Close event on already closed window

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19043
ChimeraX Version: 1.3.dev202110020016 (2021-10-02 00:16:37 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3.dev202110020016 (2021-10-02)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "D:\Science\Kinase\R-Subunit\Chimera X\site I tyr.cxs" format session

registering illegal selector name "site 2 tyr"  

Log from Sun Oct 17 16:34:10 2021UCSF ChimeraX version: 1.3.dev202110020016
(2021-10-02)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "D:\Science\Kinase\R-Subunit\Chimera X\site I tyr.cxs" format session

registering illegal selector name "site 2 tyr"  

Log from Sun Oct 17 16:26:29 2021UCSF ChimeraX version: 1.3.dev202110020016
(2021-10-02)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open D:\Science\Kinase\Xray-data-kinases\1rgs.pdb format pdb

1rgs.pdb title:  
Regulatory subunit of camp dependent protein kinase [more info...]  
  
Chain information for 1rgs.pdb #1  
---  
Chain | Description | UniProt  
A | RI(α) | KAP0_BOVIN  
  
Non-standard residues in 1rgs.pdb #1  
---  
CMP — adenosine-3',5'-cyclic-monophosphate (cyclic amp; camp)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select /A:113

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /A:113-285

1349 atoms, 1373 bonds, 173 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui mousemode right select

Drag select of 22 atoms, 25 bonds  

> delete atoms sel

> delete bonds sel

> select /A:286

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

> select /A:286-376

666 atoms, 679 bonds, 91 residues, 1 model selected  

> name frozen "site 2 tyr" sel

registering illegal selector name "site 2 tyr"  

> ui tool show "Basic Actions"

> hide /A target c

[Repeated 1 time(s)]

> hide /A target abp

[Repeated 1 time(s)]

> hide /A target c

[Repeated 1 time(s)]

> show /A target abp

[Repeated 1 time(s)]

> hide /A target abp

[Repeated 1 time(s)]

> hide /A target c

[Repeated 1 time(s)]

> show /A target c

[Repeated 1 time(s)]

> select /A

688 atoms, 704 bonds, 92 residues, 1 model selected  

> undo

[Repeated 5 time(s)]

> show /A target c

[Repeated 1 time(s)]

> select ::name="CMP"

22 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel target ab

> name frozen cAMP sel

[Repeated 1 time(s)]

> hide cAMP target abp

> show cAMP target abp

> show cAMP target s

> hide cAMP target s

> hide /A target c

[Repeated 1 time(s)]

> cd "D:/Science/Kinase/R-Subunit/Chimera X"

Current working directory is: D:\Science\Kinase\R-Subunit\Chimera X  

> save "D:/Science/Kinase/R-Subunit/Chimera X/site I tyr.cxs"

——— End of log from Sun Oct 17 16:26:29 2021 ———

opened ChimeraX session  

> ui mousemode right translate

> select clear

> save "D:/Science/Kinase/R-Subunit/Chimera X/site I tyr.cxs"

——— End of log from Sun Oct 17 16:34:10 2021 ———

opened ChimeraX session  

> addh

Summary of feedback from adding hydrogens to 1rgs.pdb #1  
---  
warnings | Not adding hydrogens to /A SER 297 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A ARG 303 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 304 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A SER 305 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A GLU 306 CB because it is missing heavy-atom bond
partners  
8 messages similar to the above omitted  
notes | No usable SEQRES records for 1rgs.pdb (#1) chain A; guessing termini
instead  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A PRO 286  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A SER 376  
55 hydrogen bonds  
/A SER 376 is not terminus, removing H atom from 'C'  
644 hydrogens added  
  

> ui tool show "Structure Modification"

> ui mousemode right select

> select /A:601@H2

1 atom, 1 residue, 1 model selected  

> substitute sel substituents NCH3_2 guessAttachment true modify true minimize
> false useRemoteness false newResidue false

> preset seqcrow sticks

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202110020016\bin\lib\site-
packages\chimerax\ui\gui.py", line 2251, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "C:\Program Files\ChimeraX 1.3.dev202110020016\bin\lib\site-
packages\chimerax\ui\gui.py", line 648, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
KeyError: <SEQCROW.tools.structure_editing.EditStructure object at
0x0000018E81DCEE20>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX 1.3.dev202110020016\bin\lib\site-
packages\chimerax\ui\gui.py", line 648, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
  
See log for complete Python traceback.  
  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  




OpenGL version: 3.3.0 NVIDIA 461.09
OpenGL renderer: Quadro P620/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 30CF000YGE
OS: Microsoft Windows 10 Pro (Build 19043)
Memory: 17,010,741,248
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8700T CPU @ 2.40GHz
OSLanguage: de-DE
Locale: ('de_DE', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1
    charset-normalizer: 2.0.6
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.1
    ChimeraX-AtomicLibrary: 4.1.4
    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
    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.dev202110020016
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    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: 2.1.1
    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: 2.0.1
    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
    ChimeraX-ModelPanel: 1.2
    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: 2.6.3
    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
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.4
    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
    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: 1.13.2
    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
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.10.0
    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: 3.4.0
    html2text: 2020.1.16
    idna: 3.2
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    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: 4.8.1
    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: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.20
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    Send2Trash: 1.8.0
    SEQCROW: 1.3
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    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
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1