Opened 6 months ago

Closed 6 months ago

#17372 closed defect (can't reproduce)

Keystroke forwarding to dead tool

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: UI Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.15.0-135-generic-x86_64-with-debian-bookworm-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/fernando/Postdoc/UTD/LGL_Results/DUF/PF10011/AlphaFold/Seq_1/1/test_e95be_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb

Chain information for
test_e95be_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Model Panel"

> ui tool show "Model Panel"

> ui tool show "Color Actions"

> ui tool show "Side View"

> select #1

2755 atoms, 2808 bonds, 355 residues, 1 model selected  

> show target m

> hide target m

> show target m

> view clip false

> toolshed show

> color bfactor sel

2755 atoms, 355 residues, atom bfactor range 52.6 to 96.9  

> select clear

> ui tool show "Conference Call"

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset cartoons/nucleotides licorice/ovals

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> preset "initial styles" "space-filling (chain colors)"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "space-filling (single color)"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "molecular surfaces" "atomic coloring (transparent)"

Changed 2755 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> preset "molecular surfaces" "ghostly white"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> set bgColor white

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> show cartoons

> hide cartoons

> hide atoms

> show atoms

> hide surfaces

> show cartoons

> hide atoms

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> show cartoons

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> color bfactor palette alphafold

Fetching url
http://www.colourlovers.com/api/palettes?keywords=alphafold&format=json&numResults=100
failed: HTTP Error 403: Forbidden  

> select #1 color bfactor palette alphafold

Expected a keyword  

> color bfactor palette red

2755 atoms, 355 residues, 1 surfaces, atom bfactor range 52.6 to 96.9  

> color bfactor palette yellow

Could not find palette yellow at COLOURlovers.com using keyword search  

> color bfactor palette alphafold

Fetching url
http://www.colourlovers.com/api/palettes?keywords=alphafold&format=json&numResults=100
failed: HTTP Error 403: Forbidden  

> color bfactor palette red

2755 atoms, 355 residues, 1 surfaces, atom bfactor range 52.6 to 96.9  

> color bfactor palette red:low orange: yellow: cornflowerblue: blue:high

> color byattribute bfactor palette red:low orange: yellow: cornflowerblue:
> blue:high

Invalid "palette" argument: Invalid color name or specifier  

> color bfactor palette red

2755 atoms, 355 residues, 1 surfaces, atom bfactor range 52.6 to 96.9  

> color bfactor palette blue

2755 atoms, 355 residues, 1 surfaces, atom bfactor range 52.6 to 96.9  

> color bfactor palette red

2755 atoms, 355 residues, 1 surfaces, atom bfactor range 52.6 to 96.9  

> color bfactor palette AlphaFold

Fetching url
http://www.colourlovers.com/api/palettes?keywords=AlphaFold&format=json&numResults=100
failed: HTTP Error 403: Forbidden  

> color bfactor #1 palette alphafold

Fetching url
http://www.colourlovers.com/api/palettes?keywords=alphafold&format=json&numResults=100
failed: HTTP Error 403: Forbidden  

> rangecolor bfactor 0 red 50 yellow 70 cyan 90 blue

Unknown command: rangecolor bfactor 0 red 50 yellow 70 cyan 90 blue  

> color bfactor 0 red 50 yellow 70 cyan 90 blue

> color byattribute bfactor 0 red 50 yellow 70 cyan 90 blue

Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword  

> color bfactor pallete 0 red 50 yellow 70 cyan 90 blue

> color byattribute bfactor pallete 0 red 50 yellow 70 cyan 90 blue

Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword  

> color bfactor #1 pallete 0 red 50 yellow 70 cyan 90 blue

> color byattribute bfactor #1 pallete 0 red 50 yellow 70 cyan 90 blue

Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword  

> select #1

2755 atoms, 2808 bonds, 355 residues, 1 model selected  

> select clear

> select clear

> ui tool show Updates

Successfully installed ChimeraX-PDBImages-1.2 ChimeraX-SignalViewer-1.0
ChimeraX-StrudelScore-0.2 MolecularDynamicsViewer-1.1  
Installed ChimeraX-PDBImages (1.2)  
Installed ChimeraX-SignalViewer (1.0)  
Installed ChimeraX-StrudelScore (0.2)  
Installed MolecularDynamicsViewer (1.1)  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 1993, in _forward_keystroke  
if not self.floating and not isinstance(self.ui_area.focusWidget(),
(QLineEdit, QComboBox)):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 1826, in _get_floating  
return self.__toolkit.dock_widget.isFloating()  
AttributeError: 'NoneType' object has no attribute 'dock_widget'  
  
AttributeError: 'NoneType' object has no attribute 'dock_widget'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 1826, in _get_floating  
return self.__toolkit.dock_widget.isFloating()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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.  
  




OpenGL version: 3.3.0 NVIDIA 550.120
OpenGL renderer: NVIDIA GeForce MX110/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: SAMSUNG ELECTRONICS CO., LTD.
Model: 550XCJ/550XCR
OS: Linux Mint 21.3 virginia
Architecture: 64bit ELF
CPU: 8 Intel(R) Core(TM) i5-10210U CPU @ 1.60GHz
Cache Size: 6144 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           7.6Gi       5.4Gi       276Mi       106Mi       1.9Gi       1.8Gi
	Swap:          2.0Gi       1.1Gi       971Mi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Comet Lake UHD Graphics [8086:9bca] (rev 04)	
	DeviceName: Onboard - Video	
	Subsystem: Samsung Electronics Co Ltd Comet Lake UHD Graphics [144d:c834]
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
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    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
    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: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 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-PDBImages: 1.2
    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-SignalViewer: 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-StrudelScore: 0.2
    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
    distro: 1.5.0
    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
    MolecularDynamicsViewer: 1.1
    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

Change History (2)

comment:1 by pett, 6 months ago

Component: Unassigned → UI
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Keystroke forwarding to dead tool

comment:2 by pett, 6 months ago

Resolution: → can't reproduce
Status: accepted → closed

The code has changed significantly since the 1.1 release being used here.

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