id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8746 ORCA file: 'utf-8' codec can't decode byte steffen@… Tony Schaefer "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.22621 ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description Opening an actual orca output brings this error. OS is windows 11 (german) Log: Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > toolshed show Downloading bundle SEQCROW-1.6.4-py3-none-any.whl Errors may have occurred when running pip: pip standard error: \--- [notice] A new release of pip available: 22.2.2 -> 23.0.1 [notice] To update, run: C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\wotan\downloads\seqcrow-1.6.4-py3-none-any.whl Collecting Send2Trash Using cached Send2Trash-1.8.0-py3-none-any.whl (18 kB) Requirement already satisfied: jinja2 in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.6.4) (3.1.2) Requirement already satisfied: ChimeraX-Core<=1.6,>=1.3 in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.6.4) (1.5) Requirement already satisfied: psutil in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.6.4) (5.9.1) Collecting basis-set-exchange Downloading basis_set_exchange-0.9.tar.gz (32.2 MB) \---------------------------------------- 32.2/32.2 MB 6.4 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Requirement already satisfied: scipy in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.6.4) (1.9.0) Collecting jsonschema Using cached jsonschema-4.17.3-py3-none-any.whl (90 kB) Collecting argcomplete Downloading argcomplete-3.0.5-py3-none-any.whl (40 kB) \---------------------------------------- 40.2/40.2 kB 2.0 MB/s eta 0:00:00 Collecting regex Downloading regex-2023.3.23-cp39-cp39-win_amd64.whl (267 kB) \-------------------------------------- 268.0/268.0 kB 5.5 MB/s eta 0:00:00 Requirement already satisfied: MarkupSafe>=2.0 in c:\program files\chimerax\bin\lib\site-packages (from jinja2->SEQCROW==1.6.4) (2.1.1) Requirement already satisfied: numpy<1.25.0,>=1.18.5 in c:\program files\chimerax\bin\lib\site-packages (from scipy->SEQCROW==1.6.4) (1.23.1) Collecting pyrsistent!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0 Downloading pyrsistent-0.19.3-cp39-cp39-win_amd64.whl (62 kB) \---------------------------------------- 62.7/62.7 kB 3.3 MB/s eta 0:00:00 Collecting attrs>=17.4.0 Using cached attrs-22.2.0-py3-none-any.whl (60 kB) Building wheels for collected packages: basis-set-exchange Building wheel for basis-set-exchange (setup.py): started Building wheel for basis-set-exchange (setup.py): finished with status 'done' Created wheel for basis-set-exchange: filename=basis_set_exchange-0.9-py3-none-any.whl size=34927000 sha256=2a3811b9796b2cd67493c4cdde50d4aebd30a3826527b593c05bb3cf9dcbcf35 Stored in directory: c:\users\wotan\appdata\local\pip\cache\wheels\91\3c\d5\a297a1089086aa777b3ccbd3e9ee227d715882482a7e6a1eea Successfully built basis-set-exchange Installing collected packages: Send2Trash, regex, pyrsistent, attrs, argcomplete, jsonschema, basis-set-exchange, SEQCROW Successfully installed SEQCROW-1.6.4 Send2Trash-1.8.0 argcomplete-3.0.5 attrs-22.2.0 basis-set-exchange-0.9 jsonschema-4.17.3 pyrsistent-0.19.3 regex-2023.3.23 \--- Successfully installed SEQCROW-1.6.4 Send2Trash-1.8.0 argcomplete-3.0.5 attrs-22.2.0 basis-set-exchange-0.9 jsonschema-4.17.3 pyrsistent-0.19.3 regex-2023.3.23 Installed SEQCROW (1.6.4) > ui tool show ""File Info"" > ui tool show ""AaronTools Fragment Library"" > open E:/Arbeit/orca/kalibrierung1/chloroform.out Summary of feedback from opening E:/Arbeit/orca/kalibrierung1/chloroform.out --- error | unable to open chloroform.out Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\dialog.py"", line 162, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 193, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 457, in collated_open return remember_data_format() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File ""C:\Users\wotan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\SEQCROW\\__init__.py"", line 430, in open return open_aarontools( File ""C:\Users\wotan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\SEQCROW\io.py"", line 44, in open_aarontools raise e File ""C:\Users\wotan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\SEQCROW\io.py"", line 36, in open_aarontools fr = FileReader( File ""C:\Users\wotan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\AaronTools\fileIO.py"", line 1535, in __init__ self.read_orca_out(f, get_all, just_geom) File ""C:\Users\wotan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\AaronTools\fileIO.py"", line 2189, in read_orca_out line = f.readline() File ""C:\Program Files\ChimeraX\bin\lib\codecs.py"", line 322, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 0: invalid start byte UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 0: invalid start byte File ""C:\Program Files\ChimeraX\bin\lib\codecs.py"", line 322, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) See log for complete Python traceback. > help help:quickstart > open E:/Arbeit/orca/kalibrierung1/chloroform.inp Unrecognized file suffix '.inp' > open E:/Arbeit/orca/kalibrierung1/methanol.out Summary of feedback from opening E:/Arbeit/orca/kalibrierung1/methanol.out --- error | unable to open methanol.out Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\dialog.py"", line 162, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 193, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 457, in collated_open return remember_data_format() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File ""C:\Users\wotan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\SEQCROW\\__init__.py"", line 430, in open return open_aarontools( File ""C:\Users\wotan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\SEQCROW\io.py"", line 44, in open_aarontools raise e File ""C:\Users\wotan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\SEQCROW\io.py"", line 36, in open_aarontools fr = FileReader( File ""C:\Users\wotan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\AaronTools\fileIO.py"", line 1535, in __init__ self.read_orca_out(f, get_all, just_geom) File ""C:\Users\wotan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\AaronTools\fileIO.py"", line 2189, in read_orca_out line = f.readline() File ""C:\Program Files\ChimeraX\bin\lib\codecs.py"", line 322, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 0: invalid start byte UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 0: invalid start byte File ""C:\Program Files\ChimeraX\bin\lib\codecs.py"", line 322, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 531.41 OpenGL renderer: NVIDIA GeForce RTX 3080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: de_DE.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: Alienware Model: Alienware Aurora R13 OS: Microsoft Windows 11 Pro (Build 22621) Memory: 34,141,798,400 MaxProcessMemory: 137,438,953,344 CPU: 24 12th Gen Intel(R) Core(TM) i9-12900KF OSLanguage: de-DE Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 argcomplete: 3.0.5 asttokens: 2.1.0 attrs: 22.2.0 Babel: 2.11.0 backcall: 0.2.0 basis-set-exchange: 0.9 blockdiag: 3.0.0 build: 0.8.0 certifi: 2022.9.24 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 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-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 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: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 comtypes: 1.1.10 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jsonschema: 4.17.3 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 pyrsistent: 0.19.3 python-dateutil: 2.8.2 pytz: 2022.6 pywin32: 303 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 regex: 2023.3.23 requests: 2.28.1 scipy: 1.9.0 Send2Trash: 1.8.0 SEQCROW: 1.6.4 setuptools: 65.1.1 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 WMI: 1.5.1 zipp: 3.11.0 }}} " defect closed normal Third Party fixed all ChimeraX