"boltz predict": UnicodeEncodeError

[boneekls@…]

The following bug report has been submitted:
Platform:        Linux-5.15.0-134-generic-x86_64-with-glibc2.35
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 Messages  
---  
warning | GBM is not supported with the current configuration. Fallback to Vulkan rendering in Chromium.  

UCSF ChimeraX version: 1.11 (2025-12-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/debanjan/Documents/Susobhan/apo.pdb

Chain information for apo.pdb #1  
---  
Chain | Description  
A | No description available  

1496 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  
Computing secondary structure  

> ui tool show Boltz

> boltz predict protein /A forEachSmilesLigand
> "ligand1,OC[C@H]1O[C@H]([C@@H](C1=O)O)n2c(=O)[nH]c(=O)cc2" name apo.pdb
> affinity each

Running Boltz prediction of protein with 196 residues on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 751, in _check_process_completion  
self._process_completed(stdout, stderr)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 828, in _process_completed  
f.write(stderr)  
UnicodeEncodeError: 'ascii' codec can't encode characters in position 244-253:
ordinal not in range(128)  

Error processing trigger "new frame":  
UnicodeEncodeError: 'ascii' codec can't encode characters in position 244-253:
ordinal not in range(128)  

File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 828, in _process_completed  
f.write(stderr)  

See log for complete Python traceback.  


failed to create compose table  




OpenGL version: 3.3.0 NVIDIA 570.124.06
OpenGL renderer: Quadro K2200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.13
Locale: en_IN.ISO8859-1
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=cinnamon
XDG_SESSION_DESKTOP=cinnamon
XDG_CURRENT_DESKTOP=X-Cinnamon
DISPLAY=:0
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7B17
OS: Linux Mint 21.3
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Core(TM) i7-9700K CPU @ 3.60GHz
Cache Size: 12288 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       2.8Gi       7.2Gi       103Mi        21Gi        27Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM107GL [Quadro K2200] [10de:13ba] (rev a2)	
	Subsystem: Hewlett-Packard Company GM107GL [Quadro K2200] [103c:1097]	
	Kernel driver in use: nvidia

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-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: 1.14.0
   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

[Eric Pettersen]

Reported by Debanjan

[Tom Goddard]

The error with Boltz is because apparently on your Linux system the default file encoding for text files written by Python is ASCII instead of the standard UTF-8. The error happened because the Boltz output included some non-ascii text and attempted to write it to a file. I've improved the ChimeraX Boltz code so that it always writes the output in utf-8 encoding even if the default on your operating system is to write ascii. That will be in tomorrow's daily build.

Same as ticket #19690.