Opened 12 months ago

Closed 12 months ago

#16333 closed defect (fixed)

Render by Attribute: cannot create weak reference to 'NoneType' object

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.9rc202411170711 (2024-11-17 07:11:23 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9rc202411170711 (2024-11-17)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "D:\Maestria\CURSOS\Bioinformática\Taller resuelto\Informe 4\1im5.pdb"
> format pdb

1im5.pdb title:  
Crystal structure of pyrazinamidase of pyrococcus horikoshii In complex with
zinc [more info...]  
  
Chain information for 1im5.pdb #1  
---  
Chain | Description | UniProt  
A | 180AA long hypothetical pyrazinamidase/nicotinamidase | O58727_PYRHO 1-180  
  
Non-standard residues in 1im5.pdb #1  
---  
ZN — zinc ion  
  
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> open
> C:/Users/RONALD/Downloads/test_ff74a/test_ff74a_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb

Chain information for
test_ff74a_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb #2  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> hide #!1 models

> close #1

> hide #!2 models

> show #!2 models

> open "C:/Users/RONALD/Downloads/MSD
> Aphafold/test1_ff74a/ptm0.391_r3_default.pdb"

Summary of feedback from opening C:/Users/RONALD/Downloads/MSD
Aphafold/test1_ff74a/ptm0.391_r3_default.pdb  
---  
warning | Ignored bad PDB record found on line 1  
PARENT N/A  
  
Chain information for ptm0.391_r3_default.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #!2 to #1

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ptm0.391_r3_default.pdb, chain A (#1) with
test_ff74a_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#2), sequence alignment score = 1020.6  
RMSD between 84 pruned atom pairs is 0.964 angstroms; (across all 238 pairs:
20.208)  
  

> show target m

Drag select of 2 residues  

> view sel

> ui tool show Matchmaker

> matchmaker #!2 to #1 showAlignment true

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ptm0.391_r3_default.pdb, chain A (#1) with
test_ff74a_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#2), sequence alignment score = 1020.6  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: ptm0.391_r3_default.pdb #1/A,
test_ff74a_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 84 pruned atom pairs is 0.964 angstroms; (across all 238 pairs:
20.208)  
  

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> show #2.1 models

> show #1.1 models

> log metadata #1

No models had metadata

> log chains #1

Chain information for ptm0.391_r3_default.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> help help:user

> select #1/A:10-50,53-57,60,90-91,95-98,100-131
> #2/A:10-50,53-57,60,90-91,95-98,100-131

1306 atoms, 1320 bonds, 2 pseudobonds, 168 residues, 4 models selected  

> view #1 clip false

[Repeated 1 time(s)]

> log metadata #1

No models had metadata

> log chains #1

Chain information for ptm0.391_r3_default.pdb #1  
---  
Chain | Description  
A | No description available  
  

> log metadata #1

No models had metadata

> log chains #1

Chain information for ptm0.391_r3_default.pdb #1  
---  
Chain | Description  
A | No description available  
  

> hide #!1 target m

[Repeated 1 time(s)]

> show #!1 target m

> ui tool show "Modeller Comparative"

> ui tool show "Similar Structures"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9rc202411170711\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 358, in _show_ligands  
pdb_hits = [hit for hit in self.results.hits if
hit['database'].startswith('pdb')]  
^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'hits'  
  
AttributeError: 'NoneType' object has no attribute 'hits'  
  
File "C:\Program Files\ChimeraX 1.9rc202411170711\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 358, in _show_ligands  
pdb_hits = [hit for hit in self.results.hits if
hit['database'].startswith('pdb')]  
^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Must run search first  
You must press the similar structures Search button before you can open
matching structures.  

> ui tool show "Map Statistics"

> measure mapstats

> toolshed show

> ui tool show Matchmaker

> select #1/A:3 #2/A:3

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select #1/A:51 #2/A:51

8 atoms, 6 bonds, 2 residues, 2 models selected  

> select #1/A:6 #2/A:6

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select #1/A:4 #2/A:4

8 atoms, 6 bonds, 2 residues, 2 models selected  

> select #1/A:2 #2/A:2

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select #1/A:1 #2/A:1

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A:67 #2/A:67

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select #1/A:69 #2/A:69

22 atoms, 22 bonds, 2 residues, 2 models selected  

> select #1/A:72 #2/A:72

24 atoms, 24 bonds, 2 residues, 2 models selected  

> select #1/A:73 #2/A:73

14 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A:75 #2/A:75

20 atoms, 20 bonds, 2 residues, 2 models selected  

> select #1/A:76 #2/A:76

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A:77 #2/A:77

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select #1/A:78 #2/A:78

22 atoms, 20 bonds, 2 residues, 2 models selected  

> select #1/A:139 #2/A:139

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A:142 #2/A:142

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A:187 #2/A:187

8 atoms, 6 bonds, 2 residues, 2 models selected  

> select #1/A:189 #2/A:189

8 atoms, 6 bonds, 2 residues, 2 models selected  

> select #1/A:192 #2/A:192

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A:193 #2/A:193

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A:195 #2/A:195

16 atoms, 14 bonds, 2 residues, 2 models selected  

> ui tool show "Render/Select by Attribute"

All 'seq_identity' values are 100  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9rc202411170711\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 649, in _new_render_attr  
self._update_markers(None, markers_attr, None, self._prev_model_value,  
File "C:\Program Files\ChimeraX 1.9rc202411170711\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 880, in _update_markers  
self._render_markers[markers_attr].setdefault(model, {})[prev_attr_name] =
prev_markers  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202411170711\bin\Lib\weakref.py", line
508, in setdefault  
return self.data.setdefault(ref(key, self._remove),default)  
^^^^^^^^^^^^^^^^^^^^^^  
TypeError: cannot create weak reference to 'NoneType' object  
  
TypeError: cannot create weak reference to 'NoneType' object  
  
File "C:\Program Files\ChimeraX 1.9rc202411170711\bin\Lib\weakref.py", line
508, in setdefault  
return self.data.setdefault(ref(key, self._remove),default)  
^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 20.19.15.4531
OpenGL renderer: Intel(R) HD Graphics 4600
OpenGL vendor: Intel

Python: 3.11.4
Locale: es_PE.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 3020
OS: Microsoft Windows 10 Pro (Build 19044)
Memory: 8,504,782,848
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-4570 CPU @ 3.20GHz
OSLanguage: es-MX

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 2.4.1
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2024.8.30
    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
    ChimeraX-Atomic: 1.58.7
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.7
    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
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9rc202411170711
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.11
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    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
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.3.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    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
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.8
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.12.1
    html2text: 2024.2.26
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.1
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 12 months ago

Component: Unassigned → Structure Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Render by Attribute: cannot create weak reference to 'NoneType' object

comment:2 by Eric Pettersen, 12 months ago

Resolution: → fixed
Status: accepted → closed

Fix: ​https://github.com/RBVI/ChimeraX/commit/648271e6c63468f3f8b44ba7c3adedf129e23cd3

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