Opened 8 hours ago

Last modified 7 hours ago

#20564 assigned defect

Several volume file readers use numpy fromstring() which does not work in numpy 2

Reported by: goddard@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-26.5.2-arm64-arm-64bit
ChimeraX Version: 1.13.dev202606302219 (2026-06-30 22:19:15 UTC)
Description
Reading an EMDB tomogram broken with numpy 2.

Log:
UCSF ChimeraX version: 1.13.dev202606302219 (2026-06-30)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1273 fromDatabase emdb

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 322, in execute  
cmd.run(cmd_text)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 138, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 184, in provider_open  
models, status = collated_open(session, database_name, ident,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 547, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 518, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 169, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/emdb_fetch.py", line 95, in fetch_emdb  
models, status = session.open_command.open_data(filename, format = 'ccp4',  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/manager.py", line 226, in open_data  
return provider_open(self.session, [path], _return_status=True,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 212, in provider_open  
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 548, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 518, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open  
return open_map(session, path, format=_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3941, in open_map  
smodels, smsg = open_grids(session, sgrids, name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4043, in open_grids  
v.update_drawings()  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 836, in update_drawings  
self.image_levels, self.image_colors = self.initial_image_levels()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 656, in initial_image_levels  
mstats = self.matrix_value_statistics()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1759, in matrix_value_statistics  
matrices = self.displayed_matrices(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1794, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1277, in matrix  
m = self.region_matrix(r, read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1301, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.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
"/Users/goddard/ucsf/chimerax/ChimeraX.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
"/Users/goddard/ucsf/chimerax/ChimeraX.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
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/readarray.py", line 67, in read_array  
slice = fromstring(data, type)  
^^^^^^^^^^^^^^^^^^^^^^  
ValueError: The binary mode of fromstring is removed, use frombuffer instead  
  
ValueError: The binary mode of fromstring is removed, use frombuffer instead  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/readarray.py", line 67, in read_array  
slice = fromstring(data, type)  
^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




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

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.11.0, Qt 6.11.0
Qt runtime version: 6.11.1
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: 1 day, 2 hours, 55 minutes

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: 2.6.2
    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: 4.7.0
    build: 1.5.0
    certifi: 2025.8.3
    cftime: 1.6.5
    charset-normalizer: 3.4.7
    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: 1.69.2
    ChimeraX-AtomicLibrary: 14.4.1
    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: 1.4.1
    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.dev202606302219
    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: 1.8.3
    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: 2.19.1
    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: 1.8.2
    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: 1.52
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.4
    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
    click: 8.4.2
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.14.3
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    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: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.16.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.18
    ihm: 2.2
    imagecodecs: 2024.6.1
    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
    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: 4.3.2
    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
    ndindex: 1.10.1
    nest-asyncio2: 1.7.2
    netCDF4: 1.6.5
    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
    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: 0.19.0
    Pygments: 2.18.0
    pynmrstar: 3.5.1
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6: 6.11.0
    PyQt6-Qt6: 6.11.1
    PyQt6-WebEngine: 6.11.0
    PyQt6-WebEngine-Qt6: 6.11.1
    PyQt6_sip: 13.11.1
    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
    scipy: 1.17.1
    setuptools: 82.0.1
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Change History (4)

comment:1 by Tom Goddard, 8 hours ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Several volume file readers use numpy fromstring() which does not work in numpy 2

comment:2 by Tom Goddard, 8 hours ago

PIF, DSN6, IMAGIC, Delphi, TomEM, Spider, Priism, UHBD, DeltaVision, DOCK formats all used fromstring(), in addition to the generic map reading code that extracted subvolumes from binary files in MRC, CCP4 and other formats.

comment:3 by Tom Goddard, 8 hours ago

Also writing DSN6, MRC, IMAGIC files was broken due to use of the numpy tostring() method.

And IMS and netcdf readers were also broken from use of tostring().

comment:4 by Tom Goddard, 7 hours ago

I fixed the fromstring problems in a dozen file readers and tested. I have not yet tested the file writing fixes caused by tostring.

NetCDF, DSN6, and HDF5 readers have additional numpy 2 problems I've reported as #20566, #20567 and #20568.

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