TypeError: setChecked(self, a0: bool): argument 1 has unexpected type 'numpy.bool'

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-26.5.2-arm64-arm-64bit-Mach-O
ChimeraX Version: 1.13.dev202607102107 (2026-07-10 21:07:32 UTC)
Description
Restoring a session hit this numpy 2 setChecked(numpy.bool) error this time in Volume Viewer that Eric saw yesterday in selection inspector.

Log:
UCSF ChimeraX version: 1.13.dev202607102107 (2026-07-10)  
© 2016-2026 Regents of the University of California. All rights reserved.  

> open /Users/goddard/Desktop/test.cxs format session

Opened emdb 55878 as #1, grid size 440,440,440, pixel 0.65, shown at level
0.122, step 1, values float32  
Opened emdb 55878 gaussian as #3, grid size 440,440,440, pixel 0.65, shown at
level 0.0403, step 1, values float32  
Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
~~~~~~~~~~^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 5178, in models_opened  
cb(vlist)  
~~^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 190, in volume_opened_cb  
self.display_volume_info(v)  
~~~~~~~~~~~~~~~~~~~~~~~~^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 235, in display_volume_info  
p.update_panel_widgets(volume)  
~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 1628, in update_panel_widgets  
self.add_histogram_pane(volume)  
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 1508, in add_histogram_pane  
hp.set_data_region(v)  
~~~~~~~~~~~~~~~~~~^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 2112, in set_data_region  
self.update_threshold_gui()  
~~~~~~~~~~~~~~~~~~~~~~~~~^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 2675, in update_threshold_gui  
self.update_shown_icon()  
~~~~~~~~~~~~~~~~~~~~~~^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 2375, in update_shown_icon  
s.setChecked(shown)  
~~~~~~~~~~~~^^^^^^^  
TypeError: setChecked(self, a0: bool): argument 1 has unexpected type
'numpy.bool'  
  
Error processing trigger "add models":  
TypeError: setChecked(self, a0: bool): argument 1 has unexpected type
'numpy.bool'  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 2375, in update_shown_icon  
s.setChecked(shown)  
~~~~~~~~~~~~^^^^^^^  
  
See log for complete Python traceback.  
  
Opened volume difference as #4, grid size 440,440,440, pixel 0.65, shown at
level 0.122, step 1, values float32  
Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
~~~~~~~~~~^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 5178, in models_opened  
cb(vlist)  
~~^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 190, in volume_opened_cb  
self.display_volume_info(v)  
~~~~~~~~~~~~~~~~~~~~~~~~^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 235, in display_volume_info  
p.update_panel_widgets(volume)  
~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 1628, in update_panel_widgets  
self.add_histogram_pane(volume)  
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 1508, in add_histogram_pane  
hp.set_data_region(v)  
~~~~~~~~~~~~~~~~~~^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 2112, in set_data_region  
self.update_threshold_gui()  
~~~~~~~~~~~~~~~~~~~~~~~~~^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 2675, in update_threshold_gui  
self.update_shown_icon()  
~~~~~~~~~~~~~~~~~~~~~~^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 2375, in update_shown_icon  
s.setChecked(shown)  
~~~~~~~~~~~~^^^^^^^  
TypeError: setChecked(self, a0: bool): argument 1 has unexpected type
'numpy.bool'  
  
Error processing trigger "add models":  
TypeError: setChecked(self, a0: bool): argument 1 has unexpected type
'numpy.bool'  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/map/volume_viewer.py", line 2375, in update_shown_icon  
s.setChecked(shown)  
~~~~~~~~~~~~^^^^^^^  
  
See log for complete Python traceback.  
  
Log from Tue Jul 14 14:48:37 2026UCSF ChimeraX version: 1.13.dev202607102107
(2026-07-10)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 55878 format ccp4 fromDatabase emdb

Opened emdb 55878 as #1, grid size 440,440,440, pixel 0.65, shown at level
0.122, step 1, values float32, fit PDB 9tfv  

> open 9tfv format mmcif fromDatabase pdb

9tfv title:  
Cryo-EM structure of the inward rectifying potassium channel 7.1 (Kir7.1)
[more info...]  
  
Chain information for 9tfv #2  
---  
Chain | Description | UniProt  
A B C D | Inward rectifier potassium channel 13 | KCJ13_HUMAN -16-360  
  
Non-standard residues in 9tfv #2  
---  
K — potassium ion  
  

> vop gaussian #1 sdev 1.95

Opened emdb 55878 gaussian as #3, grid size 440,440,440, pixel 0.65, shown at
step 1, values float32  

> vop subtract #1 #3 minrms True

Opened volume difference as #4, grid size 440,440,440, pixel 0.65, shown at
step 1, values float32  
Minimum RMS scale factor for "emdb 55878 gaussian #3" above level 0.040251 is
1.8434  
  

> transparency #4.1 50

> transparency #4.1 0

> volume #!4 showOutlineBox true

> volume #!4 showOutlineBox false

> volume #!4 region all imageMode "full region"

> volume unzone #!4

> mousemode rightMode "crop volume"

> volume #!4 region all imageMode "full region"

> volume unzone #!4

> mousemode rightMode "crop volume"

> volume #!4 projectionMode 3d

> volume #!4 projectionMode 2d-xyz

> volume #!4 projectionMode rays

> volume #!4 projectionMode 3d

> volume #4 style surface

> fitmap #2 inMap #4

Fit molecule 9tfv (#2) to map volume difference (#4) using 17050 atoms  
average map value = 0.129, steps = 60  
shifted from previous position = 0.186  
rotated from previous position = 0.156 degrees  
atoms outside contour = 10740, contour level = 0.122  
  
Position of 9tfv (#2) relative to volume difference (#4) coordinates:  
Matrix rotation and translation  
0.99999625 0.00271638 -0.00013520 -0.37481905  
-0.00271637 0.99999634 0.00006726 0.38194553  
0.00013538 -0.00006689 1.00000004 0.17593505  
Axis -0.02465377 -0.04972999 -0.99845837  
Axis point 137.02415586 139.85416498 0.00000000  
Rotation angle (degrees) 0.15587735  
Shift along axis -0.18541727  
  

> ui tool show "Color Zone"

> color zone #4 near #2 distance 3.9

> color single #4

> color bychain

> color zone #4 near #2 distance 3.9

> volume splitbyzone #4

Opened volume difference 0 as #5.1, grid size 440,440,440, pixel 0.65, shown
at level 0.122, step 1, values float32  
Opened volume difference 1 as #5.2, grid size 440,440,440, pixel 0.65, shown
at level 0.122, step 1, values float32  
Opened volume difference 2 as #5.3, grid size 440,440,440, pixel 0.65, shown
at level 0.122, step 1, values float32  
Opened volume difference 3 as #5.4, grid size 440,440,440, pixel 0.65, shown
at level 0.122, step 1, values float32  
Opened volume difference 4 as #5.5, grid size 440,440,440, pixel 0.65, shown
at level 0.122, step 1, values float32  

> hide #!5.1 models

> hide #!5.2 models

> show #!5.2 models

> close #5

> show #!1 models

> color single #4

> color zone #1 near #2 distance 3.9

> color zone #1 near #2 distance 4

> color zone #1 near #2 distance 2.34

> color single #1

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule 9tfv (#2) to map emdb 55878 (#1) using 17050 atoms  
average map value = 0.2424, steps = 44  
shifted from previous position = 0.00951  
rotated from previous position = 0.0126 degrees  
atoms outside contour = 6705, contour level = 0.122  
  
Position of 9tfv (#2) relative to emdb 55878 (#1) coordinates:  
Matrix rotation and translation  
0.99999663 0.00257110 0.00001105 -0.36501687  
-0.00257110 0.99999668 -0.00000848 0.37346891  
-0.00001107 0.00000845 0.99999998 0.19084826  
Axis 0.00329158 0.00430192 -0.99998533  
Axis point 145.39276053 141.91233461 0.00000000  
Rotation angle (degrees) 0.14731542  
Shift along axis -0.19044031  
  
Opened 9tfv map 5 as #5, grid size 68,68,84, pixel 1.67, shown at level 0.115,
step 1, values float32  

> fitmap #2 inMap #1 resolution 5

Fit map 9tfv map 5 in map emdb 55878 using 34635 points  
correlation = 0.4842, correlation about mean = 0.6234, overlap = 2049  
steps = 40, shift = 0.0403, angle = 0.0107 degrees  
  
Position of 9tfv map 5 (#5) relative to emdb 55878 (#1) coordinates:  
Matrix rotation and translation  
0.99999717 0.00239314 0.00002183 -0.35199047  
-0.00239314 0.99999709 -0.00006173 0.35115167  
-0.00002198 0.00006168 1.00000012 0.22334933  
Axis 0.02577582 0.00914998 -0.99962587  
Axis point 147.43512105 144.79145887 0.00000000  
Rotation angle (degrees) 0.13716846  
Shift along axis -0.22912558  
  
Average map value = 0.2423 for 17050 atoms, 6703 outside contour  

> close #5

> ui tool show "Hide Dust"

> surface dust #1 size 3.9

> surface dust #1 size 3.82

> surface dust #1 size 3.52

> surface undust #1

> ui tool show "Map Coordinates"

> save test.cxs

——— End of log from Tue Jul 14 14:48:37 2026 ———

> view name session-start

opened ChimeraX session  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple

Python: 3.14.6
Locale: C.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac14,14
      Model Number: Z1800003VLL/A
      Chip: Apple M2 Ultra
      Total Number of Cores: 24 (16 Performance and 8 Efficiency)
      Memory: 64 GB
      System Firmware Version: 18000.121.3
      OS Loader Version: 18000.121.3

Software:

    System Software Overview:

      System Version: macOS 26.5.2 (25F84)
      Kernel Version: Darwin 25.5.0
      Time since boot: 14 days, 22 hours, 1 minute

Graphics/Displays:

    Apple M2 Ultra:

      Chipset Model: Apple M2 Ultra
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 60
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        PHL 278B1:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.7.1
    aiohttp: 3.13.4
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.14.1
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.8.0
    build: 1.5.0
    certifi: 2026.6.17
    cftime: 1.6.5
    charset-normalizer: 3.4.9
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.3.1
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.70.2
    ChimeraX-AtomicLibrary: 14.4.2
    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: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.4
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.13.dev202607102107
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.6
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DAQplugin: 1.0.0
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.2.2
    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: 2.5.4
    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: 1.8.5
    ChimeraX-Label: 1.5
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.3
    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-MatchAlign: 1.2.1
    ChimeraX-MatchMaker: 2.4.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.4.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.17
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.24
    ChimeraX-ModelPanel: 1.6.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.16.2
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.13
    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: 1.10.2
    ChimeraX-ProNA3D: 0.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    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: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.19.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.20
    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: 2.5.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.4
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.53.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.5
    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: 8.4.2
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.15.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.8
    debugpy: 1.8.21
    decorator: 5.3.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    flatbuffers: 25.12.19
    fonttools: 4.63.0
    frozenlist: 1.8.0
    funcparserlib: 1.0.1
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h2: 4.3.0
    h5py: 3.16.0
    hpack: 4.2.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    hyperframe: 6.1.0
    idna: 3.18
    ihm: 2.2
    imagecodecs: 2026.6.26
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.3.0
    ipython: 9.14.1
    ipython_pygments_lexers: 1.1.1
    jedi: 0.20.0
    Jinja2: 3.1.6
    joblib: 1.5.3
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.9.1
    jupyter_core: 5.9.1
    kiwisolver: 1.5.0
    line_profiler: 5.0.0
    llvmlite: 0.47.0
    lxml: 6.0.2
    lz4: 4.4.5
    Markdown: 3.8.2
    markdown-it-py: 4.2.0
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.2
    mcp: 1.18.0
    mdurl: 0.1.2
    mlx: 0.31.2
    mlx-metal: 0.31.2
    mrcfile: 1.5.4
    msgpack: 1.1.1
    multidict: 6.7.1
    narwhals: 2.23.0
    ndindex: 1.10.1
    nest-asyncio2: 1.7.2
    netCDF4: 1.7.4
    networkx: 3.3
    numba: 0.65.1
    numexpr: 2.14.1
    numpy: 2.4.6
    onnxruntime: 1.26.0
    OpenMM: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.7
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 26.1.2
    pkginfo: 1.12.1.2
    platformdirs: 4.10.0
    plotly: 6.8.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.5.2
    protobuf: 7.34.1
    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: 2.13.4
    pydantic-settings: 2.14.2
    pydantic_core: 2.46.4
    pydata-sphinx-theme: 0.20.0
    Pygments: 2.18.0
    pyKVFinder: 0.9.3
    pynmrstar: 3.5.1
    pynndescent: 0.6.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6: 6.10.2
    PyQt6-Qt6: 6.10.2
    PyQt6-WebEngine: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.2
    PyQt6_sip: 13.10.3
    pytest: 9.1.1
    pytest-cov: 7.1.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.32
    pyzmq: 27.1.0
    qtconsole: 5.7.2
    QtPy: 2.4.3
    qtshim: 1.2.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    rich: 15.0.0
    roman-numerals: 4.1.0
    rpds-py: 2026.6.3
    scikit-learn: 1.9.0
    scipy: 1.17.1
    setuptools: 82.0.1
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.1.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.4
    Sphinx: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    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: 3.4.5
    stack-data: 0.6.3
    starlette: 1.3.1
    superqt: 0.7.6
    tables: 3.11.1
    threadpoolctl: 3.6.0
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tomlkit: 0.15.0
    tornado: 6.5.7
    tqdm: 4.68.3
    traitlets: 5.15.1
    typing-inspection: 0.4.2
    typing_extensions: 4.16.0
    umap-learn: 0.5.12
    urllib3: 2.7.0
    uv: 0.11.26
    uvicorn: 0.51.0
    wcwidth: 0.8.2
    webcolors: 24.11.1
    wheel: 0.47.0
    wheel-filename: 1.4.2
    yarl: 1.24.2

[Tom Goddard]

Fixed.

Cast from numpy.bool to Python bool in volume viewer gui code.