Color button accessed after C++ deleted

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3rc202110252002 (2021-10-25 20:02:00 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3rc202110252002 (2021-10-25)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/hrenault/Desktop/METABEVO/Bioinformatics/Homology-
> modelling/PpCYP73/2020-12/Autodock Vina command
> line/PpCYP73A48/PpCYP73A48_docked_heme_R213-S214-Gln218 flexible - Docking
> cinnamate/PpCYP73A48_docked_heme_R213-S214-Gln218flex_tCA_out.pdbqt"

Summary of feedback from opening
/Users/hrenault/Desktop/METABEVO/Bioinformatics/Homology-
modelling/PpCYP73/2020-12/Autodock Vina command
line/PpCYP73A48/PpCYP73A48_docked_heme_R213-S214-Gln218 flexible - Docking
cinnamate/PpCYP73A48_docked_heme_R213-S214-Gln218flex_tCA_out.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -7.0 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK 3 active torsions:  
  
Ignored bad PDB record found on line 4  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 5  
REMARK 1 A between atoms: C1_1 and C2_2  
  
Ignored bad PDB record found on line 6  
REMARK 2 A between atoms: C1_1 and O1_10  
  
535 messages similar to the above omitted  
  
Chain information for PpCYP73A48_docked_heme_R213-S214-Gln218flex_tCA_out.pdb  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A | No description
available  
  
Opened PpCYP73A48_docked_heme_R213-S214-Gln218flex_tCA_out.pdbqt containing 9
structures (333 atoms, 306 bonds)  

> hide #!1.2 models

> hide #!1.3 models

> hide #!1.5 models

> hide #!1.4 models

> hide #!1.6 models

> hide #!1.7 models

> hide #!1.8 models

> hide #!1.9 models

> color #1.1 #8eea51

> color #1.1 #97f333

> color #1.1 #93ea3d

> set bgColor white

> color #!1.1 byhetero

> open "/Users/hrenault/Desktop/METABEVO/Bioinformatics/Homology-
> modelling/PpCYP73/2020-12/Autodock Vina command
> line/PpCYP73A48/PpCYP73A48_docked_heme_R213-S214-Gln218 flexible - Docking
> cinnamate/PpCYP73A48_docked_heme_R213-S214-Gln218_Receptor_rigid.pdbqt"

Chain information for
PpCYP73A48_docked_heme_R213-S214-Gln218_Receptor_rigid.pdb #2  
---  
Chain | Description  
A | No description available  
  
Opened PpCYP73A48_docked_heme_R213-S214-Gln218_Receptor_rigid.pdbqt containing
1 structures (4678 atoms, 4765 bonds)  

> hide #!1 models

> select ::name="HEM"

47 atoms, 50 bonds, 1 residue, 1 model selected  

> select ~sel

4964 atoms, 5021 bonds, 18 pseudobonds, 507 residues, 20 models selected  

> hide sel & #2 atoms

> select ::name="HEM"

47 atoms, 50 bonds, 1 residue, 1 model selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3-rc2021.10.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 47, in
_make_color_callback  
_color_callback(*args)  
File
"/Applications/ChimeraX-1.3-rc2021.10.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 128, in _color_changed_cb  
self.set_color(color)  
File
"/Applications/ChimeraX-1.3-rc2021.10.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 191, in set_color  
ColorButton.set_color(self, color)  
File
"/Applications/ChimeraX-1.3-rc2021.10.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 88, in set_color  
self.setStyleSheet('background-color: %s' % hex_color_name(color))  
RuntimeError: wrapped C/C++ object of type MultiColorButton has been deleted  
  
RuntimeError: wrapped C/C++ object of type MultiColorButton has been deleted  
  
File
"/Applications/ChimeraX-1.3-rc2021.10.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 88, in set_color  
self.setStyleSheet('background-color: %s' % hex_color_name(color))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3-rc2021.10.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 47, in
_make_color_callback  
_color_callback(*args)  
File
"/Applications/ChimeraX-1.3-rc2021.10.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 128, in _color_changed_cb  
self.set_color(color)  
File
"/Applications/ChimeraX-1.3-rc2021.10.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 191, in set_color  
ColorButton.set_color(self, color)  
File
"/Applications/ChimeraX-1.3-rc2021.10.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 88, in set_color  
self.setStyleSheet('background-color: %s' % hex_color_name(color))  
RuntimeError: wrapped C/C++ object of type MultiColorButton has been deleted  
  
RuntimeError: wrapped C/C++ object of type MultiColorButton has been deleted  
  
File
"/Applications/ChimeraX-1.3-rc2021.10.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 88, in set_color  
self.setStyleSheet('background-color: %s' % hex_color_name(color))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3-rc2021.10.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 47, in
_make_color_callback  
_color_callback(*args)  
File
"/Applications/ChimeraX-1.3-rc2021.10.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 128, in _color_changed_cb  
self.set_color(color)  
File
"/Applications/ChimeraX-1.3-rc2021.10.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 191, in set_color  
ColorButton.set_color(self, color)  
File
"/Applications/ChimeraX-1.3-rc2021.10.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 88, in set_color  
self.setStyleSheet('background-color: %s' % hex_color_name(color))  
RuntimeError: wrapped C/C++ object of type MultiColorButton has been deleted  
  
RuntimeError: wrapped C/C++ object of type MultiColorButton has been deleted  
  
File
"/Applications/ChimeraX-1.3-rc2021.10.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 88, in set_color  
self.setStyleSheet('background-color: %s' % hex_color_name(color))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-16.5.2
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.8 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0)

Software:

    System Software Overview:

      System Version: macOS 11.6 (20G165)
      Kernel Version: Darwin 20.6.0
      Time since boot: 4:00

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        PHL 328P6A:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 59.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          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
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1
    charset-normalizer: 2.0.7
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.2
    ChimeraX-AtomicLibrary: 4.1.5
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3rc202110252002
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
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    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
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    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.2
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
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    ChimeraX-Mol2: 2.0
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    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.4
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
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    ChimeraX-PickBlobs: 1.0
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    ChimeraX-ResidueFit: 1.0
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    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
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    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
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    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.6
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    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
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    ChimeraX-Zone: 1.0
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    grako: 3.16.5
    h5py: 3.5.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
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    kiwisolver: 1.3.2
    lxml: 4.6.3
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    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
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    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
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    Pillow: 8.3.2
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    wheel: 0.37.0
    wheel-filename: 1.3.0

[Eric Pettersen]

There's further bulletproofing I can do.

[Eric Pettersen]

Instead of relying on __del__ (which doesn't get called for the button whose callback is connected to the dialog) or the destroyed() signal (which seems to not fire), just catch RuntimeError when the button callback runs and disconnect the callback.