name 'notImplemented' is not defined

[Elaine Meng]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.5.dev202208172335 (2022-08-17 23:35:46 UTC)
Description
choosing helix and centroid in Axes/Planes/Centroids gave a traceback

open 2gbp
rainbow
define axis perHelix true name "helix axes"
select ligand
define centroid sel name ligcenter

...then in the dialog I chose helix 8 and ligcenter  (actually I had chosen helix 9 and ligcenter and then used cmd key to unchoose helix 9 and choose helix 8 instead, maybe that is the problem)


Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start toolshed show $1

> alias whereprefs info path user unversioned config

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

> alias btut open
> http://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html

> alias segtest open 0557 from emdb; vol threshold #1 min 0; vol scale #2
> value uint8; open 6nzk

executed startup.cxc  

> windowsize 500 500

UCSF ChimeraX version: 1.5.dev202208172335 (2022-08-17)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 2gbp format mmcif fromDatabase pdb

2gbp title:  
Sugar and signal-transducer binding sites of the escherichia coli galactose
chemoreceptor protein [more info...]  
  
Chain information for 2gbp #1  
---  
Chain | Description | UniProt  
A | D-galactose/D-glucose binding protein | DGAL_ECOLI  
  
Non-standard residues in 2gbp #1  
---  
BGC — β-D-glucose  
CA — calcium ion  
  

> start Axes

Unknown command: ui tool start Axes  

> ui tool show Axes/Planes/Centroids

> rainbow

> define axis perHelix true name "helix axes"

Axis '2gbp #1/helix axes/helix 1' centered at [41.94068834 17.9871022
43.2924425 ] with direction [0.00263177 0.70450231 0.70969682], radius
1.84467, and length 25.563  
Axis '2gbp #1/helix axes/helix 2' centered at [52.97159584 32.15992026
34.14510536] with direction [ 0.14671884 -0.56207749 -0.81396712], radius
1.87812, and length 22.0975  
Axis '2gbp #1/helix axes/helix 3' centered at [44.70660898 37.57171271
29.54211045] with direction [ 0.27998106 -0.38932796 -0.87751601], radius
1.76687, and length 18.4062  
Axis '2gbp #1/helix axes/helix 4' centered at [33.70013048 39.82193445
31.49869013] with direction [-0.05644812 0.26791848 0.96178651], radius
1.7319, and length 9.50889  
Axis '2gbp #1/helix axes/helix 5' centered at [21.45642839 31.98893042
57.98509719] with direction [-0.37003933 -0.13595692 0.91901393], radius
1.85885, and length 24.8955  
Axis '2gbp #1/helix axes/helix 6' centered at [25.19600685 39.12756093
53.54406649] with direction [-0.85606486 0.07066697 0.51201478], radius
1.97453, and length 26.9017  
Axis '2gbp #1/helix axes/helix 7' centered at [42.21939276 36.72862917
65.79220674] with direction [-0.27736483 0.53540915 0.79775046], radius
1.95706, and length 18.9356  
Axis '2gbp #1/helix axes/helix 8' centered at [38.5746438 30.29659401
66.46297586] with direction [0.18473448 0.07398902 0.97999939], radius
1.88752, and length 22.086  
Axis '2gbp #1/helix axes/helix 9' centered at [33.29035517 19.65831334
62.42809014] with direction [-0.47821699 -0.09329239 0.87327261], radius
1.82907, and length 14.9005  
Axis '2gbp #1/helix axes/helix 10' centered at [36.04106545 20.60187451
35.06704001] with direction [ 3.00798339e-01 -3.53026548e-04 -9.53687703e-01],
radius 1.90574, and length 27.2435  

> select ligand

12 atoms, 12 bonds, 1 residue, 1 model selected  

> define centroid sel name ligcenter

Centroid 'ligcenter' placed at [37.42883333 30.59608333 49.61083333]  

> select strand & @ca

67 atoms, 67 residues, 1 model selected  

> define plane sel

Plane 'plane' placed at [35.43074627 30.51623881 47.97234328] with normal
[-0.88487927 0.10890405 -0.45291123]  

> color #1.3 #9090f7

> color #1.3 #9090f8

> color #1.4 #aafff9

plane #1.4 to helix 10 #1.2.10: distance: 1.968Å; angle: 9.539  
helix 9 #1.2.9 to ligcenter #1.3: no distance/angle  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 203, in _apc_selection_changed  
if a is not notImplemented:  
NameError: name 'notImplemented' is not defined  
  
NameError: name 'notImplemented' is not defined  
  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 203, in _apc_selection_changed  
if a is not notImplemented:  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-14.0.32 355.11.11.10.10.143
OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation

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

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac13,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 3.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 8 GB
      Boot ROM Version: 429.0.0.0.0
      SMC Version (system): 2.11f16

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2026)
      Kernel Version: Darwin 19.6.0
      Time since boot: 14 days 1:03

Graphics/Displays:

    NVIDIA GeForce GTX 675MX:

      Chipset Model: NVIDIA GeForce GTX 675MX
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 1 GB
      Vendor: NVIDIA (0x10de)
      Device ID: 0x11a2
      Revision ID: 0x00a2
      ROM Revision: 3707
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        iMac:
          Display Type: LCD
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


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
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.1
    charset-normalizer: 2.1.0
    ChimeraX-AddCharge: 1.2.4
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.5.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41
    ChimeraX-AtomicLibrary: 7.0.2
    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
    ChimeraX-ChangeChains: 1.0
    ChimeraX-CheckWaters: 1.1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.1
    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.dev202208172335
    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-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: 2.3
    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: 1.1.6
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    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-StdCommands: 1.9
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    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: 1.23
    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: 0.10.0
    filelock: 3.7.1
    fonttools: 4.36.0
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 4.12.0
    ipykernel: 6.15.1
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.1
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.5
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.3
    numpy: 1.23.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.1
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.30
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.1
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.1
    python-dateutil: 2.8.2
    pytz: 2022.2.1
    pyzmq: 23.2.1
    qtconsole: 5.3.1
    QtPy: 2.2.0
    RandomWords: 0.3.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 63.3.0
    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: 0.4.0
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.11
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.8.1