ImportError: cannot import name 'normalize_vector' from 'chimerax.core'

[Elaine Meng]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.1.dev202008030205 (2020-08-03 02:05:22 UTC)
Description
trying to specify shape ribbon "yaxis" option

The documentation is wrong (possibly my fault) in saying the "shape ribbon" command option "yaxis" can be specified as x, y, z, or vector of three comma-separated values.  I get an error with the first three and a traceback included here with the comma-sep values, from command:
shape ribbon @p yaxis 0,1,0

Structure is 6bna but that probably doesn't matter.

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

> alias reset view orient; view initial

> alias start tool 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

executed startup.cxc  
UCSF ChimeraX version: 1.1.dev202008030205 (2020-08-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 4enl format mmcif fromDatabase pdb

4enl title:  
Crystal structure of holoenzyme refined At 1.9 angstroms resolution: trigonal-
bipyramidal geometry of the cation binding site [more info...]  
  
Chain information for 4enl #1  
---  
Chain | Description  
A | enolase  
  
Non-standard residues in 4enl #1  
---  
SO4 — sulfate ion  
ZN — zinc ion  
  
4enl mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> select /A:369

7 atoms, 6 bonds, 1 model selected  

> select up

42 atoms, 42 bonds, 1 model selected  

> select down

7 atoms, 6 bonds, 1 model selected  

> select clear

> close

> open 6bna

Summary of feedback from opening 6bna fetched from pdb  
---  
notes | Fetching compressed mmCIF 6bna from
http://files.rcsb.org/download/6bna.cif  
Fetching CCD NT from http://ligand-expo.rcsb.org/reports/N/NT/NT.cif  
  
6bna title:  
Binding of an antitumor drug to DNA. Netropsin and C-G-C-G-A-A-T-T-BRC-G-C-G
[more info...]  
  
Chain information for 6bna #1  
---  
Chain | Description  
A B | DNA (5'-D(*CP*GP*CP*GP*ap*ap*TP*TP*(CBR)P*GP*CP*G)-3')  
  
Non-standard residues in 6bna #1  
---  
NT — netropsin  
  

> ~cartoon

> shape tube @P

> close #2

> shape ribbon @P

> ribbon

> close #2

> shape ribbon @p yaxis y

Invalid "yaxis" argument: Expected a number  

> shape ribbon @p yaxis z

Invalid "yaxis" argument: Expected a number  

> shape ribbon @p yaxis x

Invalid "yaxis" argument: Expected a number  

> shape ribbon @p yaxis 0,1,0

Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 269, in execute  
cmd.run(cmd_text)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shape/shape.py", line 361, in shape_ribbon  
follow_bonds, color)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/tube.py", line 276, in ribbon_through_atoms  
follow_bonds, color)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/tube.py", line 300, in _atom_extrusion  
segment_subdivisions, band_length, shape)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/tube.py", line 163, in banded_extrusion  
va, na, ta = s.geometry()  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/tube.py", line 404, in geometry  
tflist = extrusion_transforms(self.path, self.tangents, self.yaxis)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/tube.py", line 187, in extrusion_transforms  
from chimerax.core import normalize_vector, cross_product  
ImportError: cannot import name 'normalize_vector' from 'chimerax.core'
(/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/__init__.py)  
  
ImportError: cannot import name 'normalize_vector' from 'chimerax.core'
(/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/__init__.py)  
  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/tube.py", line 187, in extrusion_transforms  
from chimerax.core import normalize_vector, cross_product  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.22
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro11,4
      Processor Name: Intel Core i7
      Processor Speed: 2.2 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
      Boot ROM Version: 199.0.0.0.0
      SMC Version (system): 2.29f24

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G6020)
      Kernel Version: Darwin 18.7.0
      Time since boot: 6:34

Graphics/Displays:

    Intel Iris Pro:

      Chipset Model: Intel Iris Pro
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0d26
      Revision ID: 0x0008
      Metal: Supported, feature set macOS GPUFamily1 v4
      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
          Rotation: Supported
          Automatically Adjust Brightness: No

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.0
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.2
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.dev202008030205
    ChimeraX-CoreFormats: 1.0
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
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    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
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    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.2
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
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    PyQt5-commercial: 5.12.3
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    PyQtWebEngine-commercial: 5.12.1
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    suds-jurko: 0.6
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[Tom Goddard]

Fixed.

Wrong import statements used when running shape ribbon with yaxis option. The yaxis option only accepts 3 comma-separated floats, not "x" or "y" or "z".