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#20793 closed defect (fixed)

Various Match→Align errors

Reported by:	chimerax-bug-report@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Sequence	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.26200
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.12 (2026-06-12)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\Stefane\OneDrive - Cornell University\PhD thesis\Chapter 2-
> 4\Chapter 3 mitochondrial freeze-
> injury\RNAseq\Isoform_alignment\OPA1_structure\Alphafold_collab\TU517_ecea7_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> format pdb

Chain information for
TU517_ecea7_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> toolshed show

> ui tool show "Color Actions"

> ui tool show "Task Manager"

> ui tool show "Predicted Aligned Error Plot"

> color byhetero

> ui tool show "Color Actions"

[Repeated 1 time(s)]

> ui tool show "Render/Select by Attribute"

> color byattribute a:bfactor target csab palette
> 18.97,#0fc7cf:57.235,white:95.5,#9e205e

9950 atoms, 1221 residues, atom bfactor range 19 to 95.5  

> color byattribute a:bfactor target csab palette
> 18.97,#0fc7cf:57.235,white:95.5,#9e205e

9950 atoms, 1221 residues, atom bfactor range 19 to 95.5  

> ui tool show "Render/Select by Attribute"

> color byattribute a:bfactor target csab palette
> 18.97,#0fc7cf:57.235,white:95.5,#9e205e

9950 atoms, 1221 residues, atom bfactor range 19 to 95.5  

> color byattribute a:bfactor target csab palette
> 18.97,#0fc7cf:57.235,white:95.5,#9e205e

9950 atoms, 1221 residues, atom bfactor range 19 to 95.5  

> open "C:/Users/Stefane/OneDrive - Cornell University/PhD thesis/Chapter 2-
> 4/Chapter 3 mitochondrial freeze-
> injury/RNAseq/Isoform_alignment/OPA1_structure/Alphafold_collab/TU518_4c256_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"

Chain information for
TU518_4c256_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #2  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> ui tool show Match→Align

> msa3d #1/A#2/A cutoffDistance 8

Match→Align cutoff: 8.0, in column if within cutoff of: any  
195 residue pairs aligned  
195 fully populated columns  
Pairwise RMSDs across all fully populated columns  
---  
Model | 1 | 2  
1 | 0.000 | 4.982  
2 | 4.982 | 0.000  
  
Overall RMSD: 4.982  
Sequence lengths: 1221 1207  
SDM (cutoff 8.0): 151.559  
Q-score: 0.007  
Alignment identifier is MA-1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment MA-1  
Chains used in RMSD evaluation for alignment MA-1:
TU517_ecea7_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #1/A,
TU518_4c256_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment MA-1  

> ui tool show "Render/Select by Attribute"

> color byattribute a:bfactor #2 target csab palette
> 18.98,#e5f5e0:57.365,#a1d99b:95.75,#31a354

9843 atoms, 1207 residues, atom bfactor range 19 to 95.8  

> color byattribute a:bfactor #2 target csab palette
> 18.98,#e5f5e0:57.365,#a1d99b:95.75,#31a354

9843 atoms, 1207 residues, atom bfactor range 19 to 95.8  

> ui tool show "Render/Select by Attribute"

> color byattribute a:bfactor #1 target csab palette
> 18.97,#fee6ce:57.235,#fdae6b:95.5,#e6550d

9950 atoms, 1221 residues, atom bfactor range 19 to 95.5  

> select #1 & bfactor>70

Expected a keyword  

> select #2 & bfactor>70

Expected a keyword  

> select #2 & bfactor>70

Expected a keyword  

> select @@bfactor>=69.86924871995441 & @@bfactor<=95.75

11579 atoms, 11755 bonds, 1405 residues, 2 models selected  

> select @@bfactor>=69.86924871995441 & @@bfactor<=95.75

11579 atoms, 11755 bonds, 1405 residues, 2 models selected  

> select ~sel & ##selected

8214 atoms, 8437 bonds, 1023 residues, 2 models selected  

> hide sel target a

[Repeated 2 time(s)]

> hide #1 target m

[Repeated 1 time(s)]

> show #1 models

> hide sel target a

> show (sel-residues & sidechain) target ab

> undo

> hide sel atoms

> hide sel cartoons

> ui tool show Match→Align

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 467, in _save  
settings.save(settings=save_settings)  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\settings.py", line 232, in save  
ConfigFile.save(self)  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\configfile.py", line 335, in save  
with SaveTextFile(self._filename) as f:  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\safesave.py", line 195, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\safesave.py", line 88, in __init__  
self._f = open(self._tmp_filename)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\safesave.py", line 194, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
OSError: [Errno 22] Invalid argument:
'C:\\\Users\\\Stefane\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\match->align-1.25224.1784998647.9958613.tmp'  
  
OSError: [Errno 22] Invalid argument:
'C:\\\Users\\\Stefane\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\match->align-1.25224.1784998647.9958613.tmp'  
  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\safesave.py", line 194, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> msa3d #1/A#2/A maxIterations none minStretch 1 refChain #2/A

Match→Align cutoff: 5.0, in column if within cutoff of: any  
103 residue pairs aligned  
103 fully populated columns  
Matching TU517_ecea7_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A onto
TU518_4c256_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\match_align\tool.py", line 259, in match_align  
run(self.session, "msa3d " + ' '.join(args))  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\match_align\cmd.py", line 131, in make_alignment  
aligned = [copy(chain) for chain in ordered]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\match_align\cmd.py", line 131, in <listcomp>  
aligned = [copy(chain) for chain in ordered]  
^^^^  
NameError: name 'copy' is not defined  
  
NameError: name 'copy' is not defined  
  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\match_align\cmd.py", line 131, in  
aligned = [copy(chain) for chain in ordered]  
^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 462.59
OpenGL renderer: GeForce GTX 1050/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.9
Locale: en_CA.cp1252
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: VivoBook_ASUSLaptop X570DD_M570DD
OS: Microsoft Windows 11 Home (Build 26200.8894)
Memory: 6,387,326,976
MaxProcessMemory: 137,438,953,344
CPU: 8 AMD Ryzen 5 3500U with Radeon Vega Mobile Gfx  
OSLanguage: en-US

Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.2
    aiohttp: 3.13.4
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.13.0
    appdirs: 1.4.4
    asttokens: 3.0.1
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.4.3
    bs4: 0.0.2
    build: 1.3.0
    certifi: 2026.5.20
    cftime: 1.6.5
    charset-normalizer: 3.4.7
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2
    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: 1.67.1
    ChimeraX-AtomicLibrary: 14.4
    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: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.4
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.12
    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: 1.2.2
    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: 1.8.2
    ChimeraX-Label: 1.5
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.3
    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-MatchAlign: 1.2
    ChimeraX-MatchMaker: 2.4.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.9
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.23
    ChimeraX-ModelPanel: 1.6.1
    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: 1.15.4
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.13
    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: 1.6
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8.2
    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: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.18
    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-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.3
    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: 2.5.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.4
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.50.8
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.2
    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: 8.4.1
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.14.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.21
    decorator: 5.3.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.63.0
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.16.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.18
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.8.0
    jupyter_core: 5.9.1
    kiwisolver: 1.5.0
    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: 0.2.2
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.1
    narwhals: 2.22.1
    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: 8.4.0
    OpenMM-CUDA-12: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.7
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.10.0
    plotly: 6.8.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.5.2
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.13.4
    pydantic-settings: 2.14.1
    pydantic_core: 2.46.4
    pydata-sphinx-theme: 0.18.0
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.5.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.10.2
    PyQt6-Qt6: 6.10.2
    PyQt6-WebEngine-commercial: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.2
    PyQt6_sip: 13.10.3
    pytest: 9.0.3
    pytest-cov: 7.1.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.32
    pywin32: 311
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    rpds-py: 2026.5.1
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.1.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.4
    Sphinx: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    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: 3.4.4
    stack-data: 0.6.3
    starlette: 1.3.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 3.2.1
    threadpoolctl: 3.6.0
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.7
    tqdm: 4.68.2
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2026.2
    Unidecode: 1.4.0
    urllib3: 2.7.0
    uvicorn: 0.49.0
    wcwidth: 0.8.1
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    WMI: 1.5.1
    yarl: 1.24.2

Change History (2)

comment:1 by Eric Pettersen, 7 hours ago

Component:	Unassigned → Sequence
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Various Match→Align errors

comment:2 by Eric Pettersen, 7 hours ago

Resolution:	→ fixed
Status:	accepted → closed

The first one I cannot reproduce on our Windows box. The second is fixed, even in the 1.12 source, and the commit is early enough that it should be in the release, but perhaps the *push* was late and missed the release.

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