UnicodeDecodeError in numpy checking SVE

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.1.0-21-amd64-x86_64-with-glibc2.35
ChimeraX Version: 1.7.dev202312142006 (2023-12-14 20:06:35 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.7.dev202312142006 (2023-12-14)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1OKE format mmcif fromDatabase pdb

1oke title:  
Crystal structure of the dengue 2 virus envelope protein in complex with
n-octyl-beta-D-glucoside [more info...]  
  
Chain information for 1oke #1  
---  
Chain | Description | UniProt  
A B | MAJOR ENVELOPE PROTEIN E | POLG_DEN2P 1-394  
  
Non-standard residues in 1oke #1  
---  
BMA — beta-D-mannopyranose  
BOG — octyl beta-D-glucopyranoside  
FUL — beta-L-fucopyranose (6-deoxy-β-L-galactose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  

> hide cartoons

> show cartoons

> style sphere

Changed 6426 atom styles  

> show surfaces

[Repeated 1 time(s)]

> color bychain

> color byhetero

> color bypolymer

> rainbow

> color bychain

> graphics silhouettes true

> lighting flat

> lighting full

> graphics silhouettes false

> lighting simple

[Repeated 1 time(s)]

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting full

> lighting soft

> lighting full

> lighting soft

> open /home/doncho/Descargas/Cypfarma.pdb format pdb

Summary of feedback from opening /home/doncho/Descargas/Cypfarma.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Accelrys Discovery Studio PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2023-10-29T11:17:38Z  
note | Combining 2 symmetry atoms into HEM /A:601 FE  
  
Chain information for Cypfarma.pdb #2  
---  
Chain | Description  
A | No description available  
  

> hide #!1 target m

> view #2 clip false

> select /?:SUB 1

Expected a keyword  

> select /?:SUB1

Nothing selected  

> cartoon style #2 modeHelix tube sides 20

Traceback (most recent call last):  
File "/app/lib/python3.11/site-packages/chimerax/core/triggerset.py", line
149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/app/lib/python3.11/site-packages/chimerax/atomic/structure.py", line
1891, in _update_graphics_if_needed  
s[i].update_graphics_if_needed()  
File "/app/lib/python3.11/site-packages/chimerax/atomic/structure.py", line
357, in update_graphics_if_needed  
self._create_ribbon_graphics()  
File "/app/lib/python3.11/site-packages/chimerax/atomic/structure.py", line
667, in _create_ribbon_graphics  
ribbons_drawing.compute_ribbons(self)  
File "/app/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 600,
in compute_ribbons  
_make_ribbon_graphics(structure, self)  
File "/app/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 141,
in _make_ribbon_graphics  
centers = _arc_helix_geometry(coords, xs_mgr, displays, start, end, geometry)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/app/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 980,
in _arc_helix_geometry  
hc = HelixCylinder(coords[start:end])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/app/lib/python3.11/site-packages/chimerax/atomic/sse.py", line 196, in
__init__  
self._straight_optimize()  
File "/app/lib/python3.11/site-packages/chimerax/atomic/sse.py", line 409, in
_straight_optimize  
opt = OptLine(self.coords, centroid, axis)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/app/lib/python3.11/site-packages/chimerax/atomic/sse.py", line 36, in
__init__  
from scipy.optimize import minimize  
File "/app/lib/python3.11/site-packages/scipy/optimize/__init__.py", line 410,
in <module>  
from ._minimize import *  
File "/app/lib/python3.11/site-packages/scipy/optimize/_minimize.py", line 27,
in <module>  
from ._trustregion_constr import _minimize_trustregion_constr  
File "/app/lib/python3.11/site-
packages/scipy/optimize/_trustregion_constr/__init__.py", line 4, in <module>  
from .minimize_trustregion_constr import _minimize_trustregion_constr  
File "/app/lib/python3.11/site-
packages/scipy/optimize/_trustregion_constr/minimize_trustregion_constr.py",
line 5, in <module>  
from .._constraints import (  
File "/app/lib/python3.11/site-packages/scipy/optimize/_constraints.py", line
8, in <module>  
from numpy.testing import suppress_warnings  
File "/app/lib/python3.11/site-packages/numpy/testing/__init__.py", line 11,
in <module>  
from ._private.utils import *  
File "/app/lib/python3.11/site-packages/numpy/testing/_private/utils.py", line
1253, in <module>  
_SUPPORTS_SVE = check_support_sve()  
^^^^^^^^^^^^^^^^^^^  
File "/app/lib/python3.11/site-packages/numpy/testing/_private/utils.py", line
1247, in check_support_sve  
output = subprocess.run(cmd, capture_output=True, text=True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/app/lib/python3.11/subprocess.py", line 550, in run  
stdout, stderr = process.communicate(input, timeout=timeout)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/app/lib/python3.11/subprocess.py", line 1207, in communicate  
stdout, stderr = self._communicate(input, endtime, timeout)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/app/lib/python3.11/subprocess.py", line 2097, in _communicate  
stdout = self._translate_newlines(stdout,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/app/lib/python3.11/subprocess.py", line 1084, in _translate_newlines  
data = data.decode(encoding, errors)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 64:
ordinal not in range(128)  
  
Error processing trigger "graphics update":  
UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 64:
ordinal not in range(128)  
  
File "/app/lib/python3.11/subprocess.py", line 1084, in _translate_newlines  
data = data.decode(encoding, errors)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 550.54.15
OpenGL renderer: NVIDIA GeForce RTX 3050 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: es_MX.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=plasma
XDG_SESSION_DESKTOP=KDE
XDG_CURRENT_DESKTOP=KDE
DISPLAY=:0
Manufacturer: Acer
Model: Nitro AN517-55
OS: Freedesktop SDK 22.08 Flatpak runtime
Architecture: 64bit ELF
Virtual Machine: detection failed
CPU: 16 12th Gen Intel(R) Core(TM) i5-12500H
Cache Size: 18432 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            15Gi       3.5Gi       9.1Gi       524Mi       2.8Gi        11Gi
	Swap:          7.4Gi          0B       7.4Gi

Graphics:
	0000:00:02.0 VGA compatible controller [0300]: Intel Corporation Alder Lake-P Integrated Graphics Controller [8086:4626] (rev 0c)	
	Subsystem: Acer Incorporated [ALI] Device [1025:1597]	
	Kernel driver in use: i915

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202312142006
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.46.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.3
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.0
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

[Tom Goddard]

This is a bug in numpy, the Python numeric array library. The ChimeraX daily build uses a newer version of numpy and this bug has not been reported for the newer numpy, so it may be fixed. You can try the ChimeraX daily build.

The command that caused this error is switching the ribbon style to tube helices

cartoon style #2 modeHelix tube sides 20

That uses numpy in computing the curve of the helix. You can test that in the current ChimeraX daily build to see if the problem is fixed.

Duplicate of bug #14721.