ChimeraX bug report submission

[goddard@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26200
ChimeraX Version: 1.13.dev202606291945 (2026-06-29 19:45:43 UTC)
Description
Testing ChimeraX with numpy 2 and scipy 1.17.1.  Session saving with an atomic structure and map open failed.

Log:
UCSF ChimeraX version: 1.13.dev202606291945 (2026-06-29)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6out format mmcif fromDatabase pdb

6out title:  
Asymmetric focused reconstruction of human norovirus GI.1 Norwalk strain VLP
asymmetric unit in T=3 symmetry [more info...]  
  
Chain information for 6out #1  
---  
Chain | Description | UniProt  
A B C | Capsid protein VP1 | CAPSD_NVN68 1-530  
  

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> open 20205 format ccp4 fromDatabase emdb

Opened emdb 20205 as #2, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at
level 0.12, step 1, values float32, fit PDB 6out  

> ui tool show "Fit in Map"

> fitmap #1 inMap #2

Fit molecule 6out (#1) to map emdb 20205 (#2) using 11505 atoms  
average map value = 0.2199, steps = 40  
shifted from previous position = 0.0158  
rotated from previous position = 0.00955 degrees  
atoms outside contour = 2078, contour level = 0.12  
  
Position of 6out (#1) relative to emdb 20205 (#2) coordinates:  
Matrix rotation and translation  
1.00000005 -0.00008842 0.00010416 0.00121584  
0.00008841 0.99999999 0.00009545 -0.01067205  
-0.00010417 -0.00009544 1.00000002 0.02653727  
Axis -0.57266673 0.62499114 0.53050814  
Axis point 220.56907337 0.00000000 -48.55415867  
Rotation angle (degrees) 0.00954947  
Shift along axis 0.00671203  
  
Opened 6out map 5 as #3, grid size 70,77,74, pixel 1.67, shown at level 0.101,
step 1, values float32  

> fitmap #1 inMap #2 resolution 5

Fit map 6out map 5 in map emdb 20205 using 44837 points  
correlation = 0.6634, correlation about mean = 0.7988, overlap = 1388  
steps = 40, shift = 0.0406, angle = 0.018 degrees  
  
Position of 6out map 5 (#3) relative to emdb 20205 (#2) coordinates:  
Matrix rotation and translation  
1.00000000 -0.00004464 0.00037953 -0.00815716  
0.00004455 1.00000009 0.00024108 -0.03235670  
-0.00037955 -0.00024106 0.99999979 0.08545076  
Axis -0.53353471 0.83999859 0.09870707  
Axis point 228.87199518 0.00000000 41.76951126  
Rotation angle (degrees) 0.02588816  
Shift along axis -0.01439286  
  
Average map value = 0.2195 for 11505 atoms, 2091 outside contour  

> show #!3 models

> hide #!3 models

> close #3

> ui tool show "Hide Dust"

> surface dust #2 size 6.42

> surface undust #2

> surface dust #2 size 6.42

> surface dust #2 size 2.23

> surface undust #2

> help help:user/tools/hidedust.html

> ui tool show "Map Coordinates"

> ui tool show "Map Eraser"

> volume erase #2 center 26.67,97.205,32.403 radius 20.743

Opened emdb 20205 copy as #4, grid size 98,112,104, pixel 1.07, shown at step
1, values float32  

> close #4

> save test.cxs

Traceback (most recent call last):  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\Lib\site-
packages\chimerax\core\session.py", line 1048, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\Lib\site-
packages\chimerax\core\session.py", line 696, in save  
from . import serialize  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\Lib\site-
packages\chimerax\core\serialize.py", line 52, in <module>  
from . import _serialize  
File "src/_serialize.pyx", line 58, in init chimerax.core._serialize  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\Lib\site-
packages\numpy\\__init__.py", line 805, in __getattr__  
raise AttributeError(f"module {__name__!r} has no attribute {attr!r}")  
AttributeError: module 'numpy' has no attribute 'bool8'  
  
AttributeError: module 'numpy' has no attribute 'bool8'  
  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\Lib\site-
packages\numpy\\__init__.py", line 805, in __getattr__  
raise AttributeError(f"module {__name__!r} has no attribute {attr!r}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 322, in execute  
cmd.run(cmd_text)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\Lib\site-
packages\chimerax\core\session.py", line 1048, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\Lib\site-
packages\chimerax\core\session.py", line 696, in save  
from . import serialize  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\Lib\site-
packages\chimerax\core\serialize.py", line 52, in <module>  
from . import _serialize  
File "src/_serialize.pyx", line 58, in init chimerax.core._serialize  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\Lib\site-
packages\numpy\\__init__.py", line 805, in __getattr__  
raise AttributeError(f"module {__name__!r} has no attribute {attr!r}")  
AttributeError: module 'numpy' has no attribute 'bool8'  
  
AttributeError: module 'numpy' has no attribute 'bool8'  
  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\Lib\site-
packages\numpy\\__init__.py", line 805, in __getattr__  
raise AttributeError(f"module {__name__!r} has no attribute {attr!r}")  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 595.95
OpenGL renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.9
Locale: en_US.cp1252
Qt version: PyQt6 6.11.0, Qt 6.11.0
Qt runtime version: 6.11.1
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 7000
OS: Microsoft Windows 11 Pro (Build 26200.8655)
Memory: 68,393,086,976
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700K
OSLanguage: en-US

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
    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: 2026.6.17
    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.dev202606291945
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.6
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    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-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
    comtypes: 1.4.11
    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
    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
    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
    msgpack: 1.1.1
    multidict: 6.7.1
    ndindex: 1.10.1
    nest-asyncio2: 1.7.2
    netCDF4: 1.6.5
    networkx: 3.3
    numexpr: 2.14.1
    numpy: 2.4.6
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.4.0
    OpenMM-CUDA-12: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.7
    pep517: 0.13.1
    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
    psutil: 7.0.0
    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
    pywin32: 311
    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
    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: 3.10.2
    threadpoolctl: 3.6.0
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.7
    traitlets: 5.15.1
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    urllib3: 2.7.0
    uvicorn: 0.49.0
    wcwidth: 0.8.2
    webcolors: 24.11.1
    wheel: 0.47.0
    wheel-filename: 1.4.2
    WMI: 1.5.1
    yarl: 1.24.2