'ArrayGridData' object has no attribute 'dicom_data'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.3-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/inesbenhammouche/Desktop/WAT1 cryo-
> EM/WAT1_1UProteinA_IAA_pH75/P1337_WAT1_IAA_inward_occluded_fit.cxs"

Opened cryosparc_P1338_J131_004_volume_map_sharp.mrc z flip as #3, grid size
96,96,96, pixel 2.59, shown at level 0.937, step 1, values float32  
Opened cryosparc_P1338_J131_004_volume_map_sharp.mrc as #4, grid size
96,96,96, pixel 2.59, shown at level 1, step 1, values float32  
Log from Wed Feb 12 01:49:36 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/inesbenhammouche/Desktop/P1337_WAT1_IAA_inward_occluded_fit.cxs

Opened cryosparc_P1338_J131_004_volume_map_sharp.mrc z flip as #3, grid size
96,96,96, pixel 2.59, shown at level 0.937, step 1, values float32  
Opened cryosparc_P1338_J131_004_volume_map_sharp.mrc as #4, grid size
96,96,96, pixel 2.59, shown at level 1, step 1, values float32  
Log from Wed Feb 12 01:28:23 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/inesbenhammouche/Desktop/P1337_WAT1_IAA_inward_occluded_fit.cxs

Opened cryosparc_P1338_J131_004_volume_map_sharp.mrc as #1, grid size
96,96,96, pixel 2.59, shown at level 0.937, step 1, values float32  
Opened cryosparc_P1338_J131_004_volume_map_sharp.mrc z flip as #3, grid size
96,96,96, pixel 2.59, shown at level 0.937, step 1, values float32  
Log from Wed Jan 29 16:13:38 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> set bgColor white

> lighting soft

> camera ortho

> graphics silhouettes true

> graphics silhouettes width 3

> ui mousemode right zoom

> ui tool show "Side View"

> alias tubes cartoon style protein modeh tube rad 2 sides 24 divisions 10
> thickness 1

> graphics quality 100

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/inesbenhammouche/Downloads/cryosparc_P1338_J131_004_volume_map_sharp.mrc

Opened cryosparc_P1338_J131_004_volume_map_sharp.mrc as #1, grid size
96,96,96, pixel 2.59, shown at level 0.408, step 1, values float32  

> volume #1 level 0.9371

> surface dust #1 size 25.9

> open "/Users/inesbenhammouche/Desktop/AI
> prediction/AF3/WAT1_FL/WAT1_FL/WAT1_FL_AF3_0.cif"

Chain information for WAT1_FL_AF3_0.cif #2  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> view

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,108.18,0,1,0,39.332,0,0,1,152.82

> view matrix models #2,1,0,0,101.12,0,1,0,71.064,0,0,1,111.71

> view matrix models #2,1,0,0,116.46,0,1,0,103.44,0,0,1,143.58

> view matrix models #2,1,0,0,118.54,0,1,0,121.42,0,0,1,133.32

> volume #1 flipNormals

Missing "flipNormals" keyword's argument  

> volume flip #3

> volume flip #&

Missing or invalid "volumes" argument: invalid density maps specifier  

> volume flip #1

Opened cryosparc_P1338_J131_004_volume_map_sharp.mrc z flip as #3, grid size
96,96,96, pixel 2.59, shown at step 1, values float32  

> surface dust #3 size 25.9

> view matrix models #2,1,0,0,114.42,0,1,0,76.47,0,0,1,158.57

> ui mousemode right "rotate selected models"

> select add #2

3010 atoms, 3086 bonds, 389 residues, 1 model selected  

> view matrix models
> #2,0.56793,0.78452,-0.24895,108.46,-0.64897,0.61286,0.45083,51.745,0.50626,-0.094477,0.85719,173.86

> ui mousemode right "move picked models"

> view matrix models
> #2,0.56793,0.78452,-0.24895,118.35,-0.64897,0.61286,0.45083,132.88,0.50626,-0.094477,0.85719,127.36

> fitmap #2 inMap #3

Fit molecule WAT1_FL_AF3_0.cif (#2) to map
cryosparc_P1338_J131_004_volume_map_sharp.mrc z flip (#3) using 3010 atoms  
average map value = 0.2602, steps = 168  
shifted from previous position = 5.94  
rotated from previous position = 16.1 degrees  
atoms outside contour = 2457, contour level = 0.93714  
  
Position of WAT1_FL_AF3_0.cif (#2) relative to
cryosparc_P1338_J131_004_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.50823369 0.86120837 0.00432137 118.74497126  
-0.78617800 0.46189503 0.41058147 130.00594961  
0.35160018 -0.21206870 0.91181369 132.44197185  
Axis -0.34687210 -0.19346550 -0.91774225  
Axis point 116.26447003 4.18398596 0.00000000  
Rotation angle (degrees) 63.83413589  
Shift along axis -187.88857778  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.44567,0.44966,-0.77407,135.8,0.75429,0.27704,0.59522,162.24,0.4821,-0.84915,-0.21571,162.4

> ui mousemode right "move picked models"

> view matrix models
> #2,0.44567,0.44966,-0.77407,123.48,0.75429,0.27704,0.59522,150.62,0.4821,-0.84915,-0.21571,111.67

> view matrix models
> #2,0.44567,0.44966,-0.77407,120.08,0.75429,0.27704,0.59522,127.9,0.4821,-0.84915,-0.21571,130.48

> view matrix models
> #2,0.44567,0.44966,-0.77407,121.06,0.75429,0.27704,0.59522,130.2,0.4821,-0.84915,-0.21571,119.89

> fitmap #2 inMap #3

Fit molecule WAT1_FL_AF3_0.cif (#2) to map
cryosparc_P1338_J131_004_volume_map_sharp.mrc z flip (#3) using 3010 atoms  
average map value = 0.7321, steps = 124  
shifted from previous position = 5.03  
rotated from previous position = 36.9 degrees  
atoms outside contour = 1844, contour level = 0.93714  
  
Position of WAT1_FL_AF3_0.cif (#2) relative to
cryosparc_P1338_J131_004_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.42623971 0.42779226 -0.79706556 119.29943735  
0.33001682 0.74685194 0.57732235 126.10895320  
0.84226399 -0.50912274 0.17715931 122.20354461  
Axis -0.55174920 -0.83253059 -0.04965509  
Axis point -63.44240373 0.00000000 72.90020407  
Rotation angle (degrees) 79.91403963  
Shift along axis -176.88095862  
  

> hide #!3 models

> show #!1 models

> select subtract #2

Nothing selected  

> select add #1

2 models selected  

> view matrix models #1,1,0,0,11.785,0,1,0,19.468,0,0,1,-44.075

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.98352,-0.17812,0.031003,32.583,-0.13558,-0.6132,0.77821,144.73,-0.1196,-0.76959,-0.62724,269.21

> ui mousemode right "move picked models"

> view matrix models
> #2,0.42624,0.42779,-0.79707,130.38,0.33002,0.74685,0.57732,145.37,0.84226,-0.50912,0.17716,78.623

> fitmap #2 inMap #1

Fit molecule WAT1_FL_AF3_0.cif (#2) to map
cryosparc_P1338_J131_004_volume_map_sharp.mrc (#1) using 3010 atoms  
average map value = 0.3112, steps = 96  
shifted from previous position = 4.05  
rotated from previous position = 13.3 degrees  
atoms outside contour = 2357, contour level = 0.93714  
  
Position of WAT1_FL_AF3_0.cif (#2) relative to
cryosparc_P1338_J131_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.47544092 0.41385258 -0.77632597 118.16403351  
-0.84194376 -0.04185515 -0.53793947 130.25767365  
-0.25512087 0.90938122 0.32854094 126.85951599  
Axis 0.72883371 -0.26246557 -0.63238694  
Axis point 0.00000000 20.06991632 189.46823433  
Rotation angle (degrees) 96.83073733  
Shift along axis -28.29052461  
  

> select subtract #1

Nothing selected  

> select add #3

2 models selected  

> hide #!1 models

> select subtract #3

Nothing selected  

> show #!3 models

> select add #2

3010 atoms, 3086 bonds, 389 residues, 1 model selected  

> view matrix models
> #2,0.60966,0.44268,-0.65753,116.94,0.25328,0.67724,0.69079,123.04,0.75111,-0.58769,0.30077,120.9

> fitmap #2 inMap #3

Fit molecule WAT1_FL_AF3_0.cif (#2) to map
cryosparc_P1338_J131_004_volume_map_sharp.mrc z flip (#3) using 3010 atoms  
average map value = 0.7321, steps = 80  
shifted from previous position = 3.95  
rotated from previous position = 13.3 degrees  
atoms outside contour = 1842, contour level = 0.93714  
  
Position of WAT1_FL_AF3_0.cif (#2) relative to
cryosparc_P1338_J131_004_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.42565633 0.42818600 -0.79716590 119.29967827  
0.33022965 0.74669350 0.57740559 126.11135610  
0.84247557 -0.50902415 0.17643510 122.19729111  
Axis -0.55166851 -0.83257898 -0.04974038  
Axis point -63.35277072 0.00000000 72.88505110  
Rotation angle (degrees) 79.95669468  
Shift along axis -176.88967931  
  

> select subtract #2

Nothing selected  

> save /Users/inesbenhammouche/Desktop/P1337_WAT1_IAA_inward_occluded_fit.cxs

——— End of log from Wed Jan 29 16:13:38 2025 ———

opened ChimeraX session  

> open
> /Users/inesbenhammouche/Downloads/cryosparc_P1338_J131_004_volume_map_sharp.mrc

Opened cryosparc_P1338_J131_004_volume_map_sharp.mrc as #4, grid size
96,96,96, pixel 2.59, shown at level 0.408, step 1, values float32  

> hide #2 models

> hide #!3 models

> volume #4 level 1.005

> surface dust #4 size 25.9

> show #!1 models

[Repeated 1 time(s)]

> hide #!1 models

> show #!1 models

> show #2 models

> hide #!1 models

> close #1

> show #!3 models

> hide #!4 models

> hide #2 models

> show #!4 models

> hide #!3 models

> show #!3 models

> hide #!4 models

> ui tool show "Map Eraser"

> volume erase #3 center 108.3,102.78,104.3 radius 11.386

> volume erase #3 center 84.562,123.23,86.66 radius 11.386

> volume erase #3 center 131.82,107.05,124.63 radius 7.9705

> show #2 models

> volume erase #3 center 144.93,107.5,123.13 radius 7.9503

> volume erase #3 center 148.72,108.64,112.89 radius 7.9503

> volume erase #3 center 119.06,105.48,124.68 radius 7.9503

> volume erase #3 center 132.91,113.32,111.02 radius 4.5963

> volume erase #3 center 132.67,123.83,148.45 radius 4.5963

> save /Users/inesbenhammouche/Desktop/P1337_WAT1_IAA_inward_occluded_fit.cxs

——— End of log from Wed Feb 12 01:28:23 2025 ———

opened ChimeraX session  

> color #3 #748299ff models

> color #3 #748299e4 models

> color #3 #748299f3 models

> color #3 #748299ed models

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> hide #2 models

> lighting full

> lighting soft

> lighting simple

> color #3 #a3b7d6ff models

> lighting full

> lighting flat

> lighting simple

> lighting soft

> lighting full

> lighting flat

[Repeated 1 time(s)]

> lighting shadows true intensity 0.5

> lighting shadows false

> graphics silhouettes false

> lighting simple

> lighting full

> save WAT1_1UproteinA_final_map_IAA.tiff format tiff supersample 3
> transparentBackground true width 8000 height 7000

> open
> /Users/inesbenhammouche/Downloads/cryosparc_P1217_J109_class_04_final_volume.mrc

Opened cryosparc_P1217_J109_class_04_final_volume.mrc as #1, grid size
120,120,120, pixel 2.59, shown at level 0.129, step 1, values float32  

> volume #1 level 0.3132

> volume #1 level 0.2965

> surface dust #1 size 25.9

> close #1

> show #!3 models

> save "/Users/inesbenhammouche/Desktop/WAT1 cryo-
> EM/WAT1_1UProteinA_IAA_pH75/P1337_WAT1_IAA_inward_occluded_fit.cxs"

——— End of log from Wed Feb 12 01:49:36 2025 ———

opened ChimeraX session  

> ui tool show "Map Eraser"

> volume erase #3 center 109.82,125.26,117.11 radius 3.8143

> volume erase #3 center 110.23,126.17,118.79 radius 2.7245

[Repeated 1 time(s)]

> volume erase #3 center 110.5,129.2,124.24 radius 2.7245

> volume erase #3 center 114.27,126.2,117.46 radius 2.7245

> show #!4 models

> hide #!4 models

> select #3:1-100

Nothing selected  

> 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 M1
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 Air
      Model Identifier: MacBookAir10,1
      Model Number: MGN63FN/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 11881.81.2
      OS Loader Version: 11881.81.2

Software:

    System Software Overview:

      System Version: macOS 15.3 (24D60)
      Kernel Version: Darwin 24.3.0
      Time since boot: 2 days, 14 hours, 54 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          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
    babel: 2.16.0
    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-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-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
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    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: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    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: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    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
    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
    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
    tornado: 6.4.2
    traitlets: 5.14.3
    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-filename: 1.4.1
    widgetsnbextension: 4.0.13