Opened 8 months ago

Last modified 8 months ago

#17039 assigned defect

ISOLDE flip_if_necessary: AttributeError: 'NoneType' object has no attribute 'coord'

Reported by: chimerax-bug-report@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/swatibalakrishnan/Desktop/HTT-Macrocycle-
> structures/Complex2/deepEMhancer_highRes_J230.mrc format mrc

Opened deepEMhancer_highRes_J230.mrc as #1, grid size 512,512,512, pixel
0.732, shown at level 0.000654, step 2, values float32  

> open /Users/swatibalakrishnan/Desktop/HTT-Macrocycle-
> structures/PDB_deposition/Complex2/C2_validation2_chimera2_py_Dpep.pdb

Chain information for C2_validation2_chimera2_py_Dpep.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 41250 atom styles  

> volume #1 step 1

> volume #1 level 0.07261

> volume #1 level 0.0822

> color bychain

> select /C

318 atoms, 328 bonds, 17 residues, 1 model selected  

> ui tool show ISOLDE

> set selectionWidth 4

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for C2_validation2_chimera2_py_Dpep.pdb  
---  
Chain | Description  
2.2/A | No description available  
2.2/B | No description available  
2.2/C | No description available  
2.2/D | No description available  
2.2/E | No description available  
  

> clipper associate #1 toModel #2

Opened deepEMhancer_highRes_J230.mrc as #2.1.1.1, grid size 512,512,512, pixel
0.732, shown at step 1, values float32  

> transparency 50

> select clear

> volume #2.1.1.1 level 0.1255

> isolde sim start /C:1

ISOLDE: started sim  

> volume #2.1.1.1 level 0.01993

> select clear

> volume #2.1.1.1 level 0.06218

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /C:7

Sim termination reason: None  
ISOLDE: stopped sim  

MD template ARG for residue ARG B107 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG B273 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

> select clear

> isolde sim start /C:7

Sim termination reason: None  
ISOLDE: stopped sim  
Fetching CCD NMM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/NMM/NMM.cif  
Fetching CCD DA2 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/DA2/DA2.cif  
Fetching CCD 2MR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/2MR/2MR.cif  
Fetching CCD AAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/AAG/AAG.cif  

> isolde sim start /C:7

ISOLDE: started sim  

> volume #2.1.1.1 level 0.2364

> volume #2.1.1.1 level 0.1572

> volume #2.1.1.1 level 0.04633

> volume #2.1.1.1 level 0.1678

> volume #2.1.1.1 level 0.1203

> volume #2.1.1.1 level 0.05161

> select clear

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> volume #2.1.1.1 level 0.02845

> volume #2.1.1.1 level 0.05934

> isolde sim start /C:14

ISOLDE: started sim  

> select clear

[Repeated 2 time(s)]

> isolde sim pause

> select /B

3803 atoms, 3837 bonds, 2 pseudobonds, 250 residues, 2 models selected  

> hide (#!2.2 & sel) target a

> undo

> isolde sim resume

> volume #2.1.1.1 level 0.09108

> select clear

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> volume #2.1.1.1 level 0.07644

> isolde sim start /C:7

ISOLDE: started sim  

> select clear

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /C:3

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /C:2

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Users/swatibalakrishnan/Desktop/HTT-Macrocycle-
> structures/PDB_deposition/Complex2/C2_validation2_chimera2_py_Dpep_Cfit.pdb
> relModel #2.1.1.1

> close session

> open /Users/swatibalakrishnan/Desktop/HTT-Macrocycle-
> structures/Complex2/deepEMhancer_highRes_J230.mrc format mrc

Opened deepEMhancer_highRes_J230.mrc as #1, grid size 512,512,512, pixel
0.732, shown at level 0.000654, step 2, values float32  

> open /Users/swatibalakrishnan/Desktop/HTT-Macrocycle-
> structures/PDB_deposition/Complex2/C2_validation2_chimera2_py_Dpep_Cfit2.pdb

Chain information for C2_validation2_chimera2_py_Dpep_Cfit2.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 41250 atom styles  

> color bychain

> volume #1 level 0.0585

> volume #1 step 1

> volume #1 level 0.09916

> select /C

318 atoms, 328 bonds, 17 residues, 1 model selected  

> ui tool show ISOLDE

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Traceback (most recent call last):  
File "/Users/swatibalakrishnan/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/main_win.py", line 157, in _set_selected_model  
self.isolde.selected_model = model  
File "/Users/swatibalakrishnan/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/isolde.py", line 436, in selected_model  
self.change_selected_model(model)  
File "/Users/swatibalakrishnan/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/isolde.py", line 773, in change_selected_model  
self._change_selected_model(self, model=model, force=True)  
File "/Users/swatibalakrishnan/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/isolde.py", line 814, in _change_selected_model  
correct_pseudosymmetric_sidechain_atoms(session, m.residues)  
File "/Users/swatibalakrishnan/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/atomic/util.py", line 28, in
correct_pseudosymmetric_sidechain_atoms  
if flip_if_necessary(r, ('CD','NE','CZ',('NH2','NH1'))):  
File "/Users/swatibalakrishnan/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/atomic/util.py", line 64, in flip_if_necessary  
dihedrals.append(dihedral(*[a.coord for a in atoms]))  
File "/Users/swatibalakrishnan/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/atomic/util.py", line 64, in <listcomp>  
dihedrals.append(dihedral(*[a.coord for a in atoms]))  
AttributeError: 'NoneType' object has no attribute 'coord'  
  
AttributeError: 'NoneType' object has no attribute 'coord'  
  
File "/Users/swatibalakrishnan/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/atomic/util.py", line 64, in  
dihedrals.append(dihedral(*[a.coord for a in atoms]))  
  
See log for complete Python traceback.  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Traceback (most recent call last):  
File "/Users/swatibalakrishnan/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/main_win.py", line 157, in _set_selected_model  
self.isolde.selected_model = model  
File "/Users/swatibalakrishnan/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/isolde.py", line 436, in selected_model  
self.change_selected_model(model)  
File "/Users/swatibalakrishnan/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/isolde.py", line 773, in change_selected_model  
self._change_selected_model(self, model=model, force=True)  
File "/Users/swatibalakrishnan/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/isolde.py", line 814, in _change_selected_model  
correct_pseudosymmetric_sidechain_atoms(session, m.residues)  
File "/Users/swatibalakrishnan/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/atomic/util.py", line 28, in
correct_pseudosymmetric_sidechain_atoms  
if flip_if_necessary(r, ('CD','NE','CZ',('NH2','NH1'))):  
File "/Users/swatibalakrishnan/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/atomic/util.py", line 64, in flip_if_necessary  
dihedrals.append(dihedral(*[a.coord for a in atoms]))  
File "/Users/swatibalakrishnan/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/atomic/util.py", line 64, in <listcomp>  
dihedrals.append(dihedral(*[a.coord for a in atoms]))  
AttributeError: 'NoneType' object has no attribute 'coord'  
  
AttributeError: 'NoneType' object has no attribute 'coord'  
  
File "/Users/swatibalakrishnan/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/atomic/util.py", line 64, in  
dihedrals.append(dihedral(*[a.coord for a in atoms]))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-16.5.14
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 2020.0.1.0.0 (iBridge: 21.16.365.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 11.7.10 (20G1427)
      Kernel Version: Darwin 20.6.0
      Time since boot: 1 day 3:21

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a53
      Revision ID: 0x0007
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    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: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    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-ISOLDE: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    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-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
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    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    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: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
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    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
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    executing: 1.2.0
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    funcparserlib: 1.0.1
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    h5py: 3.8.0
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    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
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    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
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    pydicom: 2.3.0
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    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
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    PyQt6-sip: 13.4.1
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    python-dateutil: 2.8.2
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    qtconsole: 5.4.0
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    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
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    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
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    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (1)

comment:1 by Tom Goddard, 8 months ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE flip_if_necessary: AttributeError: 'NoneType' object has no attribute 'coord'
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