id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15253 UnicodeDecodeError in numpy checking SVE chimerax-bug-report@… Tom Goddard "{{{ 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 from ._minimize import * File ""/app/lib/python3.11/site-packages/scipy/optimize/_minimize.py"", line 27, in from ._trustregion_constr import _minimize_trustregion_constr File ""/app/lib/python3.11/site- packages/scipy/optimize/_trustregion_constr/__init__.py"", line 4, in 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 from .._constraints import ( File ""/app/lib/python3.11/site-packages/scipy/optimize/_constraints.py"", line 8, in from numpy.testing import suppress_warnings File ""/app/lib/python3.11/site-packages/numpy/testing/__init__.py"", line 11, in from ._private.utils import * File ""/app/lib/python3.11/site-packages/numpy/testing/_private/utils.py"", line 1253, in _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 }}} " defect closed normal Core nonchimerax Greg Couch all ChimeraX