Bond Tool
Most structures are drawn with the Bond tool. You drag bonds out of atoms, connect existing atoms, click bonds to change their order, and click atoms to relabel them to the active element. Press B to activate it.
To draw acetone, for example, click empty canvas to place a carbon and drag three bonds out of it. Press O and click the end of one bond to make it an oxygen, then click that C–O bond once to make it double.
Drawing bonds
Press on any atom and drag outward. A preview line follows the cursor, and releasing creates a new atom at the endpoint plus a bond to it. New carbon atoms are unlabeled, matching skeletal convention.
If you release the drag near an existing atom, the endpoint snaps onto it (a snap ring highlights the target) and the bond connects the two atoms. If those atoms are already bonded, the existing bond’s order cycles instead.
A single click on empty space places a lone atom of the active element. Carbon is placed with a hidden label; other elements show their symbol.
Pressing Esc mid-gesture cancels the bond and removes the start atom if it has no bonds (including a pre-existing isolated atom you started the drag from).
Drawing without dragging
If dragging is difficult, turn on View > Single-Pointer Editing. The Bond tool then creates bonds with two clicks: click a start atom (or empty canvas), move the pointer to see a preview, and click the destination atom or an empty spot. Clicking the start again, pressing Esc, or clicking the on-screen Cancel bond button cancels. While this setting is on, every Bond tool click starts or finishes a bond, so clicking to cycle bond orders or relabel atoms is unavailable. Use hover-type (see Atoms and Elements) or the canvas keyboard cursor (see Keyboard Shortcuts) for those edits, or turn the setting off. The setting is off by default and is remembered in your browser.
Clicking existing bonds
Clicking a bond with the default single-bond tool cycles its order: single, double, triple, then back to single. A bond that carries a stereo style (wedge, dash, and so on) loses the stereo style on the first click, then cycles order on later clicks.
Two refinements:
- A click within 10 px of a bond endpoint starts a new bond from that atom; the clicked bond keeps its order.
- A double bond inside a ring cycles its inner line first: inside the ring, outside the ring, centered, and only then advances to triple. This lets you flip which ring the second line faces in fused systems.
With a specific bond type selected in the flyout, clicking a bond applies that type. Clicking again with the same wedge, dash, or dative type swaps the bond’s direction. With the double-bond tool, repeated clicks on a double bond cycle the second line’s placement: auto-detected side, opposite side, centered.
Clicking atoms
Clicking an atom with the Bond tool relabels it to the active element (chosen from the element picker or an element shortcut; see Atoms and Elements). If the atom already matches the active element and that element is carbon, the click toggles the carbon label between hidden and visible.
Snapping and modifier keys
While dragging, the bond angle snaps to 15 degree increments and the length snaps to the standard bond length, which is 40 px in the Traditional and Textbook presets and 28 px in Compact. Angle snapping requires both the canvas Snap to Angle setting and Smart Guides (Ctrl+;) to be on. The angle goes to the nearest 15 degree step, and the bond lands exactly where the preview showed it.
To put bonds that ended up slightly off a 15 degree line back on it, use Structure > Straighten Bonds; see Straightening bonds.
Modifier keys during the drag relax each snap independently:
| Modifier | Angle | Length |
|---|---|---|
| None | Snapped (15 degrees) | Standard |
Shift | Snapped | Free |
Alt or Ctrl | Free | Standard |
Shift+Alt or Shift+Ctrl | Free | Free |
Shift alone is the extension gesture: the bond stays on a snapped angle but reaches as far as you drag. Shift+Alt or Shift+Ctrl is fully free drawing.
Straightening bonds
Structure > Straighten Bonds puts bonds that are a little off a 15 degree line exactly on it: up to 2 degrees off, or 3 degrees near horizontal or vertical. It slides the far side of the molecule rather than turning it, so no other bond angle changes. A ring system tilted as a whole is turned back. Bonds further off than that are treated as deliberate (VSEPR angles, a pentagon’s angles) and left alone.
With atoms selected, it works on the whole molecules they belong to; with nothing selected, on every molecule. It is also on the right-click menu when atoms are selected. The change is one undo step, and a message says how many bonds and rings were straightened, or that all bonds are already on their angles.
Bond types
The Bond toolbar button opens a flyout with every bond variant. Picking one makes it the active type for new bonds and for clicks on existing bonds.
| Group | Types |
|---|---|
| Basic | Single, Double, Triple, Quadruple |
| Stereo | Wedge, Wedge (outline), Dash, Wavy |
| Coordinate and weak | Dative, Dative (dots), Hydrogen, Coordination |
| Aromatic and crossed | Aromatic, Crossed, Double X |
| Style variants | Bold, Dotted, Dashed Double, Dashed Triple |
The flyout also offers the squiggle line, a wavy annotation drawn free-floating or anchored across a terminal bond as a cut-off mark. It has no chemical meaning.
Aromatic rings can render in Kekulé style (alternating double bonds) or with an inscribed circle. The display mode is part of the structure preset and can be switched from the Structure menu; see Presets.
Per-bond styling overrides (color, thickness, wedge and hash geometry, crossing gaps, aromatic display) are documented on the Bond Styling panel page.
Bond crossings
Where two bonds cross, the bond drawn on top gets a short white break in the bond underneath so the crossing reads correctly. To control which bond is on top, select a bond, right-click, and choose Bring Bond to Front or Send Bond to Back. Reset Bond Crossing Order removes the manual override and returns to draw order.