add_restraint: __init__() takes 3 positional arguments but 4 were given

[sai.raghavan@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5.dev202209210054 (2022-09-21 00:54:47 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5.dev202209210054 (2022-09-21)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show ISOLDE

> set selectionWidth 4

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/tool.py", line 42, in _launch_main_gui  
tw = self.tool_window = IsoldeMainWin(self)  
File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/main_win.py", line 56, in __init__  
self.restraints_tab = RestraintsTab(self.session, self.isolde, self, tabw)  
File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/ui_base.py", line 226, in __init__  
self.populate()  
File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/__init__.py", line 20, in populate  
self.addWidget(ReferenceModelPanel(session, isolde, parent, gui))  
File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 16, in
__init__  
cd = self.content = ReferenceModelDialog(session, isolde, gui, self)  
File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 85, in
__init__  
opt = self.options = ReferenceModelOptions(self.session, gui, options_frame)  
File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 464, in
__init__  
drfi = self.distance_fuzziness_indicator =
DistanceRestraintFuzzinessIndicator(session, dsl, dfl)  
File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 636, in
__init__  
self._create_dummy_model()  
File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 704, in
_create_dummy_model  
dr = self._dummy_restraint = drm.add_restraint(a1, a2)  
File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 2883, in add_restraint  
r = self._get_restraints(Atoms([atom1]), Atoms([atom2]), True)  
File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 2864, in _get_restraints  
return self._plural_restraint_getter(ret[:num])  
File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 97, in
_adaptive_distance_restraints  
return AdaptiveDistanceRestraints(p)  
File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molarray.py", line 556, in __init__  
super().__init__(c_pointers, AdaptiveDistanceRestraint,  
TypeError: __init__() takes 3 positional arguments but 4 were given  
  
Error processing trigger "new frame":  
TypeError: __init__() takes 3 positional arguments but 4 were given  
  
File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molarray.py", line 556, in __init__  
super().__init__(c_pointers, AdaptiveDistanceRestraint,  
  
See log for complete Python traceback.  
  
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 1790, in _get_and_process_changes  
return self._process_changes(changes)  
File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 1775, in _process_changes  
changed_obj = class_funcs[1](changed_ptrs)  
File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 97, in
_adaptive_distance_restraints  
return AdaptiveDistanceRestraints(p)  
File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molarray.py", line 556, in __init__  
super().__init__(c_pointers, AdaptiveDistanceRestraint,  
TypeError: __init__() takes 3 positional arguments but 4 were given  
  
Error processing trigger "new frame":  
TypeError: __init__() takes 3 positional arguments but 4 were given  
  
File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molarray.py", line 556, in __init__  
super().__init__(c_pointers, AdaptiveDistanceRestraint,  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.10.12
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 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 (22E261)
      Kernel Version: Darwin 22.4.0
      Time since boot: 1 day, 23 hours, 6 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        HP U28 4K HDR:
          Resolution: 6016 x 3384
          UI Looks like: 3008 x 1692 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 1CR24100KL  
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    biopython: 1.81
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.3
    ChimeraX-AtomicLibrary: 7.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0
    ChimeraX-CheckWaters: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0.2
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5.dev202209210054
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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-ISOLDE: 1.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.7
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.7
    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
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 2.7.2
    ChimeraX-Shape: 1.0.1
    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-StarMap: 1.1.75
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-StrudelScore: 0.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.1
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.0.0
    filelock: 3.7.1
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    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 4.12.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
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    kiwisolver: 1.4.4
    line-profiler: 3.5.1
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    matplotlib: 3.5.2
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    mrcfile: 1.4.3
    msgpack: 1.0.4
    nest-asyncio: 1.5.5
    netCDF4: 1.6.0
    networkx: 2.8.5
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    openvr: 1.23.701
    packaging: 21.3
    pandas: 2.0.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
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    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
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    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    pyqtgraph: 0.13.3
    python-dateutil: 2.8.2
    pytz: 2022.2.1
    pyzmq: 24.0.0
    qtconsole: 5.3.1
    QtPy: 2.2.0
    RandomWords: 0.4.0
    recordtype: 1.4
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    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
    stack-data: 0.5.0
    tables: 3.7.0
    threed-strudel: 0.9.18
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    tzdata: 2023.3
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.8.1

[Tristan Croll]

This was fixed in the ISOLDE 1.5 release (to get it just install the official ChimeraX 1.5 release and install ISOLDE into that - or you could wait a couple of weeks for 1.6). Was caused by a minor change in the ChimeraX API going from 1.4 to 1.5.