Bond Styling
When you select one or more bonds, the Object Properties panel shows a Bond section with per-bond style overrides. 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 mixed multi-selections show “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) |
The Length input moves atoms, not just pixels: 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 appear based on the atoms at the bond’s endpoints.
- Clearance (0 to 8, default 2.1): the gap between the bond line and a visible endpoint label. Shown only when at least one endpoint has a visible label.
- Phantom clearance (checkbox): shortens the bond as if an unlabeled terminal atom had a label. Shown when the bond ends in an unlabeled terminal atom.
- Extend past label (checkbox): elongates the bond so the rendered line matches the unlabeled length, compensating for the space the label consumes. Shown when the bond ends in a labeled terminal atom.
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 |
Which bond breaks is a z-order question, not a styling one. Change which bond renders on top 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:
- Wedge Settings (wedge or 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 or triple bonds): Offset 1 to 5 (2.5) controls the spacing between parallel lines.
- Arrow Settings (dative bonds): Arrow Size 3 to 12 (6) and 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.
- Display (Auto / Kekulé / Circle): a 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) controls the inner-line spacing in Kekulé mode.
- Arc Display (checkbox): draws a partial arc on the bond. Turning it on reveals Arc Style (Dashed or Solid), Arc Curvature (0 to 2, default 0.87), and Arc Color. Arc edits propagate 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 you have selected every bond of a complete aromatic ring 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.