ChimeraX bug report submission

[iamkaant@…]

The following bug report has been submitted:
Platform:        macOS-26.5.2-arm64-arm-64bit-Mach-O
ChimeraX Version: 1.13.dev202607182018 (2026-07-18 20:18:57 UTC)
Description
I've noticed that mouse wheel zoom stops working sometimes if I disconnect and reconnect the mouse while the session is open. The pinch movement on trackpad still works as expected.

Log:
UCSF ChimeraX version: 1.13.dev202607182018 (2026-07-18)  
© 2016-2026 Regents of the University of California. All rights reserved.  

> open
> /Users/ak87/ownCloud/owncloud/Calculations/PLA2G15/RECEPTOR/4X91/4X91-Ash13/4x91-ash13-grids.cxs

Opened trim.electrostatics.dx as #3, grid size 67,67,67, pixel 0.469, shown at
level -99.2,99.2, step 1, values float32  
Log from Tue Aug 4 21:16:42 2026UCSF ChimeraX version: 1.13.dev202607182018
(2026-07-18)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/ak87/ownCloud/owncloud/Calculations/PLA2G15/RECEPTOR/4X91/4X91-Ash13/rec_minimized_final_delHC.pdb

rec_minimized_final_delHC.pdb title:  
Crystal structure of lysosomal phospholipase A2 In complex with isopropyl
dodec-11-enylfluorophosphonate (IDFP) [more info...]  
  
Chain information for rec_minimized_final_delHC.pdb #1  
---  
Chain | Description  
A | No description available  
  
75 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
3013 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> open
> /Users/ak87/ownCloud/owncloud/Calculations/PLA2G15/RECEPTOR/4X91/4X91-Ash13/xtal-
> lig.pdb

> select clear

> select #2/?:0@C8

1 atom, 1 residue, 1 model selected  

> select up

30 atoms, 33 bonds, 1 residue, 1 model selected  

> select sel :< 5

259 atoms, 253 bonds, 24 residues, 2 models selected  

> show sel atoms

> view sel

> label sel text "{0.name} {0.number}{0.insertion_code}"

> ui tool show "Selection Inspector"

> size =sel stickRadius 0.06

Changed 253 bond radii  

> select clear

> hide cartoons

> open
> /Users/ak87/ownCloud/owncloud/Calculations/PLA2G15/RECEPTOR/4X91/4X91-Ash13/dockfiles/ligdesolv.dx

Opened ligdesolv.dx as #3, grid size 61,58,56, pixel 0.5, shown at level
-0.875,0.875, step 1, values float32  

> volume #3 level -0.875 level 0.88

> volume #3 level -0.875 level 0.8421

> volume #3 level -0.875 level 0.8626

> volume #3 style mesh

> volume #3 level -0.875 level 0.3261

> volume #3 style surface

> volume #3 level -0.875 level 0.8721

> close #3

> open
> /Users/ak87/ownCloud/owncloud/Calculations/PLA2G15/RECEPTOR/4X91/4X91-Ash13/dockfiles/vdw.dx

Opened vdw.dx as #3, grid size 154,145,141, pixel 0.2, shown at level -1,1,
step 1, values float32  

> volume #3 level -1 level 0.6661

> lighting full

> volume #3 level -1 level 0.8887

> volume #3 style mesh

> volume #3 style surface

> ui tool show "Side View"

> volume #3 style mesh

> close #3

> open
> /Users/ak87/ownCloud/owncloud/Calculations/PLA2G15/RECEPTOR/4X91/4X91-Ash13/dockfiles/trim.electrostatics.dx

Opened trim.electrostatics.dx as #3, grid size 67,67,67, pixel 0.469, shown at
level -112,112, step 1, values float32  

> volume #3 level -112.1 level 112.1

> volume #3 color white color #ff2600

> volume #3 level -112.1 level 112.1

> volume #3 color #0096ff color #ff2600

> close #3

> open
> /Users/ak87/ownCloud/owncloud/Calculations/PLA2G15/RECEPTOR/4X91/4X91-Ash13/dockfiles/trim.electrostatics.dx

Opened trim.electrostatics.dx as #3, grid size 67,67,67, pixel 0.469, shown at
level -159,159, step 1, values float32  

> volume #3 level -100 level 158.9

[Repeated 3 time(s)]

> volume #3 level -100 level 100

> volume #3 style mesh

> open
> /Users/ak87/ownCloud/owncloud/Calculations/PLA2G15/RECEPTOR/4X91/4X91-Ash13/dockfiles/vdw.dx

Opened vdw.dx as #4, grid size 154,145,141, pixel 0.2, shown at level -1,1,
step 1, values float32  

> volume #4 level 0.0377 level 1

> volume #4 style mesh

> set bgColor white

Desktop color scheme is dark  

> close #3

> close #4

> open
> /Users/ak87/ownCloud/owncloud/Calculations/PLA2G15/RECEPTOR/4X91/4X91-Ash13/dockfiles/vdw.dx

Opened vdw.dx as #3, grid size 154,145,141, pixel 0.2, shown at level -1,1,
step 1, values float32  

> volume #3 level 0.2621 level 1

> close #3

> open
> /Users/ak87/ownCloud/owncloud/Calculations/PLA2G15/RECEPTOR/4X91/4X91-Ash13/dockfiles/trim.electrostatics.dx

Opened trim.electrostatics.dx as #3, grid size 67,67,67, pixel 0.469, shown at
level -118,118, step 1, values float32  

> volume #3 level -114.3 level 118.1

> volume #3 level -99.25 level 118.1

> volume #3 color #0433ff color #b2b2b2

> volume #3 level -99.25 level 118.1

> volume #3 level -99.25 level 125.6

> volume #3 level -99.25 level 121.8

> volume #3 level -99.25 level 118.1

> volume #3 level -99.25 level 114.3

> volume #3 level -99.25 level 110.5

> volume #3 level -99.25 level 103

> volume #3 level -99.25 level 99.25

> volume #3 color #0433ff color #ff2600

> save
> /Users/ak87/ownCloud/owncloud/Calculations/PLA2G15/RECEPTOR/4X91/4X91-Ash13/4x91-ash13-grids.cxs

——— End of log from Tue Aug 4 21:16:42 2026 ———

> view name session-start

opened ChimeraX session  

> open
> /Users/ak87/ownCloud/owncloud/Calculations/PLA2G15/DOCKING/4X91/4X91-Ash13/pag15_4x91_ash13.mol2

Opened pag15_4x91_ash13.mol2 containing 413 structures (19786 atoms, 20729
bonds)  

### ViewDock hotkeys on

If clicked into ViewDock dialog or main 3D graphics area, the following keys
are active:

g/m/b/u

    Assign good/maybe/bad/(unrated) rating to chosen compounds
up/down arrow

    Move up/down compound list*
Escape

    Turn hotkeys off (have to use context menu to re-enable)
*Unless in 3D graphics with a selection, in which case normal selection widening/narrowing happens  

> ui windowfill toggle

[Repeated 2 time(s)]

> save
> /Users/ak87/ownCloud/owncloud/Calculations/PLA2G15/DOCKING/4X91/4X91-Ash13/4x91_ash13_poses.cxs

> hbonds #4.1-413 restrict #!1-2 & (main|ligand) reveal true

137 hydrogen bonds found  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M5 Pro
OpenGL vendor: Apple

Python: 3.14.6
Locale: C.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac17,8
      Model Number: MGE44LL/A
      Chip: Apple M5 Pro
      Total Number of Cores: 18 (6 Super and 12 Performance)
      Memory: 24 GB
      System Firmware Version: 18000.121.3
      OS Loader Version: 18000.121.3

Software:

    System Software Overview:

      System Version: macOS 26.5.2 (25F84)
      Kernel Version: Darwin 25.5.0
      Time since boot: 15 days, 1 hour, 54 minutes

Graphics/Displays:

    Apple M5 Pro:

      Chipset Model: Apple M5 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 20
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.7.1
    aiohttp: 3.11.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.14.2
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.2
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.9.1
    build: 1.5.0
    certifi: 2026.6.17
    cffi: 2.1.0
    cftime: 1.6.5
    charset-normalizer: 3.4.9
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.3.1
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2.2
    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: 1.70.2
    ChimeraX-AtomicLibrary: 14.4.2
    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: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.4
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.13.dev202607182018
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.6
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.3
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.2.2
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.4
    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: 1.8.5
    ChimeraX-Label: 1.5
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.3
    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-MatchAlign: 1.2.1
    ChimeraX-MatchMaker: 2.4.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.4.3
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.17
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.24
    ChimeraX-ModelPanel: 1.6.1
    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-NMRSTAR: 1.0.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.16.2
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.13
    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: 1.11
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8.3
    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: 1.5.3
    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: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.19.1
    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-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.20
    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: 2.5.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.4
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.53.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.5
    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: 8.4.2
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.15.2
    cryptography: 49.0.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.21
    decorator: 5.3.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.63.0
    frozenlist: 1.8.0
    funcparserlib: 1.0.1
    glfw: 2.10.1
    grako: 3.16.5
    h11: 0.16.0
    h2: 4.3.0
    h5py: 3.16.0
    hpack: 4.2.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    hyperframe: 6.1.0
    idna: 3.18
    ihm: 2.2
    imagecodecs: 2026.6.26
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.3.0
    ipython: 9.14.1
    ipython_pygments_lexers: 1.1.1
    jedi: 0.20.0
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.9.1
    jupyter_core: 5.9.1
    kiwisolver: 1.5.0
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.4.5
    Markdown: 3.8.2
    markdown-it-py: 4.2.0
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.2
    mcp: 1.28.1
    mdurl: 0.1.2
    msgpack: 1.1.1
    multidict: 6.7.1
    ndindex: 1.10.1
    nest-asyncio2: 1.7.2
    netCDF4: 1.7.4
    networkx: 3.3
    numexpr: 2.14.2
    numpy: 2.4.6
    OpenMM: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.7
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 12.3.0
    pip: 26.1.2
    pkginfo: 1.12.1.2
    platformdirs: 4.10.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.5.2
    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
    pycparser: 3.0
    pydantic: 2.13.4
    pydantic-settings: 2.14.2
    pydantic_core: 2.46.4
    pydata-sphinx-theme: 0.20.0
    Pygments: 2.18.0
    PyJWT: 2.13.0
    pynmrstar: 3.5.1
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.10.2
    PyQt6-Qt6: 6.10.2
    PyQt6-WebEngine-commercial: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.2
    PyQt6_sip: 13.10.3
    pytest: 9.1.1
    pytest-cov: 7.1.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.32
    pyzmq: 27.1.0
    qtconsole: 5.7.2
    QtPy: 2.4.3
    qtshim: 1.2.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    rich: 15.0.0
    roman-numerals: 4.1.0
    rpds-py: 2026.6.3
    scipy: 1.18.0
    setuptools: 82.0.1
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.1.1
    sortedcontainers: 2.4.0
    soupsieve: 2.9
    Sphinx: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    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: 3.4.5
    stack-data: 0.6.3
    starlette: 1.3.1
    superqt: 0.7.6
    tables: 3.11.1
    threadpoolctl: 3.6.0
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.7
    tqdm: 4.69.0
    traitlets: 5.15.1
    typing-inspection: 0.4.2
    typing_extensions: 4.16.0
    urllib3: 2.7.0
    uv: 0.11.26
    uvicorn: 0.51.0
    wcwidth: 0.8.2
    webcolors: 24.11.1
    wheel: 0.47.0
    wheel-filename: 1.4.2
    yarl: 1.24.2