REST server attempting to encode Atom into response

[rohou.alexis@…]

The following bug report has been submitted:
Platform:        macOS-14.7.6-arm64-arm-64bit
ChimeraX Version: 1.11.dev202510220024 (2025-10-22 00:24:07 UTC)
Description
Came across this bug when developing the MCP bridge

Log:
Startup Messages  
---  
notes | available bundle cache has not been initialized yet  
Updated animation length to 0:05.00  
  

> set bgColor white

> lighting soft

> clipper init

Error running startup command 'clipper init': Unknown command: clipper init  

> remotecontrol rest start port 8080 json true log true

UCSF ChimeraX version: 1.11.dev202510220024 (2025-10-22)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
REST server started on host 127.0.0.1 port 8080  
Visit http://127.0.0.1:8080/cmdline.html for CLI interface  

> open 7msa

7msa title:  
GDC-9545 in complex with estrogen receptor α [more info...]  
  
Chain information for 7msa #1  
---  
Chain | Description | UniProt  
A B C D | Estrogen receptor | ESR1_HUMAN 298-553  
  
Non-standard residues in 7msa #1  
---  
G9J — (2S)-3-(3-hydroxyphenyl)-2-(4-iodophenyl)-4-methyl-2H-1-benzopyran-6-ol  
ZNM —
3-[(1R,3R)-1-(2,6-difluoro-4-{[1-(3-fluoropropyl)azetidin-3-yl]amino}phenyl)-3-methyl-1,3,4,9-tetrahydro-2H-pyrido[3,4-b]indol-2-yl]-2,2-difluoropropan-1-ol  
  
7msa mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
22 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
6984 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> info

> info chains #1/A attribute chain_id

chain id /A chain_id A  

> info chains #1/A attribute polymer_type

chain id /A polymer_type 1  

> info chains #1/A attribute description

chain id /A description "Estrogen receptor"  

> info chains #1/A attribute num_residues

chain id /A num_residues 280  

> info chains #1/A attribute num_existing_residues

chain id /A num_existing_residues 225  

> hide #1/B,C,D target c

> show #1/A target c

> show #1/A target m

> style :ZNM stick

Changed 74 atom styles  

> color #1/A lightblue

> color :ZNM byhetero

> view :ZNM

> show :ZNM target a

> show :ZNM target m

> style :ZNM<5 & protein stick

Expected a keyword  

> label :ZNM residues

> lighting soft

> save /Users/rohoua/work/tmp/estrogen_receptor_giredestrant.png width 1920
> height 1080 supersample 3

> show :ZNM <5 & protein target a

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> style (:ZNM <5 & protein) stick

Expected a keyword  

> color :ZNM <5 & protein tan

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

> save /Users/rohoua/work/tmp/estrogen_receptor_giredestrant_binding.png width
> 1920 height 1080 supersample 3

> select :ZNM zr<5

Expected a keyword  

> show sel & protein target a

> show sel & protein target m

> style sel & protein stick

Changed 0 atom styles  

> color sel & protein tan

> ~select

Nothing selected  

> save /Users/rohoua/work/tmp/estrogen_receptor_giredestrant_final.png width
> 1920 height 1080 supersample 3

> select (:ZNM :< 5) & protein

409 atoms, 390 bonds, 49 residues, 1 model selected  

> show sel target a

> show sel target m

> style sel stick

Changed 409 atom styles  

> color sel tan

> ~select

Nothing selected  

> save /Users/rohoua/work/tmp/giredestrant_binding_site.png width 1920 height
> 1080 supersample 3

> close

> open 7msa

7msa title:  
GDC-9545 in complex with estrogen receptor α [more info...]  
  
Chain information for 7msa #1  
---  
Chain | Description | UniProt  
A B C D | Estrogen receptor | ESR1_HUMAN 298-553  
  
Non-standard residues in 7msa #1  
---  
G9J — (2S)-3-(3-hydroxyphenyl)-2-(4-iodophenyl)-4-methyl-2H-1-benzopyran-6-ol  
ZNM —
3-[(1R,3R)-1-(2,6-difluoro-4-{[1-(3-fluoropropyl)azetidin-3-yl]amino}phenyl)-3-methyl-1,3,4,9-tetrahydro-2H-pyrido[3,4-b]indol-2-yl]-2,2-difluoropropan-1-ol  
  
7msa mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
22 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
6984 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> info

[Repeated 1 time(s)]

> info chains #1/D attribute chain_id

chain id /D chain_id D  

> info chains #1/D attribute polymer_type

chain id /D polymer_type 1  

> info chains #1/D attribute description

chain id /D description "Estrogen receptor"  

> info chains #1/D attribute num_residues

chain id /D num_residues 280  

> info chains #1/D attribute num_existing_residues

chain id /D num_existing_residues 234  

> info chains #1/A attribute chain_id

chain id /A chain_id A  

> info chains #1/A attribute polymer_type

chain id /A polymer_type 1  

> info chains #1/A attribute description

chain id /A description "Estrogen receptor"  

> info chains #1/A attribute num_residues

chain id /A num_residues 280  

> info chains #1/A attribute num_existing_residues

chain id /A num_existing_residues 225  

> info chains #1/C attribute chain_id

chain id /C chain_id C  

> info chains #1/C attribute polymer_type

chain id /C polymer_type 1  

> info chains #1/C attribute description

chain id /C description "Estrogen receptor"  

> info chains #1/C attribute num_residues

chain id /C num_residues 280  

> info chains #1/C attribute num_existing_residues

chain id /C num_existing_residues 225  

> info chains #1/B attribute chain_id

chain id /B chain_id B  

> info chains #1/B attribute polymer_type

chain id /B polymer_type 1  

> info chains #1/B attribute description

chain id /B description "Estrogen receptor"  

> info chains #1/B attribute num_residues

chain id /B num_residues 280  

> info chains #1/B attribute num_existing_residues

chain id /B num_existing_residues 228  

> hide #1/B,C,D target abcs

> style #1/A:ZNM stick

Changed 37 atom styles  

> view #1/A:ZNM

> show #1/A:ZNM z<5 target a

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> style #1/A:ZNM z<5 & protein stick

Expected a keyword  

> color #1/A:ZNM cyan

> label #1/A:ZNM text ZNM size 20

> style #1/A & protein & #1/A:ZNM <5 stick

Expected a keyword  

> color #1/A & protein byhetero

> show #1/A:ZNM :<5 & protein target a

> show #1/A:ZNM :<5 & protein target m

> style #1/A:ZNM :<5 & protein stick

Changed 216 atom styles  

> label #1/A:ZNM :<5 & protein residues height 0.7

> save /Users/rohoua/work/tmp/giredestrant_binding_site.png width 1920 height
> 1080 supersample 3

> color byhetero

> close

> open 7msa

7msa title:  
GDC-9545 in complex with estrogen receptor α [more info...]  
  
Chain information for 7msa #1  
---  
Chain | Description | UniProt  
A B C D | Estrogen receptor | ESR1_HUMAN 298-553  
  
Non-standard residues in 7msa #1  
---  
G9J — (2S)-3-(3-hydroxyphenyl)-2-(4-iodophenyl)-4-methyl-2H-1-benzopyran-6-ol  
ZNM —
3-[(1R,3R)-1-(2,6-difluoro-4-{[1-(3-fluoropropyl)azetidin-3-yl]amino}phenyl)-3-methyl-1,3,4,9-tetrahydro-2H-pyrido[3,4-b]indol-2-yl]-2,2-difluoropropan-1-ol  
  
7msa mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
22 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
6984 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> info

[Repeated 1 time(s)]

> info chains #1/D attribute chain_id

chain id /D chain_id D  

> info chains #1/D attribute polymer_type

chain id /D polymer_type 1  

> info chains #1/D attribute description

chain id /D description "Estrogen receptor"  

> info chains #1/D attribute num_residues

chain id /D num_residues 280  

> info chains #1/D attribute num_existing_residues

chain id /D num_existing_residues 234  

> info chains #1/A attribute chain_id

chain id /A chain_id A  

> info chains #1/A attribute polymer_type

chain id /A polymer_type 1  

> info chains #1/A attribute description

chain id /A description "Estrogen receptor"  

> info chains #1/A attribute num_residues

chain id /A num_residues 280  

> info chains #1/A attribute num_existing_residues

chain id /A num_existing_residues 225  

> info chains #1/C attribute chain_id

chain id /C chain_id C  

> info chains #1/C attribute polymer_type

chain id /C polymer_type 1  

> info chains #1/C attribute description

chain id /C description "Estrogen receptor"  

> info chains #1/C attribute num_residues

chain id /C num_residues 280  

> info chains #1/C attribute num_existing_residues

chain id /C num_existing_residues 225  

> info chains #1/B attribute chain_id

chain id /B chain_id B  

> info chains #1/B attribute polymer_type

chain id /B polymer_type 1  

> info chains #1/B attribute description

chain id /B description "Estrogen receptor"  

> info chains #1/B attribute num_residues

chain id /B num_residues 280  

> info chains #1/B attribute num_existing_residues

chain id /B num_existing_residues 228  

> hide #1/B,C,D target abpcs

> view #1/A:ZNM

> color #1/A:ZNM cyan

> style #1/A:ZNM stick

Changed 37 atom styles  

> show #1/A:ZNM target a

> show #1/A:ZNM target m

> label #1/A:ZNM residues text {0.name}

> style #1/A:ZNM zr<5 stick

Expected a keyword  

> show #1/A & ligand target a

> show #1/A & ligand target m

> select #1/A:ZNM zr<5

Expected a keyword  

> show sel target a

> show sel target m

> style sel stick

Changed 0 atom styles  

> color sel byhetero

> save /Users/rohoua/work/tmp/7msa_giredestrant_binding.png width 1920 height
> 1080 supersample 3

> select #1/A:ZNM zr<5

Expected a keyword  

> show sel target a

> show sel target m

> style sel stick

Changed 0 atom styles  

> color sel byhetero

> color #1/A:ZNM hotpink

> save /Users/rohoua/work/tmp/7msa_giredestrant_final.png width 1920 height
> 1080 supersample 3

> select #1/A:ZNM :<5

254 atoms, 247 bonds, 28 residues, 1 model selected  

> show sel target a

> show sel target m

> style sel stick

Changed 254 atom styles  

> color sel byhetero

> style #1/A:ZNM ball

Changed 37 atom styles  

> size #1/A:ZNM stickRadius 0.3

Changed 41 bond radii  

> save /Users/rohoua/work/tmp/7msa_giredestrant_binding_pocket.png width 1920
> height 1080 supersample 3

> label #1/A:ZNM residues text "Giredestrant (ZNM)" height 1.5 color white
> bgColor black

> lighting soft

> save /Users/rohoua/work/tmp/7msa_estrogen_receptor_giredestrant.png width
> 1920 height 1080 supersample 3

> select clear

> color #1/A:ZNM gold

> color #1/A:ZNM byhetero

> contacts #1/A:ZNM restrict #1/A & protein

54 contacts  
Traceback (most recent call last):  
File
"/Users/rohoua/work/git/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 875, in customEvent  
func(*args, **kw)  
File
"/Users/rohoua/work/git/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/rest_server/server.py", line 286, in f  
q.put(JSONEncoder(default=lambda x: None).encode(response))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/rohoua/work/git/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/encoder.py",
line 200, in encode  
chunks = self.iterencode(o, _one_shot=True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/rohoua/work/git/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/encoder.py",
line 258, in iterencode  
return _iterencode(o, 0)  
^^^^^^^^^^^^^^^^^  
TypeError: keys must be str, int, float, bool or None, not Atom  
  
TypeError: keys must be str, int, float, bool or None, not Atom  
  
File
"/Users/rohoua/work/git/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/encoder.py",
line 258, in iterencode  
return _iterencode(o, 0)  
^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.9
Locale: UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: Z16T0006PLL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 10151.140.19.700.2

Software:

    System Software Overview:

      System Version: macOS 14.7.6 (23H626)
      Kernel Version: Darwin 23.6.0
      Time since boot: 2 days, 37 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      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: Yes
          Connection Type: Internal


Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.11.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.10.2
    build: 1.3.0
    certifi: 2025.8.3
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.0.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.17
    ChimeraX-AtomicLibrary: 14.2.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.dev202510220024
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.2
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    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: 1.0.1
    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: 1.15.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.11
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    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: 1.5.2
    ChimeraX-Scenes: 0.2.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.2
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.48.4
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.0
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.11.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.17
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.60.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.7
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.25.1
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.5
    matplotlib-inline: 0.1.7
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.3
    pydantic-settings: 2.11.0
    pydantic_core: 2.41.4
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    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.2.5
    pyproject_hooks: 1.2.0
    PyQt6: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 8.4.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.1.1
    python-multipart: 0.0.20
    pytz: 2025.2
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals-py: 3.1.0
    rpds-py: 0.27.1
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    sniffio: 1.3.1
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    sse-starlette: 3.0.2
    stack-data: 0.6.3
    starlette: 0.48.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.2
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2025.2
    urllib3: 2.5.0
    uvicorn: 0.38.0
    wcwidth: 0.2.14
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    yarl: 1.22.0

[Eric Pettersen]

Duplicate of #19203