Model Archives has score index outside bounds of chain

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
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:
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 C:/Users/gsx/Desktop/test_antibody_protocol.cif

Chain information for test_antibody_protocol.cif #1  
---  
Chain | Description  
D | No description available  

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\ui\gui.py", line 816, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\ui\gui.py", line 2202, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX 1.11\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 1.11\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 297, in provider_open  
session.models.add(opened_models)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\models.py", line 827, in add  
m.added_to_session(session)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1409, in added_to_session  
self._report_model_info(session)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1757, in _report_model_info  
res = chain.residues[int(seq_id)-1]  
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^  
IndexError: list index out of range  

IndexError: list index out of range  

File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1757, in _report_model_info  
res = chain.residues[int(seq_id)-1]  
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^  

See log for complete Python traceback.  

Computing secondary structure  




OpenGL version: 3.3.0 NVIDIA 576.88
OpenGL renderer: NVIDIA GeForce GTX 1650/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.9
Locale: zh_CN.cp936
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows

Manufacturer: LENOVO
Model: 81T0
OS: Microsoft Windows 10 \u5bb6\u5ead\u4e2d\u6587\u7248 (Build 19045)
Memory: 17,095,184,384
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
OSLanguage: zh-CN

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-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
   comtypes: 1.4.11
   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
   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
   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
   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-commercial: 6.9.1
   PyQt6-Qt6: 6.9.2
   PyQt6-WebEngine-commercial: 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
   pywin32: 311
   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
   WMI: 1.5.1
   yarl: 1.22.0

[Eric Pettersen]

Would need the file to ascertain if this is a bug or a user error.