PICKLUSTER: handle_scheme: KeyError: 'chain1'

[nicollesolangepb@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed install pickluster

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/nicollesolange/Library/Application
Support/ChimeraX/1.4/site-packages  
sysconfig: /Users/nicollesolange/Library/Python/3.9/lib/python/site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/nicollesolange/Library/Application
Support/ChimeraX/1.4/site-packages  
sysconfig: /Users/nicollesolange/Library/Python/3.9/lib/python/site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/nicollesolange/Library/Application
Support/ChimeraX/include/python3.9/ChimeraX-PICKLUSTER  
sysconfig: /Users/nicollesolange/Library/Python/3.9/include/ChimeraX-
PICKLUSTER  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/nicollesolange/Library/Application Support/ChimeraX/bin  
sysconfig: /Users/nicollesolange/Library/Python/3.9/bin  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/nicollesolange/Library/Application Support/ChimeraX  
sysconfig: /Users/nicollesolange/Library/Python/3.9  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/nicollesolange/Library/Application
Support/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /Users/nicollesolange/Library/Python/3.9/include/UNKNOWN  
WARNING: You are using pip version 21.3.1; however, version 24.0 is available.  
You should consider upgrading via the
'/private/var/folders/nc/6lh7yygx43n0mvx37jsvyhcm0000gn/T/AppTranslocation/23F5E8DF-10E9-4FC9-BEBC-9002EBB446E1/d/ChimeraX-1.4.app/Contents/MacOS/ChimeraX
-m pip install --upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Collecting ChimeraX-PICKLUSTER==0.5  
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxpickluster/releases/0.5/ChimeraX_PICKLUSTER-0.5-py3-none-
any.whl (17 kB)  
Requirement already satisfied: Jinja2>=3.0 in
/private/var/folders/nc/6lh7yygx43n0mvx37jsvyhcm0000gn/T/AppTranslocation/23F5E8DF-10E9-4FC9-BEBC-9002EBB446E1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-PICKLUSTER==0.5) (3.0.3)  
Requirement already satisfied: ChimeraX-UI~=1.0 in
/private/var/folders/nc/6lh7yygx43n0mvx37jsvyhcm0000gn/T/AppTranslocation/23F5E8DF-10E9-4FC9-BEBC-9002EBB446E1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-PICKLUSTER==0.5) (1.18.3)  
Requirement already satisfied: ChimeraX-Core~=1.4 in
/private/var/folders/nc/6lh7yygx43n0mvx37jsvyhcm0000gn/T/AppTranslocation/23F5E8DF-10E9-4FC9-BEBC-9002EBB446E1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-PICKLUSTER==0.5) (1.4)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
/private/var/folders/nc/6lh7yygx43n0mvx37jsvyhcm0000gn/T/AppTranslocation/23F5E8DF-10E9-4FC9-BEBC-9002EBB446E1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-PICKLUSTER==0.5) (1.0)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/private/var/folders/nc/6lh7yygx43n0mvx37jsvyhcm0000gn/T/AppTranslocation/23F5E8DF-10E9-4FC9-BEBC-9002EBB446E1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-PICKLUSTER==0.5) (1.1)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
/private/var/folders/nc/6lh7yygx43n0mvx37jsvyhcm0000gn/T/AppTranslocation/23F5E8DF-10E9-4FC9-BEBC-9002EBB446E1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-PICKLUSTER==0.5) (1.1)  
Requirement already satisfied: MarkupSafe>=2.0 in
/private/var/folders/nc/6lh7yygx43n0mvx37jsvyhcm0000gn/T/AppTranslocation/23F5E8DF-10E9-4FC9-BEBC-9002EBB446E1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from Jinja2>=3.0->ChimeraX-PICKLUSTER==0.5) (2.1.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
/private/var/folders/nc/6lh7yygx43n0mvx37jsvyhcm0000gn/T/AppTranslocation/23F5E8DF-10E9-4FC9-BEBC-9002EBB446E1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.0->ChimeraX-
PICKLUSTER==0.5) (1.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/private/var/folders/nc/6lh7yygx43n0mvx37jsvyhcm0000gn/T/AppTranslocation/23F5E8DF-10E9-4FC9-BEBC-9002EBB446E1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.0->ChimeraX-
PICKLUSTER==0.5) (1.2)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
/private/var/folders/nc/6lh7yygx43n0mvx37jsvyhcm0000gn/T/AppTranslocation/23F5E8DF-10E9-4FC9-BEBC-9002EBB446E1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-
PICKLUSTER==0.5) (1.0)  
Installing collected packages: ChimeraX-PICKLUSTER  
Successfully installed ChimeraX-PICKLUSTER-0.5  
\---  

Successfully installed ChimeraX-PICKLUSTER-0.5  
Installed ChimeraX-PICKLUSTER (0.5)  

> ui tool show PICKLUSTER

Please register the custom scheme 'pickluster' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

Traceback (most recent call last):  
File
"/private/var/folders/nc/6lh7yygx43n0mvx37jsvyhcm0000gn/T/AppTranslocation/23F5E8DF-10E9-4FC9-BEBC-9002EBB446E1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 335, in interceptRequest  
self._callback(info)  
File
"/private/var/folders/nc/6lh7yygx43n0mvx37jsvyhcm0000gn/T/AppTranslocation/23F5E8DF-10E9-4FC9-BEBC-9002EBB446E1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File
"/private/var/folders/nc/6lh7yygx43n0mvx37jsvyhcm0000gn/T/AppTranslocation/23F5E8DF-10E9-4FC9-BEBC-9002EBB446E1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File
"/private/var/folders/nc/6lh7yygx43n0mvx37jsvyhcm0000gn/T/AppTranslocation/23F5E8DF-10E9-4FC9-BEBC-9002EBB446E1/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 399, in thread_safe  
func(*args, **kw)  
File "/Users/nicollesolange/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/PICKLUSTER/tool.py", line 330, in handle_scheme  
chain1 = query["chain1"][0].split(':')[1]  
KeyError: 'chain1'  
  

Populating font family aliases took 503 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

KeyError: 'chain1'  
  
File "/Users/nicollesolange/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/PICKLUSTER/tool.py", line 330, in handle_scheme  
chain1 = query["chain1"][0].split(':')[1]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 455 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro13,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.7 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 526.0.0.0.0
      OS Loader Version: 540.120.3~37
      SMC Version (system): 2.38f12

Software:

    System Software Overview:

      System Version: macOS 12.7.4 (21H1123)
      Kernel Version: Darwin 21.6.0
      Time since boot: 5 days 1:48

Graphics/Displays:

    Intel HD Graphics 530:

      Chipset Model: Intel HD Graphics 530
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x191b
      Revision ID: 0x0006
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal Family: Supported, Metal GPUFamily macOS 2

    Radeon Pro 455:

      Chipset Model: AMD Radeon Pro 455
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 2 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c7
      ROM Revision: 113-C980AF-908
      VBIOS Version: 113-C9801AP-028
      EFI Driver Version: 01.A0.908
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    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-PICKLUSTER: 0.5
    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-Zone: 1.0
    colorama: 0.4.4
    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
    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
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    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
    ptyprocess: 0.7.0
    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
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    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

[Eric Pettersen]

Reported by Nicolle