap #2 inMap #1

Fit molecule 10288_receptor_remodeled_full.pdb (#2) to map
10288_workflow_local.mrc (#1) using 4906 atoms  
average map value = 0.3525, steps = 44  
shifted from previous position = 0.00344  
rotated from previous position = 0.283 degrees  
atoms outside contour = 2990, contour level = 0.39465  
  
Position of 10288_receptor_remodeled_full.pdb (#2) relative to
10288_workflow_local.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999371 -0.00324883 0.00142028 0.26629744  
0.00325368 0.99998882 -0.00343182 0.12609270  
-0.00140912 0.00343642 0.99999310 -0.33548387  
Axis 0.69571307 0.28660166 0.65866746  
Axis point 0.00000000 97.78203473 36.38751315  
Rotation angle (degrees) 0.28281949  
Shift along axis 0.00043268  
  

> fitmap #2 inMap #1

Fit molecule 10288_receptor_remodeled_full.pdb (#2) to map
10288_workflow_local.mrc (#1) using 4906 atoms  
average map value = 0.3525, steps = 44  
shifted from previous position = 0.0222  
rotated from previous position = 0.0212 degrees  
atoms outside contour = 2992, contour level = 0.39465  
  
Position of 10288_receptor_remodeled_full.pdb (#2) relative to
10288_workflow_local.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999478 -0.00289861 0.00142608 0.19660125  
0.00290366 0.99998947 -0.00355378 0.18849026  
-0.00141576 0.00355790 0.99999267 -0.36751616  
Axis 0.74016389 0.29577061 0.60388506  
Axis point 0.00000000 99.89963062 54.46373960  
Rotation angle (degrees) 0.27525704  
Shift along axis -0.02067049  
  

> show #!2#!3.4 atoms

> hide H

> ui tool show "Side View"

> hide #!1 models

Drag select of 2126 atoms, 445 residues, 2 pseudobonds, 1809 bonds  

> hide sel atoms

> hide sel cartoons

> show #!1 models

> color #2 #573e90ff

> color #2 #442a7dff

> select add #2

6616 atoms, 5817 bonds, 2 pseudobonds, 519 residues, 4 models selected  

> select subtract #2

1710 atoms, 849 bonds, 1 pseudobond, 229 residues, 2 models selected  

> color #3 #442a7dff models

> color #3 #442a7d80 models

> color #3 #442a7d8a models

> color sel byhetero

> select add #3

8453 atoms, 8637 bonds, 5 pseudobonds, 1124 residues, 9 models selected  

> color #3 #ff2600ff models

> select clear

> color #!2#!3.4 byhetero

> show #!2#!3.4 cartoons

> show #!2#!3.4 atoms

> show #!2#!3.4 cartoons

> hide HC

> hide #!3 models

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

> hide #!1 models

> show #!3 models

> save /Users/kyestachowski/Desktop/image2.png supersample 3

> color #3 #442a7dff models

> color #3 #722a7dff models

> color #3 #342a7dff models

> color #3 #442a7dff models

> color #3 #4e2a7dff models

> color #3 #4e347dff models

> color #3 #4e3487ff models

> color #3 #623487ff models

> color #3 #624887ff models

> color #3 #62489bff models

> color #3 #80489bff models

> color #3 #80669bff models

> color #3 #8066b9ff models

> show #!1 models

> color #1 #ebebebff models

> transparency 50

> color #1 darkgrey models

> color #3 #8a66b9ff models

> color #3 #8a70b9ff models

> color #3 #8a70c3ff models

> color #!2#!3.4 byhetero

> color zone #1 near #2 distance 3

[Repeated 2 time(s)]

> color #2 #00a4c2ff

> color #2 #442a7dff

> color zone #1 near #2 distance 3

> volume splitbyzone #1

Opened 10288_workflow_local.mrc 0 as #4.1, grid size 300,300,300, pixel 1.03,
shown at level 0.395, step 1, values float32  
Opened 10288_workflow_local.mrc 1 as #4.2, grid size 300,300,300, pixel 1.03,
shown at level 0.395, step 1, values float32  

> hide #!4.1 models

> color #4.2 silver models

> transparency #4.2.1 50

> color #!2#!3.4 byhetero

> select #2,3/R:358-382

589 atoms, 596 bonds, 50 residues, 2 models selected  

> show min-backbone

> hide sel cartoons

> show min-backbone

> select clear

> color #3 #bc70c3ff models

> color #3 #bca2c3ff models

> color #3 #bca2f5ff models

> color #!2#!3.4 byhetero

> show #!2#!3.4 cartoons

> select #2,3/R:358-382

589 atoms, 596 bonds, 50 residues, 2 models selected  

> center

Unknown command: center  

> center sel

Unknown command: center sel  

> view sel

> view orient

> view sel

> select clear

> center sel

Unknown command: center sel  

> show min-backbone

> hide #!2#!3.4 atoms

> hide #!2#!3.4 cartoons

> show min-backbone

> show #!2#!3.4 atoms

> hide H

> show min-backbone

> hide #!2#!3.4 atoms

> hide H

> show min-backbone

> show sidechain

> hide HC

> show #!2#!3.4 cartoons

> imsave 10288_358-382

> save /Users/kyestachowski/Desktop/10288_358-382.png supersample 3
> transparentBackground true height 2800 width 2800

> hide H

> undo

[Repeated 1 time(s)]

> hide H

> show #!2#!3.4 cartoons

> cartoon style #2#3.4#4.2#!3-4 xsection oval modeHelix default

> select #2,3/R:358-382

589 atoms, 596 bonds, 50 residues, 2 models selected  

> view sel

> select clear

> imsave 10288_358-382

> save /Users/kyestachowski/Desktop/10288_358-382.png supersample 3
> transparentBackground true height 2800 width 2800

> volume #4.2 level 0.3946

> imsave 10288_247-280

> save /Users/kyestachowski/Desktop/10288_247-280.png supersample 3
> transparentBackground true height 2800 width 2800

> select #4.2

4 models selected  

> select clear

> sel#2/R:104

Unknown command: sel#2/R:104  

> select #2/R:104

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

> hide sel atoms

> hide sel cartoons

> select clear

> imsave 10288_104-112

> save /Users/kyestachowski/Desktop/10288_104-112.png supersample 3
> transparentBackground true height 2800 width 2800

> hide #!4 models

> show #!4 models

> hide #!3 models

> imsave 10288_highlights

> save /Users/kyestachowski/Desktop/10288_highlights.png supersample 3
> transparentBackground true height 2800 width 2800

> show #!1 models

> hide #!4 models

> color #1 #00a4c2ff models

> color #1 gpcr-rec

> hide #!2 models

> show #!2 models

> show #!3 models

> hide #!1 models

> hide #!3 models

> hide #!2 models

> show #!1 models

> imsave 10288_highlights

> save /Users/kyestachowski/Desktop/10288_highlights.png supersample 3
> transparentBackground true height 2800 width 2800

> save
> /Users/kyestachowski/Desktop/GPCR_Automation_Final_run/figures/modeling_improvements/10288_modeling_improvements.cxs
> includeMaps true

——— End of log from Tue May 20 16:40:26 2025 ———

opened ChimeraX session  

> open
> /Users/kyestachowski/Desktop/GPCR_Automation_Final_run/final_maps_models/10288/10288_deposited_global.map

Opened 10288_deposited_global.map as #5, grid size 240,240,240, pixel 0.86,
shown at level 0.0827, step 1, values float32  

> select add #5

3 models selected  

> ui mousemode right 'translate selected models'

> view matrix models #5,1,0,0,39.697,0,1,0,39.591,0,0,1,84.769

> volume #1 level 0.1089

> volume #5 level 0.1267

> view matrix models #5,1,0,0,37.023,0,1,0,37.315,0,0,1,79.506

> view matrix models
> #5,-0.78912,-0.03144,0.61343,171.91,0.59014,0.23821,0.77136,-22.444,-0.17038,0.9707,-0.16942,111.6

> view matrix models
> #5,-0.78912,-0.03144,0.61343,168.9,0.59014,0.23821,0.77136,-26.377,-0.17038,0.9707,-0.16942,104.12

> view matrix models
> #5,-0.78912,-0.03144,0.61343,181.47,0.59014,0.23821,0.77136,-10.628,-0.17038,0.9707,-0.16942,99.751

> view matrix models
> #5,-0.70776,0.018461,0.70621,158.62,0.67747,0.30112,0.67108,-16.686,-0.20027,0.95341,-0.22563,110.19

> view matrix models
> #5,-0.70776,0.018461,0.70621,161.67,0.67747,0.30112,0.67108,-14.496,-0.20027,0.95341,-0.22563,108.95

> view matrix models
> #5,-0.61299,-0.4801,0.62749,210.45,0.6895,0.062726,0.72156,3.8182,-0.38578,0.87497,0.29258,86.473

> view matrix models
> #5,-0.61299,-0.4801,0.62749,202.68,0.6895,0.062726,0.72156,-1.1508,-0.38578,0.87497,0.29258,90.638

> view matrix models
> #5,-0.61299,-0.4801,0.62749,203.06,0.6895,0.062726,0.72156,0.61795,-0.38578,0.87497,0.29258,76.827

> view matrix models
> #5,-0.68745,-0.51323,0.51382,225.48,0.55855,0.078553,0.82574,2.8651,-0.46416,0.85465,0.23266,93.119

> view matrix models
> #5,-0.68745,-0.51323,0.51382,220.11,0.55855,0.078553,0.82574,7.6153,-0.46416,0.85465,0.23266,96.496

> view matrix models
> #5,-0.67627,-0.52861,0.51307,220.57,0.55235,0.096976,0.82795,6.1696,-0.48742,0.84331,0.22639,100.76

> view matrix models
> #5,-0.644,-0.4472,0.6207,198.21,0.60207,0.20431,0.77187,-4.6388,-0.47199,0.87079,0.13767,104.9

> fitmap #5 inMap #1

Fit map 10288_deposited_global.map in map 10288_workflow_local.mrc using 72504
points  
correlation = 0.6256, correlation about mean = 0.04556, overlap = 3768  
steps = 104, shift = 3.3, angle = 4.07 degrees  
  
Position of 10288_deposited_global.map (#5) relative to
10288_workflow_local.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.62677418 -0.40326149 0.66673405 187.63969679  
0.62496583 0.25087097 0.73924385 -10.38062312  
-0.46537279 0.88002496 0.09478520 105.28491117  
Axis 0.09166523 0.73713612 0.66949819  
Axis point 110.88016471 0.00000000 0.11072840  
Rotation angle (degrees) 129.83351587  
Shift along axis 80.03616248  
  

> select subtract #5

Nothing selected  

> volume #4.1 level 0.8039

> volume #1 level 0.719

> volume #5 level 0.181

> volume #1 level 0.495

> hide #!1 models

> show #!4 models

> volume #4.2 level 0.4435

> volume #4.2 level 0.3675

> volume #5 level 0.1601

> transparency #5.1#4.1.1#4.2.1 0

> transparency #5.1#4.1.1#4.2.1 50

> hide #!5 models

> show #!2 models

> hide #!2 atoms

> show #!2 atoms

> hide H

> ui tool show "Side View"

> select #2/R:104

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

> hide sel cartoons

> hide sel atoms

> imsave 10288_workflow_mod_dif

> save /Users/kyestachowski/Desktop/10288_workflow_mod_dif.png supersample 3
> transparentBackground true height 2800 width 2800

> select add #2

4906 atoms, 4968 bonds, 1 pseudobond, 290 residues, 2 models selected  

> hide #!2 models

> select subtract #2

Nothing selected  

> hide #!4 models

> show #!5 models

> show #!3 models

> color #3 #ff9300ff models

> color #!3.4 byhetero

> show #!4 models

> show #!2 models

> hide #!2 models

> hide #!4 models

> volume #5 level 0.158

> volume #5 level 0.1622

> show #!2 models

> show #!4 models

> hide #!3 models

> hide #!5 models

> imsave 10288_workflow_mod_dif

> save /Users/kyestachowski/Desktop/10288_workflow_mod_dif.png supersample 3
> transparentBackground true height 2800 width 2800

> hide #!4 models

> hide #!2 models

> show #!3 models

> show #!5 models

> imsave 10288_deposited_mod_dif

> save /Users/kyestachowski/Desktop/10288_deposited_mod_dif.png supersample 3
> transparentBackground true height 2800 width 2800

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!2 models

> hide #!2#!3.4 atoms

> imsave 10288_model_differences

> save /Users/kyestachowski/Desktop/10288_model_differences.png supersample 3
> transparentBackground true height 2800 width 2800

> hide #!3 models

> show #!4 models

> show #!2 atoms

> hide H

> select #2/R:104@OD1

1 atom, 1 residue, 1 model selected  

> select #2/R:104

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

> hide cartoons sel

Expected ',' or a keyword  

> hide sel cartoons

> hide sel atoms

> imsave 10288_workflow_mod_dif

> save /Users/kyestachowski/Desktop/10288_workflow_mod_dif.png supersample 3
> transparentBackground true height 2800 width 2800

> select add #2

4906 atoms, 4968 bonds, 1 pseudobond, 290 residues, 2 models selected  

> hide #!2 models

> select subtract #2

Nothing selected  

> show #!3 models

> hide #!4 models

> show #!5 models

> show #!3.4 atoms

> imsave 10288_deposited_mod_dif

> save /Users/kyestachowski/Desktop/10288_deposited_mod_dif.png supersample 3
> transparentBackground true height 2800 width 2800

> hide #!5 models

> show #!1 models

> hide #!1 models

> show #!5 models

> volume #5 level 0.1141

> save
> /Users/kyestachowski/Desktop/GPCR_Automation_Final_run/figures/modeling_improvements/10288/10288_modeling_improvements.cxs
> includeMaps true

——— End of log from Wed May 21 16:48:09 2025 ———

opened ChimeraX session  

> hide #!3 models

> hide #!5 models

> show #!4 models

> show #!2 models

> graphics silhouettes true width 2 depthJump 0.1

> ui tool show "Side View"

> show #!3 models

> hide #!3 models

> imsave 10288_workflow_map-model

> save /Users/kyestachowski/Desktop/10288_workflow_map-model.png supersample 3
> transparentBackground true height 2800 width 2800

> hide #!2 models

> hide #!4 models

> show #!3 models

> show #!5 models

> volume #5 level 0.1622

> volume #5 level 0.158

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> imsave 10288_deposited_map-model

> save /Users/kyestachowski/Desktop/10288_deposited_map-model.png supersample
> 3 transparentBackground true height 2800 width 2800

> show #!2 models

> hide #!5 models

> hide #!2#!3.4 atoms

> imsave 10288_model_comparison

> save /Users/kyestachowski/Desktop/10288_model_comparison.png supersample 3
> transparentBackground true height 2800 width 2800

> save
> /Users/kyestachowski/Desktop/GPCR_Automation_Final_run/figures/modeling_improvements/10288/10288_modeling_improvements.cxs
> includeMaps true

——— End of log from Fri May 23 10:43:32 2025 ———

opened ChimeraX session  

> graphics silhouettes true width 4 depthJump 0.1

> imsave 10288_model_comparison

> save /Users/kyestachowski/Desktop/10288_model_comparison.png supersample 3
> transparentBackground true height 2800 width 2800

Cell requested for row 1 is out of bounds for table with 10 rows! Resizing
table model.  

> hide #!2 models

> show #!5 models

> imsave 10288_deposited_map-model

> save /Users/kyestachowski/Desktop/10288_deposited_map-model.png supersample
> 3 transparentBackground true height 2800 width 2800

> hide #!5 models

> show #!4 models

> show #!2 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!5 models

> hide #!5 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!5 models

> hide #!4 models

> hide #!2 models

> show #!3.4 atoms

> imsave 10288_deposited_map-model

> save /Users/kyestachowski/Desktop/10288_deposited_map-model.png supersample
> 3 transparentBackground true height 2800 width 2800

> hide #!3 models

> hide #!5 models

> show #!4 models

> show #!2 models

> show #!2 atoms

> hide H

> imsave 10288_workflow_map-model

> save /Users/kyestachowski/Desktop/10288_workflow_map-model.png supersample 3
> transparentBackground true height 2800 width 2800

> save
> /Users/kyestachowski/Desktop/GPCR_Automation_Final_run/figures/modeling_improvements/10288/10288_modeling_improvements.cxs
> includeMaps true

——— End of log from Fri May 23 11:23:34 2025 ———

opened ChimeraX session  

> open
> /Users/kyestachowski/Desktop/GPCR_Automation_Final_run/final_maps_models/10288/10288_workflow_local_11119-mask.mrc

Opened 10288_workflow_local_11119-mask.mrc as #6, grid size 300,300,300, pixel
1.03, shown at level 0.0563, step 2, values float32  

> fitmap #6 inMap #1

Fit map 10288_workflow_local_11119-mask.mrc in map 10288_workflow_local.mrc
using 33430 points  
correlation = 0.9679, correlation about mean = 0.9434, overlap = 1277  
steps = 48, shift = 0.0705, angle = 0.211 degrees  
  
Position of 10288_workflow_local_11119-mask.mrc (#6) relative to
10288_workflow_local.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999854 0.00108698 -0.00131640 0.04379375  
-0.00109128 0.99999406 -0.00326796 0.61843325  
0.00131284 0.00326940 0.99999379 -0.74719710  
Axis 0.88638803 -0.35649282 -0.29534576  
Axis point 0.00000000 225.38332336 193.08976776  
Rotation angle (degrees) 0.21128669  
Shift along axis 0.03903274  
  

> volume #6 step 1

> volume #6 level 0.373

> hide #!4 models

> show #!4 models

> transparency #6.1#4.1.1#4.2.1 0

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> volume #6 level 0.367

> transparency #6.1 50

> ui tool show "Side View"

> graphics silhouettes true depthJump 0.1 width 5

> imsave 10288_modelling_improvements

> save /Users/kyestachowski/Desktop/10288_modelling_improvements.png
> supersample 3 transparentBackground true height 2800 width 2800

> save
> /Users/kyestachowski/Desktop/GPCR_Automation_Final_run/figures/modeling_improvements/10288_modeling_improvements.cxs
> includeMaps true

——— End of log from Thu Jun 5 10:58:06 2025 ———

opened ChimeraX session  

> graphics silhouettes true depthJump 0.1 width 5

> hide #!2 models

> hide #!6 models

> show #!3 models

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #!5 models

> show #!6 models

> fitmap #5 inMap #6

Fit map 10288_deposited_global.map in map 10288_workflow_local_11119-mask.mrc
using 52664 points  
correlation = 0.6341, correlation about mean = -0.0107, overlap = 3452  
steps = 84, shift = 0.14, angle = 0.161 degrees  
  
Position of 10288_deposited_global.map (#5) relative to
10288_workflow_local_11119-mask.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.62744637 -0.40458874 0.66529617 188.03129872  
0.62162074 0.25428612 0.74089555 -10.54679400  
-0.46893358 0.87843413 0.09194985 106.22345038  
Axis 0.08955845 0.73855545 0.66821788  
Axis point 111.36815636 0.00000000 0.57393801  
Rotation angle (degrees) 129.83696267  
Shift along axis 80.03080868  
  

> show #!2 models

> show #!3 models

> mmaker #3 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 10288_receptor_remodeled_full.pdb, chain R (#2) with
10288_deposited_model.pdb A, chain A (#3.1), sequence alignment score = 35.3  
RMSD between 21 pruned atom pairs is 0.702 angstroms; (across all 39 pairs:
13.594)  
  
Matchmaker 10288_receptor_remodeled_full.pdb, chain R (#2) with
10288_deposited_model.pdb B, chain B (#3.2), sequence alignment score = 30  
RMSD between 16 pruned atom pairs is 1.236 angstroms; (across all 32 pairs:
10.922)  
  
Matchmaker 10288_receptor_remodeled_full.pdb, chain R (#2) with
10288_deposited_model.pdb C, chain C (#3.3), sequence alignment score = 19.4  
RMSD between 9 pruned atom pairs is 1.366 angstroms; (across all 57 pairs:
20.010)  
  
Matchmaker 10288_receptor_remodeled_full.pdb, chain R (#2) with
10288_deposited_model.pdb R, chain R (#3.4), sequence alignment score = 1307.8  
RMSD between 260 pruned atom pairs is 0.766 angstroms; (across all 276 pairs:
1.478)  
  
Matchmaker 10288_receptor_remodeled_full.pdb, chain R (#2) with
10288_deposited_model.pdb S, chain S (#3.5), sequence alignment score = 8.3  
RMSD between 3 pruned atom pairs is 0.377 angstroms; (across all 4 pairs:
3.435)  
  

> hide #!3 models

> hide #!5 models

> imsave 10288_workflow_map-model

> save /Users/kyestachowski/Desktop/10288_workflow_map-model.png supersample 3
> transparentBackground true height 2800 width 2800

> hide #!2 models

> hide #!6 models

> show #!5 models

> show #!3 models

> imsave 10288_deposited_map-model

> save /Users/kyestachowski/Desktop/10288_deposited_map-model.png supersample
> 3 transparentBackground true height 2800 width 2800

> hide #!5 models

> show #!2 models

> imsave 10288_model_comparison

> save /Users/kyestachowski/Desktop/10288_model_comparison.png supersample 3
> transparentBackground true height 2800 width 2800

> save
> /Users/kyestachowski/Desktop/GPCR_Automation_Final_run/figures/modeling_improvements/10288_modeling_improvements.cxs
> includeMaps true

——— End of log from Thu Jun 5 11:59:25 2025 ———

> view name session-start

opened ChimeraX session  

> view name p2

[Repeated 1 time(s)]

> view p2

> ui tool show "Side View"

> view p2

> show #!6 models

> transparency #6.1 0

> transparency #6.1 50

> transparency #6.1 0

> hide #!2 models

> hide #!3 models

> graphics silhouettes true depthJump 0.1 width 3

> graphics silhouettes true depthJump 0.1 width 1

> graphics silhouettes true depthJump 0.1 width 2

> view name p1

> fly p1 p2

> view p2

> fly p1 p2

> p1

Unknown command: p1  

> view p1

> fly p1 p2

> view p2

> ui tool show "Side View"

> view p1

> view p2

> fly p1 p2

[Repeated 1 time(s)]

> view p1

> rotate

Unknown command: rotate  

> roll

> stop

> view p1

> roll

> wait 10

> stop

> fly p1 p2

> rock

> view p1

> wait 10

> roll

> stop

> fly p1 p2

> rock

> view p1

> stop

> runscript /Users/kyestachowski/Documents/scripts/gpcr_10288_video.cxc

> volume #6.1 transparency 0

No volumes specified  

> transparency #6.1 50

> transparency #6.1 0

> runscript /Users/kyestachowski/Documents/scripts/gpcr_10288_video.cxc

> transparency #6.1 0

> view p1

> turn y 90 10

> wait 10

> fly p1 p2

> transparency #6.1 50

> show #3.4

> rock y 30 2

> wait 10

> view p2

> rock y 30 2

> view p1

> transparency #6.1 0

> roll y 360 10

> roll y 90 10

[Repeated 9 time(s)]

> roll y 3 90

> roll y 3 60

> roll y 3 30

> roll y 3 120

> roll y 3 60

> roll y 3 90

[Repeated 1 time(s)]

> roll y 3 120

> roll y 4 90

> roll y 2 180

> roll y 1 360

> roll y 2 180

> roll y 1.5 270

> roll y 1.5 240

> fly p1 p2

> crossfade view p2

Expected an integer >= 1 or a keyword  

> fly p1 p2

> crossfade

> view p2

> wait 30

> view p1

> fly p1 p2

> wait 30

> crossfade

> view p2

> wait 30

> view p1

> wait30; fly p1 p2; wait 30; crossfade; view p2; wait 30

Unknown command: wait30; fly p1 p2; wait 30; crossfade; view p2; wait 30  

> view p1

> wait 30

> fly p1 p2

> wait 30

> crossfade

> view p2

> wait 30

> view p1

> wait 30

> fly p1 p2

> wait 30

> crossfade

> view p2

> wait 30

> view p1

> wait 30

> fly p1 p2

> wait 30

> crossfade

> wait 30

> view p2

> wait 30

> view p1

> wait 100

> fly p1 p2

> wait 100

> crossfade

> wait 100

> view p2

> wait 100

> view p1

> wait 100

> fly p1 p2

> wait 200

> crossfade

> wait 100

> view p2

> wait 100

> viw p1

Unknown command: viw p1  

> view p1

> fly p1 p2

> view p1

> fly p1 p2

> view 2

Expected an objects specifier or a view name or a keyword  

> view p2

> view p1

> fly p1 p2

> help wait

> view p1

> wait

wait requires a frame count argument unless motion is in progress  

> fly p1 p2

> wait

> crossfade

> wait

wait requires a frame count argument unless motion is in progress  

> view p2

> view p1

> roll y 1.5 240

> wait

> fly p1 p2

> wait

> crossfade

> wait

wait requires a frame count argument unless motion is in progress  

> view p2

> view p1

> roll y 1.5 240

> wait

> fly p1 p2

> wait

> crossfade

> view p2

> view p1

> roll y 1.5 240

> wait

> fly p1 p2

> wait

> crossfade

> view p2

> wait 60

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait

> crossfade

> view p2

> wait 60

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait

> crossfade

> view p2

> wait 30

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait

> crossfade

> view p2

> wait 120

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade

> view p2

> wait 120

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade

> view p2

> wait 30

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade

> view p2

> wait 30

> rock y 2 30

> wait 10

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade

> view p2

> wait 30

> rock y

> wait 10

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade

> view p2

> wait 30

> rock y

> wait 10

> stop

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade

> view p2

> wait 30

> rock y

> wait 10

> stop

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade

> view p2

> wait 30

> rock y

> wait 90

> stop

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade

> view p2

> wait 30

> rock y

> wait 270

> stop

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade

> view p2

> wait 30

> rock y

> wait 360

> stop

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade

> view p2

> wait 30

> rock y

> wait 360

> stop

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade

> view p2

> wait 60

> crossfade

> transparency #6.1 0

> wait 30

> crossfade

> show #3.4

> wait 30

> wait rock y; wait 360; stop

Expected an integer >= 1 or a keyword  

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade

> view p2

> wait 60

> crossfade

> transparency #6.1 0

> wait 30

> crossfade

> show #3.4

> wait 30

> rock y

> wait 360

> stop

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade 60

> view p2

> wait 60

> crossfade

> transparency #6.1 0

> wait 30

> crossfade

> show #3.4

> wait 30

> rock y

> wait 360

> stop

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade 120

> view p2

> wait 120

> crossfade

> transparency #6.1 0

> wait 30

> crossfade

> show #3.4

> wait 30

> rock y

> wait 360

> stop

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade

> view p2

> wait 60

> crossfade

> transparency #6.1 0

> wait 30

> crossfade

> show #3.4

> wait 30

> rock y

> wait 360

> stop

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade

> view p2

> wait 60

> transparency #6.1 0

> crossfade

> show #3.4

> wait 30

> rock y

> wait 360

> stop

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade

> view p2

> wait 60

> crossfade

> transparency #6.1 50

> wait 30

> show #3.4

> wait 30

> rock y

> wait 360

> stop

> show #!3 models

> view p1

> hide #3.4

> hide #3

> hide models #3

Expected ',' or a keyword  

> hide #!3.4 models

> show #!3.4 models

> hide #!3.4 models

> show #!3.4 models

> hide #!3.4 models

[Repeated 1 time(s)]

> show #!3.4 models

> hide #!3.4 models

> transparency #6.1 0

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade

> view p2

> wait 60

> crossfade

> transparency #6.1 50

> wait 30

> show #!3.4 models

> wait 30

> rock y

> wait 360

> stop

> hide #!3.4 models

> show #!2 models

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade

> view p2

> wait 60

> crossfade

> transparency #6.1 50

> wait 30

> show #!2 models

> wait 30

> rock y

> wait 360

> stop

> transparency #6.1 0

> hide#!2 models

Unknown command: hide#!2 models  

> transparency #6.1 0

> hide #!2 models

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade

> view p2

> wait 60

> crossfade

> transparency #6.1 50

> wait 30

> show #!2 models

> wait 30

> rock y

> wait 360

> stop

> transparency #6.1 0

> hide #!2 models

No help found for 'help:user/movies'  
No help found for 'help:user/movie'  

> help movie

> help movie record

> movie record

> view p1

> roll y 1.5 240

> wait

> clip off

> fly p1 p2

> wait 120

> crossfade

> view p2

> wait 60

> crossfade

> transparency #6.1 50

> wait 30

> show #!2 models

> wait 30

> rock y

> wait 360

> stop

> movie encode /Users/kyestachowski/Desktop/10288_movie.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/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
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 - 88.1
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: 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: Mac14,6
      Model Number: Z17500103LL/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 64 GB
      System Firmware Version: 11881.41.5
      OS Loader Version: 10151.140.19.700.2

Software:

    System Software Overview:

      System Version: macOS 14.7.1 (23H222)
      Kernel Version: Darwin 23.6.0
      Time since boot: 52 days, 2 hours, 34 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 30
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        HP X27q:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 120.00Hz
          Main Display: Yes
          Mirror: On
          Mirror Status: Master Mirror
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Mirror: On
          Mirror Status: Hardware Mirror
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        HP X27q:
          Resolution: 1440 x 2560
          UI Looks like: 1440 x 2560 @ 144.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


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

[kstachowski@…]

I updated to v1.10.1 and this resolved the problem.

On Fri, Sep 12, 2025 at 4:21 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>

[Eric Pettersen]

Hi Kye,

Thanks for reporting this problem. Yes, as you discovered it is fixed in the 1.10.1 release. Sorry for the inconvenience.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab