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Selection Inspector

The Selection Inspector is a lightweight third tab in the pipeline panel (alongside Editor and Chat) for the most common task in molecular visualization: select a subset of atoms and change how it looks. It is inspired by OVITO's Expression Select, but you rarely have to type an expression — you build selections by clicking chips for the elements, residues, and chains that are actually present in your structure, or by picking atoms directly in the 3D view.

Everything the Inspector does is compiled straight into ordinary pipeline nodes, so a selection you make here appears as a filter → color / representation / modify chain in the Editor tab. The Inspector is just a friendlier front end to the same pipeline — nothing is hidden or parallel.

Layers​

Each layer is one "select these atoms, style them like this" rule. Add as many as you need — e.g. a layer that colors the protein backbone, another that draws the ligand as licorice, another that hides the solvent. Layers are drawn on top of the base structure, so atoms no layer selects keep their default appearance.

Building a selection​

  • Chips — click the elements, residues, or chains present in the loaded structure. Selected categories are AND-ed together (e.g. carbons and chain A).
  • Within (Å) — expand the current selection to every atom within a distance of it (within R of (…)), handy for "everything around the active site".
  • Expression — the raw selection expression is always shown and editable for full control. Editing it directly overrides the chips.
  • From the 3D view — turn on Box select and drag a rectangle in the viewer to select atoms, or click an atom and choose same element / same residue / same chain / same molecule / just this. The current selection is highlighted live in green.

The selection language supports the fields element, index, x/y/z, resname, resid, chain, mass, and molecule_id, combined with and / or / not, parentheses, and within R of (…).

Appearance​

For the active layer you can set the color (uniform or by element/residue/chain/B-factor/illustrative), the representation (ball, licorice, cartoon, surface, line, illustrative…), the atom size and opacity, and toggle visibility. Changes apply immediately and are reflected in the Editor tab.

Availability​

The Inspector is available everywhere the visual pipeline editor is — the standalone web app, the JupyterLab extension, and the VS Code extension. It is not shown in the in-cell Jupyter widget, which does not mount the pipeline editor.