ffmpeg: Permission denied

[chimerax-bug-report@…]

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
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/dmargulies/open model M142-Ly49C.cxs" format session

Log from Wed Jul 23 05:49:59 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/dmargulies/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/_M142-Ly49-models-and paper/8tq4-1p4l-trans.cxs"
> format session

Log from Mon Jul 21 14:20:24 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/dmargulies/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/M142fromJJ/P14J284-m142dd-267a.cxs format session

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "ZoneColor" returned None  

[Repeated 4 time(s)]Log from Wed Jul 3 17:19:29 2024UCSF ChimeraX version:
1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/jiangji/Projects/JJ-CryoEM-antiMHCI-
> mAb/M142+Dd/P14J261-m142dd-276a.cxs

Error opening map "/Users/jiangji/Projects/JJ-CryoEM-antiMHCI-
mAb/M142+Dd/m142dd-J261-276a_rsr28.pdb": File m142dd-J261-276a_rsr28.pdb,
format mrc  
MRC header value nsymbt (1229934138) is invalid  
  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Opened cryosparc_P14_J261_003_volume_map.mrc as #1, grid size 256,256,256,
pixel 0.83, shown at level 0.0827, step 1, values float32  

restore_snapshot for "ZoneColor" returned None  

Log from Wed Jun 19 18:25:07 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/jiangji/Projects/M142Fab+Dd-
> cryoEM/Skyline/P14J257-m142dd-315a.cxs

Opened cryosparc_P14_J245flipJ244_map.mrc as #4, grid size 256,256,256, pixel
0.83, shown at level 0.0677, step 1, values float32  
Opened cryosparc_P14_J257_006_volume_map.mrc as #6, grid size 256,256,256,
pixel 0.83, shown at level 0.0797, step 1, values float32  
Opened cryosparc_P14_J257_006_volume_map_sharp.mrc as #8, grid size
256,256,256, pixel 0.83, shown at level 0.128, step 1, values float32  
Log from Wed Jun 19 17:06:46 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/jiangji/Projects/M142Fab+Dd-
> cryoEM/Skyline/P14J245flipJ244-m142dd.cxs

Opened cryosparc_P14_J244_003_volume_map.mrc as #1, grid size 256,256,256,
pixel 0.83, shown at level 0.0922, step 1, values float32  
Opened cryosparc_P14_J244_003_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 0.83, shown at level 0.125, step 1, values float32  
Opened cryosparc_P14_J245flipJ244_map.mrc as #4, grid size 256,256,256, pixel
0.83, shown at level 0.0677, step 1, values float32  
Opened cryosparc_P14_J240flipJ238_map.mrc as #5, grid size 256,256,256, pixel
0.83, shown at level 0.0722, step 1, values float32  
Log from Fri Jun 14 15:56:04 2024 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/jiangji/Projects/M142Fab+Dd-
> cryoEM/Skyline/cryosparc_P14_J244_003_volume_map.mrc

Opened cryosparc_P14_J244_003_volume_map.mrc as #1, grid size 256,256,256,
pixel 0.83, shown at level 0.0373, step 1, values float32  

> volume #1 level 0.09219

> open /Users/jiangji/Projects/M142Fab+Dd-
> cryoEM/CryoEM/models/8tq4-one-b50.pdb

Chain information for 8tq4-one-b50.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
H | No description available  
L | No description available  
P | No description available  
  

> hide atoms

> show cartoons

> ui mousemode right "rotate selected models"

> select add #2

6370 atoms, 6538 bonds, 816 residues, 1 model selected  

> view matrix models
> #2,0.96438,-0.22394,0.14081,11.536,0.2404,0.96404,-0.11328,-9.1767,-0.11038,0.14309,0.98353,-1.4049

> view matrix models
> #2,0.6389,-0.53686,-0.551,157.41,-0.59613,-0.79821,0.086495,243.63,-0.48625,0.27321,-0.83001,229.71

> view matrix models
> #2,0.73771,-0.63261,-0.23578,121.37,-0.64306,-0.76477,0.039928,250.38,-0.20558,0.12216,-0.97099,231.47

> view matrix models
> #2,0.73925,-0.63837,-0.21446,119.4,-0.63495,-0.76683,0.093879,243.64,-0.22438,0.06677,-0.97221,239.46

> view matrix models
> #2,0.76682,-0.63784,-0.071764,100.3,-0.63713,-0.76994,0.035463,250.79,-0.077874,0.018529,-0.99679,231.63

> view matrix models
> #2,0.74978,-0.65069,-0.12014,108.93,-0.66092,-0.7452,-0.088693,264.74,-0.031813,0.1459,-0.98879,212.37

> view matrix models
> #2,0.76191,-0.63004,-0.15016,108.85,-0.6476,-0.74479,-0.16092,271.42,-0.010453,0.21985,-0.97548,200.79

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.76191,-0.63004,-0.15016,112.47,-0.6476,-0.74479,-0.16092,269.33,-0.010453,0.21985,-0.97548,190.22

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.76677,-0.63891,-0.062125,102.95,-0.63729,-0.74607,-0.19295,271.98,0.07693,0.18754,-0.97924,184.69

> view matrix models
> #2,-0.82805,0.48388,-0.28318,180.33,0.52652,0.8447,-0.096249,-31.24,0.19263,-0.2288,-0.95422,213.36

> open /Users/jiangji/Projects/M142Fab+Dd-
> cryoEM/Skyline/cryosparc_P14_J244_003_volume_map_sharp.mrc

Opened cryosparc_P14_J244_003_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 0.83, shown at level 0.0516, step 1, values float32  

> volume #3 level 0.1247

> hide #!1 models

> open /Users/jiangji/Projects/M142Fab+Dd-
> cryoEM/Skyline/cryosparc_P14_J245flipJ244_map.mrc

Opened cryosparc_P14_J245flipJ244_map.mrc as #4, grid size 256,256,256, pixel
0.83, shown at level 0.0373, step 1, values float32  

> hide #!3 models

> volume #4 level 0.06453

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.83838,-0.09114,0.53742,149.48,0.10064,-0.99485,-0.011715,198.73,0.53572,0.044264,0.84324,-54.923

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.96907,-0.02525,0.24547,189.46,0.0062678,-0.99695,-0.077805,216.51,0.24669,-0.07386,0.96628,-25.399

> view matrix models
> #2,0.91564,-0.20486,0.34588,-4.7693,0.079798,0.93591,0.34307,-42.571,-0.394,-0.28653,0.87331,76.117

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.91564,-0.20486,0.34588,-2.1935,0.079798,0.93591,0.34307,-28.732,-0.394,-0.28653,0.87331,73.303

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.90631,-0.15734,0.39224,-11.432,0.032504,0.95132,0.30649,-21.165,-0.42137,-0.26503,0.8673,74.646

> view matrix models
> #2,0.99498,-0.048959,0.08726,2.0506,0.056765,0.99438,-0.08934,16.349,-0.082396,0.093845,0.99217,-13.569

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.99498,-0.048959,0.08726,1.6069,0.056765,0.99438,-0.08934,3.2751,-0.082396,0.093845,0.99217,-6.5071

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.99499,-0.019226,0.098071,-2.7479,0.024214,0.99846,-0.049928,1.8856,-0.09696,0.052053,0.99393,-0.74027

> view matrix models
> #2,0.99916,-0.033215,-0.023798,12.027,0.033029,0.99942,-0.0081568,-3.8718,0.024055,0.0073639,0.99968,-9.639

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.99916,-0.033215,-0.023798,6.2049,0.033029,0.99942,-0.0081568,-1.491,0.024055,0.0073639,0.99968,-4.8069

> ui tool show "Fit in Map"

> fitmap #2 inMap #4

Fit molecule 8tq4-one-b50.pdb (#2) to map cryosparc_P14_J245flipJ244_map.mrc
(#4) using 6370 atoms  
average map value = 0.1011, steps = 56  
shifted from previous position = 1.78  
rotated from previous position = 1.49 degrees  
atoms outside contour = 1784, contour level = 0.064526  
  
Position of 8tq4-one-b50.pdb (#2) relative to
cryosparc_P14_J245flipJ244_map.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99978708 -0.01099710 -0.01746052 3.02431164  
0.01106911 0.99993061 0.00403316 -1.41251006  
0.01741495 -0.00422558 0.99983942 -1.34061754  
Axis -0.19622423 -0.82862672 0.52428409  
Axis point 74.76733031 0.00000000 170.88235504  
Rotation angle (degrees) 1.20582923  
Shift along axis -0.12586409  
  

> view matrix models
> #2,0.99979,-0.010997,-0.017461,3.0724,0.011069,0.99993,0.0040332,-1.1886,0.017415,-0.0042256,0.99984,-1.7712

> fitmap #2 inMap #4

Fit molecule 8tq4-one-b50.pdb (#2) to map cryosparc_P14_J245flipJ244_map.mrc
(#4) using 6370 atoms  
average map value = 0.1011, steps = 48  
shifted from previous position = 0.49  
rotated from previous position = 0.00429 degrees  
atoms outside contour = 1786, contour level = 0.064526  
  
Position of 8tq4-one-b50.pdb (#2) relative to
cryosparc_P14_J245flipJ244_map.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99978696 -0.01097712 -0.01748008 3.01797778  
0.01104801 0.99993112 0.00396398 -1.41135562  
0.01743537 -0.00415625 0.99983936 -1.35289581  
Axis -0.19300355 -0.82987883 0.52349858  
Axis point 75.57810340 0.00000000 170.41215717  
Rotation angle (degrees) 1.20539015  
Shift along axis -0.11946531  
  

> select subtract #2

Nothing selected  

> save /Users/jiangji/Projects/M142Fab+Dd-
> cryoEM/Skyline/P14J245flipJ244-m142dd.cxs

> volume #4 level 0.07394

> volume #4 level 0.0959

> open /Users/jiangji/Projects/M142Fab+Dd-
> cryoEM/Skyline/cryosparc_P14_J240flipJ238_map.mrc

Opened cryosparc_P14_J240flipJ238_map.mrc as #5, grid size 256,256,256, pixel
0.83, shown at level 0.0383, step 1, values float32  

> volume #5 level 0.09376

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #!4 models

> show #!4 models

> hide #!5 models

> volume #5 level 0.1092

> volume #4 level 0.1294

> hide #!4 models

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!4 models

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!4 models

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> volume #4 level 0.1105

> show #!5 models

> hide #!4 models

> show #!4 models

> volume #5 level 0.08657

> volume #5 level 0.08349

> volume #4 level 0.1032

> hide #!5 models

> volume #4 level 0.07708

> hide #!4 models

> show #!5 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!5 models

> volume #4 level 0.08126

> volume #5 level 0.08246

> hide #!4 models

> hide #!5 models

> show #!4 models

> show #!5 models

> volume #5 level 0.08965

> volume #4 level 0.08335

> volume #5 level 0.07218

> volume #4 level 0.06766

> save /Users/jiangji/Projects/M142Fab+Dd-
> cryoEM/Skyline/P14J245flipJ244-m142dd.cxs includeMaps true

——— End of log from Fri Jun 14 15:56:04 2024 ———

opened ChimeraX session  

> open /Users/jiangji/Projects/M142Fab+Dd-
> cryoEM/Skyline/cryosparc_P14_J257_006_volume_map.mrc

Opened cryosparc_P14_J257_006_volume_map.mrc as #6, grid size 256,256,256,
pixel 0.83, shown at level 0.0379, step 1, values float32  

> hide #!5 models

> hide #!4 models

> transparency #2,6 50

> set bgColor white

> open /Users/jiangji/Projects/M142Fab+Dd-
> cryoEM/CryoEM/models/m142dd-p14j245-287a-mod_rsr21.pdb

Chain information for m142dd-p14j245-287a-mod_rsr21.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
H | No description available  
L | No description available  
P | No description available  
  

> hide atoms

> show cartoons

> hide #2 models

> ui tool show "Fit in Map"

> fitmap #7 inMap #6

Fit molecule m142dd-p14j245-287a-mod_rsr21.pdb (#7) to map
cryosparc_P14_J257_006_volume_map.mrc (#6) using 6130 atoms  
average map value = 0.1093, steps = 76  
shifted from previous position = 0.235  
rotated from previous position = 3.66 degrees  
atoms outside contour = 413, contour level = 0.037937  
  
Position of m142dd-p14j245-287a-mod_rsr21.pdb (#7) relative to
cryosparc_P14_J257_006_volume_map.mrc (#6) coordinates:  
Matrix rotation and translation  
0.99830424 -0.05443913 0.02061620 3.67079117  
0.05496391 0.99815480 -0.02580610 -2.69261950  
-0.01917330 0.02689548 0.99945436 -0.77248457  
Axis 0.41241526 0.31137202 0.85613148  
Axis point 51.27539755 65.72497618 0.00000000  
Rotation angle (degrees) 3.66334233  
Shift along axis 0.01413555  
  

> color #6/A, lime

> sequence chain #7/A

Alignment identifier is 7/A  

> select #7/A:2-274

2115 atoms, 2177 bonds, 1 pseudobond, 270 residues, 2 models selected  

> select #7/A:2-274

2115 atoms, 2177 bonds, 1 pseudobond, 270 residues, 2 models selected  

> color #6/A green

> color #7/A, green

> color #7/A green

> select add #7

6130 atoms, 6298 bonds, 3 pseudobonds, 798 residues, 2 models selected  

> select subtract #7

Nothing selected  

> color #7/A lime

> ui tool show "Color Actions"

> color #7/A chartreuse

> color #7/B royle blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #7/B royal blue

> color #7/H sandy brown

> color #7/L light gray

> color zone #6 near #7 distance 4.98

> color #7/P red

> color zone #6 near #7 distance 4.98

> volume #1 level 0.0905

> volume #1 level 0.08881

> hide #!1 models

> volume #6 level 0.02574

> volume #6 level 0.06232

> color #7/L dark gray

> color zone #6 near #7 distance 4.98

> open /Users/jiangji/Projects/M142Fab+Dd-
> cryoEM/Skyline/cryosparc_P14_J257_006_volume_map_sharp.mrc

Opened cryosparc_P14_J257_006_volume_map_sharp.mrc as #8, grid size
256,256,256, pixel 0.83, shown at level 0.0701, step 1, values float32  

> volume #8 level 0.2041

> hide #!6 models

> volume #3 level 0.08928

> close #3

> close #1

> close #5

> volume #8 level 0.1281

> hide #!8 models

> show #!6 models

> save /Users/jiangji/Projects/M142Fab+Dd-
> cryoEM/Skyline/P14J257-m142dd-315a.cxs

> volume #6 level 0.07974

> hide #!7 models

> color #7/B slate blue

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

> color #7/B slate blue

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

> show #!7 models

> color zone #6 near #7 distance 4.98

> hide #!7 models

> save /Users/jiangji/Projects/M142Fab+Dd-
> cryoEM/Skyline/P14J257-m142dd-315a.cxs

——— End of log from Wed Jun 19 17:06:46 2024 ———

opened ChimeraX session  

> open /Users/jiangji/Projects/M142Fab+Dd-
> cryoEM/Skyline/cryosparc_P14_J261_003_volume_map.mrc

Opened cryosparc_P14_J261_003_volume_map.mrc as #1, grid size 256,256,256,
pixel 0.83, shown at level 0.0376, step 1, values float32  

> hide #!6 models

> transparency #1 50

> show #!7 models

> ui tool show "Fit in Map"

> fitmap #7 inMap #1

Fit molecule m142dd-p14j245-287a-mod_rsr21.pdb (#7) to map
cryosparc_P14_J261_003_volume_map.mrc (#1) using 6130 atoms  
average map value = 0.1109, steps = 52  
shifted from previous position = 0.0455  
rotated from previous position = 0.388 degrees  
atoms outside contour = 400, contour level = 0.037585  
  
Position of m142dd-p14j245-287a-mod_rsr21.pdb (#7) relative to
cryosparc_P14_J261_003_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99797237 -0.05883880 0.02427226 3.73984141  
0.05954143 0.99779520 -0.02931835 -2.76102535  
-0.02249368 0.03070410 0.99927538 -0.80187225  
Axis 0.42652192 0.33232065 0.84121462  
Axis point 48.67913303 61.86130252 0.00000000  
Rotation angle (degrees) 4.03481853  
Shift along axis 0.00303193  
  

> volume #4 level 0.06851

> volume #4 level 0.05919

> hide #!1 models

> volume #1 level 0.0903

> hide #!1 models

> show #!1 models

> hide #!4 models

> volume #1 level 0.07475

> volume #4 level 0.06089

> volume #4 level 0.07698

> hide #!4 models

> close #4

> color zone #1 near #7 distance 4.98

> transparency #1,7 50

> hide #!7 models

> volume #1 level 0.09117

> close #8

> show #!7 models

> color zone #1 near #7 distance 4.98

> volume #1 level 0.08273

> hide #!7 models

> volume #1 level 0.08273

> show #!7 models

> hide #!7 models

> save /Users/jiangji/Projects/M142Fab+Dd-cryoEM/Skyline/P14J261-map-
> color-276a.png width 941 height 655 supersample 4

> save /Users/jiangji/Projects/M142Fab+Dd-cryoEM/Skyline/m142dd-J261-276a.pdb
> models #7

> save /Users/jiangji/Projects/M142Fab+Dd-
> cryoEM/Skyline/P14J261-m142dd-276a.cxs

——— End of log from Wed Jun 19 18:25:07 2024 ———

opened ChimeraX session  

> close #2

> open /Users/jiangji/Projects/JJ-CryoEM-antiMHCI-
> mAb/M142+Dd/cryosparc_P14_J284_003_volume_map.mrc

Opened cryosparc_P14_J284_003_volume_map.mrc as #2, grid size 256,256,256,
pixel 0.83, shown at level 0.0387, step 1, values float32  

> hide #!1 models

> show #!7 models

> color zone #2 near #7 distance 4.98

> hide #!7 models

> hide #!2 models

> show #!7 models

> show #!1 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> volume #1 level 0.05267

> volume #2 level 0.05382

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> open /Users/jiangji/Projects/JJ-CryoEM-antiMHCI-
> mAb/M142+Dd/m142dd-J261-276a_rsr28.pdb

Chain information for m142dd-J261-276a_rsr28.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
H | No description available  
L | No description available  
P | No description available  
  

> hide #!7 models

> show #!2 models

> hide #!1 models

> hide #!3 atoms

> show #!3 cartoons

> color #3/P red

> color #3/L dark gray

> color #3/B dark cyan

> color #3/H tomato

> color #3/A spring green

> color zone #2 near #3 distance 4.98

> volume #2 level 0.05707

> open /Users/jiangji/Projects/JJ-CryoEM-antiMHCI-
> mAb/M142+Dd/cryosparc_P14_J284_003_volume_map_half_A.mrc

Opened cryosparc_P14_J284_003_volume_map_half_A.mrc as #4, grid size
256,256,256, pixel 0.83, shown at level 0.0844, step 1, values float32  

> volume #4 level 0.1243

> hide #!4 models

> close #4

> open /Users/jiangji/Projects/JJ-CryoEM-antiMHCI-
> mAb/M142+Dd/cryosparc_P14_J287_007_volume_map.mrc

Opened cryosparc_P14_J287_007_volume_map.mrc as #4, grid size 256,256,256,
pixel 0.83, shown at level 0.0389, step 1, values float32  

> volume #1 level 0.08468

> hide #!1 models

> hide #!2 models

> close #7

> volume #1 level 0.06014

> close #4

> show #!2 models

> hide #!1 models

> volume #2 level 0.08157

> save /Users/jiangji/Projects/JJ-CryoEM-antiMHCI-
> mAb/M142+Dd/P14J284-m142dd-267a.cxs

> hide #!3 models

> volume #2 level 0.076

> show #!3 models

> ui tool show "Color Actions"

> color #3/A yellow green

> color #3/B state blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color blue

> color #3/H linen

> color zone #2 near #3 distance 4.98

> color #3/H orange

> color zone #2 near #3 distance 4.98

> color #3/H khaki

> color #3/B state blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #3/A yellow green

> color #3/B state blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #3/B slate blue

> color #3/A spring green

> color zone #2 near #3 distance 4.98

> color #3/P red

> color zone #2 near #3 distance 4.98

> color #3/L dark gray

> color zone #2 near #3 distance 4.98

> volume #2 level 0.07712

> color #3/H burly wood

> color zone #2 near #3 distance 4.98

> color #3/A ywllow green

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #3/A yellow green

> color zone #2 near #3 distance 4.98

> hide #!3 models

> show #!3 models

> save /Users/jiangji/Projects/JJ-CryoEM-antiMHCI-
> mAb/M142+Dd/P14J284-m142dd-267a.cxs

——— End of log from Wed Jul 3 17:19:29 2024 ———

> view name session-start

opened ChimeraX session  

> close #3

> open 8tq4 fromDatabase pdb

8tq4 title:  
Crystal structure of Fab M142 in complex with MHC-I (H2-Dd) [more info...]  
  
Chain information for 8tq4 #1  
---  
Chain | Description | UniProt  
A E | H2 class I histocompatibility antigen D-d alpha chain (H2-Dd) | HA12_MOUSE 2-274  
B F | Beta-2-microglobulin | B2MG_MOUSE 1-98  
C H | Fab M142 Heavy Chain |   
D L | Fab M142 Light Chain |   
G P | HV1: HIV-1 P18-I10 |   
  
8tq4 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_defined_assembly  
  

> sym #1 assembly 2

Made 1 copies for 8tq4 assembly 2  

> view

> show #2.1 cartoons

> hide #2.1 atoms

> hide #!2 models

> show #!2 models

> hide #2.1 models

> show #2.1 models

> open 8tq4 fromDatabase pdb

8tq4 title:  
Crystal structure of Fab M142 in complex with MHC-I (H2-Dd) [more info...]  
  
Chain information for 8tq4 #3  
---  
Chain | Description | UniProt  
A E | H2 class I histocompatibility antigen D-d alpha chain (H2-Dd) | HA12_MOUSE 2-274  
B F | Beta-2-microglobulin | B2MG_MOUSE 1-98  
C H | Fab M142 Heavy Chain |   
D L | Fab M142 Light Chain |   
G P | HV1: HIV-1 P18-I10 |   
  
8tq4 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_defined_assembly  
  

> sym #3 assembly 2

Made 1 copies for 8tq4 assembly 2  

> view

> open 3c8k fromDatabase pdb

3c8k title:  
The crystal structure of Ly49C bound to H-2Kb [more info...]  
  
Chain information for 3c8k #5  
---  
Chain | Description | UniProt  
A | H-2 class I histocompatibility antigen, K-B alpha chain | HA1B_MOUSE 1-274  
B | beta-2 microglobulin | Q91XJ8_MOUSE 1-99  
D | Natural killer cell receptor Ly-49C | Q61198_MOUSE 138-262  
P | Ovalbumin peptide |   
  

> hide #5 models

> show #5 models

> hide #5 models

> show #5 models

> close #5

> open 1p4l fromDatabase pdb

1p4l title:  
Crystal structure of NK receptor Ly49C mutant with its MHC class I ligand
H-2Kb [more info...]  
  
Chain information for 1p4l #5  
---  
Chain | Description | UniProt  
A | MHC CLASS I H-2KB HEAVY CHAIN | HA1B_MOUSE 1-274  
B | Beta-2-microglobulin | B2MG_MOUSE 1-99  
D | LY49-C | KLRA3_MOUSE 138-259  
P | Ovalbumin peptide | OVAL_CHICK 1-8  
  
1p4l mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> sym #5 assembly 1

Made 2 copies for 1p4l assembly 1  

> view

> hide #6.2 models

> show #6.2 models

> hide #6.1 models

> show #6.1 models

> show #2.1#4.1#6.1-2 cartoons

> hide #2.1#4.1#6.1-2 atoms

> mmaker #2.1 to #6.1

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 1p4l, chain A (#6.1) with 8tq4, chain E (#2.1), sequence alignment
score = 1267.3  
RMSD between 260 pruned atom pairs is 1.042 angstroms; (across all 273 pairs:
1.171)  
  

> mmaker #4.1 to #6.2

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 1p4l, chain A (#6.2) with 8tq4, chain E (#4.1), sequence alignment
score = 1267.3  
RMSD between 260 pruned atom pairs is 1.042 angstroms; (across all 273 pairs:
1.171)  
  

> open /Users/dmargulies/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/_M142-Ly49-models/fold_2025_03_04_16_09_ly49c_2_kb_2_b2m_2_siinfekl_2/fold_2025_03_04_16_09_ly49c_2_kb_2_b2m_2_siinfekl_2_model_0.cif

Chain information for
fold_2025_03_04_16_09_ly49c_2_kb_2_b2m_2_siinfekl_2_model_0.cif #7  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
G H | .  
  

> show #7#2.1#4.1#6.1-2 cartoons

Computing secondary structure  

> hide #7#2.1#4.1#6.1-2 atoms

> mmaker #7 to #6.1

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 1p4l, chain A (#6.1) with
fold_2025_03_04_16_09_ly49c_2_kb_2_b2m_2_siinfekl_2_model_0.cif, chain C (#7),
sequence alignment score = 1390.9  
RMSD between 272 pruned atom pairs is 0.600 angstroms; (across all 273 pairs:
0.616)  
  

> hide #6.2 models

> hide #6.1 models

> hide #!6 models

> hide #4.1 models

> hide #2.1 models

> hide #!4 models

> select #7 lysine

Expected a keyword  

> select #7 lys

Expected a keyword  

> ui tool show "Show Sequence Viewer"

[Repeated 1 time(s)]

> sequence chain #7/A #7/B

Alignment identifier is 1  

> select #7/A-B:5

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #7/A-B:5

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #7/A-B:2-89,121-131,141-150,178-186

1968 atoms, 1994 bonds, 236 residues, 1 model selected  

> select #7/A-B:26-27

40 atoms, 40 bonds, 4 residues, 1 model selected  

> select #7/A-B:26-27

40 atoms, 40 bonds, 4 residues, 1 model selected  

> select #7/A-B:2-89,121-131,141-150,178-186

1968 atoms, 1994 bonds, 236 residues, 1 model selected  

> select #7/A-B:92-96,100-108,110-116,160-163,168-171,193-197,200-204,212-217

766 atoms, 778 bonds, 90 residues, 1 model selected  

> select #7 :lys

774 atoms, 696 bonds, 86 residues, 1 model selected  

> select #7 /A:lys

198 atoms, 179 bonds, 22 residues, 1 model selected  

> show sel atoms

> select clear

> hide #!2 models

> color #7 orange

> color bychain

> select #7 /A:lys

198 atoms, 179 bonds, 22 residues, 1 model selected  

> color sel yellow

> select #7 /A:cys

66 atoms, 55 bonds, 11 residues, 1 model selected  

> color sel lime

> show sel atoms

> select #7 /A:cys /B:cys

132 atoms, 110 bonds, 22 residues, 1 model selected  

> show sel atoms

> color sel yellow

> select #7 /A:lys /B:lys

396 atoms, 358 bonds, 44 residues, 1 model selected  

> color sel cornflower blue

> select clear

> select #7 /A:lys /B:lys

396 atoms, 358 bonds, 44 residues, 1 model selected  

> show sel atoms

> select clear

> show #!4 models

> show #4.1 models

> show #6.2 models

> hide #6.2 models

> show #6.1 models

> hide #6.1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #4.1 models

> show #4.1 models

> show #2.1 models

> save "/Users/dmargulies/OneDrive - National Institutes of
> Health/_M142-Ly49-models/8tq4-1p4l-trans.cxs"

——— End of log from Mon Jul 21 14:20:24 2025 ———

> view name session-start

opened ChimeraX session  

> color bymolecule

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color bymodel

> save "/Users/dmargulies/open model M142-Ly49C.cxs"

——— End of log from Wed Jul 23 05:49:59 2025 ———

> view name session-start

opened ChimeraX session  

> open "/Users/dmargulies/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/_M142-Ly49-models-and
> paper/fold_ly49c_2_copies_lumenal/fold_ly49c_2_copies_lumenal_model_0.cif"

Chain information for fold_ly49c_2_copies_lumenal_model_0.cif #8  
---  
Chain | Description  
A B | .  
  
Computing secondary structure  

> hide #7 models

> show #7 models

> mmaker #8 to #7

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 fold_2025_03_04_16_09_ly49c_2_kb_2_b2m_2_siinfekl_2_model_0.cif,
chain B (#7) with fold_ly49c_2_copies_lumenal_model_0.cif, chain B (#8),
sequence alignment score = 1164.3  
RMSD between 125 pruned atom pairs is 0.466 angstroms; (across all 223 pairs:
54.538)  
  

> hide #7 models

> show #7 models

> hide #!2 models

> show #!2 models

> hide #2.1 models

> show #2.1 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> show #6.1 models

> show #6.2 models

> hide #!2 models

> hide #2.1 models

> hide #4.1 models

> hide #!6 models

> hide #6.1 models

> hide #8 models

> hide #6.2 models

> color bychain

> hide #7 models

> show #6.2 models

> show #6.1 models

> hide #6.1 models

> lighting simple

> show #6.1 models

> hide #6.2 models

> hide #6.1 models

> show #7 models

> hide #7 atoms

> show #8 models

> hide #7 models

> show #7 models

> select #7 /B,A

3696 atoms, 3778 bonds, 446 residues, 1 model selected  

> hide sel cartoons

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/dmargulies/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 Metal - 89.4
OpenGL renderer: Apple M4 Max
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: Mac16,6
      Model Number: MX2K3LL/A
      Chip: Apple M4 Max
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 36 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: 5 days, 1 hour, 52 minutes

Graphics/Displays:

    Apple M4 Max:

      Chipset Model: Apple M4 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U4323QE:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Television: Yes


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