QScore: model is None

[rohou.alexis@…]

The following bug report has been submitted:
Platform:        macOS-14.7.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Here's how to reproduce:
- download 8i5b and the associated EMDB map
- calculate Q scores for chain A
- color byattr the atoms of chain A with Q scores (from 0.2 to 1.0)
- close

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> set bgColor white

> lighting soft

> clipper init

> cofr centerOfView showPivot true

> camera ortho

> lighting simple

UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open pdb:8i5b

Summary of feedback from opening 8i5b fetched from pdb  
---  
warnings | Unable to fetch template for 'LPE': will use incomplete information in mmCIF file  
Unable to fetch template for 'OJ0': will use incomplete information in mmCIF
file  
Unable to fetch template for 'P5S': will use incomplete information in mmCIF
file  
Unable to fetch template for 'PCW': will use incomplete information in mmCIF
file  
note | Fetching compressed mmCIF 8i5b from http://files.rcsb.org/download/8i5b.cif  
  
8i5b title:  
Structure of human Nav1.7 in complex with bupivacaine [more info...]  
  
Chain information for 8i5b #1  
---  
Chain | Description | UniProt  
A | Sodium channel protein type 9 subunit alpha | SCN9A_HUMAN 1-1988  
B | Sodium channel subunit beta-1 | SCN1B_HUMAN 1-218  
C | Sodium channel subunit beta-2 | SCN2B_HUMAN 1-215  
  
Non-standard residues in 8i5b #1  
---  
LPE — 1-O-octadecyl-Sn-glycero-3-phosphocholine (LPC-ether)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
OJ0 — Levobupivacaine
((2~{S})-1-butyl-~{N}-(2,6-dimethylphenyl)piperidine-2-carboxamide)  
P5S —
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
(phosphatidyl serine)  
PCW — 1,2-dioleoyl-Sn-glycero-3-phosphocholine
((Z,Z)-4-hydroxy-N,N,N-trimethyl-10-oxo-7-[(1-oxo-9-octadecenyl)oxy]-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium-4-oxide)  
Y01 — cholesterol hemisuccinate  
  

> log metadata #1

Metadata for 8i5b #1  
---  
Title | Structure of human Nav1.7 in complex with bupivacaine  
Citation | Wu, Q., Huang, J., Fan, X., Wang, K., Jin, X., Huang, G., Li, J., Pan, X., Yan, N. (2023). Structural mapping of Na v 1.7 antagonists. Nat Commun, 14, 3224-3224. PMID: 37270609. DOI: 10.1038/s41467-023-38942-3  
Non-standard residues | LPE — 1-O-octadecyl-Sn-glycero-3-phosphocholine (LPC-ether)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
OJ0 — Levobupivacaine
((2~{S})-1-butyl-~{N}-(2,6-dimethylphenyl)piperidine-2-carboxamide)  
P5S —
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
(phosphatidyl serine)  
PCW — 1,2-dioleoyl-Sn-glycero-3-phosphocholine
((Z,Z)-4-hydroxy-N,N,N-trimethyl-10-oxo-7-[(1-oxo-9-octadecenyl)oxy]-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium-4-oxide)  
Y01 — cholesterol hemisuccinate  
Gene source | Homo sapiens (human)  
CryoEM Map | EMDB 35193 — open map  
Experimental method | Electron microscopy  
Resolution | 2.7Å  
  
> open 35193 fromDatabase emdb

Summary of feedback from opening 35193 fetched from emdb  
---  
notes | Fetching compressed map 35193 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-35193/map/emd_35193.map.gz  
Fetching map header 35193 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-35193/header/emd-35193.xml  
  
Opened emdb 35193 as #2, grid size 288,288,288, pixel 0.865, shown at level
0.35, step 2, values float32, fit PDB 8i5b  

> volume #2 step 1

> volume #2 level 0.5512

> view /A:OJ0

> volume #2 level 0.3692

> volume #2 color #b2b2b2a1

> show water

> show :HOH

> select zone /A:OJ0 5.0 residues true

Selected 99 atoms, 2 surfaces  

> show sel

> label sel

> select clear

> ui tool show "Model-map Q-Score"

> style #1 stick

Changed 13440 atom styles  

> color #1 byhetero

> transparency #2 60

> qscore #1 toVolume #2 useGui false pointsPerShell 8 shellRadiusStep 0.100
> maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false assignAttr
> true

Overall mean Q-Score: 0.64  

> color byattribute /A qscore

Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword  

> color byattribute /A atoms qscore

Expected ',' or a keyword  

> color byattribute a:qscore /A

10930 atoms, 1293 residues, atom qscore range -0.828 to 0.93  

> color byattribute a:qscore /A range 0.2,1.0

10930 atoms, 1293 residues, atom qscore range -0.828 to 0.93  

> save /Users/rohoua/work/Genentech/sidechain_remodel/8i5b.cxs

> close

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/rohoua/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/qscore/ui.py", line 307, in _toggle_save_button_enabled  
for atom in model.atoms:  
^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
Error processing trigger "selected model changed":  
AttributeError: 'NoneType' object has no attribute 'atoms'  
  
File "/Users/rohoua/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/qscore/ui.py", line 307, in _toggle_save_button_enabled  
for atom in model.atoms:  
^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: Z16T0006PLL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.41.5
      OS Loader Version: 10151.140.19.700.2

Software:

    System Software Overview:

      System Version: macOS 14.7.1 (23H222)
      Kernel Version: Darwin 23.6.0
      Time since boot: 49 days, 12 hours, 31 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL P4317Q:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 3840 x 2160 @ 30.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Television: Yes


Installed Packages:
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    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
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    autocommand: 2.2.2
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    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
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    ChimeraX-AtomicLibrary: 14.1.11
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    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
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    ChimeraX-CommandLine: 1.2.5
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    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
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    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
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    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
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    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
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    ChimeraX-IMOD: 1.0
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    ChimeraX-IUPAC: 1.0
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    ChimeraX-LigandRecognizer: 0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
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    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
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    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
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    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
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    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
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    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-QScore: 1.2
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    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
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    ChimeraX-SelInspector: 1.0
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    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
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[pett]

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