Render by Attribute: attribute monitoring still on in dead tool

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.27686
ChimeraX Version: 1.9.dev202408250821 (2024-08-25 08:21:02 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  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9.dev202408250821 (2024-08-25)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/DELL/Documents/Data from Jelle's
> Lab/data_nigeria/Data/Scaffolds/Bats/Metagenomic analysis/SaV VP1
> structure/7dod.cif/7dod.pdb"

7dod.pdb title:  
Capsid structure of human sapovirus [more info...]  
  
Chain information for 7dod.pdb #1  
---  
Chain | Description  
A B C | calicivirin  
  

> delete /B,C

> open "C:/Users/DELL/Desktop/Tim_Protein
> analysis/fold_btsava2_2024_10_25_16_24/fold_btsava2_2024_10_25_16_24_model_0.cif"

Chain information for fold_btsava2_2024_10_25_16_24_model_0.cif #2  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> 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 7dod.pdb, chain A (#1) with
fold_btsava2_2024_10_25_16_24_model_0.cif, chain A (#2), sequence alignment
score = 1219.4  
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: 7dod.pdb #1/A,
fold_btsava2_2024_10_25_16_24_model_0.cif #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 204 pruned atom pairs is 0.882 angstroms; (across all 496 pairs:
7.190)  
  

> save C:\Users\DELL/Desktop\image1.png supersample 3

> ui tool show "Render/Select by Attribute"

> key red-white-blue :1 :3 :5 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color byattribute r:seq_rmsd #2#!1 target sabc palette 1,red:3,white:5,blue
> noValueColor #55ff7f

7852 atoms, 1047 residues, atom seq_rmsd range 0.103 to 22.8  

> color byattribute r:seq_rmsd #2#!1 target sabc palette 1,red:3,white:5,blue
> noValueColor #55ff7f

7852 atoms, 1047 residues, atom seq_rmsd range 0.103 to 22.8  

> hide #!1 models

> set bgColor white

> lighting simple

> lighting soft

> lighting full

> set bgColor white

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #2 models

> show #2 models

> hide #!1 models

> save C:\Users\DELL/Desktop\image2.png supersample 3

> show #!1 models

> show cartoons

> show surfaces

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> select add #1

3896 atoms, 4003 bonds, 1 pseudobond, 513 residues, 3 models selected  

> select subtract #1

1 model selected  

> hide surfaces

> hide cartoons

> show cartoons

> show atoms

> hide #!2 models

> show #!2 models

> hide #!1 models

> hide #!2 atoms

> style #!2 sphere

Changed 3956 atom styles  

> color #!2 byhetero

> color #!2 bychain

> color #!2 byhetero

> color #!2 bychain

> color #!2 bypolymer

> rainbow #!2

> coulombic #!2

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for fold_btsava2_2024_10_25_16_24_model_0.cif_A SES surface
#2.1: minimum, -19.08, mean -2.91, maximum 7.76  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp #!2

Map values for surface "fold_btsava2_2024_10_25_16_24_model_0.cif_A SES
surface": minimum -30.8, mean -5.318, maximum 22.84  
To also show corresponding color key, enter the above mlp command and add key
true  

> mlp #!2

Map values for surface "fold_btsava2_2024_10_25_16_24_model_0.cif_A SES
surface": minimum -30.8, mean -5.318, maximum 22.84  
To also show corresponding color key, enter the above mlp command and add key
true  

> mlp #!2

Map values for surface "fold_btsava2_2024_10_25_16_24_model_0.cif_A SES
surface": minimum -30.8, mean -5.318, maximum 22.84  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic #!2

Coulombic values for fold_btsava2_2024_10_25_16_24_model_0.cif_A SES surface
#2.1: minimum, -19.08, mean -2.91, maximum 7.76  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp #!2

Map values for surface "fold_btsava2_2024_10_25_16_24_model_0.cif_A SES
surface": minimum -30.8, mean -5.318, maximum 22.84  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor #!2

3956 atoms, 534 residues, 1 surfaces, atom bfactor range 18.7 to 98.2  

> color #!2 bynucleotide

> show #!2 cartoons

> hide #!2 cartoons

> show #!2 cartoons

> clear

Unknown command: clear  

> close

> open "C:\Users\DELL\Documents\Data from Jelle's
> Lab\data_nigeria\Data\Scaffolds\Bats\Metagenomic analysis\SaV VP1
> structure\7dod.cif\7dod.pdb" format pdb

7dod.pdb title:  
Capsid structure of human sapovirus [more info...]  
  
Chain information for 7dod.pdb #1  
---  
Chain | Description  
A B C | calicivirin  
  
Associated 7dod.pdb chain A to 7dod.pdb, chain A with 0 mismatches  
Associated 7dod.pdb chain B to 7dod.pdb, chain A with 0 mismatches  
Associated 7dod.pdb chain C to 7dod.pdb, chain A with 0 mismatches  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9.dev202408250821\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9.dev202408250821\bin\Lib\site-
packages\chimerax\atomic\\__init__.py", line 175, in handler  
callback()  
File "C:\Program Files\ChimeraX 1.9.dev202408250821\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 689, in update_hist  
self._update_render_histogram(attr_name)  
File "C:\Program Files\ChimeraX 1.9.dev202408250821\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 739, in
_update_render_histogram  
any_None = self._update_histogram(self.render_histogram, attr_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9.dev202408250821\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 709, in _update_histogram  
attr_info = self._cur_attr_info()  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9.dev202408250821\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 464, in _cur_attr_info  
target = self.target_menu_button.text()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
RuntimeError: wrapped C/C++ object of type QPushButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QPushButton has been deleted  
  
File "C:\Program Files\ChimeraX 1.9.dev202408250821\bin\Lib\site-
packages\chimerax\render_by_attr\tool.py", line 464, in _cur_attr_info  
target = self.target_menu_button.text()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.2127
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_GB.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Latitude 5591
OS: Microsoft Windows 11 Pro Insider Preview (Build 27686)
Memory: 16,962,301,952
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8850H CPU @ 2.60GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 2.4.1
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2024.7.4
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.14
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.6
    ChimeraX-AtomicLibrary: 14.1.5
    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
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.10
    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: 1.9.dev202408250821
    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-DeepMutationalScan: 1.0
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    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-Foldseek: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.4
    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-Label: 1.1.10
    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: 2.7.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    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: 1.4.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3
    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: 3.1.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.13
    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-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: 1.40.1
    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: 1.2.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.5
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.0.1
    filelock: 3.15.4
    fonttools: 4.53.1
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.8
    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: 1.4.5
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.8
    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: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.47
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    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: 3.1.4
    pyproject_hooks: 1.1.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.2
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.2
    PyQt6-WebEngineSubwheel-Qt6: 6.7.2
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.1
    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: 2024.1
    urllib3: 2.2.2
    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

[Eric Pettersen]

Duplicate of #16185