Follow-on error to: 'ClipCap' object has no attribute 'data'

[julia.charl@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
How do I get out of the segmentation view, where my model is split into axial, coronal and sagittal orthoplanes?

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open C:\Users\Julia\Documents\Uni\FtsH_stuff\cryo-EM\ATP-bound-
> FtsH_map_with_structure.cxs format session

Opened protease-ring_C6_flipped.mrc as #2, grid size 340,340,340, pixel 0.84,
shown at level 0.0713, step 2, values float32  
Opened cryosparc_P4_J375_017_ATPase_zflip.mrc as #7, grid size 340,340,340,
pixel 0.84, shown at level 0.0613, step 2, values float32  
Log from Tue Feb 28 10:55:03 2023UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open C:/Users/Julia/Documents/Uni/FtsH_stuff/cryo-EM/ATPase-Protease_with-
> model-built-in.cxs

Opened J666_volume_zflip.mrc as #1, grid size 340,340,340, pixel 0.84, shown
at level 0.0378, step 2, values float32  
Opened protease-ring_C6_flipped.mrc as #2, grid size 340,340,340, pixel 0.84,
shown at level 0.0713, step 2, values float32  
Opened cryosparc_P4_J562_008_zflipped.mrc as #3, grid size 340,340,340, pixel
0.84, shown at level 0.0652, step 2, values float32  
Opened cryosparc_P4_J375_017_ATPase_zflip_deepemhancer.mrc as #6, grid size
340,340,340, pixel 0.84, shown at level 0.053, step 2, values float32  
Opened cryosparc_P4_J375_017_ATPase_zflip.mrc as #7, grid size 340,340,340,
pixel 0.84, shown at level 0.0524, step 2, values float32  
Log from Wed Feb 15 21:28:11 2023 Startup Messages  
---  
warning | No presets found in custom preset folder C:/Users/Julia/Documents/Uni/FtsH_stuff/cryo-EM/Chimera custom presets  
  

> chimera_trimmings.com

Error running startup command 'chimera_trimmings.com': Unknown command:
chimera_trimmings.com  
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\\\Users\\\Julia\\\Documents\\\Uni\\\FtsH_stuff\\\cryo-
> EM\\\J666_volume_zflip.mrc

Opened J666_volume_zflip.mrc as #1, grid size 340,340,340, pixel 0.84, shown
at level 0.0241, step 2, values float32  

> volume #1 level 0.05253

> volume #1 level 0.05901

[Repeated 1 time(s)]

> open C:/Users/Julia/Documents/Uni/FtsH_stuff/cryo-EM/protease-
> ring_C6_flipped.mrc

Opened protease-ring_C6_flipped.mrc as #2, grid size 340,340,340, pixel 0.84,
shown at level 0.0448, step 2, values float32  

> close #2

> open C:/Users/Julia/Documents/Uni/FtsH_stuff/cryo-EM/J622_ATPase-only.mrc

Opened J622_ATPase-only.mrc as #2, grid size 340,340,340, pixel 0.84, shown at
level 0.0383, step 2, values float32  

> vop flip #2

Opened J622_ATPase-only.mrc z flip as #3, grid size 340,340,340, pixel 0.84,
shown at step 1, values float32  

> volume #3 level 0.066

> hide #!1 models

> close #2

> close #3

> show #!1 models

> volume #1 level 0.0655

> open C:/Users/Julia/Documents/Uni/FtsH_stuff/cryo-EM/protease-
> ring_C6_flipped.mrc

Opened protease-ring_C6_flipped.mrc as #2, grid size 340,340,340, pixel 0.84,
shown at level 0.0448, step 2, values float32  

> volume #2 level 0.07421

> volume #2 level 0.07127

> select #2

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.13784,-0.29917,0.94419,61.545,-0.21815,0.93905,0.2657,-0.5717,-0.96613,-0.16935,-0.19471,343.92

> view matrix models
> #2,0.10084,-0.27627,0.95577,22.428,-0.53756,0.79324,0.28601,62.771,-0.83718,-0.54262,-0.068522,359.61

> view matrix models
> #2,-0.025114,-0.34278,0.93908,52.452,-0.56388,0.78053,0.26983,70.807,-0.82547,-0.52275,-0.21289,377.07

> view matrix models
> #2,-0.15649,-0.090314,0.98354,28.396,-0.58309,0.8122,-0.018196,112.85,-0.79719,-0.57634,-0.17977,375.65

> view matrix models
> #2,-0.1571,-0.076365,0.98463,26.326,-0.52481,0.85104,-0.017734,98.913,-0.8366,-0.51953,-0.17378,372.25

> view matrix models
> #2,-0.081456,-0.056445,0.99508,11.089,-0.54123,0.84087,0.0033932,99.496,-0.83692,-0.53829,-0.099044,363.6

> hide #!2 models

> open C:/Users/Julia/Documents/Uni/FtsH_stuff/cryo-
> EM/cryosparc_P4_J562_008_zflipped.mrc

Opened cryosparc_P4_J562_008_zflipped.mrc as #3, grid size 340,340,340, pixel
0.84, shown at level 0.0652, step 2, values float32  

> show #!2 models

> view matrix models
> #2,0.002752,-0.021068,0.99977,-6.7027,-0.54066,0.84102,0.019211,96.984,-0.84124,-0.54059,-0.0090763,350.86

> view matrix models
> #2,0.19353,0.20561,0.95931,-60.158,-0.31143,0.9401,-0.13867,74.124,-0.93036,-0.27192,0.24597,286.41

> view matrix models
> #2,0.077626,0.20674,0.97531,-46.203,-0.21033,0.95964,-0.18668,64.202,-0.97454,-0.19065,0.11798,300.59

> view matrix models
> #2,0.065125,0.069476,0.99546,-27.882,-0.20846,0.97651,-0.054516,41.417,-0.97586,-0.20396,0.078078,308.75

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.065125,0.069476,0.99546,-24.469,-0.20846,0.97651,-0.054516,36.196,-0.97586,-0.20396,0.078078,301.21

> view matrix models
> #2,0.065125,0.069476,0.99546,-19.148,-0.20846,0.97651,-0.054516,42.316,-0.97586,-0.20396,0.078078,301.96

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.025405,0.053256,0.99826,-11.586,-0.32594,0.94445,-0.042091,61.78,-0.94505,-0.3243,0.041352,320.33

> view matrix models
> #2,0.048031,0.0077156,0.99882,-8.3991,-0.32359,0.94616,0.0082517,53.54,-0.94498,-0.3236,0.047942,319.22

> view matrix models
> #2,0.054413,-0.0051898,0.99851,-7.4202,-0.32271,0.94623,0.022504,51.237,-0.94493,-0.32346,0.049812,318.91

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.054413,-0.0051898,0.99851,-7.263,-0.32271,0.94623,0.022504,49.805,-0.94493,-0.32346,0.049812,316

> view matrix models
> #2,0.054413,-0.0051898,0.99851,-7.278,-0.32271,0.94623,0.022504,51.905,-0.94493,-0.32346,0.049812,316.24

> view matrix models
> #2,0.054413,-0.0051898,0.99851,-7.259,-0.32271,0.94623,0.022504,52.015,-0.94493,-0.32346,0.049812,316.1

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.055773,-0.0086902,0.99841,-6.9383,-0.29444,0.95535,0.024764,46.332,-0.95404,-0.29535,0.050724,313.25

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.055773,-0.0086902,0.99841,-4.8721,-0.29444,0.95535,0.024764,46.064,-0.95404,-0.29535,0.050724,312.79

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.056606,-0.0041962,0.99839,-5.6301,-0.35558,0.93434,0.024087,57.898,-0.93293,-0.35637,0.051397,318.39

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.056606,-0.0041962,0.99839,-5.6463,-0.35558,0.93434,0.024087,57.221,-0.93293,-0.35637,0.051397,319.03

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.056466,-0.0056507,0.99839,-5.4187,-0.27776,0.96042,0.021145,42.832,-0.95899,-0.2785,0.052661,311.44

> ~select #2

Nothing selected  

> volume align #2,3

Expected a density maps specifier or a keyword  

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 3 maps.  

> select #2

2 models selected  

> select #3

2 models selected  

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 3 maps.  

> hide #!1 models

> fitmap #3 inMap #2

Fit map cryosparc_P4_J562_008_zflipped.mrc in map protease-ring_C6_flipped.mrc
using 49105 points  
correlation = 0.8184, correlation about mean = 0.5759, overlap = 325.7  
steps = 68, shift = 0.964, angle = 1.18 degrees  
  
Position of cryosparc_P4_J562_008_zflipped.mrc (#3) relative to protease-
ring_C6_flipped.mrc (#2) coordinates:  
Matrix rotation and translation  
0.04977736 -0.28199089 -0.95812491 312.88966884  
-0.02434838 0.95868641 -0.28342111 49.86148426  
0.99846350 0.03743674 0.04085486 -11.98912839  
Axis 0.16047773 -0.97859179 0.12886044  
Axis point 166.80327725 0.00000000 161.15834159  
Rotation angle (degrees) 88.58698198  
Shift along axis -0.12714016  
  

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> open C:/Users/Julia/Documents/Uni/FtsH_stuff/cryo-EM/C6-protease-
> structure_FtsHE255Q-ATP.pdb

Chain information for C6-protease-structure_FtsHE255Q-ATP.pdb #4  
---  
Chain | Description  
A C E | No description available  
B D F | No description available  
  

> show cartoons

> hide atoms

> select ::name="HG"::name="HOH"

50 atoms, 50 residues, 1 model selected  

> show sel atoms

> select ::name="HOH"

44 atoms, 44 residues, 1 model selected  

> delete sel

> select #4

15170 atoms, 15275 bonds, 12 pseudobonds, 1041 residues, 2 models selected  

> view matrix models
> #4,0.76024,-0.50774,0.40526,38.083,-0.11518,0.50858,0.85327,-57.783,-0.63935,-0.69537,0.32816,304

> view matrix models
> #4,-0.10278,-0.16927,0.9802,15.772,-0.24595,0.95914,0.13984,17.281,-0.96382,-0.22671,-0.14021,362.69

> view matrix models
> #4,0.083387,0.12332,0.98886,-53.98,-0.32865,0.9402,-0.089538,70.572,-0.94076,-0.31752,0.11893,328.53

> view matrix models
> #4,0.0034368,-0.011277,0.99993,-25.251,-0.34048,0.94018,0.011774,55.132,-0.94025,-0.3405,-0.00060845,351.94

> view matrix models
> #4,0.044712,0.033168,0.99845,-37.228,-0.49884,0.86667,-0.0064514,91.295,-0.86554,-0.49778,0.055296,354.25

> ui mousemode right "move picked models"

> view matrix models
> #4,0.044712,0.033168,0.99845,-14.637,-0.49884,0.86667,-0.0064514,77.192,-0.86554,-0.49778,0.055296,341.21

> view matrix models
> #4,0.044712,0.033168,0.99845,-19.539,-0.49884,0.86667,-0.0064514,88.329,-0.86554,-0.49778,0.055296,329.01

> view matrix models
> #4,0.044712,0.033168,0.99845,-11.3,-0.49884,0.86667,-0.0064514,85.051,-0.86554,-0.49778,0.055296,324.79

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.12301,0.044229,0.99142,-22.863,-0.33931,0.94067,0.00013362,50.618,-0.9326,-0.33642,0.13072,298.6

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.12301,0.044229,0.99142,-19.922,-0.33931,0.94067,0.00013362,58.323,-0.9326,-0.33642,0.13072,301.76

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.034917,-0.020133,0.99919,0.51367,-0.31886,0.94732,0.030231,49.367,-0.94716,-0.31966,0.026658,319.05

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.034917,-0.020133,0.99919,0.57195,-0.31886,0.94732,0.030231,49.52,-0.94716,-0.31966,0.026658,318.97

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.046768,-0.024201,0.99861,-0.44229,-0.28329,0.95834,0.036492,41.813,-0.95789,-0.28461,0.037964,313.59

> view matrix models
> #4,0.036528,0.0048548,0.99932,-3.2433,-0.2785,0.96042,0.0055141,46.07,-0.95974,-0.27851,0.036434,313.24

> view matrix models
> #4,0.030473,-0.020592,0.99932,1.2487,-0.27876,0.95994,0.028281,42.327,-0.95988,-0.27944,0.023512,315.58

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.030473,-0.020592,0.99932,1.2129,-0.27876,0.95994,0.028281,41.904,-0.95988,-0.27944,0.023512,315.18

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.040268,-0.013808,0.99909,-1.1136,-0.28209,0.95907,0.024624,43.121,-0.95854,-0.28282,0.034725,313.58

> hide #!1 models

> fitmap #4 inMap #2

Fit molecule C6-protease-structure_FtsHE255Q-ATP.pdb (#4) to map protease-
ring_C6_flipped.mrc (#2) using 15170 atoms  
average map value = 0.1143, steps = 68  
shifted from previous position = 1.75  
rotated from previous position = 1.03 degrees  
atoms outside contour = 4216, contour level = 0.071267  
  
Position of C6-protease-structure_FtsHE255Q-ATP.pdb (#4) relative to protease-
ring_C6_flipped.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999985 -0.00033555 0.00044301 0.00733999  
0.00033514 0.99999952 0.00091993 -0.19353761  
-0.00044332 -0.00091978 0.99999948 0.18817092  
Axis -0.85591468 0.41236265 0.31203703  
Axis point 0.00000000 213.75734301 198.22472552  
Rotation angle (degrees) 0.06157582  
Shift along axis -0.02737379  
  

> transparency #2.1 50

> show #!1 models

> set bgColor white

> ~select #4

Nothing selected  

> open C:/Users/Julia/Phenix/RealSpaceRefine_57/FtsH-fit_to_YME1_ATPase-
> only_real_space_refined_052-coot-3_real_space_refined_057.pdb

Chain information for FtsH-fit_to_YME1_ATPase-
only_real_space_refined_052-coot-3_real_space_refined_057.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> show cartoons

> hide atoms

> select ::name="ADP"::name="ATP"::name="HG"

216 atoms, 220 bonds, 11 residues, 2 models selected  

> show sel atoms

> volume #1 level 0.06297

> transparency #1.1#2.1 0

> transparency #1.1#2.1 50

> select #5

20320 atoms, 20494 bonds, 8 pseudobonds, 1467 residues, 2 models selected  

> select #4

15170 atoms, 15275 bonds, 12 pseudobonds, 1041 residues, 2 models selected  

> select #5

20320 atoms, 20494 bonds, 8 pseudobonds, 1467 residues, 2 models selected  

> ~select #5

Nothing selected  

> volume #1 level 0.03784

> open C:/Users/Julia/Documents/Uni/FtsH_stuff/cryo-
> EM/cryosparc_P4_J375_017_ATPase_zflip_deepemhancer.mrc

Opened cryosparc_P4_J375_017_ATPase_zflip_deepemhancer.mrc as #6, grid size
340,340,340, pixel 0.84, shown at level -0.00175, step 2, values float32  

> volume #6 level 0.0151

> hide #!1 models

> volume #6 level 0.05303

> transparency #2.1#6.1 0

> transparency #2.1#6.1 50

> open C:/Users/Julia/Documents/Uni/FtsH_stuff/cryo-
> EM/cryosparc_P4_J375_017_ATPase_zflip.mrc

Opened cryosparc_P4_J375_017_ATPase_zflip.mrc as #7, grid size 340,340,340,
pixel 0.84, shown at level 0.0275, step 2, values float32  

> hide #!6 models

> volume #7 level 0.05242

[Repeated 1 time(s)]

> transparency #2.1#7.1 0

> transparency #2.1#7.1 50

> open C:/Users/Julia/Documents/Uni/FtsH_stuff/cryo-EM/FtsH-
> fit_to_YME1_ATPase-only_real_space_refined_052-coot-4.pdb

Chain information for FtsH-fit_to_YME1_ATPase-
only_real_space_refined_052-coot-4.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> show cartoons

> hide atoms

> select ::name="ADP"::name="ATP"::name="HG"

426 atoms, 440 bonds, 16 residues, 3 models selected  

> show sel atoms

> select #8

20320 atoms, 20494 bonds, 8 pseudobonds, 1467 residues, 2 models selected  

> ~select #8

Nothing selected  

> hide #!5 models

> spin

Unknown command: spin  

> roll

> stop

> roll

> stop

> yroll

Unknown command: yroll  

> roll y

> roll x

> stop

> roll x

> roll x hald

Expected a number or a keyword  

> roll x half

Expected a number or a keyword  

> stop

> roll x 180

> stop

> roll x 180

> stop

> roll x 2

> stop

> roll x 1

> stop

> roll x 0.5

> stop

> roll z

> stop

> rock 1/2

Expected an axis vector or a keyword  

> rock x 1/2

Expected a number or a keyword  

> rock x 0.5

> rock

> rock x

> stop

> rock x

> stop

> wobble

> stop

> turn x

[Repeated 4 time(s)]

> turn x 190

> turn x 180

> save C:/Users/Julia/Documents/Uni/FtsH_stuff/cryo-EM/ATPase-Protease_with-
> model-built-in.cxs

——— End of log from Wed Feb 15 21:28:11 2023 ———

opened ChimeraX session  

> open C:/Users/Julia/Documents/Uni/FtsH_stuff/cryo-EM/ALA-
> coot-0_centralpore_substrate.pdb format pdb

Chain information for ALA-coot-0_centralpore_substrate.pdb #9  
---  
Chain | Description  
A | No description available  
  

> close #9

> open C:/Users/Julia/Documents/Uni/FtsH_stuff/cryo-EM/ALA-
> coot-0_centralpore_substrate.pdb

Chain information for ALA-coot-0_centralpore_substrate.pdb #9  
---  
Chain | Description  
A | No description available  
  

> volume #7 level 0.0577

> select #8:228

120 atoms, 120 bonds, 6 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 120 atom styles  

> ui mousemode right select

> select #9/A:-5@CA

1 atom, 1 residue, 1 model selected  

> select up

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

45 atoms, 44 bonds, 9 residues, 1 model selected  

> ui mousemode right "translate selected atoms"

> ui mousemode right select

> select #7

2 models selected  

> save C:/Users/Julia/Documents/Uni/FtsH_stuff/cryo-EM/ATPase-Protease_with-
> model-built-in.cxs

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> hide #!4 models

> hide #!7 models

> hide #!8 models

> hide #9 models

> ui mousemode right clip

> ui tool show "Side View"

> color #3 #5555ff models transparency 0

> color #3 #aaaaff models transparency 0

> color #3 #00aaff models transparency 0

> color #3 #aaaaff models transparency 0

> color #3 #9797e2 models transparency 0

> lighting full

> color #3 #9c9cea models transparency 0

> color #3 #a5a5f8 models transparency 0

> ui mousemode right "map eraser"

> volume erase #3 center 87.797,136.88,138.55 radius 30.9

Opened cryosparc_P4_J562_008_zflipped.mrc copy as #11, grid size 340,340,340,
pixel 0.84, shown at step 1, values float32  

> volume erase #11 center 82.769,132.18,159.22 radius 30.845

> volume erase #11 center 82.828,139.54,162.28 radius 30.845

> volume erase #11 center 81.311,116.99,155.51 radius 30.845

> close #10

[Repeated 1 time(s)]

> ui mousemode right translate

> ui mousemode right clip

> lighting full

> lighting shadows false

> lighting shadows true

> graphics silhouettes true

> lighting shadows false

> lighting shadows true

> graphics silhouettes false

> graphics silhouettes true

> ui tool show "Color Actions"

> lighting simple

> lighting full

> save C:\Users\Julia\Desktop\image31.png supersample 3

> open C:/Users/Julia/Downloads/cryosparc_P4_J562_008_volume_map_sharp.mrc

Opened cryosparc_P4_J562_008_volume_map_sharp.mrc as #10, grid size
340,340,340, pixel 0.84, shown at level 0.0704, step 2, values float32  

> hide #!11 models

> surface dust #10 size 8.4

> volume #10 level 0.07575

> close #12

> color #10 #aaaaff models transparency 0

> color #10 #9999e5 models transparency 0

> hide #!10 models

> show #9 models

> show #!8 models

> show #!4 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!2 models

> show #!7 models

> hide #!7 models

> show #!6 models

> ui mousemode right translate

> show #!5 models

> hide #!5 models

> show #!7 models

> hide #!6 models

> select #8:228

120 atoms, 120 bonds, 6 residues, 1 model selected  

> select clear

> color #4 white transparency 0

> color #4 #b2ffb2 transparency 0

> color #4 #c30052 transparency 0

> color #4 #e0e08c transparency 0

> color #7 #cce4f7 models transparency 0

> color #7 #b2ffb2 models transparency 0

> color #7 white models transparency 0

> color #7 #b2ffb2 models transparency 0

> color #7 #fdfdfd models transparency 0

> color #7 #b2ffb2 models transparency 0

> color #7 #55aa7f models transparency 0

[Repeated 1 time(s)]

> color #7 #00aa7f models transparency 0

> color #7 #00cc96 models transparency 0

> color #7 #46cca4 models transparency 0

> color #7 #4ddfb3 models transparency 0

> transparency #2.1#7.1 0

> transparency #2.1#7.1 50

> transparency #2,4,7-9 70

> hide #!2 models

> hide #!4 models

> show #!2 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!7 models

> hide #!8 models

> hide #9 models

> select Zn

Nothing selected  

> ui mousemode right select

> select #4/D:2001@HG

1 atom, 1 residue, 1 model selected  

> select ::name="HG"

6 atoms, 6 residues, 1 model selected  

> color sel medium blue

> select clear

> ui mousemode right translate

> save C:\Users\Julia\Desktop\image32.png supersample 3

> show #!7 models

> show #!8 models

> hide #!7 models

> hide #!2 models

> show #!7 models

> hide #!8 models

> show #!8 models

> hide #!4 models

> select #8:228

120 atoms, 120 bonds, 6 residues, 1 model selected  

> hide sel atoms

> select clear

> show #9 models

> save C:\Users\Julia\Desktop\image33.png supersample 3

> select #8:228

120 atoms, 120 bonds, 6 residues, 1 model selected  

> show sel atoms

> view selected

Expected an objects specifier or a view name or a keyword  

> view sel

> volume #7 level 0.07054

> color sel byhetero

> color sel byelement

> undo

> ui tool show "Color Actions"

> color sel byelement

> color sel byhetero

> undo

[Repeated 1 time(s)]

> color sel byelement

> undo

> color sel lime

> undo

> color sel light sea green

> undo

> color sel purple

> undo

> color sel hot pink

> undo

> color sel byelement

> graphics silhouettes false

> graphics silhouettes true

> select clear

> lighting shadows false

> lighting soft

> hide #!7 models

> show #!7 models

> transparency #7-9 80

> select #7

4 models selected  

> graphics silhouettes false

> graphics silhouettes true

> ~select #7

Nothing selected  

> ui mousemode right select

> select #9/A:-1@C

1 atom, 1 residue, 1 model selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select #9/A:3@O

1 atom, 1 residue, 1 model selected  

> select #9/A

45 atoms, 44 bonds, 9 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #9,1,0,0,0.3442,0,1,0,-0.19713,0,0,1,0.07561

> ~select #9

Nothing selected  

> save C:\Users\Julia\Desktop\image34.png supersample 3

> select ::name="ATP"

344 atoms, 360 bonds, 8 residues, 2 models selected  

> view sel

> view matrix models
> #5,1,0,0,-1.2681,0,1,0,-11.735,0,0,1,-10.128,#8,1,0,0,-1.2681,0,1,0,-11.735,0,0,1,-10.128

> undo

> ui mousemode right translate

> lighting full

> lighting simple

> volume #7 level 0.07373

> save C:\Users\Julia\Desktop\image35.png supersample 3

> select #5

20320 atoms, 20494 bonds, 8 pseudobonds, 1467 residues, 2 models selected  

> ~select #5

Nothing selected  

> select #5

20320 atoms, 20494 bonds, 8 pseudobonds, 1467 residues, 2 models selected  

> save C:\Users\Julia\Desktop\image36.png supersample 3

> select ::name="ADP"

76 atoms, 80 bonds, 2 residues, 2 models selected  

> view sel

> select #5

20320 atoms, 20494 bonds, 8 pseudobonds, 1467 residues, 2 models selected  

> save C:\Users\Julia\Desktop\image37.png supersample 3

> volume #7 level 0.05699

> ui mousemode right select

> select #8/B:221

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

> select add #8/B:222

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

> select add #8/B:223

30 atoms, 27 bonds, 3 residues, 1 model selected  

> select add #8/B:224

50 atoms, 47 bonds, 4 residues, 1 model selected  

> select add #8/B:225

66 atoms, 62 bonds, 5 residues, 1 model selected  

> hide sel cartoons

> select clear

> ui mousemode right translate

> save C:\Users\Julia\Desktop\image38.png supersample 3

> view

> hide #!7 models

> hide #9 models

> hide #!8 atoms

> style #!8 stick

Changed 20320 atom styles  

> lighting full

> save C:\Users\Julia\Desktop\image39.png supersample 3

> show #!4 models

> hide #!8 models

> show #!8 models

> select #4

15170 atoms, 15275 bonds, 12 pseudobonds, 1041 residues, 2 models selected  

> ~select #4

Nothing selected  

> graphics silhouettes false

> graphics silhouettes true

> color #8 #005500 transparency 0

> undo

> color #8 #55aa7f transparency 0

> color #8 #458a66 transparency 0

> save C:\Users\Julia\Desktop\image40.png supersample 3

> undo

[Repeated 1 time(s)]

> color #8 #aa007f transparency 0

> save C:\Users\Julia\Desktop\image41.png supersample 3

> undo

> show #9 models

> show #!7 models

> select down

Nothing selected  

> select #8:228

120 atoms, 120 bonds, 6 residues, 1 model selected  

> show sel atoms

> select #8

20320 atoms, 20494 bonds, 8 pseudobonds, 1467 residues, 2 models selected  

> select #8:228

120 atoms, 120 bonds, 6 residues, 1 model selected  

> show sel

> view sel

> select #9

45 atoms, 44 bonds, 9 residues, 1 model selected  

> view sel

> spin x

Unknown command: spin x  

> roll x

> stop

> roll y

> stop

> roll y center #9

> stop

> ~select #9

Nothing selected  

> undo

> ~select #9

Nothing selected  

> save C:\Users\Julia\Desktop\image43.png supersample 3

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\Julia\Desktop\movie4.mp4

Movie saved to \C:Users\\...\Desktop\movie4.mp4  
  

> lighting soft

> save C:\Users\Julia\Desktop\image43.png supersample 3

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\Julia\Desktop\movie4.mp4

Movie saved to \C:Users\\...\Desktop\movie4.mp4  
  

> movie record

> turn y 2 180 center #9

> movie encode

Movie saved to C:\Users\Julia/Desktop/movie.mp4  
  

> select #8:228

120 atoms, 120 bonds, 6 residues, 1 model selected  

> hide sel atoms

> hide #!4 models

> hide #!8 models

> show #!8 models

> select ::name="ADP"

76 atoms, 80 bonds, 2 residues, 2 models selected  

> show sel & #!8 atoms

> select ::name="ATP"

344 atoms, 360 bonds, 8 residues, 2 models selected  

> show sel & #!8 atoms

> select #5

20320 atoms, 20494 bonds, 8 pseudobonds, 1467 residues, 2 models selected  

> ~select #5

Nothing selected  

> select ::name="ATP"

344 atoms, 360 bonds, 8 residues, 2 models selected  

> volume zone #7 nearAtoms sel & #8 range 5.04

> volume #7 level 0.09444

> volume #7 level 0.06974

> volume #7 level 0.1263

> volume #7 level 0.09524

> volume #7 level 0.09604

> hide #!7 models

> show #!7 models

> volume #!7 region all imageMode "full region"

> volume unzone #!7

> mousemode rightMode "crop volume"

> volume #7 region 30,0,0,339,339,339

> ui mousemode right select

Drag select of 7 cryosparc_P4_J375_017_ATPase_zflip.mrc , 43 atoms, 33
residues, 45 bonds  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  
Drag select of 7 cryosparc_P4_J375_017_ATPase_zflip.mrc , 37 atoms, 14
residues, 41 bonds  

> select ::name="ATP"

344 atoms, 360 bonds, 8 residues, 2 models selected  

> ui mousemode right "translate selected atoms"

> ui mousemode right "select fragment"

> ui mousemode right select

> select #8/D:501@PG

1 atom, 1 residue, 1 model selected  

> select #8/D:501@O1G

1 atom, 1 residue, 1 model selected  

> select add #8/D:501@O2G

1 atom, 3 bonds, 1 residue, 1 model selected  

> select add #8/D:501@O1G

2 atoms, 3 bonds, 1 residue, 1 model selected  

> select add #8/D:501@O3G

3 atoms, 3 bonds, 1 residue, 1 model selected  

> select add #8/D:501@O3B

4 atoms, 5 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected atoms"

> undo

> ui mousemode right select

> select add #8/D:501@PG

5 atoms, 5 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected atoms"

> undo

> volume #7 level 0.08262

> undo

[Repeated 8 time(s)]

> ui mousemode right "bond rotation"

> torsion #8/D:501@O1B,PB,O3A,PA 125.04

> torsion #8/D:501@O1B,PB,O3A,PA 33.04

> torsion #8/D:501@O1G,PG,O3B,PB -128.92

> torsion #8/D:501@O1G,PG,O3B,PB -162.92

> torsion #8/D:501@PG,O3B,PB,O1B 120.10

> torsion #8/D:501@O1B,PB,O3A,PA 19.04

> torsion #8/D:501@O1B,PB,O3A,PA -38.96

> ui mousemode right select

> select #7

4 models selected  

> ui mousemode right translate

> ~select #7

Nothing selected  

> select #7

4 models selected  

> ~select #7

Nothing selected  

> volume #7 level 0.06132

> select ::name="ATP"

344 atoms, 360 bonds, 8 residues, 2 models selected  

> ui mousemode right "select fragment"

> ui mousemode right "select similar fragments"

> ui mousemode right "select fragment"

> save C:/Users/Julia/Documents/Uni/FtsH_stuff/cryo-EM/ATPase-Protease_with-
> model-built-in.cxs

> select ::name="ATP"

344 atoms, 360 bonds, 8 residues, 2 models selected  

> select add ::name="ADP"

420 atoms, 440 bonds, 10 residues, 2 models selected  

> volume zone #7 nearAtoms sel & #8 range 5.04

[Repeated 1 time(s)]

> volume #!7 region all imageMode "full region"

> volume unzone #!7

> mousemode rightMode "crop volume"

> volume zone #7 nearAtoms sel & #8 range 5.04

> vop gaussian #7 sdev 2.52

Opened cryosparc_P4_J375_017_ATPase_zflip.mrc gaussian as #12, grid size
340,340,340, pixel 0.84, shown at step 1, values float32  

> hide #!12 models

> show #!7 models

> volume #7 region 3,0,0,339,339,339

[Repeated 1 time(s)]

> open 6az0

Summary of feedback from opening 6az0 fetched from pdb  
---  
notes | Fetching compressed mmCIF 6az0 from http://files.rcsb.org/download/6az0.cif  
Fetching CCD ATP from http://ligand-expo.rcsb.org/reports/A/ATP/ATP.cif  
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif  
  
6az0 title:  
Mitochondrial ATPase Protease YME1 [more info...]  
  
Chain information for 6az0  
---  
Chain | Description | UniProt  
13.1/A 13.2/A 13.3/A 13.4/A 13.5/A 13.1/B 13.2/B 13.3/B 13.4/B 13.5/B 13.1/C 13.2/C 13.3/C 13.4/C 13.5/C 13.1/D 13.2/D 13.3/D 13.4/D 13.5/D 13.1/E 13.2/E 13.3/E 13.4/E 13.5/E 13.1/F 13.2/F 13.3/F 13.4/F 13.5/F | Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1 | B3LL85_YEAS1  
13.1/G 13.2/G 13.3/G 13.4/G 13.5/G | poly(UNK) |   
  

> hide #!7 models

> hide #!8 models

> hide #9 models

> view sel

> view

> show #!13.1-5 cartoons

> hide #!13.1-5 atoms

> show #!13.1-5 atoms

> hide #!13.1-5 cartoons

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting soft

> graphics silhouettes true

> select #13

102310 atoms, 103805 bonds, 155 pseudobonds, 13295 residues, 11 models
selected  

> show sel surfaces

> lighting flat

> lighting soft

> lighting simple

> lighting full

> lighting soft

> select #13

102310 atoms, 103805 bonds, 155 pseudobonds, 13295 residues, 41 models
selected  

> ~select #13

35 models selected  

> show #!13.1-5 cartoons

> hide #!13.1-5 surfaces

> hide #!13.1-5 atoms

> hide #!13.2 models

> hide #!13.3 models

> hide #!13.4 models

> hide #!13.5 models

> show #!13.1 surfaces

> save C:\Users\Julia\Desktop\image44.png supersample 3

> hide #!13 models

> show #!8 models

> show #!8 surfaces

> hide #!8 atoms

> show #!4 models

> show #!4,8 surfaces

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> close #13

> hide #!4 models

> hide #!8 models

> show #!1 models

> close #1

> show #!2 models

> hide #!2 models

> show #!2 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> show #!4 models

> show #!5 models

> hide #!5 models

> show #!8 models

> show #!5 models

> hide #!8 models

> show #!7 models

> volume #!7 region all imageMode "full region"

> volume unzone #!7

> mousemode rightMode "crop volume"

> show #!8 models

> hide #!4-5,8 surfaces

> select ::name="ADP"

76 atoms, 80 bonds, 2 residues, 2 models selected  

> show sel atoms

> select ::name="ATP"

344 atoms, 360 bonds, 8 residues, 2 models selected  

> show sel atoms

> hide #!5 models

> close #5

> show #!6 models

> hide #!6 models

> close #6

> close #3

> show #!10 models

> close #10

> show #!11 models

> volume #11 level 0.07178

> show #!12 models

> close #12

> close #11

> show #!2 models

> save C:/Users/Julia/Documents/Uni/FtsH_stuff/cryo-EM/ATP-bound-
> FtsH_map_with_structure.cxs

——— End of log from Tue Feb 28 10:55:03 2023 ———

opened ChimeraX session  

> ui tool show Segmentations

> ui view fourup

> segmentations mouseModes false

Mouse bindings not saved; ignoring 'mouseModes false'  

> ui view fourup

> segmentations create #2

Opened segmentation 1 of protease-ring_C6_flipped.mrc as #6, grid size
340,340,340, pixel 0.84, shown at level 0.501, step 1, values float64  

> segmentations mouseModes false

Mouse bindings not saved; ignoring 'mouseModes false'  

> ui tool show "Segment Map"

> volume #2 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 142.8 tiltedSlabSpacing 0.84 tiltedSlabPlaneCount 10

> mousemode rightMode "rotate slab"

> volume #7 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 142.8 tiltedSlabSpacing 0.84 tiltedSlabPlaneCount 10

> mousemode rightMode "rotate slab"

> volume #6 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 142.8 tiltedSlabSpacing 0.84 tiltedSlabPlaneCount 10

> mousemode rightMode "rotate slab"

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1327, in
_surfaceChosen  
v = copy_volume_for_auxiliary_display(self.model_menu.value)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\segmentation.py", line 115, in
copy_volume_for_auxiliary_display  
volume.data, volume.session, style=None, show_dialog=False, open_model=False  
^^^^^^^^^^^  
AttributeError: 'ClipCap' object has no attribute 'data'  
  
AttributeError: 'ClipCap' object has no attribute 'data'  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\segmentation.py", line 115, in
copy_volume_for_auxiliary_display  
volume.data, volume.session, style=None, show_dialog=False, open_model=False  
^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> view

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1318, in
_surfaceChosen  
v.delete()  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\volume.py", line 1912, in delete  
Image3d.delete(self)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\image3d.py", line 752, in delete  
b.remove_image(self)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\image3d.py", line 1517, in remove_image  
del dbi[image_render]  
~~~^^^^^^^^^^^^^^  
KeyError: <chimerax.map.volume.VolumeImage object at 0x000001A4E99D3710>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\image3d.py", line 1517, in remove_image  
del dbi[image_render]  
~~~^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 546.80
OpenGL renderer: NVIDIA GeForce RTX 3050 Ti Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: de_DE.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: HP
Model: HP Pavilion Gaming Laptop 15-dk2xxx
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 16,913,522,688
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i7-11370H @ 3.30GHz
OSLanguage: de-DE

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    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
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.1
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
    WMI: 1.5.1