Bond Styling
To make one bond of acetone heavier than the rest, or to widen the wedges on a single stereocenter, select the bonds and use the Bond section of the Object Properties panel. Everything here applies only to the selected bonds and overrides the document-wide defaults set in Structure Settings. Most rows appear only when they apply to the current selection, so the section grows and shrinks as you click different bond types. Sliders with a default reset on double-click, and a multi-selection whose bonds disagree shows “Mixed” until you edit.
Core controls
These rows are available for any selected bond.
| Control | Values | Default | What it does |
|---|---|---|---|
| Hide | checkbox | off | Suppresses rendering; connectivity, hit-testing, and SMILES still see the bond |
| Element Color | Auto / On / Off | Auto | Per-bond override of the document’s color-by-element setting |
| Color | hex + reset | scheme color | Bond stroke color; hidden while element coloring is in effect |
| Vertex Color | hex + reset | matches bond | Junction fill at unlabeled endpoints with two or more bonds; only shown when such a vertex exists |
| Thickness | 0.5 to 5 | 1.5 | Line thickness |
| Line Cap | default / Butt / Round | default | End cap style |
| Length | 5 to 9999 px | preset value | Type a length; reset returns to the preset’s default (40 in the standard presets) |
Typing a Length moves atoms. Molkit walks outward from each end of the bond and translates the lighter side (the side with fewer atoms) along the bond axis. Ring bonds are skipped, since both ends connect back to the same structure.
Label clearance
These rows depend on the atoms at the bond’s endpoints.
| Control | Shown when | What it does |
|---|---|---|
| Clearance (0 to 8, default 2.1) | at least one endpoint has a visible label | Gap between the bond line and the label |
| Phantom clearance (checkbox) | the bond ends in an unlabeled terminal atom | Shortens the bond as if that atom had a label |
| Extend past label (checkbox) | the bond ends in a labeled terminal atom | Lengthens the bond so the drawn line matches the unlabeled length, making up for the space the label takes |
Crossing bonds
When a selected bond crosses another bond on the canvas, three extra sliders appear:
| Control | Range | Default | What it does |
|---|---|---|---|
| Gap | 0 to 10 | 1 | Width of the break where the lower bond passes under |
| Len →1 | -1 to 30 | auto | Break length on the atom-1 side; -1 means automatic |
| Len →2 | -1 to 30 | auto | Break length on the atom-2 side; -1 means automatic |
The bond drawn underneath is the one that breaks. To swap them, change the stacking order with the ordering commands in Right-click menus.
Bond-type sub-sections
Each sub-section appears only when a matching bond is in the selection. Defaults are in parentheses.
| Sub-section | Appears for | Controls |
|---|---|---|
| Wedge Settings | wedge and outlined-wedge bonds | Max Width 1 to 6 (2.5), Narrow Gap 0 to 5 (0.5); hash bonds add Hash Lines 3 to 15 (7) |
| Wavy Settings | wavy bonds | Amplitude 1 to 5 (2.5), Frequency 4 to 16 (8) |
| Multi-Bond Settings | double and triple bonds | Offset 1 to 5 (2.5), the spacing between the parallel lines |
| Arrow Settings | dative bonds | Arrow Size 3 to 12 (6), Arrow Width 1 to 5 (2.5) |
Aromatic display
The aromatic sub-section appears for aromatic bonds, or for bonds in a ring that carries an aromatic circle. In benzene, for example, select one ring bond to see Display and Arc Display; select all six to add the circle controls.
| Control | What it does |
|---|---|
| Display (Auto / Kekulé / Circle) | Per-bond override of the rendering mode. Shown when a selected bond belongs to a ring with an aromatic circle. Offset (1 to 5, default 2.5) sets the inner-line spacing in Kekulé mode. |
| Arc Display (checkbox) | Draws a partial arc on the bond and reveals Arc Style (Dashed or Solid), Arc Curvature (0 to 2, default 0.87) and Arc Color. Arc edits spread to every connected aromatic bond, so styling one bond styles the whole conjugated path. |
| Circle Radius (0.2 to 0.9, default 0.6) and Circle Color | Shown only when every bond of a complete aromatic ring is selected and circle display is active. |
Stereo configuration
When a double bond is selected, a Config dropdown (None / E / Z) appears at the bottom of the section. It sets the bond’s stereo descriptor; see Stereo labels for how descriptors render on the canvas.
To draw bonds in the first place, see the Bond tool and Ring tool. The preset values these overrides start from are listed under Structure presets.