Qt 6.5: menus only show up on second monitor

[Tony Schaefer]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.7.dev202307260053 (2023-07-26 00:53:22 UTC)
Description
Menus only show up on my 2nd monitor (ChimeraX also opens by default on my 2nd monitor and not my main monitor). It seems like all QMenus do this, including context menus. The previous daily build I have is from June 23rd, and it doesn't do this. 

Log:
> cd C:\Users\normn/Desktop

Current working directory is: C:\Users\normn\Desktop  

> graphics selection width 2

UCSF ChimeraX version: 1.7.dev202307260053 (2023-07-26)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show "Build QM Input"




OpenGL version: 3.3.0 NVIDIA 532.03
OpenGL renderer: NVIDIA GeForce RTX 2070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_US.cp1252
Qt version: PyQt6 6.5.2, Qt 6.5.2
Qt runtime version: 6.5.2
Qt platform: windows

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.7.22
    cftime: 1.6.2
    charset-normalizer: 3.2.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.46.1
    ChimeraX-AtomicLibrary: 10.0.8
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.4
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202307260053
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.2
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.2
    ChimeraX-OpenCommands: 1.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.9
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-TestManager: 0.3
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.31.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.1.0
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    flake8: 6.0.0
    fonttools: 4.41.1
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.9.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.38
    imagecodecs: 2023.7.10
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.7
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.3.1
    jupyterlab-widgets: 3.0.8
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    mccabe: 0.7.0
    msgpack: 1.0.4
    mypy: 1.4.1
    mypy-extensions: 1.0.0
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 10.0.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.9.1
    prompt-toolkit: 3.0.39
    psutil: 5.9.5
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycodestyle: 2.10.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    pydocstyle: 6.3.0
    pyflakes: 3.0.1
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.5.2
    PyQt6-Qt6: 6.5.2
    PyQt6-sip: 13.5.2
    PyQt6-WebEngine-commercial: 6.5.0
    PyQt6-WebEngine-Qt6: 6.5.2
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.1.0
    qtconsole: 5.4.3
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    Send2Trash: 1.8.2
    SEQCROW: 1.8
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.2
    traitlets: 5.9.0
    typing-extensions: 4.7.1
    tzdata: 2023.3
    urllib3: 2.0.4
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.8
    WMI: 1.5.1
File attachment: Screenshot 2023-07-26 193923.png

Screenshot 2023-07-26 193923.png​

[Tony Schaefer]

Added by email2trac

[Tom Goddard]

Your explanation of the problem isn't very clear to me. Do you mean clicking on a menu with ChimeraX on the first display causes it to appear on the second display?

I tested the ChimeraX July 27, 2023 daily build on Windows 10 with two displays and menus worked correctly on both displays but there was one glitch. The one glitch was that if I started ChimeraX with display mirroring so both displays show the same thing, then switched to no-mirroring, then the ChimeraX menu bar vanished. If I moved the window even slightly the menu bar reappeared and again the menus worked on the first display and also when I drag it to the second display they work.

My daily build is 1 day newer than yours but I don't think there is any difference, both are using Qt 6.5.2 which we started using 2 days ago.

We decided to revert to Qt 6.3 for the daily builds and the next ChimeraX release because Qt 6.5 dropped support for macOS 10.15. So in any case your menu problem should go away in tomorrow's daily build, since whatever you are observing is surely a Qt 6.5 bug.

It would be useful to know how to reproduce your problem though because after the Nov/Dec 2023 ChimeraX release we will be updating Qt to the current version. Hopefully the bug will be fixed in Qt by then.

[Tony Schaefer]

Tom,

I agree that this bug is certainly something to do with Qt (or maybe my
graphics driver or Windows version, given that you can't reproduce it).

I realize my explanation isn't as clear as I thought it was at the time.
All QMenus are opening on my second display, even if ChimeraX is on my
primary display. I tried the ribbon menus at the top of ChimeraX, as well
as context menus. I also tried the menu on my QM Input File Builder tool,
which uses QMenu. They all did the same thing.

In the screenshot from the original report, ChimeraX is maximized on the
primary display. I clicked the 'Help' menu, and the menu appears on the
edge of my second display. When I get home this evening, I'll check and see
if the issue is still happening. If I can reproduce it, I'll record a video.

Tony

On Thu, Jul 27, 2023 at 1:49 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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[Tom Goddard]

Ok. I wonder if the problem appears when ChimeraX is maximized on a display. I tried that. Still works fine with menus always appearing on the correct display. This is very unlikely to be a graphics driver issue. Are your displays configured as "extended display" in the Windows Display settings? In my tests one is an HD display with 100% scaling and one is a 4K display with 300% scaling.

Does a new window, e.g. menu Help / User Guide appear on the same display ChimeraX is on? I'm wondering if what you observe is a "feature" where if your app is maximized and there is a second display then any new windows are put on the other display.

[Tony Schaefer]

If I recall correctly, I have two 1920x1080 monitors connected as extended
displays, both scaled to 100% and my primary display is on the right. I
don't remember the behavior of new windows, as I basically just reported
the bug and went back to a previous ChimeraX version. This daily build is
installed on my home PC, so I'll have to get home to double check this.

On Thu, Jul 27, 2023 at 2:50 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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[Tom Goddard]

Ok. Don't spend too much time on it. Tonight's daily build will be using Qt 6.3 and should work correctly. (Today we decided not to switch to Qt 6.5 because it requires macOS 11 minimum and we'd like to still support older macOS versions for the next release.)

[Tony Schaefer]

video of problem: https://www.youtube.com/watch?v=ENupBF0OdBw

I also show my display settings at the start. After recording it, I noticed
that tooltips show up on the other display as well, and the balloons when
you hover over atoms don't show up at all.

On Thu, Jul 27, 2023 at 3:22 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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[Tom Goddard]

I'm somewhat baffled why you have this problem and I don't. Here are a few things to try if you are so inclined. I wonder if your two HD monitors are hard for Qt to distinguish. Can you plugin a different monitor (different resolution or manufacturer or cable type) and see if the problem changes? You also have your primary display on the right while I tested on the left. Could see if that makes a difference. Could try if ChimeraX 1.6 has the problem, or if tonight's daily build using Qt 6.3 (same version as from old ChimeraX 1.5) has the problem. Could try not full-screened. Could try starting ChimeraX on the primary display.

It is probably a new Qt 6.5 bug and since we are reverting to Qt 6.3 until the ChimeraX 1.7 release and by that time Qt 6.6 will be out so we will probably be using Qt 6.6 next and probably the Qt bug will have been fixed. So feel free to give up testing now, except to see if the new daily build fixes it.

[Tony Schaefer]

I only have two monitors, but I did try swapping them around. The same
thing happened. This daily build only opens on the 2nd monitor. I tried a
few other ChimeraX versions I have installed, including a 1.5 release
candidate (I guess I skipped the full release), and none of them have this
issue.

I did try installing the 7/26 daily build on my laptop (also windows 10)
and plugged one of my monitors in. It worked flawlessly.

I think I'll ignore the problem and hope it goes away.

On Thu, Jul 27, 2023 at 7:47 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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[Tom Goddard]

That sounds like the right plan. I changed the Qt used in the daily builds last night to version 6.3 instead of 6.5. I expect the problem will be gone by the time we update Qt again after the ChimeraX 1.7 release at the end of the year.