Opened 3 weeks ago

Last modified 10 days ago

#19781 feedback defect

CliX: QTextCursor::setPosition: Position '1' out of range

Reported by: jianghai.zhu@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: Hanjin Liu, chimera-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.8.3-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
ChimeraX 1.11.1 and plugin Clix 0.25 on MacOS 14.8.3 gave me the following errors. 

ui tool show CliX
QTextCursor::setPosition: Position '1' out of range

[Repeated 55 time(s)]

There is no error in ChimeraX 1.10.1 on MacOX or ChimeraX 1.11.1 on Ubuntu. It seems to be a MacOS only problem. Here is the related discussion on Clix github https://github.com/hanjinliu/Chimerax-clix/issues/59.

Log:
> mousemode middleMode "center or translate"

> functionkey F1 clip near -2

> functionkey F2 clip near 2

> functionkey F3 clip far -2

> functionkey F4 clip far 2

> ui tool hide "command line interface"

> ui tool show clix

Error running startup command 'ui tool show clix': No running or installed
tool named "clix"  
UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Shell

> toolshed show

Installed ChimeraX-clix (0.2.5)  

> ui tool show CliX

QTextCursor::setPosition: Position '1' out of range  

[Repeated 55 time(s)]




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,10
      Model Number: MNW83LL/A
      Chip: Apple M2 Pro
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 13822.61.10
      OS Loader Version: 10151.140.19.700.2

Software:

    System Software Overview:

      System Version: macOS 14.8.3 (23J220)
      Kernel Version: Darwin 23.6.0
      Time since boot: 3 days, 58 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 19
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        BenQ PD3200Q:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-clix: 0.2.5
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    ChimeraX-Map: 1.3
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.12
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    roman-numerals-py: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.3
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    sse-starlette: 3.2.0
    stack-data: 0.6.3
    starlette: 0.52.1
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    urllib3: 2.6.3
    uvicorn: 0.40.0
    wcwidth: 0.3.2
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    yarl: 1.22.0

Change History (17)

comment:1 by Eric Pettersen, 3 weeks ago

Cc: Hanjin Liu chimera-programmers added
Component: Unassigned → Third Party
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → CliX: QTextCursor::setPosition: Position '1' out of range

comment:2 by Eric Pettersen, 3 weeks ago

Does not happen for me with ARM Mac running OSX 15.7.2. Will try on OSX 14.

comment:3 by Eric Pettersen, 3 weeks ago

Should have said running ChimeraX 1.11

comment:4 by Eric Pettersen, 3 weeks ago

Could not reproduce using ChimeraX 1.11.1 on Intel Mac running 12.7.6.

Not sure we have a Mac running OSX 14, but I'll look around.

comment:5 by Eric Pettersen, 3 weeks ago

Also failed to reproduce with 1.11.1 on an Intel Mac running 13.7.8

comment:6 by Eric Pettersen, 3 weeks ago

Status: accepted → feedback

Hi Jianghai,

Can you try commenting out all lines that have movePosition() calls? That would be 4 lines in widgets/cli_widget.py, 4 lines in widgets/popups.py, and 1 line in widgets/hist_button.py.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:7 by jianghai.zhu@…, 3 weeks ago 

I commented out all lines with movePosition(), reinstalled Clix, and still got the same error.



Best,


— Jianghai


From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Thursday, January 29, 2026 at 6:02 PM
To: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>, Zhu, Jianghai (NIH/NIAID) [C] <jianghai.zhu@nih.gov>
Cc: chimera-programmers@cgl.ucsf.edu <chimera-programmers@cgl.ucsf.edu>, liuhanjin.sc@gmail.com <liuhanjin.sc@gmail.com>
Subject: [EXTERNAL] Re: [ChimeraX] #19781: CliX: QTextCursor::setPosition: Position '1' out of range

#19781: CliX: QTextCursor::setPosition: Position '1' out of range
-------------------------------------+----------------------------
          Reporter:  jianghai.zhu@…  |      Owner:  Eric Pettersen
              Type:  defect          |     Status:  feedback
          Priority:  normal          |  Milestone:
         Component:  Third Party     |    Version:
        Resolution:                  |   Keywords:
        Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
           Project:  ChimeraX        |
-------------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => feedback

Comment:

 Hi Jianghai,
         Can you try commenting out all lines that have movePosition()
 calls?  That would be 4 lines in widgets/cli_widget.py, 4 lines in
 widgets/popups.py, and 1 line in widgets/hist_button.py.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab
--
Ticket URL: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F19781%23comment%3A6&data=05%7C02%7Cjianghai.zhu%40nih.gov%7C799b88fd2e4545bcd6db08de5f8a6780%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C639053245280376695%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=vZY5kPi3tR4nU%2FJTAxHaTPhfuMaiTH8%2F7A77Zonjcp8%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/19781#comment:6>>
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comment:8 by Eric Pettersen, 3 weeks ago

I'm not sure what you mean when you say you reinstalled CliX. You should edit those files in the already-installed version of CliX, i.e. ~/Library/Application Support/ChimeraX/1.11/lib/python/site-packages/chimerax/clix/widgets/<filename>.py and restart ChimeraX. Maybe that's what you meant?

comment:9 by jianghai.zhu@…, 3 weeks ago 

Ah, I have a local clone of Clix. I changed the files there and reinstalled it. I also installed Clix through ChimeraX and edited files as you described. Both still gave me the same error.



Best,


— Jianghai


From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Thursday, January 29, 2026 at 6:18 PM
To: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>, Zhu, Jianghai (NIH/NIAID) [C] <jianghai.zhu@nih.gov>
Cc: chimera-programmers@cgl.ucsf.edu <chimera-programmers@cgl.ucsf.edu>, liuhanjin.sc@gmail.com <liuhanjin.sc@gmail.com>
Subject: [EXTERNAL] Re: [ChimeraX] #19781: CliX: QTextCursor::setPosition: Position '1' out of range

#19781: CliX: QTextCursor::setPosition: Position '1' out of range
-------------------------------------+----------------------------
          Reporter:  jianghai.zhu@…  |      Owner:  Eric Pettersen
              Type:  defect          |     Status:  feedback
          Priority:  normal          |  Milestone:
         Component:  Third Party     |    Version:
        Resolution:                  |   Keywords:
        Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
           Project:  ChimeraX        |
-------------------------------------+----------------------------
Comment (by Eric Pettersen):

 I'm not sure what you mean when you say you reinstalled CliX.  You should
 edit those files in the already-installed version of CliX, i.e.
 ~/Library/Application Support/ChimeraX/1.11/lib/python/site-
 packages/chimerax/clix/widgets/<filename>.py and restart ChimeraX.  Maybe
 that's what you meant?
--
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comment:10 by Eric Pettersen, 3 weeks ago

Can you try the daily build? The daily build uses a newer version of Qt than 1.11.1 does, so it could possibly fix this problem...

comment:11 by jianghai.zhu@…, 3 weeks ago 

I just installed the daily build, and I still got the same error.



Best,


— Jianghai


From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Thursday, January 29, 2026 at 7:02 PM
To: Zhu, Jianghai (NIH/NIAID) [C] <jianghai.zhu@nih.gov>, pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Cc: chimera-programmers@cgl.ucsf.edu <chimera-programmers@cgl.ucsf.edu>, liuhanjin.sc@gmail.com <liuhanjin.sc@gmail.com>
Subject: [EXTERNAL] Re: [ChimeraX] #19781: CliX: QTextCursor::setPosition: Position '1' out of range

#19781: CliX: QTextCursor::setPosition: Position '1' out of range
-------------------------------------+----------------------------
          Reporter:  jianghai.zhu@…  |      Owner:  Eric Pettersen
              Type:  defect          |     Status:  feedback
          Priority:  normal          |  Milestone:
         Component:  Third Party     |    Version:
        Resolution:                  |   Keywords:
        Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
           Project:  ChimeraX        |
-------------------------------------+----------------------------
Comment (by Eric Pettersen):

 Can you try the daily build?  The daily build uses a newer version of Qt
 than 1.11.1 does, so it could possibly fix this problem...
--
Ticket URL: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F19781%23comment%3A10&data=05%7C02%7Cjianghai.zhu%40nih.gov%7Cd232653792be4894859d08de5f92cfc3%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C639053281315668621%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=0bkcbeFaIgmd%2BqpX0EVoy8OAW3Sx5vvYHLUzsI8iblY%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/19781#comment:10>>
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comment:12 by jianghai.zhu@…, 3 weeks ago 

I tested it on my Intel Mac running 13.7.8 and was able to reproduce this error. I found that I can reliably reproduce the error when I start ChimeraX 1.11.1 from Terminal, whether I'm using macOS 13.7.8 or 14.8.3. However, if I start ChimeraX 1.11.1 by double-clicking the app, I don’t always encounter the error.



Best,


— Jianghai


From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Thursday, January 29, 2026 at 5:42 PM
To: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>, Zhu, Jianghai (NIH/NIAID) [C] <jianghai.zhu@nih.gov>
Cc: chimera-programmers@cgl.ucsf.edu <chimera-programmers@cgl.ucsf.edu>, liuhanjin.sc@gmail.com <liuhanjin.sc@gmail.com>
Subject: [EXTERNAL] Re: [ChimeraX] #19781: CliX: QTextCursor::setPosition: Position '1' out of range

#19781: CliX: QTextCursor::setPosition: Position '1' out of range
-------------------------------------+----------------------------
          Reporter:  jianghai.zhu@…  |      Owner:  Eric Pettersen
              Type:  defect          |     Status:  accepted
          Priority:  normal          |  Milestone:
         Component:  Third Party     |    Version:
        Resolution:                  |   Keywords:
        Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
           Project:  ChimeraX        |
-------------------------------------+----------------------------
Comment (by Eric Pettersen):

 Also failed to reproduce with 1.11.1 on an Intel Mac running 13.7.8
--
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comment:13 by Eric Pettersen, 2 weeks ago

Just tried it on a 13.7.8 Intel Mac launched from the command line and still get no errors.

Is this problem actually interfering with the operation of CliX or ChimeraX in any way (other than spamming the log)? If not, you could just suppress the message by editing ChimeraX.app/Contents/lib/python/site-packages/chimerax/ui/gui.py and changing the embedded cx_qt_msg_handler() function (embedded in the redirect_qt_messages() method) to add the string 'QTextCursor::setPosition: Position' to the list of Qt message strings that are ignored.

comment:14 by jianghai.zhu@…, 2 weeks ago 

OK, this is weird. I haven’t used the new version long enough to notice anything else besides the log spam.

Anyway, I modified the file ~/Applications/ChimeraX-1.11.1.app/Contents/lib/python3.11/site-packages/chimerax/ui/gui.py  as you suggested, but still got the error.

        def cx_qt_msg_handler(msg_type, msg_log_context, msg_string,
                              log_fatal_error = self._log_qt_fatal_error):
            if msg_string.startswith((
                    'delivering touch release to same window',   # Qt 6.2
                    'skipping QEventPoint',   # Qt 6.2
                    'doh set to',  # Qt 6.2
                    'Path override failed for key base::DIR_APP_DICTIONARIES',  # Qt 6.6.3
                    'Already setting window visible!', # Qt 6.6.3
                    'Compositor returned null texture', # Qt 6.6.3
                    'QTextCursor::setPosition:Position', # Clix error
                    )):
                return  # Supress Qt warnings
            if 'QWindowsWindow::setDarkBorderToWindow' in msg_string:
                return  # Supress Qt 6.4 warning, ChimeraX ticket #8541
            if msg_type == QtMsgType.QtFatalMsg:
                log_fatal_error('Qt fatal error: %s\n' % msg_string)
            log_level = qt_to_cx_log_level_map[msg_type]
            if log_level is None:
                return
            if msg_string.strip().endswith(" null"):
                # downgrade Javascript errors
                log_level = Log.LEVEL_INFO
            self.session.logger.method_map[log_level](msg_string)



Best,


— Jianghai


From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Monday, February 2, 2026 at 8:56 PM
To: Zhu, Jianghai (NIH/NIAID) [C] <jianghai.zhu@nih.gov>, pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Cc: chimera-programmers@cgl.ucsf.edu <chimera-programmers@cgl.ucsf.edu>, liuhanjin.sc@gmail.com <liuhanjin.sc@gmail.com>
Subject: [EXTERNAL] Re: [ChimeraX] #19781: CliX: QTextCursor::setPosition: Position '1' out of range

#19781: CliX: QTextCursor::setPosition: Position '1' out of range
-------------------------------------+----------------------------
          Reporter:  jianghai.zhu@…  |      Owner:  Eric Pettersen
              Type:  defect          |     Status:  feedback
          Priority:  normal          |  Milestone:
         Component:  Third Party     |    Version:
        Resolution:                  |   Keywords:
        Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
           Project:  ChimeraX        |
-------------------------------------+----------------------------
Comment (by Eric Pettersen):

 Just tried it on a 13.7.8 Intel Mac launched from the command line and
 still get no errors.

 Is this problem actually interfering with the operation of CliX or
 ChimeraX in any way (other than spamming the log)?  If not, you could just
 suppress the message by editing ChimeraX.app/Contents/lib/python/site-
 packages/chimerax/ui/gui.py and changing the embedded cx_qt_msg_handler()
 function (embedded in the redirect_qt_messages() method) to add the string
 'QTextCursor::setPosition: Position' to the list of Qt message strings
 that are ignored.
--
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comment:15 by Eric Pettersen, 2 weeks ago

Hi Jinghai,

The string in that list has to match the start of the string being logged, so you need a space between the "setPosition:" and the "Position" in that string.

--Eric

comment:16 by jianghai.zhu@…, 2 weeks ago 

Thanks! You are right. For whatever reason, my copy-and-paste removed a space there. Now, the error messages are suppressed. I will see if it causes other problems.



Best,


— Jianghai


From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Tuesday, February 3, 2026 at 12:42 PM
To: Zhu, Jianghai (NIH/NIAID) [C] <jianghai.zhu@nih.gov>, pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Cc: chimera-programmers@cgl.ucsf.edu <chimera-programmers@cgl.ucsf.edu>, liuhanjin.sc@gmail.com <liuhanjin.sc@gmail.com>
Subject: [EXTERNAL] Re: [ChimeraX] #19781: CliX: QTextCursor::setPosition: Position '1' out of range

#19781: CliX: QTextCursor::setPosition: Position '1' out of range
-------------------------------------+----------------------------
          Reporter:  jianghai.zhu@…  |      Owner:  Eric Pettersen
              Type:  defect          |     Status:  feedback
          Priority:  normal          |  Milestone:
         Component:  Third Party     |    Version:
        Resolution:                  |   Keywords:
        Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
           Project:  ChimeraX        |
-------------------------------------+----------------------------
Comment (by Eric Pettersen):

 Hi Jinghai,
         The string in that list has to match the start of the string being
 logged, so you need a space between the "setPosition:" and the "Position"
 in that string.

 --Eric
--
Ticket URL: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F19781%23comment%3A15&data=05%7C02%7Cjianghai.zhu%40nih.gov%7Cc2116954e5ee4315eb7308de634ba2ed%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C639057373681760834%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=PXBCJ9mj%2FurVsNhoNVbfCsBYDXQVal1WSHCWyeYr%2FXk%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/19781#comment:15>>
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comment:17 by jianghai.zhu@…, 10 days ago 

After using it for a while, I discovered that there is a real problem beyond the log spamming. All the suggestion popups, one of the most useful features of Clix,  disappeared. Doesn’t matter how I start ChimeraX 1.11.1.



Best,


— Jianghai


From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Tuesday, February 3, 2026 at 12:56 PM
To: Zhu, Jianghai (NIH/NIAID) [C] <jianghai.zhu@nih.gov>, pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Cc: chimera-programmers@cgl.ucsf.edu <chimera-programmers@cgl.ucsf.edu>, liuhanjin.sc@gmail.com <liuhanjin.sc@gmail.com>
Subject: [EXTERNAL] Re: [ChimeraX] #19781: CliX: QTextCursor::setPosition: Position '1' out of range

#19781: CliX: QTextCursor::setPosition: Position '1' out of range
-------------------------------------+----------------------------
          Reporter:  jianghai.zhu@…  |      Owner:  Eric Pettersen
              Type:  defect          |     Status:  feedback
          Priority:  normal          |  Milestone:
         Component:  Third Party     |    Version:
        Resolution:                  |   Keywords:
        Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
           Project:  ChimeraX        |
-------------------------------------+----------------------------
Comment (by jianghai.zhu@…):

 {{{
 Thanks! You are right. For whatever reason, my copy-and-paste removed a
 space there. Now, the error messages are suppressed. I will see if it
 causes other problems.



 Best,


 — Jianghai


 From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
 Date: Tuesday, February 3, 2026 at 12:42 PM
 To: Zhu, Jianghai (NIH/NIAID) [C] <jianghai.zhu@nih.gov>,
 pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
 Cc: chimera-programmers@cgl.ucsf.edu <chimera-programmers@cgl.ucsf.edu>,
 liuhanjin.sc@gmail.com <liuhanjin.sc@gmail.com>
 Subject: [EXTERNAL] Re: [ChimeraX] #19781: CliX: QTextCursor::setPosition:
 Position '1' out of range

 #19781: CliX: QTextCursor::setPosition: Position '1' out of range
 -------------------------------------+----------------------------
           Reporter:  jianghai.zhu@…  |      Owner:  Eric Pettersen
               Type:  defect          |     Status:  feedback
           Priority:  normal          |  Milestone:
          Component:  Third Party     |    Version:
         Resolution:                  |   Keywords:
         Blocked By:                  |   Blocking:
 Notify when closed:                  |   Platform:  all
            Project:  ChimeraX        |
 -------------------------------------+----------------------------
 Comment (by Eric Pettersen):

  Hi Jinghai,
          The string in that list has to match the start of the string
 being
  logged, so you need a space between the "setPosition:" and the "Position"
  in that string.

  --Eric
 --
 Ticket URL:
 <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F19781%23comment%3A15&data=05%7C02%7Cjianghai.zhu%40nih.gov%7C9f34a828bcac4563a03d08de634d8250%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C639057381715565173%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=i5HL3QZMQ0UBCq%2FHCR5dkWQWHGEnEHBseRWQdU2o5Qk%3D&reserved=0<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F19781%23comment%3A15&data=05%7C02%7Cjianghai.zhu%40nih.gov%7C9f34a828bcac4563a03d08de634d8250%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C639057381715590313%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=2rrlB68qklz6FY6dyvSUZ8XlzC%2FE%2F3WpsfCCcxYuda4%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/19781#comment:15>>>
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 }}}
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