ISOLDE: 'NoneType' object has no attribute 'is_difference_map'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/kurumizaka-lab/Desktop/Fukushima/211124_KpNCP_32.pdb

Chain information for 211124_KpNCP_32.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D H | No description available  
E | No description available  
F | No description available  
G | No description available  
I | No description available  
J | No description available  
  

> open "/Users/kurumizaka-lab/Desktop/211019_fukushima
> 2/211117_postprocess_masked.mrc"

Opened 211117_postprocess_masked.mrc as #2, grid size 180,180,180, pixel 1.06,
shown at level 0.0346, step 1, values float32  

> isolde start

> set selectionWidth 4

Chain information for 211124_KpNCP_32.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D 1.2/H | No description available  
1.2/E | No description available  
1.2/F | No description available  
1.2/G | No description available  
1.2/I | No description available  
1.2/J | No description available  
  
Done loading forcefield  
Traceback (most recent call last):  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2650, in _choose_map_color  
if v.is_difference_map:  
AttributeError: 'NoneType' object has no attribute 'is_difference_map'  
  
AttributeError: 'NoneType' object has no attribute 'is_difference_map'  
  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2650, in _choose_map_color  
if v.is_difference_map:  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2650, in _choose_map_color  
if v.is_difference_map:  
AttributeError: 'NoneType' object has no attribute 'is_difference_map'  
  
AttributeError: 'NoneType' object has no attribute 'is_difference_map'  
  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2650, in _choose_map_color  
if v.is_difference_map:  
  
See log for complete Python traceback.  
  
Opened 211117_postprocess_masked.mrc as #1.1.1.1, grid size 180,180,180, pixel
1.06, shown at step 1, values float32  

> select /A:35

Nothing selected  
Traceback (most recent call last):  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2599, in _xtal_mask_to_selection  
self._xtal_mask_to_atoms(sel, focus)  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2607, in _xtal_mask_to_atoms  
sh.isolate_and_cover_selection(  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/symmetry.py", line 987, in
isolate_and_cover_selection  
self.map_mgr.cover_atoms(atoms, transforms=transforms,
transform_indices=indices,  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms  
zm.set_symmetry_map(atoms, transforms, transform_indices)  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 119, in set_symmetry_map  
self.structure = self._unique_structure(atoms)  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
TypeError: All atoms for zone mask must be from a single model!  
  
TypeError: All atoms for zone mask must be from a single model!  
  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
  
See log for complete Python traceback.  
  

> select /A:35

Nothing selected  

> select /A:35

Nothing selected  
Traceback (most recent call last):  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2599, in _xtal_mask_to_selection  
self._xtal_mask_to_atoms(sel, focus)  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2607, in _xtal_mask_to_atoms  
sh.isolate_and_cover_selection(  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/symmetry.py", line 987, in
isolate_and_cover_selection  
self.map_mgr.cover_atoms(atoms, transforms=transforms,
transform_indices=indices,  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms  
zm.set_symmetry_map(atoms, transforms, transform_indices)  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 119, in set_symmetry_map  
self.structure = self._unique_structure(atoms)  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
TypeError: All atoms for zone mask must be from a single model!  
  
TypeError: All atoms for zone mask must be from a single model!  
  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.6.20
OpenGL renderer: AMD Radeon HD - FirePro D700 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: Mac Pro
      Model Identifier: MacPro6,1
      Processor Name: 12-Core Intel Xeon E5
      Processor Speed: 2.7 GHz
      Number of Processors: 1
      Total Number of Cores: 12
      L2 Cache (per Core): 256 KB
      L3 Cache: 30 MB
      Hyper-Threading Technology: Enabled
      Memory: 64 GB
      System Firmware Version: 428.140.7.0.0
      SMC Version (system): 2.20f18
      Panel Illumination Version: 1.4a6

Software:

    System Software Overview:

      System Version: macOS 11.6 (20G165)
      Kernel Version: Darwin 20.6.0
      Time since boot: 25 days 19:08

Graphics/Displays:

    AMD FirePro D700:

      Chipset Model: AMD FirePro D700
      Type: GPU
      Bus: PCIe
      Slot: Slot-1
      PCIe Lane Width: x16
      VRAM (Total): 6 GB
      Vendor: AMD (0x1002)
      Device ID: 0x6798
      Revision ID: 0x0000
      ROM Revision: 113-C3861J-687
      VBIOS Version: 113-C3861XA-028
      EFI Driver Version: 01.0D.687
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.11 [3.2.8]
      Metal Family: Supported, Metal GPUFamily macOS 2
      Connection Type: No Display Connected

    AMD FirePro D700:

      Chipset Model: AMD FirePro D700
      Type: GPU
      Bus: PCIe
      Slot: Slot-2
      PCIe Lane Width: x16
      VRAM (Total): 6 GB
      Vendor: AMD (0x1002)
      Device ID: 0x6798
      Revision ID: 0x0000
      ROM Revision: 113-C3861J-687
      VBIOS Version: 113-C3861XB-028
      EFI Driver Version: 01.0D.687
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.11 [3.2.8]
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Thunderbolt Display:
          Display Type: LCD
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: C02N864QF2GC
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes
          Connection Type: Thunderbolt/DisplayPort

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
    biopython: 1.79
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    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: 1.13.2
    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-Clipper: 0.16.1
    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: 1.2.5
    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: 1.1.3
    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-ISOLDE: 1.2.2
    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-Phenix: 0.3
    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-StrudelScore: 0.1.9
    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: 1.7.6
    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: 5.0.9
    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: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    mrcfile: 1.3.0
    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
    pandas: 1.3.3
    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
    recordtype: 1.3
    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
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    threed-strudel: 0.9.7
    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

[Tristan Croll]

I've been meaning to fix that for ages, but kept forgetting: the map settings dialogue doesn't have callbacks for model add/remove. Will fix for the new release.