volume flip: 'NoneType' object is not subscriptable

[um18fa@…]

The following bug report has been submitted:
Platform:        macOS-13.3-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
TypeError: 'NoneType' object is not subscriptable

File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map_filter/flip.py", line 87, in flip_matrix
m = m[::-1,:,:]
~^^^^^^^^^^

See log for complete Python traceback.


Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/francescappadoo/Desktop/EVs/160Sa_450box_round8_popro_masked.mrc

Opened 160Sa_450box_round8_popro_masked.mrc as #1, grid size 450,450,450,
pixel 0.82, shown at level 0.0056, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.00112

> volume #1 step 2

> volume flip #1 axis z

Opened 160Sa_450box_round8_popro_masked.mrc z flip as #2, grid size
450,450,450, pixel 0.82, shown at step 1, values float32  

> close #1

> ui tool show "Surface Color"

> color radial #2.1 palette #ff0000:#ffffff:#0000ff center 184.5,184.5,183.68

> color radial #2.1 palette 114.6,#00f900:141.8,#ff9300:168.9,#ff2600 center
> 184.5,184.5,183.68

> color radial #2.1 palette 114.6,#ff2600:141.8,#ff9300:168.9,#00f900 center
> 184.5,184.5,183.68

> ui tool show "Side View"

> close

> open /Users/francescappadoo/Desktop/EVs/160Sa_450box_round8_popro.mrc

Opened 160Sa_450box_round8_popro.mrc as #1, grid size 450,450,450, pixel 0.82,
shown at level 0.00683, step 2, values float32  

> volume flip #1 axis z

Opened 160Sa_450box_round8_popro.mrc z flip as #2, grid size 450,450,450,
pixel 0.82, shown at step 1, values float32  

> surface dust #2 size 8.2

> volume #1 level 0.00112

> close #1

> volume #2 level 0.00112

> color radial #2.1 palette 114.6,#ff2600:141.8,#ff9300:168.9,#00f900 center
> 184.5,184.5,183.68

> surface dust #2 size 8.2

> volume #2 level 0.002564

> volume #2 step 2

> volume #2 level 0.00112

> color radial #2.1 palette 114.6,#ff2600:141.8,#ff9300:168.9,#00f900 center
> 184.5,184.5,183.68

[Repeated 1 time(s)]

> color radial #2.1 palette 114.6,#ff2600:141.8,#ff9300:168.9,#00f900 center
> 183.68,183.68,183.68

> color single #2.1

> color radial #2.1 palette 114.6,#ff2600:141.8,#ff9300:168.9,#00f900 center
> 183.68,183.68,183.68

> color single #2.1

> color radial #2.1 palette 114.6,#ff2600:141.8,#ff9300:168.9,#00f900 center
> 183.68,183.68,183.68

> close #2

> open /Users/francescappadoo/Desktop/EVs/160Sa_450box_round8_popro_masked.mrc

Opened 160Sa_450box_round8_popro_masked.mrc as #1, grid size 450,450,450,
pixel 0.82, shown at level 0.0056, step 2, values float32  

> volume flip #1 axis z

Opened 160Sa_450box_round8_popro_masked.mrc z flip as #2, grid size
450,450,450, pixel 0.82, shown at step 1, values float32  

Surface Color: surface has no bounding box  

> color radial #1.1 palette 114.6,#ff2600:141.8,#ff9300:168.9,#00f900 center
> 184.5,184.5,184.5

> color radial #2.1 palette 114.6,#ff2600:141.8,#ff9300:168.9,#00f900 center
> 184.5,184.5,184.5

> volume #1 level 0.001616

> volume #1 level 0.00112

> color radial #2.1 palette 114.6,#ff2600:141.8,#ff9300:168.9,#00f900 center
> 184.5,184.5,184.5

[Repeated 3 time(s)]

> close

> open /Users/francescappadoo/Desktop/EVs/160ish_refine3D_r1.mrc

Opened 160ish_refine3D_r1.mrc as #1, grid size 450,450,450, pixel 0.82, shown
at level 0.00433, step 2, values float32  

> volume flip #1 axis z

Opened 160ish_refine3D_r1.mrc z flip as #2, grid size 450,450,450, pixel 0.82,
shown at step 1, values float32  

> volume #2 step 2

> volume #2 level 0.00112

Surface Color: surface has no bounding box  

[Repeated 1 time(s)]

> color radial #2.1 palette 114.6,#ff2600:141.8,#ff9300:168.9,#00f900 center
> 184.5,184.5,182.86

[Repeated 2 time(s)]

> surface dust #2 size 8.2

> color radial #2.1 palette 114.6,#ff2600:141.8,#ff9300:168.9,#00f900 center
> 184.5,184.5,182.86

No map chosen for coloring  

[Repeated 2 time(s)]

> open /Users/francescappadoo/Desktop/EVs/160ish_refine3D_r2.mrc

Opened 160ish_refine3D_r2.mrc as #3, grid size 450,450,450, pixel 0.82, shown
at level 0.00192, step 2, values float32  

> volume flip #3 axis z

Opened 160ish_refine3D_r2.mrc z flip as #4, grid size 450,450,450, pixel 0.82,
shown at step 1, values float32  

> volume #4 level 0.00112

> color radial #4.1 palette 114.6,#ff2600:141.8,#ff9300:168.9,#00f900 center
> 184.5,184.5,183.68

> surface dust #4 size 8.2

Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.  

> surface dust #4 size 8.2

> open /Users/francescappadoo/Desktop/EVs/3vbu_RBF_symmates_178zflip.pdb

Chain information for 3vbu_RBF_symmates_178zflip.pdb #5  
---  
Chain | Description  
A D E F G H I J | No description available  
B K L M N O P Q | No description available  
C R S T U V W X | No description available  
  

> hide #!4 models

> volume flip #3 axis z

Opened 160ish_refine3D_r2.mrc z flip as #6, grid size 450,450,450, pixel 0.82,
shown at step 1, values float32  

> hide #!6 models

> tile

1 model tiled  

> hide #!5 models

> show #!6 models

> hide #!6 models

> close #6

> show #!4 models

Error processing trigger "graphics update":  
  
You deleted or moved a volume file that is still open in ChimeraX.  
  
/Users/francescappadoo/Desktop/EVs/160ish_refine3D_r2.mrc  
  
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.  

> tile

1 model tiled  

> color radial #4.1 palette 114.6,#ff2600:141.8,#ff9300:168.9,#00f900 center
> 184.5,184.5,183.68

> color radial #4.1 palette 50,#ff2600:100,#ff9300:168.9,#00f900 center
> 184.5,184.5,183.68

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> color radial #4.1 palette 50,#ff2600:100,#ff9300:180,#00f900 center
> 184.5,184.5,183.68

> close

> open /Users/francescappadoo/Desktop/EVs/300c18.mrc

Opened 300c18.mrc as #1, grid size 450,450,450, pixel 0.82, shown at level
0.00363, step 2, values float32  

> volume flip #1 axis z

Opened 300c18.mrc z flip as #2, grid size 450,450,450, pixel 0.82, shown at
step 1, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2740, in update_cb  
s.update_histogram(rm, m, rz, delay = 0)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2748, in update_histogram  
s = v.matrix_value_statistics(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics  
matrices = self.displayed_matrices(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix  
m = self.region_matrix(r, read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix  
mf = flip_matrix(m, self.axes)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> close #2

> show #!1 models

> volume flip #1 axis z

Opened 300c18.mrc z flip as #2, grid size 450,450,450, pixel 0.82, shown at
step 1, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2740, in update_cb  
s.update_histogram(rm, m, rz, delay = 0)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2748, in update_histogram  
s = v.matrix_value_statistics(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics  
matrices = self.displayed_matrices(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix  
m = self.region_matrix(r, read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix  
mf = flip_matrix(m, self.axes)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> volume flip #1 axis z

Opened 300c18.mrc z flip as #3, grid size 450,450,450, pixel 0.82, shown at
step 1, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2740, in update_cb  
s.update_histogram(rm, m, rz, delay = 0)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2748, in update_histogram  
s = v.matrix_value_statistics(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics  
matrices = self.displayed_matrices(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix  
m = self.region_matrix(r, read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix  
mf = flip_matrix(m, self.axes)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix  
m = m[::-1,:,:]  
~^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Model Number: MGNA3B/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 8422.100.650
      OS Loader Version: 8422.100.650

Software:

    System Software Overview:

      System Version: macOS 13.3 (22E252)
      Kernel Version: Darwin 22.4.0
      Time since boot: 4 days, 4 hours, 25 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      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: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    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: 2.2.4
    ChimeraX-Clipper: 0.23.1
    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: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    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: 1.1.1
    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-ISOLDE: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    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-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    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: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    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: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    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: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

[Eric Pettersen]

Reported by Fran

[Tom Goddard]

I believe this is fixed in ChimeraX version 1.9. The code had a bug where opening a volume which is displayed at step 2 then trying to flip it about the z axis which displays it as step 1 failed because it tried to get the step 1 data from memory and it wasn't available. If you show the original volume at step 1 (command "volume #1 step 1") in ChimeraX 1.8 then I would expect the flip to work. But best to update to ChimeraX 1.9.