XMAS: 'Tabular' object has no attribute 'peptide_pairs'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26200
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  

> import 4f5fc

Unknown command: import 4f5fc  

> open 4f5s

Summary of feedback from opening 4f5s fetched from pdb  
---  
notes | Fetching compressed mmCIF 4f5s from http://files.rcsb.org/download/4f5s.cif  
Fetching CCD PGE from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/PGE/PGE.cif  
  
4f5s title:  
Crystal Structure of Bovine Serum Albumin [more info...]  
  
Chain information for 4f5s #1  
---  
Chain | Description | UniProt  
A B | Serum albumin | ALBU_BOVIN 1-583  
  
Non-standard residues in 4f5s #1  
---  
PGE — triethylene glycol  
  
4f5s mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
32 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
9306 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> ui tool show XMAS

Please select pseudobonds  

> show target m

Unsupported evidence file format  
Traceback (most recent call last):  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 290, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 447, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 460, in map_crosslinks  
evidence = Evidence(evidence_file)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\read_evidence.py", line 38, in __init__  
self.peptide_pairs = evidence.peptide_pairs  
^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'  
  
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'  
  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\read_evidence.py", line 38, in __init__  
self.peptide_pairs = evidence.peptide_pairs  
^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> style stick

Changed 9643 atom styles  
Please check one or more files  
Please check one or more files  
  
Peptide pair mapping of pLink evidence file: H:/pLink-data-
analyze/US1/reports/result_2026.01.13.filtered_cross-linked_peptides.csv  
Unique peptide pairs: 68 out of 70  
Unique peptide pairs with pseudobonds: 66  
Pseudobonds are stored in H:/pLink-data-
analyze/US1/reports/result_2026.01.13.filtered_cross-linked_peptides_1.pb  
Mapping information is stored in H:/pLink-data-
analyze/US1/reports/result_2026.01.13.filtered_cross-linked_peptides_1.tsv  
Please select pseudobonds  
Please select pseudobonds  

> ui tool show "Selection Inspector"

Please select pseudobonds  
Please select pseudobonds  
Please select pseudobonds  
Please select pseudobonds  

> ui tool show XMAS

Please select pseudobonds  
Please select pseudobonds  
  
Peptide pair mapping of pLink evidence file: H:/pLink-data-
analyze/US1/reports/result_2026.01.13.filtered_cross-linked_peptides.csv  
Unique peptide pairs: 68 out of 70  
Unique peptide pairs with pseudobonds: 66  
Pseudobonds are stored in H:/pLink-data-
analyze/US1/reports/result_2026.01.13.filtered_cross-linked_peptides_1.pb  
Mapping information is stored in H:/pLink-data-
analyze/US1/reports/result_2026.01.13.filtered_cross-linked_peptides_1.tsv  
  
Peptide pair mapping of pLink evidence file: H:/pLink-data-
analyze/US1/reports/result_2026.01.13.filtered_cross-linked_peptides.csv  
Unique peptide pairs: 68 out of 70  
Unique peptide pairs with pseudobonds: 66  
Traceback (most recent call last):  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 290, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 447, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 530, in map_crosslinks  
self.align_peptides(peptide_pairs, checked_models)  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 684, in align_peptides  
self.create_pseudobonds(peptide_pairs)  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 748, in create_pseudobonds  
self.create_files(pbonds, info_file_path)  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 761, in create_files  
created_model = self.create_pseudobonds_model(pbonds,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 795, in create_pseudobonds_model  
group = self.get_pseudobonds_model(name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 873, in get_pseudobonds_model  
self.session.models.add([group])  
File "F:\质谱软件\ChimeraX 1.11\bin\Lib\site-packages\chimerax\core\models.py",
line 796, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
ValueError: Attempted to add model result_2026.01.13.filtered_cross-
linked_peptides_1(1).pb #3 to scene twice  
  
ValueError: Attempted to add model result_2026.01.13.filtered_cross-
linked_peptides_1(1).pb #3 to scene twice  
  
File "F:\质谱软件\ChimeraX 1.11\bin\Lib\site-packages\chimerax\core\models.py",
line 796, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
  
See log for complete Python traceback.  
  
  
Peptide pair mapping of pLink evidence file: H:/pLink-data-
analyze/US1/reports/result_2026.01.13.filtered_cross-linked_peptides.csv  
Unique peptide pairs: 68 out of 70  
Unique peptide pairs with pseudobonds: 66  
Traceback (most recent call last):  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 290, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 447, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 530, in map_crosslinks  
self.align_peptides(peptide_pairs, checked_models)  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 684, in align_peptides  
self.create_pseudobonds(peptide_pairs)  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 748, in create_pseudobonds  
self.create_files(pbonds, info_file_path)  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 761, in create_files  
created_model = self.create_pseudobonds_model(pbonds,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 795, in create_pseudobonds_model  
group = self.get_pseudobonds_model(name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 873, in get_pseudobonds_model  
self.session.models.add([group])  
File "F:\质谱软件\ChimeraX 1.11\bin\Lib\site-packages\chimerax\core\models.py",
line 796, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
ValueError: Attempted to add model result_2026.01.13.filtered_cross-
linked_peptides_1(1).pb #3 to scene twice  
  
ValueError: Attempted to add model result_2026.01.13.filtered_cross-
linked_peptides_1(1).pb #3 to scene twice  
  
File "F:\质谱软件\ChimeraX 1.11\bin\Lib\site-packages\chimerax\core\models.py",
line 796, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
  
See log for complete Python traceback.  
  
  
Peptide pair mapping of pLink evidence file: H:/pLink-data-
analyze/US1/reports/result_2026.01.13.filtered_cross-linked_peptides.csv  
Unique peptide pairs: 68 out of 70  
Unique peptide pairs with pseudobonds: 66  
Traceback (most recent call last):  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 290, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 447, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 530, in map_crosslinks  
self.align_peptides(peptide_pairs, checked_models)  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 684, in align_peptides  
self.create_pseudobonds(peptide_pairs)  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 748, in create_pseudobonds  
self.create_files(pbonds, info_file_path)  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 761, in create_files  
created_model = self.create_pseudobonds_model(pbonds,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 795, in create_pseudobonds_model  
group = self.get_pseudobonds_model(name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\abyss\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 873, in get_pseudobonds_model  
self.session.models.add([group])  
File "F:\质谱软件\ChimeraX 1.11\bin\Lib\site-packages\chimerax\core\models.py",
line 796, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
ValueError: Attempted to add model result_2026.01.13.filtered_cross-
linked_peptides_1(1).pb #3 to scene twice  
  
ValueError: Attempted to add model result_2026.01.13.filtered_cross-
linked_peptides_1(1).pb #3 to scene twice  
  
File "F:\质谱软件\ChimeraX 1.11\bin\Lib\site-packages\chimerax\core\models.py",
line 796, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 555.97
OpenGL renderer: NVIDIA GeForce GTX 1650 Ti/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: ASUSTeK COMPUTER INC.
Model: ASUS TUF Gaming A15 FA506II_FA506II
OS: Microsoft Windows 11 家庭中文版 (Build 26200)
Memory: 7,968,419,840
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 4800H with Radeon Graphics         
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
    autocommand: 2.2.2
    babel: 2.17.0
    backports.tarfile: 1.2.0
    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
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    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
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    ChimeraX-IUPAC: 1.0
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    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
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    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
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    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
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    ChimeraX-PDB: 2.7.11
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
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    ChimeraX-Positions: 1.0
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    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
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    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
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    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
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    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
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    ChimeraX-SelInspector: 1.0
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    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
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    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
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    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-XMAS: 1.1.3
    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
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    executing: 2.2.1
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    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
    importlib_metadata: 8.0.0
    inflect: 7.3.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jaraco.collections: 5.1.0
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.25.1
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    jupyter_client: 8.6.3
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    OpenMM-CUDA-12: 8.2.0
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    packaging: 24.2
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    platformdirs: 4.2.2
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