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
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Fixed.
numpy.bool8 is identical numpy.bool_ in numpy 1 and all the places it was being used checked both bool8 and bool_ so I removed the bool8 checks.