XMAS: error parsing results from pLink

[emilio.cirri@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.9rc202411230619 (2024-11-23 06:19:23 UTC)
Description
I tried to upload the cross-linked peptides result from pLink but it did not work. Is ChimeraX compatible with pLink and if so, which is the document I would have to upload to visualize the cross linkers?

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9rc202411230619 (2024-11-23)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open F:\M52_SDA_Test\SDA_Test_Jena\BSA.cif format mmcif

BSA.cif title:  
Crystal structure of Bovine Serum Albumin [more info...]  
  
Chain information for BSA.cif #1  
---  
Chain | Description | UniProt  
A B | Serum albumin | ALBU_BOVIN 1-583  
  
Non-standard residues in BSA.cif #1  
---  
ACT — acetate ion  
CA — calcium ion  
  
BSA.cif mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
18 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> ui tool show XMAS

Traceback (most recent call last):  
File "C:\Users\research_ori\AppData\Local\UCSF\ChimeraX\1.9\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\research_ori\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\XMAS\tool.py", line 447, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\research_ori\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\XMAS\tool.py", line 460, in map_crosslinks  
evidence = Evidence(evidence_file)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\research_ori\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\XMAS\read_evidence.py", line 37, in __init__  
evidence = cls(evidence_file)  
^^^^^^^^^^^^^^^^^^  
File "C:\Users\research_ori\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\XMAS\read_evidence.py", line 101, in __init__  
df = self.make_df(evidence_file, delimiter, header)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\research_ori\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\XMAS\read_evidence.py", line 300, in make_df  
df = pd.read_csv(evidence_file, sep=delimiter, header=0,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\research_ori\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\pandas\io\parsers\readers.py", line 1026, in read_csv  
return _read(filepath_or_buffer, kwds)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\research_ori\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\pandas\io\parsers\readers.py", line 626, in _read  
return parser.read(nrows)  
^^^^^^^^^^^^^^^^^^  
File "C:\Users\research_ori\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\pandas\io\parsers\readers.py", line 1923, in read  
) = self._engine.read( # type: ignore[attr-defined]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\research_ori\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\pandas\io\parsers\c_parser_wrapper.py", line 234, in read  
chunks = self._reader.read_low_memory(nrows)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "pandas/_libs/parsers.pyx", line 838, in
pandas._libs.parsers.TextReader.read_low_memory  
File "pandas/_libs/parsers.pyx", line 905, in
pandas._libs.parsers.TextReader._read_rows  
File "pandas/_libs/parsers.pyx", line 874, in
pandas._libs.parsers.TextReader._tokenize_rows  
File "pandas/_libs/parsers.pyx", line 891, in
pandas._libs.parsers.TextReader._check_tokenize_status  
File "pandas/_libs/parsers.pyx", line 2061, in
pandas._libs.parsers.raise_parser_error  
pandas.errors.ParserError: Error tokenizing data. C error: Expected 11 fields
in line 4, saw 12  
  
  
pandas.errors.ParserError: Error tokenizing data. C error: Expected 11 fields
in line 4, saw 12  
  
  
File "pandas/_libs/parsers.pyx", line 2061, in
pandas._libs.parsers.raise_parser_error  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 556.39
OpenGL renderer: NVIDIA T400 4GB/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp65001
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: Precision 5820 Tower
OS: Microsoft Windows 10 Enterprise LTSC (Build 19044)
Memory: 137,106,837,504
MaxProcessMemory: 137,438,953,344
CPU: 36 Intel(R) Xeon(R) W-2295 CPU @ 3.00GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 2.4.1
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
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    ChimeraX-BasicActions: 1.1.2
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    ChimeraX-ChangeChains: 1.1
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    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
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    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9rc202411230619
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
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    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
    ChimeraX-Help: 1.3
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    ChimeraX-IHM: 1.1
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    ChimeraX-IO: 1.0.3
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    ChimeraX-MapFit: 2.0
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    ChimeraX-Mole: 1.0
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    ChimeraX-MouseModes: 1.2
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    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
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    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
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    ChimeraX-Positions: 1.0
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    ChimeraX-PubChem: 2.2
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    ChimeraX-RenderByAttr: 1.6.2
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    ChimeraX-RotamerLibsRichardson: 2.0
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    ChimeraX-Shortcuts: 1.2.0
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    ChimeraX-SideView: 1.0.1
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    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    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
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
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    ChimeraX-Tug: 1.0.1
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    ChimeraX-uniprot: 2.3.1
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    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: 1.1.4
    ChimeraX-XMAS: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    et_xmlfile: 2.0.0
    executing: 2.1.0
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    fonttools: 4.55.0
    funcparserlib: 2.0.0a0
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    h5py: 3.12.1
    html2text: 2024.2.26
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
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    inflect: 7.3.1
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    ipython: 8.26.0
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    jaraco.context: 5.3.0
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    packaging: 23.2
    packaging: 24.1
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    platformdirs: 4.3.6
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    python-dateutil: 2.9.0.post0
    pytz: 2024.2
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    RandomWords: 0.4.0
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    seaborn: 0.13.2
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    soupsieve: 2.6
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