~ attribute test

[olibclarke@…]

The following bug report has been submitted:
Platform:        macOS-14.4-arm64-arm-64bit
ChimeraX Version: 1.8.dev202403210048 (2024-03-21 00:48:29 UTC)
Description
Hi, the following command (which I have bound to an alias) works in the 1.7.1 stable build, but fails in recent daily builds. It did work in the daily release a few days ago, but fails in the most recent builds.

Command: surface unzone ##~num_residues; sel; close #10000; marker #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel distance 0; close #10000

Error: Missing or invalid "surfaces" argument: invalid surfaces specifier

Is this a bug, or has the syntax changed? A similar command with volume zone also gives the same error in the daily.

Cheers
Oli


Log:
> runscript /Users/oc2188/Dropbox/chimera_startup/chimerax_startup.py

> camera ortho

> cofr centerOfView

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"

> mousemode shift leftMode "rotate selected models"

> mousemode alt control leftMode "pick blobs"

> alias cofron cofr centerofview showpivot 7,0.25

> alias cofroff cofr centerofview showpivot false

> alias symclip cofr centerofview; clip near -$1 far $1 position cofr

> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues
> cornflower blue

> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ##~num_residues #3d60ffff; transparency 50

> alias project_map set bgColor black; lighting depthcue false; volume $1
> style image sdlevel 0,0 color white sdlevel 100,0.15 color white
> projectionmode 3d maximumIntensityProjection false dimTransparentVoxels
> false btcorrection true showOutlineBox false linearinterpolation true

> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1

> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1

> alias map_sphere_15 volume unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; volume zone ##~num_residues nearAtoms sel
> minimalBounds true range 15; close #10000

> alias map_unsphere volume unzone ##~num_residues

> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft

> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000

> alias showmaps surface unzone ##~num_residues

> alias caps_off surface cap false

> alias caps_on surface cap true

> alias open_vseries "open browse vseries true"

> alias selbetween ks ri

> alias helix setattr $1 res is_helix true

> alias strand setattr $1 res is_strand true

> alias coil setattr $1 res is_strand false; setattr $1 res is_helix false

> alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136;
> movie encode ~/Desktop/rock_movie.mp4; stop

> buttonpanel Shortcuts rows 3 columns 5

> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"

> buttonpanel Shortcuts add Model_Panel command "tool show Models"

> buttonpanel Shortcuts add Log command "tool show Log"

> buttonpanel Shortcuts add default_disp command default_mol_display

> buttonpanel Shortcuts add map_sphere command map_sphere_15

> buttonpanel Shortcuts add map_unsphere command map_unsphere

> buttonpanel Shortcuts add cofron command cofron

> buttonpanel Shortcuts add cofroff command cofroff

> buttonpanel Shortcuts add cootmode command cootmode

> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr"

> buttonpanel Shortcuts add hidemaps command hidemaps

> buttonpanel Shortcuts add showmaps command showmaps

> buttonpanel Shortcuts add reset_mouse command "mousemode alt right contour ;
> mousemode right clip ; mousemode alt left 'translate selected models' ;
> mousemode shift left 'rotate selected models' ; mousemode alt control left
> 'pick blobs'; help https://github.com/olibclarke/chimerax-
> trimmings/blob/main/default_mousemodes.md"

> buttonpanel Shortcuts add previous_model command prevmodel

> buttonpanel Shortcuts add next_model command nextmodel

> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true

Saved volume settings  
UCSF ChimeraX version: 1.8.dev202403210048 (2024-03-21)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/oc2188/Downloads/cryosparc_P48_J686_00385_volume_series/J686_class_00_00385_volume.mrc

Opened J686_class_00_00385_volume.mrc as #1, grid size 100,100,100, pixel
2.82, shown at level 0.288, step 1, values float32  

> open
> /Users/oc2188/Downloads/cryosparc_P48_J686_00385_volume_series/J686_class_01_00385_volume.mrc

Opened J686_class_01_00385_volume.mrc as #2, grid size 100,100,100, pixel
2.82, shown at level 0.294, step 1, values float32  

> open
> /Users/oc2188/Downloads/cryosparc_P48_J686_00385_volume_series/J686_class_02_00385_volume.mrc

Opened J686_class_02_00385_volume.mrc as #3, grid size 100,100,100, pixel
2.82, shown at level 0.299, step 1, values float32  

> open
> /Users/oc2188/Downloads/cryosparc_P48_J686_00385_volume_series/J686_class_03_00385_volume.mrc

Opened J686_class_03_00385_volume.mrc as #4, grid size 100,100,100, pixel
2.82, shown at level 0.297, step 1, values float32  

> open
> /Users/oc2188/Downloads/cryosparc_P48_J686_00385_volume_series/J686_class_04_00385_volume.mrc

Opened J686_class_04_00385_volume.mrc as #5, grid size 100,100,100, pixel
2.82, shown at level 0.292, step 1, values float32  

> open
> /Users/oc2188/Downloads/cryosparc_P48_J686_00385_volume_series/J686_class_05_00385_volume.mrc

Opened J686_class_05_00385_volume.mrc as #6, grid size 100,100,100, pixel
2.82, shown at level 0.296, step 1, values float32  

> open
> /Users/oc2188/Downloads/cryosparc_P48_J686_00385_volume_series/J686_class_06_00385_volume.mrc

Opened J686_class_06_00385_volume.mrc as #7, grid size 100,100,100, pixel
2.82, shown at level 0.298, step 1, values float32  

> open
> /Users/oc2188/Downloads/cryosparc_P48_J686_00385_volume_series/J686_class_07_00385_volume.mrc

Opened J686_class_07_00385_volume.mrc as #8, grid size 100,100,100, pixel
2.82, shown at level 0.296, step 1, values float32  

> open
> /Users/oc2188/Downloads/cryosparc_P48_J686_00385_volume_series/J686_class_08_00385_volume.mrc

Opened J686_class_08_00385_volume.mrc as #9, grid size 100,100,100, pixel
2.82, shown at level 0.297, step 1, values float32  

> open
> /Users/oc2188/Downloads/cryosparc_P48_J686_00385_volume_series/J686_class_09_00385_volume.mrc

Opened J686_class_09_00385_volume.mrc as #10, grid size 100,100,100, pixel
2.82, shown at level 0.296, step 1, values float32  

> cofron

> hidemaps

> surface unzone ##~num_residues; sel; close #10000; marker #10000 position
> cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel distance 0; close
> #10000

Missing or invalid "surfaces" argument: invalid surfaces specifier  




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

Python: 3.11.4
Locale: 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: MacBook Pro
      Model Identifier: Mac14,5
      Model Number: Z17J00171LL/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 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 (23E214)
      Kernel Version: Darwin 23.4.0
      Time since boot: 3 days, 23 hours, 35 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 30
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.1.1
    certifi: 2023.11.17
    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-Atomic: 1.56
    ChimeraX-AtomicLibrary: 14.0.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    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: 2.12.1
    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-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-Core: 1.8.dev202403210048
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4.2
    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: 1.1.4
    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: 2.1.3
    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
    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-OpenCommand: 1.13.3
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    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-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
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.9
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.1
    fonttools: 4.50.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2024.2.26
    idna: 3.6
    ihm: 0.43
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    Jinja2: 3.1.3
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.1.0
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.8
    ndindex: 1.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.2.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.9.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.3
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.2.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.3.0
    pygments: 2.17.2
    pynmrstar: 3.3.4
    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-commercial: 6.6.1
    PyQt6-Qt6: 6.6.2
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.2
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 25.1.2
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.12.0
    setuptools: 69.2.0
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.0
    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
    superqt: 0.6.1
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.1
    typing-extensions: 4.10.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10

[olibclarke@…]

It seems like the ##~num_residues syntax is broken - it also breaks a number of other shortcuts I have that use this in the context of various different commands

[Eric Pettersen]

Hi Ollie,

In implementing the "Select" tab in the Render By Attribute tool I realized I needed an attribute test for whether an attribute exists and has a value. The undocumented '~' attribute operator does not cut the mustard because it is a boolean test and if an attribute exists and just so happens to have a value of zero (e.g. a formal_charge attribute) the '~' operator will return true even though the attribute exists.
Therefore we withdrew the '~' attribute test (since it's also redundant, e.g. ##~num_residues is the same as ~##num_residues) and replaced it with the '^{' operator, which is the symbol that Chimera used for checking if an attribute exists.
For your purposes, since the attribute you're checking can't be zero, I'd replace ##~attr with ~##attr in your aliases, since that will function in all versions of ChimeraX.}

--Eric

[olibclarke@…]

Got it, thanks Eric, will do!

Cheers
Oli