Global hide/show hitting dead tool

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/chrismuriel/Downloads/AF-A0A5B7KR20-F1-model_v3.pdb

Summary of feedback from opening
/Users/chrismuriel/Downloads/AF-A0A5B7KR20-F1-model_v3.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 477 UNP A0A5B7KR20 A0A5B7KR20_ECOLX 1 477  
  
AF-A0A5B7KR20-F1-model_v3.pdb title:  
Alphafold monomer V2.0 prediction for RNA polymerase σ-54 factor (A0A5B7KR20)
[more info...]  
  
Chain information for AF-A0A5B7KR20-F1-model_v3.pdb #1  
---  
Chain | Description  
A | RNA polymerase σ-54 factor  
  
Alignment identifier is 1/A  
[Repeated 1 time(s)]

> select
> /A:17-27,30-43,71-73,120-130,135-146,158-165,172-184,195-203,213-228,232-239,243-255,260-263,291-293,301-308,313-350,352-357,359-361,367-374,378-385,399-402,417-429,439-448,455-465

1885 atoms, 1880 bonds, 234 residues, 1 model selected  

> select /A:56

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1-56

452 atoms, 454 bonds, 56 residues, 1 model selected  

> color sel blue

> select /A:85-86

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /A:56-86

243 atoms, 244 bonds, 31 residues, 1 model selected  

> color sel forest green

> select /A:85

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:85-105

153 atoms, 157 bonds, 21 residues, 1 model selected  

> color sel orange

> select /A:105-106

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select /A:105-121

136 atoms, 137 bonds, 17 residues, 1 model selected  

> select /A:105

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:105-118

112 atoms, 113 bonds, 14 residues, 1 model selected  

> select /A:105

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:105-120

127 atoms, 128 bonds, 16 residues, 1 model selected  

> color sel yellow

> select /A:120

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:120-150

248 atoms, 252 bonds, 31 residues, 1 model selected  

> color sel hot pink

> select /A:385

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:267-385

962 atoms, 979 bonds, 119 residues, 1 model selected  

> select /A:250

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:250-385

1092 atoms, 1111 bonds, 136 residues, 1 model selected  

> color sel purple

> select /A:385

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:385-477

722 atoms, 734 bonds, 93 residues, 1 model selected  

> color sel medium blue

> color sel cyan

> color sel light gray

> select #1

3791 atoms, 3852 bonds, 477 residues, 1 model selected  

> ~select #1

Nothing selected  

> open /Users/chrismuriel/Downloads/AF-A0A7H9LYA1-F1-model_v3.pdb

Summary of feedback from opening
/Users/chrismuriel/Downloads/AF-A0A7H9LYA1-F1-model_v3.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 477 UNP A0A7H9LYA1 A0A7H9LYA1_ECOLX 1 477  
  
AF-A0A7H9LYA1-F1-model_v3.pdb title:  
Alphafold monomer V2.0 prediction for RNA polymerase σ-54 factor (A0A7H9LYA1)
[more info...]  
  
Chain information for AF-A0A7H9LYA1-F1-model_v3.pdb #2  
---  
Chain | Description  
A | RNA polymerase σ-54 factor  
  

> hide #2 models

> open /Users/chrismuriel/Downloads/AF-Q84CP3-F1-model_v3.pdb

AF-Q84CP3-F1-model_v3.pdb title:  
Alphafold monomer V2.0 prediction for RNA polymerase σ-54 factor (Q84CP3)
[more info...]  
  
Chain information for AF-Q84CP3-F1-model_v3.pdb #3  
---  
Chain | Description | UniProt  
A | RNA polymerase σ-54 factor | Q84CP3_ALIFS  
  

> hide #3 models

> open /Users/chrismuriel/Downloads/AF-A0A510UNU5-F1-model_v3.pdb

Summary of feedback from opening
/Users/chrismuriel/Downloads/AF-A0A510UNU5-F1-model_v3.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 489 UNP A0A510UNU5 A0A510UNU5_ALIFS 1 489  
  
AF-A0A510UNU5-F1-model_v3.pdb title:  
Alphafold monomer V2.0 prediction for RNA polymerase σ-54 factor (A0A510UNU5)
[more info...]  
  
Chain information for AF-A0A510UNU5-F1-model_v3.pdb #4  
---  
Chain | Description  
A | RNA polymerase σ-54 factor  
  

> hide #4 models

> save /Users/chrismuriel/Ecoli_domain_rpon.tif width 704 height 570
> supersample 3

> save /Users/chrismuriel/Ecoli_domain_rpoN.tif width 704 height 570
> supersample 3 transparentBackground true

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 629, in changeEvent  
self.hide_floating_tools = self.isMinimized()  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 734, in hide_floating_tools  
tw._mw_set_shown(True)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2187, in _mw_set_shown  
self.__toolkit.shown = shown  
AttributeError: 'NoneType' object has no attribute 'shown'  
  
AttributeError: 'NoneType' object has no attribute 'shown'  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2187, in _mw_set_shown  
self.__toolkit.shown = shown  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-18.8.4
OpenGL renderer: Intel(R) HD Graphics 615
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook
      Model Identifier: MacBook10,1
      Processor Name: Dual-Core Intel Core m3
      Processor Speed: 1.2 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 451.140.1.0.0
      OS Loader Version: 540.120.3~19
      SMC Version (system): 2.42f13

Software:

    System Software Overview:

      System Version: macOS 12.5.1 (21G83)
      Kernel Version: Darwin 21.6.0
      Time since boot: 8 days 5:25

Graphics/Displays:

    Intel HD Graphics 615:

      Chipset Model: Intel HD Graphics 615
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x591e
      Revision ID: 0x0002
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2304 x 1440 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

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: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    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: 1.31
    ChimeraX-AtomicLibrary: 4.2
    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: 2.6.1
    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: 2.2.2
    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: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    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
    ChimeraX-Maestro: 1.8.1
    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: 2.0.4
    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
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    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: 1.13.7
    ChimeraX-uniprot: 2.2
    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
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0