measure center: Array argument has non-numeric values

[blz208813@…]

The following bug report has been submitted:
Platform:        macOS-15.3.2-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/kirti/Desktop/TF/Image/J58_viewing_direction_distribution_iteration_015.bild

Opened BILD data containing 3072 objects  

> open /Users/kirti/Desktop/TF/cryosparc_P2_J58_015_volume_map_sharp.mrc

Opened cryosparc_P2_J58_015_volume_map_sharp.mrc as #2, grid size 352,352,352,
pixel 0.86, shown at level 0.0774, step 2, values float32  

> volume #2 step 1

> set bgColor white

> lighting soft

> close session

> open /Users/kirti/Desktop/TF/CS/cryosparc_P2_J126_class_00_final_volume.mrc

Opened cryosparc_P2_J126_class_00_final_volume.mrc as #1, grid size
256,256,256, pixel 1.18, shown at level 0.0384, step 1, values float32  

> volume #1 level 0.05553

> volume #1 level 0.0313

> volume #1 level 0.06263

> open "/Users/kirti/Desktop/TF/CS/cryosparc_P2_whole map blur.mrc"
> /Users/kirti/Desktop/TF/CS/cryosparc_P2_J130_class_00_00045_volume_sharp.mrc

Opened cryosparc_P2_whole map blur.mrc as #2.1, grid size 256,256,256, pixel
1.18, shown at level 0.0394, step 1, values float32  
Opened cryosparc_P2_J130_class_00_00045_volume_sharp.mrc as #2.2, grid size
128,128,128, pixel 2.37, shown at level 0.158, step 1, values float32  

> volume #1 level 0.03645

> volume #2.2 level 0.1116

> volume #2.2 level 0.1908

> open
> /Users/kirti/Desktop/TF/CS/cryosparc_P2_cryosparc_P2_J126_class_00_final_volume_region_140.mrc

Opened cryosparc_P2_cryosparc_P2_J126_class_00_final_volume_region_140.mrc as
#3, grid size 256,256,256, pixel 1.18, shown at level 4.66e-06, step 1, values
float32  

> volume #3 level 0.01449

> volume #2.2 level 0.1137

> volume #2.2 level 0.09133

> volume #2.2 level 0.1055

> vop gaussian #2.2

Opened cryosparc_P2_J130_class_00_00045_volume_sharp.mrc gaussian as #4, grid
size 128,128,128, pixel 2.37, shown at step 1, values float32  

> vop gaussian #2.2 sd 2.5

Opened cryosparc_P2_J130_class_00_00045_volume_sharp.mrc gaussian as #5, grid
size 128,128,128, pixel 2.37, shown at step 1, values float32  

> volume #5 level 0.05528

> vop gaussian #2.2 sd 5

Opened cryosparc_P2_J130_class_00_00045_volume_sharp.mrc gaussian as #6, grid
size 128,128,128, pixel 2.37, shown at step 1, values float32  

> volume #6 level 0.02516

> volume #6 level 0.05262

> volume #6 level 0.01637

> ui tool show "Segment Map"

Segmenting cryosparc_P2_J130_class_00_00045_volume_sharp.mrc gaussian, density
threshold 0.016372  
Showing 6 region surfaces  
77 watershed regions, grouped to 6 regions  
Showing cryosparc_P2_J130_class_00_00045_volume_sharp gaussian.seg - 6
regions, 6 surfaces  
Smoothing and grouping, standard deviation 5 voxels  
No new groups smoothing 5 voxels  
Showing 4 region surfaces  
Got 4 regions after smoothing 6 voxels.  
Smoothing and grouping, standard deviation 7 voxels  
Showing 2 region surfaces  
Got 2 regions after smoothing 7 voxels.  
Ungrouped to 3 regions  
Ungrouped to 4 regions  
Segmenting cryosparc_P2_J130_class_00_00045_volume_sharp.mrc gaussian, density
threshold 0.016372  
Showing 19 region surfaces  
77 watershed regions, grouped to 19 regions  
Showing cryosparc_P2_J130_class_00_00045_volume_sharp gaussian.seg - 19
regions, 19 surfaces  
Got 18 regions after grouping by connections  
Got 17 regions after grouping by connections  
Got 16 regions after grouping by connections  
Got 15 regions after grouping by connections  
Got 14 regions after grouping by connections  
Got 13 regions after grouping by connections  
Got 12 regions after grouping by connections  
Got 11 regions after grouping by connections  

> select

27 models selected  

> select clear

> select add #7.1

1 model selected  

> select subtract #7.1

Nothing selected  

> select #7.1

1 model selected  
Saving 1 regions to mrc file...  
Opened cryosparc_P2_J130_class_00_00045_volume_sharp_region_143.mrc as #8,
grid size 100,64,63, pixel 2.37, shown at step 1, values float32  
Wrote cryosparc_P2_J130_class_00_00045_volume_sharp_region_143.mrc  

> vop resample #8 ongrid #2.2

Opened cryosparc_P2_J130_class_00_00045_volume_sharp_region_143.mrc resampled
as #9, grid size 128,128,128, pixel 2.37, shown at step 1, values float32  

> save /Users/kirti/Desktop/TF/chimera/cryosparc_P2_J130_class_00_maks.mrc
> models #9

> close #1

> close #2.1

> close #3

> close #4

> close #5

> close #7

> close #9

> close #8

> show #!6 models

> volume #6 level 0.08887

> volume #6 level 0.06031

> close #6

> show #!2.2 models

> volume #2.2 level 0.0893

> volume #2.2 level 0.1096

> volume #2.2 level 0.09945

> vop gaussian #2.2 sd 2.5

Opened cryosparc_P2_J130_class_00_00045_volume_sharp.mrc gaussian as #1, grid
size 128,128,128, pixel 2.37, shown at step 1, values float32  

> volume #1 level 0.09673

> vop gaussian #2.2 sd 4

Opened cryosparc_P2_J130_class_00_00045_volume_sharp.mrc gaussian as #3, grid
size 128,128,128, pixel 2.37, shown at step 1, values float32  

> volume #3 level 0.06364

> ui tool show "Segment Map"

Segmenting cryosparc_P2_J130_class_00_00045_volume_sharp.mrc gaussian, density
threshold 0.063645  
Showing 5 region surfaces  
49 watershed regions, grouped to 5 regions  
Showing cryosparc_P2_J130_class_00_00045_volume_sharp gaussian.seg - 5
regions, 5 surfaces  
Ungrouped to 5 regions  
Ungrouped to 19 regions  

> select #4.22

1 model selected  

> select add #4.21

2 models selected  
Drag select of 61, 384 of 10392 triangles, 14, 246 of 5148 triangles, 34, 244
of 2856 triangles, 40, 48 of 768 triangles, 3
cryosparc_P2_J130_class_00_00045_volume_sharp.mrc gaussian  

> select add #4.24

7 models selected  

> select add #4.22

8 models selected  

> select subtract #4.12

7 models selected  

> select subtract #4.23

6 models selected  

> select add #4.27

7 models selected  

> select add #4.25

8 models selected  

> select add #4.20

9 models selected  

> select add #4.19

10 models selected  
Drag select of 65, 194 of 14908 triangles, 64, 84 of 15444 triangles, 61, 209
of 10392 triangles, 63, 107 of 7308 triangles, 32, 26 of 4212 triangles, 60,
128 of 6316 triangles, 57, 175 of 8832 triangles, 59, 117 of 16160 triangles,
3 cryosparc_P2_J130_class_00_00045_volume_sharp.mrc gaussian  

> select clear

> select add #4.12

1 model selected  

> select add #4.13

2 models selected  

> select add #4.7

3 models selected  

> select add #4.4

4 models selected  
Drag select of 65, 194 of 14908 triangles, 64, 177 of 15444 triangles, 3
cryosparc_P2_J130_class_00_00045_volume_sharp.mrc gaussian  

> select add #4.4

7 models selected  

> select subtract #4.4

6 models selected  

> select subtract #4.2

5 models selected  

> select add #4.2

6 models selected  

> select add #4.26

7 models selected  
Showing 21 region surfaces  

> select add #4.4

8 models selected  
Showing 21 region surfaces  

> select add #4.14

9 models selected  

> select add #4.23

10 models selected  

> select subtract #4.23

9 models selected  

> select add #4.20

10 models selected  

> select subtract #4.20

9 models selected  

> select add #4.27

10 models selected  

> select subtract #4.27

9 models selected  
Showing 21 region surfaces  

> select add #4.11

10 models selected  
Showing 21 region surfaces  

> select ~sel & ##selected

Nothing selected  
Showing 21 region surfaces  

> undo

Showing 21 region surfaces  

> select ~sel & ##selected

Nothing selected  

> undo

> select ~sel

19 models selected  

> select subtract #4.1

18 models selected  
Grouped 12 regions  

> select ~sel

11 models selected  
Deleted 9 regions  

> undo

> select ~sel

2 models selected  

> open /Users/kirti/Desktop/TF/chimera/cryosparc_P2_J130_class_00_maks.mrc

Opened cryosparc_P2_J130_class_00_maks.mrc as #5, grid size 128,128,128, pixel
2.37, shown at level 0.142, step 1, values float32  

> volume #5 level 0.03637

> volume #5 level 0.02168

> close #3

> volume #1 level 0.04217

> volume #1 level 0.06247

> ui mousemode right "mark surface"

> select #5

2 models selected  

> select #5

2 models selected  

> marker #3 position 255.6,166.3,152 color #ff2600 radius 1

> ui tool show "Side View"

> marker #3 position 148.8,187.6,157.3 color #ff2600 radius 1

> volume #5 level 0.02407

> volume #5 level 0.02566

> volume #5 level 0.02088

> volume #5 level 0.02964

Drag select of 5 cryosparc_P2_J130_class_00_maks.mrc  

> marker #3 position 193.2,133.2,190.9 color #ff2600 radius 1

> marker #3 position 183.7,110.8,117.6 color #ff2600 radius 1

> marker #3 position 112.8,113,137 color #ff2600 radius 1

Drag select of 5 cryosparc_P2_J130_class_00_maks.mrc  

> marker #3 position 215.1,208.4,138 color #ff2600 radius 1

> ui mousemode right "delete markers"

> volume #5 level 0.05431

> volume #1 level 0.0612

> volume #1 level 0.0409

> ui mousemode right "delete markers"

[Repeated 2 time(s)]

> volume #5 level 0.03521

> volume #1 level 0.03456

> volume #5 level 0.01849

> centre #5

Unknown command: measure centre #5  

> measure center #5

Center of mass grid index for cryosparc_P2_J130_class_00_maks.mrc = (64.94,
66.68, 63.02)  
Center of mass xyz scene coordinates for cryosparc_P2_J130_class_00_maks.mrc =
(153.58, 157.69, 149.05)  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/measure_center.py", line 72, in measure_center  
areas = vertex_areas(surf.vertices, surf.triangles)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: Array argument has non-numeric values  
  
TypeError: Array argument has non-numeric values  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/measure_center.py", line 72, in measure_center  
areas = vertex_areas(surf.vertices, surf.triangles)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> measure center #5

Center of mass grid index for cryosparc_P2_J130_class_00_maks.mrc = (64.94,
66.68, 63.02)  
Center of mass xyz scene coordinates for cryosparc_P2_J130_class_00_maks.mrc =
(153.58, 157.69, 149.05)  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/measure_center.py", line 72, in measure_center  
areas = vertex_areas(surf.vertices, surf.triangles)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: Array argument has non-numeric values  
  
TypeError: Array argument has non-numeric values  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/measure_center.py", line 72, in measure_center  
areas = vertex_areas(surf.vertices, surf.triangles)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




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

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: MNEJ3HN/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 11881.81.4
      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: 13 days, 1 hour, 54 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:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    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
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

[pett]

Reported by Kirti

[Tom Goddard]

This bug with the measure center command is fixed in the ChimeraX release candidates and daily builds. The previous report of this error happened when clipping was being used.