Opened 3 years ago

Closed 2 years ago

Last modified 2 years ago

#8675 closed defect (fixed)

XMAS: making crosslinks: Duplicate names are not allowed

Reported by: fpastorelli1@… Owned by: Richard Scheltema
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
XMAS -  tried to max crosslinks - and it gives me: 

ValueError: Duplicate names are not allowed. 

how do i solve this ?

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show XMAS

> open C:\Users\mbp19fp\Downloads\6rqf.pdb format pdb

6rqf.pdb title:  
3.6 angstrom cryo-em structure of the dimeric cytochrome B6F complex from
spinacia oleracea with natively bound thylakoid lipids and plastoquinone
molecules [more info...]  
  
Chain information for 6rqf.pdb #1  
---  
Chain | Description | UniProt  
A I | cytochrome B6 | CYB6_SPIOL  
B J | 17 KDA polypeptide | PETD_SPIOL  
C K | cytochrome F | CYF_SPIOL  
D L | cytochrome B6-F complex iron-sulfur subunit, chloroplastic | UCRIA_SPIOL  
E M | cytochrome B6-F complex subunit 6 | PETL_SPIOL  
F N | cytochrome B6-F complex subunit 7 | PETM_SPIOL  
G O | cytochrome B6-F complex subunit 5 | PETG_SPIOL  
H P | cytochrome B6-F complex subunit 8 | PETN_SPIOL  
  
Non-standard residues in 6rqf.pdb #1  
---  
6PL —
(4S,7R)-4-hydroxy-N,N,N-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium
4-oxide (1-palmitoyl-2-stearoyl-Sn-glycero-3-phosphocholine)  
BCR — β-carotene  
CLA — chlorophyll A  
FES — FE2/S2 (inorganic) cluster  
HEC — heme C  
HEM — protoporphyrin IX containing Fe (HEME)  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
PGV —
(1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl
(11E)-octadec-11-enoate (phosphatidylglycerol, 2-vaccenoyl-1-palmitoyl-Sn-
glycerol-3-phosphoglycerol)  
PL9 —
2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone
(plastoquinone 9)  
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)  
  

> open C:/Users/mbp19fp/Downloads/1fnc.pdb

1fnc.pdb title:  
Refined crystal structure of spinach ferredoxin reductase At 1.7 angstroms
resolution: oxidized, reduced, and 2'- phospho-5'-amp bound states [more
info...]  
  
Chain information for 1fnc.pdb #2  
---  
Chain | Description | UniProt  
A | ferredoxin-nadp+ reductase | FENR_SPIOL  
  
Non-standard residues in 1fnc.pdb #2  
---  
A2P — adenosine-2'-5'-diphosphate  
FDA — dihydroflavine-adenine dinucleotide  
SO4 — sulfate ion  
  
Traceback (most recent call last):  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\tool.py", line 286, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s,  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\tool.py", line 444, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\tool.py", line 457, in map_crosslinks  
evidence = Evidence(evidence_file)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\read_evidence.py", line 37, in __init__  
evidence = cls(evidence_file)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\read_evidence.py", line 101, in __init__  
df = self.make_df(evidence_file, delimiter, header)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\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\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\util\\_decorators.py", line 211, in wrapper  
return func(*args, **kwargs)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\util\\_decorators.py", line 331, in wrapper  
return func(*args, **kwargs)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\io\parsers\readers.py", line 950, in read_csv  
return _read(filepath_or_buffer, kwds)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\io\parsers\readers.py", line 602, in _read  
_validate_names(kwds.get("names", None))  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\io\parsers\readers.py", line 564, in _validate_names  
raise ValueError("Duplicate names are not allowed.")  
ValueError: Duplicate names are not allowed.  
  
ValueError: Duplicate names are not allowed.  
  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\io\parsers\readers.py", line 564, in _validate_names  
raise ValueError("Duplicate names are not allowed.")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\tool.py", line 286, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s,  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\tool.py", line 444, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\tool.py", line 457, in map_crosslinks  
evidence = Evidence(evidence_file)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\read_evidence.py", line 37, in __init__  
evidence = cls(evidence_file)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\read_evidence.py", line 101, in __init__  
df = self.make_df(evidence_file, delimiter, header)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\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\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\util\\_decorators.py", line 211, in wrapper  
return func(*args, **kwargs)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\util\\_decorators.py", line 331, in wrapper  
return func(*args, **kwargs)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\io\parsers\readers.py", line 950, in read_csv  
return _read(filepath_or_buffer, kwds)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\io\parsers\readers.py", line 602, in _read  
_validate_names(kwds.get("names", None))  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\io\parsers\readers.py", line 564, in _validate_names  
raise ValueError("Duplicate names are not allowed.")  
ValueError: Duplicate names are not allowed.  
  
ValueError: Duplicate names are not allowed.  
  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\io\parsers\readers.py", line 564, in _validate_names  
raise ValueError("Duplicate names are not allowed.")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\tool.py", line 286, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s,  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\tool.py", line 444, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\tool.py", line 457, in map_crosslinks  
evidence = Evidence(evidence_file)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\read_evidence.py", line 37, in __init__  
evidence = cls(evidence_file)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\read_evidence.py", line 101, in __init__  
df = self.make_df(evidence_file, delimiter, header)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\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\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\util\\_decorators.py", line 211, in wrapper  
return func(*args, **kwargs)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\util\\_decorators.py", line 331, in wrapper  
return func(*args, **kwargs)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\io\parsers\readers.py", line 950, in read_csv  
return _read(filepath_or_buffer, kwds)  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\io\parsers\readers.py", line 602, in _read  
_validate_names(kwds.get("names", None))  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\io\parsers\readers.py", line 564, in _validate_names  
raise ValueError("Duplicate names are not allowed.")  
ValueError: Duplicate names are not allowed.  
  
ValueError: Duplicate names are not allowed.  
  
File "C:\Users\mbp19fp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\io\parsers\readers.py", line 564, in _validate_names  
raise ValueError("Duplicate names are not allowed.")  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.13399 Core Profile Forward-Compatible Context 15.201.1151.1008
OpenGL renderer: AMD Radeon R5 200 Series
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: en_GB.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: LENOVO
Model: 10AW009SUK
OS: Microsoft Windows 10 Education (Build 19044)
Memory: 17,124,245,504
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-4790S CPU @ 3.20GHz
OSLanguage: en-GB

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-XMAS: 1.1.2
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    et-xmlfile: 1.1.0
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openpyxl: 3.1.1
    openvr: 1.16.802
    packaging: 21.3
    pandas: 1.5.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    QtRangeSlider: 0.1.5
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    seaborn: 0.12.2
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (3)

comment:1 by pett, 3 years ago

Component: Unassigned → Third Party
Owner: set to Richard Scheltema
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → XMAS: making crosslinks: Duplicate names are not allowed

Reported by Frederica Pastorelli

comment:2 by pett, 2 years ago

Resolution: → fixed
Status: assigned → closed

comment:3 by pett, 2 years ago

Fixed with newest release of XMAS (1.1.3)

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