'ArrayGridData' object has no attribute 'dicom_data'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.3.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

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

> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/EMPEMcomposition.cxs

Opened 101F_SiteIV_purple.mrc as #1, grid size 208,208,208, pixel 2, shown at
level 0.15, step 1, values float32  
Opened A14_V_Orange.mrc as #2, grid size 208,208,208, pixel 2, shown at level
0.15, step 1, values float32  
Opened ADI-14442_SiteV-II_orange-yellow.mrc as #3, grid size 208,208,208,
pixel 2, shown at level 0.15, step 1, values float32  
Opened D25_Site0_red.mrc as #4, grid size 208,208,208, pixel 2, shown at level
0.15, step 1, values float32  
Opened Motavizumab_SiteII_yellow.mrc as #5, grid size 208,208,208, pixel 2,
shown at level 0.15, step 1, values float32  
Opened MPE8_SiteIII_green.mrc as #6, grid size 208,208,208, pixel 2, shown at
level 0.15, step 1, values float32  
Opened preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc as #8, grid size 208,208,208,
pixel 2, shown at level 0.15, step 1, values float32  
Opened RSB1_SiteV_orange.mrc as #9, grid size 208,208,208, pixel 2, shown at
level 0.15, step 1, values float32  
Opened Medi8897_Site0_red.mrc as #10, grid size 208,208,208, pixel 2, shown at
level 0.03, step 1, values float32  
Opened RSV monomer.mrc as #11, grid size 208,208,208, pixel 2, shown at level
0.026, step 1, values float32  
Log from Mon Jun 16 08:40:41 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/EMPEMcomposition.cxs

Opened 101F_SiteIV_purple.mrc as #1, grid size 208,208,208, pixel 2, shown at
level 0.15, step 1, values float32  
Opened A14_V_Orange.mrc as #2, grid size 208,208,208, pixel 2, shown at level
0.15, step 1, values float32  
Opened ADI-14442_SiteV-II_orange-yellow.mrc as #3, grid size 208,208,208,
pixel 2, shown at level 0.15, step 1, values float32  
Opened D25_Site0_red.mrc as #4, grid size 208,208,208, pixel 2, shown at level
0.15, step 1, values float32  
Opened Motavizumab_SiteII_yellow.mrc as #5, grid size 208,208,208, pixel 2,
shown at level 0.15, step 1, values float32  
Opened MPE8_SiteIII_green.mrc as #6, grid size 208,208,208, pixel 2, shown at
level 0.15, step 1, values float32  
Opened preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc as #8, grid size 208,208,208,
pixel 2, shown at level 0.15, step 1, values float32  
Opened RSB1_SiteV_orange.mrc as #9, grid size 208,208,208, pixel 2, shown at
level 0.15, step 1, values float32  
Log from Thu May 8 15:20:48 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
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/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/101F_SiteIV_purple.mrc

Opened 101F_SiteIV_purple.mrc as #1, grid size 208,208,208, pixel 2, shown at
level 1.84e-05, step 1, values float32  

> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/A14_V_Orange.mrc

Opened A14_V_Orange.mrc as #2, grid size 208,208,208, pixel 2, shown at level
1.84e-05, step 1, values float32  

> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/ADI-14442_SiteV-II_orange-yellow.mrc

Opened ADI-14442_SiteV-II_orange-yellow.mrc as #3, grid size 208,208,208,
pixel 2, shown at level 1.83e-05, step 1, values float32  

> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/D25_Site0_red.mrc

Opened D25_Site0_red.mrc as #4, grid size 208,208,208, pixel 2, shown at level
1.84e-05, step 1, values float32  

> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/Motavizumab_SiteII_yellow.mrc

Opened Motavizumab_SiteII_yellow.mrc as #5, grid size 208,208,208, pixel 2,
shown at level 1.84e-05, step 1, values float32  

> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/MPE8_SiteIII_green.mrc

Opened MPE8_SiteIII_green.mrc as #6, grid size 208,208,208, pixel 2, shown at
level 1.84e-05, step 1, values float32  

> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/MPE8_SiteIII_purple.mrc

Opened MPE8_SiteIII_purple.mrc as #7, grid size 208,208,208, pixel 2, shown at
level 1.84e-05, step 1, values float32  

> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc

Opened preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc as #8, grid size 208,208,208,
pixel 2, shown at level 0.000161, step 1, values float32  

> open /Users/szhang3/Library/CloudStorage/OneDrive-
> Moderna/RSV/EMPEM/EMPEMcomposition/RSB1_SiteV_orange.mrc

Opened RSB1_SiteV_orange.mrc as #9, grid size 208,208,208, pixel 2, shown at
level 1.76e-05, step 1, values float32  

> lighting soft

> select clear

> volume all level 0.15

> select #8

2 models selected  

> color #8.1 gray

> set bgColor white

> color #8.1 light gray

> select #1

2 models selected  

> color #1.1 purple

> select #4

2 models selected  

> color #4.1 red

> select #3

2 models selected  

> ui tool show "Color Actions"

> color sel orange

No visible atoms or bonds selected  
[Repeated 13 time(s)]

> select #5

2 models selected  

> color #5.1 yellow

> select #2

2 models selected  

> color #2.1 orange

> select #9

2 models selected  

> color #9.1 orange

> select #3

2 models selected  

> ui tool show "Color Actions"

> color sel gold

> color sel sandy brown

> color sel dark orange

> color sel gold

> select #5

2 models selected  

> ui tool show "Color Actions"

> color sel gold

> color sel yellow

[Repeated 1 time(s)]

> select clear

> select #6

2 models selected  

> color #6.1 forest green

> select clear

> select #6

2 models selected  

> color #6.1 forest green

> ui tool show "Color Actions"

> color sel forest green

> color sel green

> color sel dodger blue

> color sel turquoise

> volume #7 color #5eaf88

> volume #7 color #00f900

> color sel forest green

[Repeated 1 time(s)]

> color #6.1 forest green

> close #7

> ui mousemode right zoom

> select clear

> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/front.png" width 936 height 671
> supersample 3 transparentBackground true

> hide #!4 models

> show #!4 models

> graphics silhouettes true

> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/TopView.png" width 936 height 671
> supersample 3 transparentBackground true

> hide #!3 models

> show #!3 models

> hide #!5 models

> hide #!6 models

> show #!6 models

> show #!5 models

> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/front.png" width 936 height 671
> supersample 3 transparentBackground true

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/SideView.png" width 936 height 671
> supersample 3 transparentBackground true

> hide #!9 models

> show #!9 models

> hide #!8 models

> show #!8 models

> hide #!6 models

> show #!6 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!5 models

> hide #!3 models

> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/front.png" width 936 height 671
> supersample 3 transparentBackground true

> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/SideView.png" width 936 height 671
> supersample 3 transparentBackground true

> hide #!4 models

> show #!4 models

> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/TopView.png" width 936 height 671
> supersample 3 transparentBackground true

> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/EMPEMcomposition.cxs" includeMaps true

——— End of log from Thu May 8 15:20:48 2025 ———

opened ChimeraX session  

> show #!2 models

> open /Users/szhang3/Downloads/5udc.pdb

5udc.pdb title:  
Crystal structure of RSV F A2 bound to MEDI8897 [more info...]  
  
Chain information for 5udc.pdb #7  
---  
Chain | Description | UniProt  
A D F | protein F | FUS_HRSVA 1-513  
B E H | MEDI8897 fab heavy chain |   
C G L | MEDI8897 fab light chain |   
  
Non-standard residues in 5udc.pdb #7  
---  
BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)  
CL — chloride ion  
MAN — α-D-mannopyranose (α-D-mannose; D-mannose; mannose)  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)  
  

> hide atoms

> hide cartoons

> show cartoons

> select add #7

20324 atoms, 20737 bonds, 6 pseudobonds, 2648 residues, 2 models selected  

> select subtract #7

Nothing selected  

> select add #7

20324 atoms, 20737 bonds, 6 pseudobonds, 2648 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.88918,0.059463,0.45368,10.939,0.43217,-0.43489,-0.79,43.97,0.15033,0.89852,-0.41239,-85.347

> ui mousemode right "translate selected models"

> view matrix models
> #7,0.88918,0.059463,0.45368,122.68,0.43217,-0.43489,-0.79,296.84,0.15033,0.89852,-0.41239,5.384

> view matrix models
> #7,0.88918,0.059463,0.45368,171.33,0.43217,-0.43489,-0.79,179.17,0.15033,0.89852,-0.41239,201.23

> view matrix models
> #7,0.88918,0.059463,0.45368,240.03,0.43217,-0.43489,-0.79,163.15,0.15033,0.89852,-0.41239,168.21

> ui tool show "Fit in Map"

> fitmap #7 inMap #8

Fit molecule 5udc.pdb (#7) to map preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8)
using 20324 atoms  
average map value = 0.1316, steps = 112  
shifted from previous position = 8.08  
rotated from previous position = 18.1 degrees  
atoms outside contour = 10579, contour level = 0.15  
  
Position of 5udc.pdb (#7) relative to preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc
(#8) coordinates:  
Matrix rotation and translation  
0.82604493 0.02497455 0.56305066 249.73640605  
0.55945921 -0.15727372 -0.81379996 158.97442632  
0.06822879 0.98723920 -0.14388740 179.75571678  
Axis 0.92705817 0.25470221 0.27511804  
Axis point 0.00000000 6.52392129 85.45899564  
Rotation angle (degrees) 103.74246189  
Shift along axis 321.46535400  
  

> select clear

> hide #!9 models

> hide #!8 models

> hide #!1 models

> hide #!2 models

> hide #!4 models

> hide #!6 models

> hide #!5 models

Drag select of 470 residues  

> select up

4639 atoms, 4727 bonds, 603 residues, 1 model selected  

> select up

10429 atoms, 10603 bonds, 1345 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> show #!8 models

> show #!4 models

Drag select of 72 residues  

> select up

773 atoms, 780 bonds, 106 residues, 1 model selected  

> select up

1618 atoms, 1659 bonds, 217 residues, 1 model selected  

> select add /L:126

1627 atoms, 1667 bonds, 218 residues, 1 model selected  
Drag select of 110 residues  

> select up

3121 atoms, 3182 bonds, 416 residues, 1 model selected  

> select up

6517 atoms, 6670 bonds, 861 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide #!4 models

Drag select of 287 residues, 1 pseudobonds  

> select up

2458 atoms, 2510 bonds, 1 pseudobond, 326 residues, 2 models selected  

> select up

3249 atoms, 3326 bonds, 1 pseudobond, 429 residues, 2 models selected  

> select up

3378 atoms, 3463 bonds, 1 pseudobond, 442 residues, 2 models selected  

> select up

3378 atoms, 3463 bonds, 1 pseudobond, 442 residues, 2 models selected  

> vop gaussian #7 sd 3

> molmap #7 20 onGrid #8

Opened 5udc.pdb map 20 as #10, grid size 208,208,208, pixel 2, shown at level
0.0257, step 1, values float32  

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> select #10

2 models selected  

> select clear

Drag select of 10 5udc.pdb map 20  

> select clear

> select #10

2 models selected  

> select clear

> hide #!10 models

> select add #7

3378 atoms, 3463 bonds, 1 pseudobond, 442 residues, 2 models selected  

> show sel atoms

Drag select of 76 atoms, 84 bonds  

> select up

82 atoms, 87 bonds, 8 residues, 1 model selected  

> select up

88 atoms, 94 bonds, 8 residues, 1 model selected  

> select up

127 atoms, 137 bonds, 11 residues, 1 model selected  

> select up

3378 atoms, 3463 bonds, 442 residues, 1 model selected  

> select down

127 atoms, 137 bonds, 11 residues, 1 model selected  

> hide #!8 models

> select clear

Drag select of 1 atoms  
Drag select of 6 atoms, 6 bonds  
Drag select of 1 atoms  

> select up

12 atoms, 7 bonds, 5 residues, 1 model selected  

> select up

38 atoms, 37 bonds, 5 residues, 1 model selected  

> select up

129 atoms, 137 bonds, 13 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> show #!8 models

> hide atoms

> show cartoons

> molmap #7 20 onGrid #8

Opened 5udc.pdb map 20 as #10, grid size 208,208,208, pixel 2, shown at level
0.03, step 1, values float32  

> show #!4 models

> color #10 #ff2600ff models

> hide #!8 models

> show #!8 models

> hide #!7 models

> close #7

> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/Medi8897_Site0_red.mrc" models #10

> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/EMPEMcomposition.cxs" includeMaps true

> show #!1 models

> show #!2 models

> show #!3 models

> show #!5 models

> hide #!3 models

> hide #!4 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!2 models

> ui mousemode right zoom

> rock axis y

> movie record

> movie encode /Users/szhang3/Desktop/movie2.mp4

Movie saved to /Users/szhang3/Desktop/movie2.mp4  
  

> stop

> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/EMPEMcomposition.cxs" includeMaps true

> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/RSV_MEDI_Mota.png" width 936 height 665
> supersample 3 transparentBackground true

> open /Users/szhang3/Downloads/5udc.pdb

5udc.pdb title:  
Crystal structure of RSV F A2 bound to MEDI8897 [more info...]  
  
Chain information for 5udc.pdb #7  
---  
Chain | Description | UniProt  
A D F | protein F | FUS_HRSVA 1-513  
B E H | MEDI8897 fab heavy chain |   
C G L | MEDI8897 fab light chain |   
  
Non-standard residues in 5udc.pdb #7  
---  
BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)  
CL — chloride ion  
MAN — α-D-mannopyranose (α-D-mannose; D-mannose; mannose)  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)  
  

> hide atoms

> show cartoons

> select add #7

20324 atoms, 20737 bonds, 6 pseudobonds, 2648 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.45186,0.83609,0.31109,-39.974,0.59179,-0.019992,-0.80585,30.737,-0.66754,0.54823,-0.50382,-98.435

> ui mousemode right "translate selected models"

> view matrix models
> #7,0.45186,0.83609,0.31109,10.706,0.59179,-0.019992,-0.80585,229.92,-0.66754,0.54823,-0.50382,-81.952

> view matrix models
> #7,0.45186,0.83609,0.31109,179.34,0.59179,-0.019992,-0.80585,158.03,-0.66754,0.54823,-0.50382,186.41

> view matrix models
> #7,0.45186,0.83609,0.31109,204.92,0.59179,-0.019992,-0.80585,146.3,-0.66754,0.54823,-0.50382,186.25

> view matrix models
> #7,0.45186,0.83609,0.31109,199.52,0.59179,-0.019992,-0.80585,144.61,-0.66754,0.54823,-0.50382,185.8

> view matrix models
> #7,0.45186,0.83609,0.31109,191.86,0.59179,-0.019992,-0.80585,143.65,-0.66754,0.54823,-0.50382,176.83

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.45386,0.75421,0.47453,201.39,0.72149,0.0014847,-0.69242,150.81,-0.52294,0.65663,-0.54348,175.14

> fitmap #7 inMap #8

Fit molecule 5udc.pdb (#7) to map preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8)
using 20324 atoms  
average map value = 0.1316, steps = 236  
shifted from previous position = 23.1  
rotated from previous position = 48.8 degrees  
atoms outside contour = 10580, contour level = 0.15  
  
Position of 5udc.pdb (#7) relative to preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc
(#8) coordinates:  
Matrix rotation and translation  
0.82584349 0.02466872 0.56335955 249.77298201  
0.55968844 -0.15772236 -0.81355547 159.01791335  
0.06878502 0.98717532 -0.14406078 179.73879837  
Axis 0.92699562 0.25460131 0.27542203  
Axis point 0.00000000 6.62206876 85.41492505  
Rotation angle (degrees) 103.76674887  
Shift along axis 321.52865406  
  

> select clear

> ui mousemode right zoom

> hide #!8 models

> select /A:225

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

> select up

218 atoms, 219 bonds, 26 residues, 1 model selected  

> select up

3474 atoms, 3532 bonds, 448 residues, 1 model selected  

> select ~sel & ##selected

16850 atoms, 17205 bonds, 5 pseudobonds, 2200 residues, 2 models selected  

> delete atoms (#!7 & sel)

> delete bonds (#!7 & sel)

> vop gaussian #7 sd 3

> molmap #7 20 onGrid #8

Opened 5udc.pdb map 20 as #11, grid size 208,208,208, pixel 2, shown at level
0.026, step 1, values float32  

> save "/Users/szhang3/OneDrive - Moderna/RSV/EMPEM/EMPEMcomposition/RSV
> monomer.mrc" models #11

> color #11 #ebebebff models

> color #11 silver models

> color #11 #d6d6d6ff models

> color #11 silver models

> color #11 darkgrey models

> color #11 #d6d6d6ff models

> color #11 silver models

> save "/Users/szhang3/OneDrive -
> Moderna/RSV/EMPEM/EMPEMcomposition/EMPEMcomposition.cxs" includeMaps true

——— End of log from Mon Jun 16 08:40:41 2025 ———

opened ChimeraX session  

> open /Users/szhang3/Downloads/cryosparc_P141_J26_002_volume_map_sharp.mrc

Opened cryosparc_P141_J26_002_volume_map_sharp.mrc as #12, grid size
208,208,208, pixel 2, shown at level 0.127, step 1, values float32  

> volume #12 level 0.2952

> color #12 #7974d0ff models

> select add #12

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #12,1,0,0,19.646,0,1,0,23.526,0,0,1,-82.779

> volume #12 level 0.6635

> volume #12 level 1.358

> ui mousemode right "rotate selected models"

> view matrix models
> #12,0.59534,0.75283,-0.28073,-6.5854,-0.65365,0.65699,0.37564,160.69,0.46723,-0.040131,0.88322,-147.97

> volume flip #12

Opened cryosparc_P141_J26_002_volume_map_sharp.mrc z flip as #13, grid size
208,208,208, pixel 2, shown at step 1, values float32  

> view matrix models
> #12,0.59534,0.75283,-0.28073,-6.5854,-0.65365,0.65699,0.37564,160.69,0.46723,-0.040131,0.88322,-147.97

> select subtract #12

Nothing selected  

> select add #13

2 models selected  

> view matrix models
> #13,-0.92863,-0.13558,-0.34534,514.85,-0.30913,0.79746,0.51817,27.504,0.20514,0.58795,-0.78245,139.68

> view matrix models
> #13,0.84143,-0.48367,-0.24094,202.4,-0.24475,0.056391,-0.96794,505.32,0.48175,0.87343,-0.070931,-137.41

> view matrix models
> #13,0.47751,0.85406,0.20631,-112.48,0.15751,0.1478,-0.9764,404.43,-0.86439,0.49873,-0.063946,219.9

> view matrix models
> #13,-0.081549,-0.97627,-0.20062,490.67,-0.75932,0.19124,-0.62199,505.24,0.64559,0.10161,-0.75689,148.83

> ui mousemode right "translate selected models"

> view matrix models
> #13,-0.081549,-0.97627,-0.20062,430,-0.75932,0.19124,-0.62199,446.49,0.64559,0.10161,-0.75689,222.99

> view matrix models
> #13,-0.081549,-0.97627,-0.20062,474.01,-0.75932,0.19124,-0.62199,436.55,0.64559,0.10161,-0.75689,242.95

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.82303,0.5376,0.18331,-126.53,0.23831,-0.033884,-0.9706,357.24,-0.51559,0.84252,-0.15601,187.9

> ui mousemode right zoom

> ui mousemode right "translate selected models"

> view matrix models
> #13,0.82303,0.5376,0.18331,-101.8,0.23831,-0.033884,-0.9706,363.2,-0.51559,0.84252,-0.15601,208.74

> ui tool show "Fit in Map"

> fitmap #13 inMap #11

Fit map cryosparc_P141_J26_002_volume_map_sharp.mrc z flip in map RSV
monomer.mrc using 45702 points  
correlation = 0.5239, correlation about mean = 0.2257, overlap = 5089  
steps = 348, shift = 23.8, angle = 43.1 degrees  
  
Position of cryosparc_P141_J26_002_volume_map_sharp.mrc z flip (#13) relative
to RSV monomer.mrc (#11) coordinates:  
Matrix rotation and translation  
0.27476068 0.88401675 0.37818110 -97.29220617  
0.67757343 0.10104673 -0.72848047 186.71744101  
-0.68220290 0.45640325 -0.57122259 389.76055209  
Axis 0.73896892 0.66132297 -0.12875120  
Axis point 0.00000000 4.50037877 249.48413425  
Rotation angle (degrees) 126.70589194  
Shift along axis 1.40247832  
  

> hide #!13 models

> select subtract #13

Nothing selected  

> select add #12

2 models selected  

> show #!12 models

> view matrix models
> #12,0.59534,0.75283,-0.28073,8.723,-0.65365,0.65699,0.37564,130.34,0.46723,-0.040131,0.88322,-30.652

> ui mousemode right "rotate selected models"

> view matrix models
> #12,-0.078213,0.96461,-0.2518,96.015,-0.62153,0.1503,0.76884,158.33,0.77947,0.21663,0.58778,-94.099

> ui mousemode right "translate selected models"

> view matrix models
> #12,-0.078213,0.96461,-0.2518,97.82,-0.62153,0.1503,0.76884,142.45,0.77947,0.21663,0.58778,-106.78

> view matrix models
> #12,-0.078213,0.96461,-0.2518,89.173,-0.62153,0.1503,0.76884,130.87,0.77947,0.21663,0.58778,-88.982

> fitmap #12 inMap #11

Fit map cryosparc_P141_J26_002_volume_map_sharp.mrc in map RSV monomer.mrc
using 45702 points  
correlation = 0.5178, correlation about mean = 0.2534, overlap = 4884  
steps = 472, shift = 9.99, angle = 56.1 degrees  
  
Position of cryosparc_P141_J26_002_volume_map_sharp.mrc (#12) relative to RSV
monomer.mrc (#11) coordinates:  
Matrix rotation and translation  
-0.86656684 0.47375042 -0.15691537 326.97169745  
-0.27360204 -0.18802830 0.94328536 90.93929916  
0.41737731 0.86035219 0.29255817 -88.56225583  
Axis -0.08765204 -0.60696970 -0.78987651  
Axis point 181.53403477 27.63568693 0.00000000  
Rotation angle (degrees) 151.76546823  
Shift along axis -13.90388830  
  

> view matrix models
> #12,-0.86657,0.47375,-0.15692,226.83,-0.2736,-0.18803,0.94329,55.466,0.41738,0.86035,0.29256,-57.96

> ui mousemode right "rotate selected models"

> view matrix models
> #12,0.502,0.85752,-0.11248,-147.15,-0.50545,0.39642,0.7664,10.259,0.7018,-0.32788,0.63244,76.27

> view matrix models
> #12,0.68525,0.70828,0.16964,-206.63,-0.68354,0.70584,-0.1859,162.47,-0.25141,0.011433,0.96781,134.72

> view matrix models
> #12,0.90837,0.38486,-0.16354,-118.46,-0.30318,0.87549,0.3763,-60.637,0.288,-0.29224,0.91195,100.2

> view matrix models
> #12,0.80697,0.43047,-0.40436,-61.262,-0.16066,0.81884,0.55108,-111.24,0.56833,-0.37974,0.72993,96.341

> view matrix models
> #12,-0.26697,-0.91319,0.30792,315.27,-0.20303,0.36565,0.90834,-72.625,-0.94208,0.17998,-0.28302,480.45

> ui tool show Segmentations

> ui view fourup

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,5
      Model Number: MPHG3LL/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 32 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.81.4

Software:

    System Software Overview:

      System Version: macOS 15.3.2 (24D81)
      Kernel Version: Darwin 24.3.0
      Time since boot: 6 days, 3 hours, 27 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:
        LS34A650U:
          Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
          UI Looks like: 3440 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    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: 2.3
    ChimeraX-Clipper: 0.24.0
    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: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    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-ISOLDE: 1.9
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    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-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
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    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: 1.18.1
    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
    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: 1.41
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.0.8
    narwhals: 1.31.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 2.2.4
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    plotly: 6.0.1
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pyKVFinder: 0.7.3
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    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: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    toml: 0.10.2
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2