Orbital Lobes

The Orbital Lobes tool draws atomic and hybrid orbital shapes directly on your structure: s spheres, p dumbbells, four-lobed d orbitals, sp/sp2/sp3 hybrids, and pi overlap envelopes between two atoms. Use it for bonding diagrams, hybridization figures, and MO-style illustrations where the skeletal structure alone is not enough.

Activate it with the orbital button in the toolbar or press Shift+O. Plain O is taken: it sets the current element to oxygen. Clicking the toolbar button also opens the flyout where you pick the orbital type; right-clicking the button opens the flyout without changing your current sub-type.

Orbital types

The flyout catalog is arranged in three rows:

Pure orbitals: s, p, p½ (single-lobe p), and the five d orbitals (dxy, dxz, dyz, dx²−y², dz²). The cloverleaf d types (dxy, dxz, dyz, dx²−y²) render as four lobes at 90° intervals; dz² renders as two lobes with a central torus ring.
Hybrid orbitals: sp, sp², sp³, each with a large front lobe and a smaller back lobe, plus half versions (sp½, sp²½, sp³½) that draw only the front lobe. Half types are handy when the back lobe would clutter a bonding diagram.
Overlap orbitals: π (two-sausage overlap above and below an axis) and π* (antibonding, with a gap between the halves).

Placing orbitals

With a single-atom type selected:

Click an atom to add the orbital at an automatically chosen angle: the tool finds the largest angular gap between the atom’s bonds, lone pairs, and existing orbitals and centers the new lobe there. On a bare atom it points straight up.
Drag from an atom to set the angle yourself. A snap circle previews angles based on the atom’s geometry (VSEPR-derived positions). Hold Shift to drop the snap and place at any free angle.
Click an existing lobe to select that orbital and switch to the Select tool. If your click lands within the atom’s own hit radius, the atom wins and a new orbital is added instead.
Click or drag on empty canvas to create a freestanding orbital annotation, not attached to any atom. A plain click places it pointing right at default size; dragging sets the angle (snapped to 15° increments unless Shift is held) and the drag distance sets the scale.

The π and π* types work differently because they span two centers: click one atom, then a second atom, and the overlap is drawn between them and stays linked to both. Clicking the same atom twice cancels. Click-drag in empty space instead to create a freestanding overlap between two arbitrary points.

The tool stays active while you add atom-attached orbitals, so you can decorate several atoms in a row. Creating a freestanding orbital, finishing a π overlap, or clicking an existing lobe switches you to the Select tool.

Editing placed orbitals

Select a single atom-attached orbital and you get gold diamond adjustment handles: one at the lobe tip for length, one at the widest point for width, and one near the atom center that pulls the lobe away from the nucleus (center gap). A rotation handle floats past the tip on a dashed connector; drag it to re-aim the orbital. See Selection handles for the handle conventions.

For everything else there is an Orbitals section in the Object Properties panel with roughly 25 controls. The headline options: orbital type, fill style (outline, flat, or 3D shaded), render layer (behind bonds, above bonds, or above all), positive/negative phase colors with swap and preset pairs (blue/red, purple/green, black/white, and more), the single-lobe (half) toggle, a cover-atom-label override, and a tilt slider for foreshortened pseudo-3D lobes. See Object Properties.

Deleting

Click a lobe with the Eraser, press Delete with orbitals selected, or use the Delete Orbital button at the bottom of the panel section.

Visibility and clipping

Structure > Display > Show Orbitals hides or shows every orbital in the document without deleting anything; the panel section hides along with them.

Document-wide rendering defaults live on the Orbitals tab of Structure Settings under Lobe Clipping: clip lobes at atom labels, clip at sibling lobes on the same atom, the padding around each clipped region, and truncation of outlines where sibling lobes intersect. The per-orbital “Cover atom label” checkbox in the panel overrides label clipping for one orbital.