Surface created by surface smooth command not saved in sessions

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-14.4.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202404021803 (2024-04-02 18:03:23 UTC)
Description
Surface created by "surface smooth" command is not saved in sessions.  Restores as an empty surface.

Log:
UCSF ChimeraX version: 1.8.dev202404021803 (2024-04-02)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/goddard/ucsf/chimerax/src/bundles/surface/test.cxs format
> session

Log from Thu May 2 16:11:32 2024UCSF ChimeraX version: 1.8.dev202404021803
(2024-04-02)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open COLI_HUMAN format mmcif fromDatabase alphafold

Summary of feedback from opening COLI_HUMAN fetched from alphafold  
---  
note | Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
  
Chain information for AlphaFold COLI_HUMAN #1  
---  
Chain | Description | UniProt  
A | Pro-opiomelanocortin | COLI_HUMAN 1-267  
  
Color AlphaFold COLI_HUMAN by residue attribute pLDDT_score  

> molmap #1 5

Opened AlphaFold COLI_HUMAN map 5 as #2, grid size 90,75,81, pixel 1.67, shown
at level 0.0488, step 1, values float32  

> surface smooth #2

> close #1,2

> save test.cxs

——— End of log from Thu May 2 16:11:32 2024 ———

opened ChimeraX session  

> info bounds

Scene no bounding box  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac14,14
      Model Number: Z1800003VLL/A
      Chip: Apple M2 Ultra
      Total Number of Cores: 24 (16 performance and 8 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.101.3
      OS Loader Version: 10151.101.3

Software:

    System Software Overview:

      System Version: macOS 14.4.1 (23E224)
      Kernel Version: Darwin 23.4.0
      Time since boot: 5 hours, 23 minutes

Graphics/Displays:

    Apple M2 Ultra:

      Chipset Model: Apple M2 Ultra
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 60
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        PHL 278B1:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    aiobotocore: 2.12.3
    aiohttp: 3.9.5
    aioitertools: 0.11.0
    aiosignal: 1.3.1
    alabaster: 0.7.16
    alphashape: 1.3.1
    annotated-types: 0.6.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asciitree: 0.3.3
    asttokens: 2.4.1
    attrs: 23.2.0
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    biopython: 1.83
    blockdiag: 3.0.0
    blosc2: 2.0.0
    botocore: 1.34.69
    build: 1.2.1
    certifi: 2023.11.17
    cffi: 1.16.0
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.4.5
    ChimeraX-Atomic: 1.56.1
    ChimeraX-AtomicLibrary: 14.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    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: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-copick: 0.1.0
    ChimeraX-Core: 1.8.dev202404021803
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-crai: 0.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.2.2
    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: 1.1.9
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    ChimeraX-ModelPanel: 1.5
    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
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OME-Zarr: 0.5.3
    ChimeraX-OpenCommand: 1.13.4
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.2.2
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-TetraScapeCommand: 0.1
    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: 1.37.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    click: 8.1.7
    click-log: 0.4.0
    cloudpickle: 3.0.0
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.0
    copick: 0.1.dev45+g5a19260
    cripser: 0.0.13
    cryptography: 42.0.5
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.9
    dask: 2024.4.2
    debugpy: 1.8.1
    decorator: 5.1.1
    distributed: 2024.4.2
    docutils: 0.20.1
    executing: 2.0.1
    fasteners: 0.19
    filelock: 3.13.4
    fonttools: 4.50.0
    frozenlist: 1.4.1
    fsspec: 2024.3.1
    funcparserlib: 2.0.0a0
    geomdl: 5.3.1
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.10.0
    hatchling: 1.24.2
    html2text: 2024.2.26
    idna: 3.6
    ihm: 1.0
    imagecodecs: 2024.1.1
    imageio: 2.34.1
    imagesize: 1.4.1
    importlib-metadata: 7.1.0
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    Jinja2: 3.1.3
    jmespath: 1.0.1
    joblib: 1.4.0
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    lazy-loader: 0.4
    line-profiler: 4.1.2
    llvmlite: 0.42.0
    locket: 1.0.0
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.6
    mpmath: 1.3.0
    mrcfile: 1.5.0
    msgpack: 1.0.8
    multidict: 6.0.5
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.0.1
    nptyping: 2.5.0
    numba: 0.59.1
    numcodecs: 0.12.1
    numexpr: 2.10.0
    numpy: 1.26.4
    ome-zarr: 0.8.3
    OpenMM: 8.1.1
    openvr: 1.26.701
    packaging: 23.2
    pandas: 2.2.2
    ParmEd: 4.2.2
    parso: 0.8.3
    partd: 1.4.1
    pathspec: 0.12.1
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.0
    pluggy: 1.5.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pyarrow: 16.0.0
    pycollada: 0.8
    pycparser: 2.22
    pydantic: 2.7.1
    pydantic-core: 2.18.2
    pydicom: 2.3.0
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynndescent: 0.5.12
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3302
    pyparsing: 3.1.2
    pyproject-hooks: 1.0.0
    PyQt6: 6.6.1
    PyQt6-Qt6: 6.6.2
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.2
    pyspnego: 0.10.2
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    PyYAML: 6.0.1
    pyzmq: 25.1.2
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    Rtree: 1.1.0
    s3fs: 2024.3.1
    scikit-image: 0.23.2
    scikit-learn: 1.4.2
    scipy: 1.13.0
    setuptools: 69.2.0
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    shapely: 2.0.2
    six: 1.16.0
    smbprotocol: 1.13.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    starfile: 0.5.6
    superqt: 0.6.3
    sympy: 1.12
    tables: 3.8.0
    tblib: 3.0.0
    tcia-utils: 1.5.1
    threadpoolctl: 3.4.0
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    toolz: 0.12.1
    torch: 2.2.2
    tornado: 6.4
    tqdm: 4.66.2
    traitlets: 5.14.2
    trimesh: 4.0.10
    trove-classifiers: 2024.4.10
    typing-extensions: 4.10.0
    tzdata: 2024.1
    umap-learn: 0.5.6
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10
    wrapt: 1.16.0
    yarl: 1.9.4
    zarr: 2.17.2
    zict: 3.0.0
    zipp: 3.18.1

[Tom Goddard]

Fixed.

Command surface smooth created new surfaces but did not set SESSION_SAVE_DRAWING attribute.

Commands surface splitbycolor and measure contactarea also failed to save surfaces in sessions so I fixed those too.