Save MRC file: could not broadcast input array

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.10rc202506101855 (2025-06-10 18:55:00 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10rc202506101855 (2025-06-10)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/danylo/Desktop/TraI_cryoEM_workflows/TraIdN_monomer/3D_maps/TraIdN_monomer_J80.mrc
> /Users/danylo/Desktop/TraI_cryoEM_workflows/TraIdN_monomer/3D_maps/TraIdN_monomer_J78_class4.mrc
> /Users/danylo/Desktop/TraI_cryoEM_workflows/TraIdN_monomer/3D_maps/TraIdN_monomer_J78_class3.mrc
> /Users/danylo/Desktop/TraI_cryoEM_workflows/TraIdN_monomer/3D_maps/TraIdN_monomer_J78_class2.mrc
> /Users/danylo/Desktop/TraI_cryoEM_workflows/TraIdN_monomer/3D_maps/TraIdN_monomer_J78_class1.mrc
> /Users/danylo/Desktop/TraI_cryoEM_workflows/TraIdN_monomer/3D_maps/TraIdN_monomer_J78_class0.mrc
> /Users/danylo/Desktop/TraI_cryoEM_workflows/TraIdN_monomer/3D_maps/TraIdN_monomer_J73.mrc
> /Users/danylo/Desktop/TraI_cryoEM_workflows/TraIdN_monomer/3D_maps/TraIdN_monomer_J72.mrc
> /Users/danylo/Desktop/TraI_cryoEM_workflows/TraIdN_monomer/3D_maps/TraIdN_monomer_J69.mrc
> /Users/danylo/Desktop/TraI_cryoEM_workflows/TraIdN_monomer/3D_maps/TraIdN_monomer_J55_class2.mrc
> /Users/danylo/Desktop/TraI_cryoEM_workflows/TraIdN_monomer/3D_maps/TraIdN_monomer_J55_class1.mrc
> /Users/danylo/Desktop/TraI_cryoEM_workflows/TraIdN_monomer/3D_maps/TraIdN_monomer_J55_class0.mrc

Opened TraIdN_monomer_J80.mrc as #1.1, grid size 320,320,320, pixel 0.84,
shown at level 0.102, step 2, values float32  
Opened TraIdN_monomer_J78_class4.mrc as #1.2, grid size 60,60,60, pixel 4.48,
shown at level 1.68, step 1, values float32  
Opened TraIdN_monomer_J78_class3.mrc as #1.3, grid size 60,60,60, pixel 4.48,
shown at level 1.65, step 1, values float32  
Opened TraIdN_monomer_J78_class2.mrc as #1.4, grid size 60,60,60, pixel 4.48,
shown at level 1.72, step 1, values float32  
Opened TraIdN_monomer_J78_class1.mrc as #1.5, grid size 60,60,60, pixel 4.48,
shown at level 1.69, step 1, values float32  
Opened TraIdN_monomer_J78_class0.mrc as #1.6, grid size 60,60,60, pixel 4.48,
shown at level 1.68, step 1, values float32  
Opened TraIdN_monomer_J73.mrc as #1.7, grid size 320,320,320, pixel 0.84,
shown at level 0.097, step 2, values float32  
Opened TraIdN_monomer_J72.mrc as #1.8, grid size 128,128,128, pixel 2.1, shown
at level 0.47, step 1, values float32  
Opened TraIdN_monomer_J69.mrc as #1.9, grid size 80,80,80, pixel 3.36, shown
at level 0.898, step 1, values float32  
Opened TraIdN_monomer_J55_class2.mrc as #1.10, grid size 80,80,80, pixel 3.36,
shown at level 0.869, step 1, values float32  
Opened TraIdN_monomer_J55_class1.mrc as #1.11, grid size 80,80,80, pixel 3.36,
shown at level 0.771, step 1, values float32  
Opened TraIdN_monomer_J55_class0.mrc as #1.12, grid size 80,80,80, pixel 3.36,
shown at level 0.695, step 1, values float32  

> view

> open
> /Users/danylo/Desktop/TraI_cryoEM_workflows/TraIFL_dimer/3D_maps/TraIFL_dimer_J207.mrc

Opened TraIFL_dimer_J207.mrc as #2, grid size 320,320,320, pixel 0.84, shown
at level 0.129, step 2, values float32  

> close #2

> volume flip #1.1

Opened TraIdN_monomer_J80.mrc z flip as #2, grid size 320,320,320, pixel 0.84,
shown at step 1, values float32  

> close #1.1

> close #1.2

> close #1.3

> close #1.4

> close #1.5

> close #1.6

> close #1.7

> close #1.8

> close #1.9

> close #1.10

> close #1.11

> close #1.12

> close #2

> open
> /Users/danylo/Desktop/TraI_cryoEM_workflows/TraIdN_monomer/3D_maps/TraIdN_monomer_J78_class4.mrc

Opened TraIdN_monomer_J78_class4.mrc as #2, grid size 60,60,60, pixel 4.48,
shown at level 1.68, step 1, values float32  

> volume flip #2

Opened TraIdN_monomer_J78_class4.mrc z flip as #3, grid size 60,60,60, pixel
4.48, shown at step 1, values float32  

> close #2

> save
> /Users/danylo/Desktop/TraI_cryoEM_workflows/TraIdN_monomer/3D_maps/TraIdN_monomer_J78_class4.mrc
> models #3

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10-rc2025.06.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.10-rc2025.06.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.10-rc2025.06.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.10-rc2025.06.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.10-rc2025.06.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 200, in save  
save_map(session, path, _name, **kw)  
File
"/Applications/ChimeraX-1.10-rc2025.06.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4028, in save_map  
save_grid_data(grids, path, session, format_name, options)  
File
"/Applications/ChimeraX-1.10-rc2025.06.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/fileformats.py", line 326, in save_grid_data  
ff.save_func(garg, tpath, options = options, progress = p)  
File
"/Applications/ChimeraX-1.10-rc2025.06.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/mrc/writemrc.py", line 73, in
write_mrc2000_grid_data  
matrix = grid_data.matrix((0,0,k), (isz,jsz,1))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 39, in matrix  
m = self.data.matrix(origin, ijk_size, ijk_step, progress=progress,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/griddata.py", line 317, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 50, in read_matrix  
m = self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 287, in read_matrix  
matrix = read_array(self.path, self.data_offset,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/readarray.py", line 68, in read_array  
matrix[(k-ko)//kstep,(j-jo)//jstep,:] = slice[::istep]  
~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: could not broadcast input array from shape (0,) into shape (60,)  
  
ValueError: could not broadcast input array from shape (0,) into shape (60,)  
  
File
"/Applications/ChimeraX-1.10-rc2025.06.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/readarray.py", line 68, in read_array  
matrix[(k-ko)//kstep,(j-jo)//jstep,:] = slice[::istep]  
~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: Z16S000CRB/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
      Time since boot: 59 minutes, 5 seconds

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:
        MateView:
          Resolution: 3840 x 2560
          UI Looks like: 1920 x 1280 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.3.4
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    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: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    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
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10rc202506101855
    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: 2.5.1
    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: 1.6.2
    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: 2.2.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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
    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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    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-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: 1.45.1
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.8.2
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.2
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    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: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
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[Tom Goddard]

User did volume flip #2 ; close #2 ; save flipped.mrc models #3. The flipped map uses the volume cache from map #2. I think I've fixed this about 3 times in the past few years but I never seem to get it right. I'll try to reproduce it.

[Tom Goddard]

I see the problem and can reproduce it. The saved the new map with the same file name as the source map that was flipped and ChimeraX tried to read the data from the source map since it was not cached because the source map had been closed.

[Tom Goddard]

One day I may change volume flip so it makes a new full copy of the map in memory. The current behavior where it uses the source map was intended to allow flipping large maps that don't fit in memory. I could have an option if you need that obscure capability.

For now I think I'm not going to fix this. This basic error where the user modifies a map file on disk (often deleting it) while ChimeraX is still using it happens in other circumstances. Reading only the part of the map needed for display is an important optimization that allows fast display of maps and I think it is worth the trouble that the user fails to realize they can't delete the map file while it is being used in ChimeraX. In this volume flip case the user almost surely won't realize it is still using the source map file.