Surface Color tool: map is None

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.13.6-x86_64-i386-64bit
ChimeraX Version: 1.2.2 (2021-05-08 05:48:20 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.2 (2021-05-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/landskron/Desktop/structure figures/cluster 1 ocean -
> magnesium.cxs"

Log from Tue May 11 19:05:23 2021UCSF ChimeraX version: 1.2.2 (2021-05-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/landskron/Desktop/cluster1_1.pdb format pdb

Summary of feedback from opening /Users/landskron/Desktop/cluster1_1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK FILENAME="complex_108w.pdb0"  
  
Ignored bad PDB record found on line 2  
REMARK ===============================================================  
  
Ignored bad PDB record found on line 3  
REMARK HADDOCK run for complex  
  
Ignored bad PDB record found on line 4  
REMARK initial structure: complex_108.pdb  
  
Ignored bad PDB record found on line 5  
REMARK ===============================================================  
  
29 messages similar to the above omitted  
  
Chain information for cluster1_1.pdb #1  
---  
Chain | Description  
D | No description available  
T | No description available  
  

> hide #1 models

> show #1 models

> ui tool show "Surface Color"

> surface

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> hide #1.1 models

> show #1.1 models

> open http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup

Opened http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup  

> set bgColor white

> lighting simple

> lighting soft

> lighting full

> lighting simple

> graphics silhouettes true

> lighting soft

> lighting simple

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> lighting simple

> lighting soft

> lighting full

> lighting full

> lighting shadows false

> hide #1.1 models

> show #1.1 models

> show #1.2 models

> hide #1.2 models

> hide #* target a

> show #1.1#!1 target ab

> hide #1.1 models

> hide #!1 target a

> ui tool show "Color Key"

> ui mousemode left "color key"

> key delete

> ui mousemode left rotate

> ui tool show "Color Actions"

> show #1.1 models

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> select ::name="ZN2"

1 atom, 1 residue, 1 model selected  

> show ZN

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show ZN2

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show ZN2

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show ZN2

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show ZN2

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show ZN2

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show ZN2

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> lighting soft

> lighting simple

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting simple

> graphics silhouettes true

> save "/Users/landskron/Desktop/structure figures/cluster 1 ocean -
> magnesium.cxs"

——— End of log from Tue May 11 19:05:23 2021 ———

opened ChimeraX session  

> ui tool show "Surface Color"

> color radial #1.1 palette -10,#ff0000:-3,#ffffff:5,#0000ff

> color radial #1.1 palette -10,#ff0000:-3,#ffffff:5,#0000ff

> color radial #1.1 palette -10,#ff0000:0,#ffffff:10,#0000ff

> color radial #1.1 palette -3,#ff0000:0,#ffffff:10,#0000ff

> color radial #1.1 palette -100,#ff0000:0,#ffffff:10,#0000ff

> color radial #1.1 palette -100,#ff0000:0,#ffffff:10,#0000ff center
> -1.0552,-0.19128,-2.4173

> color radial #1.1 palette 0,#ffffff:-2.5,#0000ff center
> -1.0552,-0.19128,-2.4173

> color radial #1.1 palette 0,#ffffff:-2.5,#0000ff center
> -1.0552,-0.19128,-2.4173

No map chosen for coloring  

Traceback (most recent call last):  
File
"/Users/landskron/Desktop/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/surface/surfcolorgui.py", line 425, in _color  
% (subcmd, surf_spec, map.id_string, palette))  
AttributeError: 'NoneType' object has no attribute 'id_string'  
  
AttributeError: 'NoneType' object has no attribute 'id_string'  
  
File
"/Users/landskron/Desktop/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/surface/surfcolorgui.py", line 425, in _color  
% (subcmd, surf_spec, map.id_string, palette))  
  
See log for complete Python traceback.  
  

No map chosen for coloring  

Traceback (most recent call last):  
File
"/Users/landskron/Desktop/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/surface/surfcolorgui.py", line 425, in _color  
% (subcmd, surf_spec, map.id_string, palette))  
AttributeError: 'NoneType' object has no attribute 'id_string'  
  
AttributeError: 'NoneType' object has no attribute 'id_string'  
  
File
"/Users/landskron/Desktop/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/surface/surfcolorgui.py", line 425, in _color  
% (subcmd, surf_spec, map.id_string, palette))  
  
See log for complete Python traceback.  
  

No map chosen for coloring  

Traceback (most recent call last):  
File
"/Users/landskron/Desktop/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/surface/surfcolorgui.py", line 425, in _color  
% (subcmd, surf_spec, map.id_string, palette))  
AttributeError: 'NoneType' object has no attribute 'id_string'  
  
AttributeError: 'NoneType' object has no attribute 'id_string'  
  
File
"/Users/landskron/Desktop/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/surface/surfcolorgui.py", line 425, in _color  
% (subcmd, surf_spec, map.id_string, palette))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-10.36.19
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro12,1
      Processor Name: Intel Core i7
      Processor Speed: 3,1 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Memory: 8 GB
      Boot ROM Version: MBP121.0177.B00
      SMC Version (system): 2.28f7

Software:

    System Software Overview:

      System Version: macOS 10.13.6 (17G65)
      Kernel Version: Darwin 17.7.0
      Time since boot: 22 days 6:02

Graphics/Displays:

    Intel Iris Graphics 6100:

      Chipset Model: Intel Iris Graphics 6100
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x162b
      Revision ID: 0x0009
      Metal: Supported, feature set macOS GPUFamily1 v3
      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
          Rotation: Supported
          Automatically Adjust Brightness: No

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.3
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.2
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.2
    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: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.4
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.7
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
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    sphinxcontrib-devhelp: 1.0.2
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    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

[Tom Goddard]

Fixed.

Surface Color tool gave a traceback when coloring by volume data value when no map is chosen. It gave an error message "No map chosen for coloring" but then the code didn't return and tried to use the map which was None.