XMAS: update_distances: KeyError: None

[t.jenne@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.7.dev202304302138 (2023-04-30 21:38:49 UTC)
Description
I wanted only to plot the shortest distance, but this error occurred. The xlsx-file is attached. The analyzed protein is a homohexamer.

Log:
UCSF ChimeraX version: 1.7.dev202304302138 (2023-04-30)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/Timo/Documents/PhD/Structures/ClpG_AF_hexamer.cxs format session

Log from Mon Oct 23 18:38:47 2023UCSF ChimeraX version: 1.7.dev202304302138
(2023-04-30)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/Timo/Documents/PhD/Structures/ClpG_AF.pdb

Chain information for ClpG_AF.pdb #1  
---  
Chain | Description  
A B C D E F | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /A /B /C /D /E /F

Alignment identifier is 1  

> select

44106 atoms, 44760 bonds, 5694 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> show sel cartoons

> select :4

9 atoms, 8 bonds, 1 residue, 1 model selected  

> renumber start 1

4745 residues renumbered  

> select :1

48 atoms, 42 bonds, 6 residues, 1 model selected  

> save /Users/Timo/Documents/PhD/Structures/ClpG_AF_hexamer.cxs

——— End of log from Mon Oct 23 18:38:47 2023 ———

opened ChimeraX session  

> color :1-106 cornflower blue

> color :107-260 light sea green

> color :261-514 light gray

> color :515-572 orange

> color :573-592 light gray

> color :593-909 gray

> color :910-949 purple

> lighting simple

> ui tool show XMAS

  
Peptide pair mapping of XlinkX evidence file:
/Users/Timo/Documents/PhD/Data/Mass-
spectrometry/Analysis/new/XMAS/XMAS_Y541A_all.xlsx  
Unique peptide pairs: 100 out of 109  
Unique peptide pairs with pseudobonds: 88  
Pseudobonds are stored in /Users/Timo/Documents/PhD/Data/Mass-
spectrometry/Analysis/new/XMAS/XMAS_Y541A_all_1.pb  
Mapping information is stored in /Users/Timo/Documents/PhD/Data/Mass-
spectrometry/Analysis/new/XMAS/XMAS_Y541A_all_1.tsv  
Traceback (most recent call last):  
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/pandas/core/indexes/base.py", line 3802, in get_loc  
return self._engine.get_loc(casted_key)  
File "index.pyx", line 153, in pandas._libs.index.IndexEngine.get_loc  
File "index.pyx", line 161, in pandas._libs.index.IndexEngine.get_loc  
File "pandas/_libs/index_class_helper.pxi", line 70, in
pandas._libs.index.Int64Engine._check_type  
KeyError: None  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/pandas/core/frame.py", line 4550, in _set_value  
iindex = self.index.get_loc(index)  
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/pandas/core/indexes/base.py", line 3809, in get_loc  
raise KeyError(key) from err  
KeyError: None  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/pandas/core/indexes/base.py", line 3802, in get_loc  
return self._engine.get_loc(casted_key)  
File "index.pyx", line 153, in pandas._libs.index.IndexEngine.get_loc  
File "index.pyx", line 161, in pandas._libs.index.IndexEngine.get_loc  
File "pandas/_libs/index_class_helper.pxi", line 19, in
pandas._libs.index.Float64Engine._check_type  
KeyError: None  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/XMAS/tool.py", line 1015, in <lambda>  
self.get_names(names_menu, pbs_dict, f))  
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/XMAS/tool.py", line 1246, in get_names  
function(pbs_dict, names)  
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/chimerax/XMAS/tool.py", line 1225, in update_distances  
file.df.at[index, "Distance (A)"] = distance  
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/pandas/core/indexing.py", line 2579, in __setitem__  
return super().__setitem__(key, value)  
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/pandas/core/indexing.py", line 2535, in __setitem__  
self.obj._set_value(*key, value=value, takeable=self._takeable)  
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/pandas/core/frame.py", line 4563, in _set_value  
self.loc[index, col] = value  
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/pandas/core/indexing.py", line 912, in __setitem__  
iloc._setitem_with_indexer(indexer, value, self.name)  
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/pandas/core/indexing.py", line 1926, in _setitem_with_indexer  
nindexer.append(labels.get_loc(key))  
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/pandas/core/indexes/base.py", line 3809, in get_loc  
raise KeyError(key) from err  
KeyError: None  
  
KeyError: None  
  
File "/Users/Timo/Library/Application Support/ChimeraX/1.7/site-
packages/pandas/core/indexes/base.py", line 3809, in get_loc  
raise KeyError(key) from err  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-20.5.7
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2,4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0)
      OS Loader Version: 577~129

Software:

    System Software Overview:

      System Version: macOS 13.3.1 (a) (22E772610a)
      Kernel Version: Darwin 22.4.0
      Time since boot: 5 Tage, 20 Stunden und 25 Minuten

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.4
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.45.4
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202304302138
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.2
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.1
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.2
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
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    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
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    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
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    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.11.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-XMAS: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
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    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
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    et-xmlfile: 1.1.0
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    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
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    importlib-metadata: 6.6.0
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    pandas: 2.2.0
    ParmEd: 3.4.3
    parso: 0.8.3
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    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
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    pure-eval: 0.2.2
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    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
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    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
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    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    QtRangeSlider: 0.1.5
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    seaborn: 0.13.2
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
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    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0
File attachment: XMAS_Y541A_all.xlsx

XMAS_Y541A_all.xlsx​

[t.jenne@…]

Added by email2trac

[Eric Pettersen]

Reported by Timo Jenne