Orbital Lobes

To show why the oxygen in water is sp³ hybridized, or where the π bond in ethene sits, draw the orbitals on the structure itself. The Orbital Lobes tool places s spheres, p dumbbells, four-lobed d orbitals and sp/sp²/sp³ hybrids directly on atoms, and joins two atoms with σ and π bonds. To draw every orbital of a molecule in one step, see Orbital Pictures.

Activate it with the orbital button in the toolbar or press Shift+O. Plain O 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 shows 14 buttons in two rows, each with an icon and a caption under it.

Row	Buttons	What they draw
One atom	s, p, dxy, dxz, dyz, dx²−y², dz²	The cloverleaf d types draw four lobes at 90° intervals; dz² draws two lobes with a central torus ring.
Hybrids and bonds	sp, sp², sp³, σ, π, π*, Build All	A hybrid has a large front lobe and a smaller back lobe. σ, π and π* span two atoms (see below). Build All builds an orbital picture of the selected molecule, or of the whole drawing.

The σ button appears only while the hybridization tools are on (the default; see Hybridization tools). New lobes use the Egg shape.

Older menu entries (the half hybrids, the forced σ-sp/σ-sp²/σ-sp³ types, the p pairs, the π envelopes and the older π cloud) have left the flyout. Files that use them still open and draw as before. To draw a single lobe, place a full orbital and tick Single lobe only in the panel.

Drawing sp³ orbitals on water

Draw water as an O with two bonds to H (see Your first molecule if you have not drawn one yet).
Press Shift+O, then pick sp³ in the flyout.
Click the oxygen twice. Each click adds a lobe in the largest open gap left by the bonds and any existing lobes, so the two lobes fan out on the side away from the hydrogens.

To aim a lobe yourself, drag from the atom instead of clicking.

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. A snap circle previews angles derived from the atom’s VSEPR geometry; hold Shift to place at any angle.
Click an existing lobe to select that orbital and switch to the Select tool. If the click lands within the atom’s own hit radius, the atom wins and a new orbital is added.
Click or drag on empty canvas to create a freestanding orbital that is not attached to any atom. A click places it pointing right at default size; a drag sets the angle (snapped to 15° steps unless Shift is held) and the drag distance sets the scale.

The π, π* and σ types span two atoms. Click one atom, then a second; clicking the same atom twice cancels.

π joins the p orbitals of the two atoms with a bridge, a band from lobe to lobe with the electron pair on one face. An atom with no suitable p orbital gets one in the page. You can also click the bond. Using π again on the same two atoms joins their out-of-page p orbitals, as for the second π bond of a triple bond.
π* draws an antibonding overlap between the two atoms, linked to both. Drag in empty space to create a freestanding one between two points.
σ is described under Hybridization tools.

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 two-atom orbital, or clicking an existing lobe switches you to the Select tool.

Editing placed orbitals

Select one atom-attached orbital to 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). Double-click a diamond to reset that dimension to its default. A rotation handle floats past the tip on a dashed connector; drag it to re-aim the orbital. See Canvas Handles.

The ORBITALS section of the Object Properties panel holds the remaining controls. The main ones set the orbital type, lobe shape (Rounded, Petal, Teardrop, Egg, or Ellipse), fill (outline, flat, or 3D shaded), render layer (behind bonds, above bonds, or above all), positive and negative phase colors, the single-lobe toggle, At letter (how the lobe meets its atom’s letter), and Out of page, a 0 to 45 degree slider that draws the lobe pointing out of the page. See Object Properties.

Hybridization tools

A second set of tools draws whole bonding frameworks in one click. They are controlled by Structure > Display > Hybridization Tools (Experimental), which is checked for every new document; the menu marks them experimental, and unchecking the item hides them for that document.

With the tools off, the σ button leaves the flyout.

The σ button draws a σ bond from hybrid lobes when you click a bond or two atoms. Each end’s hybridization is detected from its own atom: on propyne, the CH₃ end gets sp³ and the alkyne end gets sp. The tool also adds the shared electron pair in the overlap of the two lobes and hides the bond line under them.

Clicking a bond with σ reads the bond order and adds the π bonds, each as p orbitals joined by a bridge: a double bond gets σ plus one π, a triple bond σ plus two. Alt-click the bond to draw the σ lobes only.

With the tools on, a hybrid or p orbital added to an atom is labeled with its type (sp, sp², sp³, p; an s orbital reads 1s).

Two right-click commands also depend on the setting:

With one lobe selected on an atom that has lone pairs, Hold Lone Pair moves the nearest lone pair (within 30° of the lobe’s direction) inside the lobe, and Release Lone Pair returns it to its usual position.
With one bond selected, Draw orbitals: σ only, Draw orbitals: σ + π (double) and Draw orbitals: σ + 2π (triple) draw that framework whatever the drawn bond order. The item that matches the bond order is marked “(recommended)”.

The atom right-click Orbitals > Build Orbital Picture and Orbitals > Fill with sp / sp² / sp³ commands are available whether or not the hybridization tools are on. See Right-click menus.

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.

Structure > Display > Auto-Clear Orbitals from Labels is checked by default. While it is on, a lobe on a labeled atom (the O in water, for example) is clipped where it would cover that atom’s own label, so the letter stays readable. It is the same setting as Clip at Label on the Orbitals tab of Structure Settings, and the per-orbital At letter choice in the panel overrides it for one orbital (Run through it draws the lobe through the label).

Overlapping outlines of lobes on the same atom are handled by Truncate at Intersections on the Orbitals tab of Structure Settings.

The Orbitals tab also sets the padding around each clipped region and whether outlines are truncated where sibling lobes intersect.