Selection Inspector
The Selection Inspector is a lightweight tab in the pipeline panel — the Inspector button on the panel's rail, under Editor — for the most common tasks in molecular visualization: change how the structure looks, and select a subset of atoms and change how that looks. The Quick style section at the top does the first; the Selections below it do the second. 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.
Quick style
A few global controls, applied to the whole structure:
| Control | What it changes in the pipeline |
|---|---|
| Style | adds a representation node (insp-global-rep) to the main particle stream |
| Color | adds a color node (insp-global-color) |
| Atom size, Atom opacity | adds a modify node (insp-global-atoms) |
| Bond width, Bond opacity | adds a modify node on the bond stream (insp-global-bonds) |
| Bond tolerance | the add_bond node's distance factor — shown only when bonds are inferred by distance |
| Labels (None / Element / Residue / Index) | adds a label_generator node (insp-global-labels) |
| Arrow scale | the vector_overlay node's scale — shown only when the pipeline draws vectors |
| Perspective, Cell axes | the viewport node's settings |
The nodes are inserted in line, between the node that feeds the viewport and
the viewport itself, so they show up in the Editor tab like any other node.
A control set back to its default removes its node again, and ↺ Reset
removes them all — an untouched Quick style leaves the pipeline exactly as it
was. Pipeline default for Style or Color means "don't override what the
pipeline already draws". Everything is read back from the pipeline, so the
panel stays correct after you edit those nodes in the Editor, apply a template
or an AI assistant result, or re-open a saved .megane.json.
If the pipeline already carries color / representation / modify nodes of
its own, the panel says how many: they also affect the look, and Quick style
does not take them over.
Selections
Each layer is one "select these atoms, style them like this" rule. Click
+ Add selection to create one, and the ✕ beside a layer to delete it. 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 Quick style: atoms no layer selects keep the global look, and a
layer's settings win for the atoms it selects (a layer at size 1.0 restores full
size under a global 0.5). Layers branch from the end of the Quick style chain,
and the Inspector recognises its nodes by their insp-<layer>-<role> ids, so
layers survive saving and re-opening the pipeline.
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. Below it the panel shows how many atoms the expression selects, or the syntax error.
- 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/property/illustrative), the style
(representation: ball, licorice, cartoon, cartoon + atoms, surface, line,
illustrative), the atom size and opacity, and toggle visibility
(a hidden layer drives its atoms to opacity 0). Color and style each have a
checkbox; only the enabled ones add a color / representation node to the
chain. Changes apply immediately and are reflected in the Editor tab — Open
generated nodes in Editor → jumps there.
Availability
The Inspector is available everywhere the visual pipeline editor is — the standalone web app, the JupyterLab extension, and the VS Code extension. The in-cell Jupyter widget does not mount the pipeline editor, but it can show the Quick style controls on their own:
from megane import MolecularViewer
viewer = MolecularViewer(quick_style=True)
viewer.set_pipeline(pipe)
viewer.quick_style = False # hide it again
The panel opens in the viewer's top-right corner and collapses to a Style
button. Its changes are written back to the widget's pipeline, so they survive
re-displaying the widget and are saved with the notebook; calling
set_pipeline() again replaces them. It needs data loaded with
set_pipeline() (it is disabled on the deprecated load() path), and the
Selections part is not available in the widget.