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Opened 5 hours ago
#19769 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: Linux-6.14.0-37-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
Startup Errors
---
errors | Bundle 'SEQCROW' custom initialization failed
Bundle 'SEQCROW' custom initialization failed
warnings | Traceback (most recent call last):
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/__init__.py", line 83, in <module>
from scipy._lib._ccallback import LowLevelCallable
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/_lib/_ccallback.py", line 1, in <module>
from . import _ccallback_c
ImportError: cannot import name '_ccallback_c' from 'scipy._lib'
(/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/_lib/__init__.py)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 387, in init_manager
return api._api_caller.init_manager(api, session, self, name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1416, in init_manager
return cls._get_func(api, "init_manager")(session, bi, name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/SEQCROW/__init__.py", line 347, in init_manager
from .managers import FileReaderManager
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/SEQCROW/managers/__init__.py", line 1, in <module>
from .filereader_manager import FileReaderManager, FILEREADER_CHANGE,
FILEREADER_REMOVED, FILEREADER_ADDED, ADD_FILEREADER
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/SEQCROW/managers/filereader_manager.py", line 10, in <module>
from AaronTools.fileIO import FileReader
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/AaronTools/fileIO.py", line 16, in <module>
from AaronTools.orbitals import Orbitals
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 6, in <module>
from scipy.spatial.distance import pdist, cdist, squareform
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/__init__.py", line 88, in <module>
raise ImportError(msg) from e
ImportError: The `scipy` install you are using seems to be broken, (extension
modules cannot be imported), please try reinstalling.
Traceback (most recent call last):
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/__init__.py", line 83, in <module>
from scipy._lib._ccallback import LowLevelCallable
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/_lib/_ccallback.py", line 1, in <module>
from . import _ccallback_c
ImportError: cannot import name '_ccallback_c' from 'scipy._lib'
(/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/_lib/__init__.py)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 376, in initialize
api._api_caller.initialize(api, session, self)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1412, in initialize
return cls._get_func(api, "initialize")(session, bi)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/SEQCROW/__init__.py", line 73, in initialize
from SEQCROW.mouse_modes import (
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/SEQCROW/mouse_modes.py", line 23, in <module>
from SEQCROW.managers.filereader_manager import apply_seqcrow_preset
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/SEQCROW/managers/__init__.py", line 1, in <module>
from .filereader_manager import FileReaderManager, FILEREADER_CHANGE,
FILEREADER_REMOVED, FILEREADER_ADDED, ADD_FILEREADER
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/SEQCROW/managers/filereader_manager.py", line 10, in <module>
from AaronTools.fileIO import FileReader
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/AaronTools/fileIO.py", line 16, in <module>
from AaronTools.orbitals import Orbitals
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 6, in <module>
from scipy.spatial.distance import pdist, cdist, squareform
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/__init__.py", line 88, in <module>
raise ImportError(msg) from e
ImportError: The `scipy` install you are using seems to be broken, (extension
modules cannot be imported), please try reinstalling.
GBM is not supported with the current configuration. Fallback to Vulkan
rendering in Chromium.
Traceback (most recent call last):
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/__init__.py", line 83, in <module>
from scipy._lib._ccallback import LowLevelCallable
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/_lib/_ccallback.py", line 1, in <module>
from . import _ccallback_c
ImportError: cannot import name '_ccallback_c' from 'scipy._lib'
(/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/_lib/__init__.py)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/SEQCROW/__init__.py", line 60, in <lambda>
lambda *args, ses=session: _SEQCROW_API.register_selector_menus(ses)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/SEQCROW/__init__.py", line 1145, in register_selector_menus
from AaronTools.geometry import Geometry
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/AaronTools/geometry.py", line 11, in <module>
from scipy.spatial import distance_matrix, distance
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/__init__.py", line 88, in <module>
raise ImportError(msg) from e
ImportError: The `scipy` install you are using seems to be broken, (extension
modules cannot be imported), please try reinstalling.
Error processing trigger "ready":
ImportError: The `scipy` install you are using seems to be broken, (extension
modules cannot be imported), please try reinstalling.
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/__init__.py", line 88, in
raise ImportError(msg) from e
See log for complete Python traceback.
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 NVIDIA 580.126.09
OpenGL renderer: NVIDIA GeForce GTX 1070 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.13
Locale: zh_CN.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: xcb
XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu-wayland
XDG_SESSION_DESKTOP=ubuntu-wayland
XDG_CURRENT_DESKTOP=ubuntu:GNOME
GNOME_SETUP_DISPLAY=:2
DISPLAY=:1
WAYLAND_DISPLAY=wayland-0
Manufacturer: HUANANZHI
Model:
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 88 Intel(R) Xeon(R) CPU E5-2696 v4 @ 2.20GHz
Cache Size: 56320 KB
Memory:
total used free shared buff/cache available
Mem: 125Gi 7.2Gi 108Gi 253Mi 11Gi 118Gi
Swap: 8.0Gi 0B 8.0Gi
Graphics:
05:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Lexa XT [Radeon PRO WX 3100] [1002:6985]
Subsystem: Dell Lexa XT [Radeon PRO WX 3100] [1028:0b0c]
Kernel driver in use: amdgpu
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.0
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.11.12
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
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: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
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
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: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DAQplugin: 0.13.0
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: 2.5.3
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: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.11
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: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
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: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
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: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.5
pyproject_hooks: 1.2.0
PyQt6: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pytz: 2025.2
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.0.0
roman-numerals-py: 4.0.0
rpds-py: 0.30.0
scipy: 1.16.1
scipy: 1.14.0
SEQCROW: 1.9.7
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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: 3.0.4
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.3
urllib3: 2.6.2
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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