self.main_window is None

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-20.1.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/mariopalma/Downloads/6zwo.pdb

6zwo.pdb title:  
Cryo-em structure of human mtor complex 2, focused on one half [more info...]  
  
Chain information for 6zwo.pdb #1  
---  
Chain | Description  
B | serine/threonine-protein kinase mtor  
D | target of rapamycin complex subunit LST8  
F | rapamycin-insensitive companion of mtor  
H | target of rapamycin complex 2 subunit MAPKAP1  
  
Non-standard residues in 6zwo.pdb #1  
---  
ACE — acetyl group  
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)  
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)  
ZN — zinc ion  
  

> select /F:25-1694

8931 atoms, 9092 bonds, 12 pseudobonds, 1117 residues, 2 models selected  

> color (#!1 & sel) purple

> select /B:791-2549

12841 atoms, 13126 bonds, 8 pseudobonds, 1592 residues, 2 models selected  

> color (#!1 & sel) medium blue

> select /H:2-146

655 atoms, 660 bonds, 2 pseudobonds, 98 residues, 2 models selected  

> color (#!1 & sel) lime

> select /D:8-326

2465 atoms, 2523 bonds, 319 residues, 1 model selected  

> color sel orange

> ui tool show "Show Sequence Viewer"

> sequence chain /F

Alignment identifier is 1/F  

> style stick

Changed 24994 atom styles  

> style stick

Changed 24994 atom styles  

> style stick

Changed 24994 atom styles  

> color cyan

> undo

> style sel stick

Changed 6 atom styles  

> style sel stick

Changed 6 atom styles  

> show sel target ab

> color sel cyan

No Surface models open  

> ui tool show Contacts

Illegal contacts 'color' attribute value (Color([0.5294118, 0.5372549,
0.015686275, 1.0])), leaving attribute unchanged  

> ui tool show Distances

> ui tool show Contacts

> contacts

14149 contacts  

> ui tool show Clashes

Illegal clashes 'color' attribute value (Color([0.827451, 0.7176471,
0.03137255, 1.0])), leaving attribute unchanged  

> color sel red

> ui tool show "Build Structure"

> open /Users/mariopalma/Downloads/6zwm.pdb

6zwm.pdb title:  
Cryo-em structure of human mtor complex 2, overall refinement [more info...]  
  
Chain information for 6zwm.pdb #2  
---  
Chain | Description  
A B | serine/threonine-protein kinase mtor  
C D | target of rapamycin complex subunit LST8  
E F | rapamycin-insensitive companion of mtor  
G H | target of rapamycin complex 2 subunit MAPKAP1  
  
Non-standard residues in 6zwm.pdb #2  
---  
ACE — acetyl group  
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)  
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)  
ZN — zinc ion  
  

> style sel stick

Changed 6 atom styles  

> color sel red

> ui tool show "Show Sequence Viewer"

> sequence chain #1/H

Alignment identifier is 1/H  

> color sel red

> close session

> open /Users/mariopalma/Downloads/6zwo.pdb format pdb

6zwo.pdb title:  
Cryo-em structure of human mtor complex 2, focused on one half [more info...]  
  
Chain information for 6zwo.pdb #1  
---  
Chain | Description  
B | serine/threonine-protein kinase mtor  
D | target of rapamycin complex subunit LST8  
F | rapamycin-insensitive companion of mtor  
H | target of rapamycin complex 2 subunit MAPKAP1  
  
Non-standard residues in 6zwo.pdb #1  
---  
ACE — acetyl group  
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)  
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)  
ZN — zinc ion  
  

> close session

> open /Users/mariopalma/Downloads/6zwm.pdb format pdb

6zwm.pdb title:  
Cryo-em structure of human mtor complex 2, overall refinement [more info...]  
  
Chain information for 6zwm.pdb #1  
---  
Chain | Description  
A B | serine/threonine-protein kinase mtor  
C D | target of rapamycin complex subunit LST8  
E F | rapamycin-insensitive companion of mtor  
G H | target of rapamycin complex 2 subunit MAPKAP1  
  
Non-standard residues in 6zwm.pdb #1  
---  
ACE — acetyl group  
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)  
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)  
ZN — zinc ion  
  

> hide #1.1 models

> hide #1.2 models

> select #1

56947 atoms, 57990 bonds, 114 pseudobonds, 7447 residues, 3 models selected  

> ~select #1

Nothing selected  

> select #1

56947 atoms, 57990 bonds, 114 pseudobonds, 7447 residues, 3 models selected  

> ~select #1.1

56947 atoms, 57990 bonds, 106 pseudobonds, 7447 residues, 2 models selected  

> ~select #1.2

56947 atoms, 57990 bonds, 7447 residues, 1 model selected  

> show sel cartoons

> show sel cartoons

> show sel cartoons

> show sel cartoons

> show sel atoms

> cartoon sel

> surface hidePatches sel

> cartoon style sel modeHelix tube sides 20

No Surface models open  
No Surface models open  

> surface hidePatches sel

> cartoon hide sel

> style sel sphere

Changed 56947 atom styles  

> style sel sphere

Changed 56947 atom styles  

> style sel sphere

Changed 56947 atom styles  

> style sel sphere

Changed 56947 atom styles  

> style sel ball

Changed 56947 atom styles  

> style sel stick

Changed 56947 atom styles  

> select /E/F

17926 atoms, 18250 bonds, 32 pseudobonds, 2238 residues, 3 models selected  

> color (#!1 & sel) purple

> color (#!1 & sel) magenta

> select /A/B

32775 atoms, 33368 bonds, 78 pseudobonds, 4373 residues, 2 models selected  

> color (#!1 & sel) blue

> select /G/H

1316 atoms, 1326 bonds, 4 pseudobonds, 198 residues, 2 models selected  

> color (#!1 & sel) lime

> select /C/D

4930 atoms, 5046 bonds, 638 residues, 1 model selected  

> color sel orange

> select helix

38488 atoms, 38820 bonds, 5033 residues, 1 model selected  

> select /E/F

17926 atoms, 18250 bonds, 32 pseudobonds, 2238 residues, 3 models selected  

> show sel atoms

> cartoon style (#!1 & sel) modeHelix tube sides 20

> rainbow sel

> show sel surfaces

> hide sel surfaces

> mlp sel

Map values for surface "6zwm.pdb_E SES surface": minimum -28.94, mean -3.652,
maximum 24.82  
Map values for surface "6zwm.pdb_F SES surface": minimum -28.84, mean -4.039,
maximum 23.81  

> style sel stick

Changed 17926 atom styles  

> style sel stick

Changed 17926 atom styles  

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> select /E/F

17926 atoms, 18250 bonds, 32 pseudobonds, 2238 residues, 3 models selected  

> hide sel surfaces

> show sel cartoons

> hide sel atoms

> select /A/B

32775 atoms, 33368 bonds, 78 pseudobonds, 4373 residues, 2 models selected  

> show sel cartoons

> hide sel atoms

> select /G/H

1316 atoms, 1326 bonds, 4 pseudobonds, 198 residues, 2 models selected  

> show sel atoms

> show sel cartoons

> hide sel atoms

> select /C/D

4930 atoms, 5046 bonds, 638 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> hide sel atoms

> ui tool show "Show Sequence Viewer"

> sequence chain /E /F

Alignment identifier is 1  

> ui tool show "Show Sequence Viewer"

> sequence chain /E /F

Alignment identifier is 2  

> show sel atoms

> style sel stick

Changed 12 atom styles  

> color (#!1 & sel) red

> set bgColor white

> set bgColor black

> lighting simple

> lighting soft

> lighting full

> show sel atoms

> show (#!1 & sel) target ab

> select sel @< 5

17862 atoms, 77 bonds, 2234 residues, 1 model selected  

> select sel :< 5

17862 atoms, 204 bonds, 2234 residues, 1 model selected  

> select sel :< 5

17862 atoms, 204 bonds, 2234 residues, 1 model selected  

> select sel :< 5

20240 atoms, 20510 bonds, 36 pseudobonds, 2512 residues, 3 models selected  

> select sel :< 5

23145 atoms, 23534 bonds, 36 pseudobonds, 2870 residues, 3 models selected  

> color (#!1 & sel) white

> select sel :< 50

24972 atoms, 20261 bonds, 20 pseudobonds, 3142 residues, 2 models selected  

> select sel :< 5

28400 atoms, 28823 bonds, 50 pseudobonds, 3560 residues, 3 models selected  

> color (#!1 & sel) white

> select sel @< 5

17862 atoms, 221 bonds, 2234 residues, 1 model selected  

> select sel :< 5

20240 atoms, 20510 bonds, 36 pseudobonds, 2512 residues, 3 models selected  

> select sel :< 0.005

17862 atoms, 10 bonds, 2234 residues, 1 model selected  

> undo

> help help:user/menu.html#selectzone

> select sel :< 5

17862 atoms, 204 bonds, 2234 residues, 1 model selected  

> select sel :< 5

20240 atoms, 20510 bonds, 36 pseudobonds, 2512 residues, 3 models selected  

> ui tool show Rotamers

> swapaa interactive sel ASP rotLib Dunbrack

/E SER 383: phi -140.6, psi 6.3 trans  
Changed 90 bond radii  
6zwm.pdb #1/F SER 383: phi -136.0, psi 5.5 trans  
Changed 90 bond radii  

> swapaa #1/E:383 ASP criteria 1 rotLib Dunbrack

Using Dunbrack library  
6zwm.pdb #1/E SER 383: phi -140.6, psi 6.3 trans  
Applying ASP rotamer (chi angles: 63.2 1.3) to 6zwm.pdb #1/E ASP 383  

> swapaa #1/F:383 ASP criteria 1 rotLib Dunbrack

Using Dunbrack library  
6zwm.pdb #1/F SER 383: phi -136.0, psi 5.5 trans  
Applying ASP rotamer (chi angles: 63.2 1.3) to 6zwm.pdb #1/F ASP 383  
Traceback (most recent call last):  
File
"/private/var/folders/nk/1w90xnld1bjd4d0fljcbqq_r0000gn/T/AppTranslocation/258F78E7-A2C8-45D8-8D70-CB0B0004DC9A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 2137, in float_changed  
self.main_window._float_changed(self.tool_window, floating)  
AttributeError: 'NoneType' object has no attribute '_float_changed'  
  
AttributeError: 'NoneType' object has no attribute '_float_changed'  
  
File
"/private/var/folders/nk/1w90xnld1bjd4d0fljcbqq_r0000gn/T/AppTranslocation/258F78E7-A2C8-45D8-8D70-CB0B0004DC9A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 2137, in float_changed  
self.main_window._float_changed(self.tool_window, floating)  
  
See log for complete Python traceback.  
  

> ui tool show Rotamers

> swapaa interactive sel ASP rotLib Dunbrack

/E ASP 383: phi -140.6, psi 6.3 trans  
Changed 90 bond radii  
6zwm.pdb #1/F ASP 383: phi -136.0, psi 5.5 trans  
Changed 90 bond radii  

> swapaa #1/F:383 ASP criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
6zwm.pdb #1/F ASP 383: phi -136.0, psi 5.5 trans  
Applying ASP rotamer (chi angles: 63.2 1.3) to 6zwm.pdb #1/F ASP 383  
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.  

> ui tool show Clashes

Illegal clashes 'color' attribute value (Color([0.81960785, 0.0, 0.039215688,
1.0])), leaving attribute unchanged  
Traceback (most recent call last):  
File
"/private/var/folders/nk/1w90xnld1bjd4d0fljcbqq_r0000gn/T/AppTranslocation/258F78E7-A2C8-45D8-8D70-CB0B0004DC9A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swap_res/tool.py", line 331, in _apply_rotamer  
rot_nums = [r.id[-1] for r in rots]  
File
"/private/var/folders/nk/1w90xnld1bjd4d0fljcbqq_r0000gn/T/AppTranslocation/258F78E7-A2C8-45D8-8D70-CB0B0004DC9A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swap_res/tool.py", line 331, in <listcomp>  
rot_nums = [r.id[-1] for r in rots]  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/private/var/folders/nk/1w90xnld1bjd4d0fljcbqq_r0000gn/T/AppTranslocation/258F78E7-A2C8-45D8-8D70-CB0B0004DC9A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swap_res/tool.py", line 331, in  
rot_nums = [r.id[-1] for r in rots]  
  
See log for complete Python traceback.  
  

> ui tool show Clashes

Restriction atom specifier must not be blank  
Illegal clashes 'color' attribute value (Color([0.81960785, 0.0, 0.13333334,
1.0])), leaving attribute unchanged  
Illegal clashes 'color' attribute value (Color([0.81960785, 0.22352941,
0.76862746, 1.0])), leaving attribute unchanged  
Traceback (most recent call last):  
File
"/private/var/folders/nk/1w90xnld1bjd4d0fljcbqq_r0000gn/T/AppTranslocation/258F78E7-A2C8-45D8-8D70-CB0B0004DC9A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swap_res/tool.py", line 460, in <lambda>  
bbox.accepted.connect(lambda sdt=sd_type: self._process_subdialog(sdt))  
File
"/private/var/folders/nk/1w90xnld1bjd4d0fljcbqq_r0000gn/T/AppTranslocation/258F78E7-A2C8-45D8-8D70-CB0B0004DC9A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swap_res/tool.py", line 400, in _process_subdialog  
base_spec = "#!%s & ~%s" % (res.structure.id_string,
res.string(style="command"))  
AttributeError: 'NoneType' object has no attribute 'structure'  
  
AttributeError: 'NoneType' object has no attribute 'structure'  
  
File
"/private/var/folders/nk/1w90xnld1bjd4d0fljcbqq_r0000gn/T/AppTranslocation/258F78E7-A2C8-45D8-8D70-CB0B0004DC9A/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/swap_res/tool.py", line 400, in _process_subdialog  
base_spec = "#!%s & ~%s" % (res.structure.id_string,
res.string(style="command"))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-16.0.49
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 650
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,2
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 3,1 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: 429.50.1.0.0
      SMC Version (system): 2.44f5

Software:

    System Software Overview:

      System Version: macOS 11.0.1 (20B29)
      Kernel Version: Darwin 20.1.0
      Time since boot: 4:30

Graphics/Displays:

    Intel Iris Plus Graphics 650:

      Chipset Model: Intel Iris Plus Graphics 650
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x5927
      Revision ID: 0x0006
      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)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

[Eric Pettersen]

Probably the "topLevelChanged" signal fired after the tool was destroyed, but couldn't manage to reproduce the behavior.