Structure Settings
The Structure Settings dialog sets document-wide drawing defaults. Open it from Structure > Structure Settings… (it is also available from the command palette). Every value you change here applies to the whole document immediately; the dialog is draggable, and the Done button closes it. These are defaults, not per-object styles. To override an individual bond or atom, use the Bond Styling or Object Properties panel instead; per-object overrides win over the defaults set here.
At the top of the dialog, a Preset dropdown switches between Traditional, Compact, and Textbook, plus any custom presets you have saved. Picking a preset rewrites the settings below in one step, while your element color scheme stays untouched. The dropdown reads Custom when your settings no longer match a named preset. See Structure Presets for what each preset bundles.
Bonds
Controls how bonds draw by default:
| Setting | Range (default) |
|---|---|
| Line Cap | Butt / Round (Butt) |
| Bond Length | 15-80 px (40) |
| Thickness | 0.5-4 px (1.5) |
| Color by Element | checkbox (off) |
| Gradient Width | 0-50% (16%) |
| Double Bond Offset | 1-5 px (2.5) |
| Triple Bond Offset | 2-6 px (3) |
| Wedge Max Width | 1.5-4 px (2.5) |
| Hash Line Count | 5-11 (7) |
| Wavy Amplitude | 1-5 px (2.5) |
| Crossing Padding | 0-10 px (1) |
| Aromatic Display | Kekulé / Circle (Kekulé) |
Color by Element has a guard: if any bonds carry their own per-bond element-coloring override, toggling the global checkbox opens an “Individual Settings Found” prompt with three choices: Preserve Settings (keep the per-bond overrides), Reset All to Auto (clear them so every bond follows the global value), or Cancel. Gradient Width controls how wide the two-color blend zone is on element-colored bonds.
Atoms
Label visibility, font, and the element color scheme:
- Show Carbon Labels (off) and Show Implicit Hydrogens (off) toggle automatic C and H labels.
- Label Font picks the atom-label typeface: Arial (default), Times New Roman, Helvetica, Georgia, Courier New, plus any fonts you have added. The + button opens the font import dialog and the x button removes the selected user font (system fonts cannot be removed). See Fonts.
- Color Scheme selects an element palette: Simple, Black & White, CPK (Jmol), Colorblind Safe, WCAG AA, or Publication. Save Current… stores your colors as a named custom scheme; Delete removes a custom scheme (it is disabled for built-ins). See Color Schemes.
- Edit Element Colors… closes this dialog and opens the Color Scheme Editor.
Electrons
Two matching blocks, one for lone pairs and one for radicals:
- Visible (on for both)
- Representation: Dots / Lines / Lobes (Dots)
- Size: 0.5-4 px (1.5)
- Dot Spacing: 1-5 px (2), lone pairs only
- Distance from the atom: 1-12 px (5)
- Color Mode: Bond / Element / Custom (Bond), with a custom color swatch
Charges
Defaults for charge rendering:
- Style: Superscript / Circle (Superscript)
- Size: 0.5-1.5 (0.85). The readout shows px, but this is a scale factor relative to the label size, not a pixel value.
- Default Position: Auto plus six fixed placements (Top Right, Top Left, Top Center, Bottom Right, Bottom Left, Bottom Center)
- Fine Tune X and Fine Tune Y: -3 to 3 px nudge (0)
Geometry
- Default Bond Length: 15-80 px (40). This is the same underlying setting as Bond Length on the Bonds tab; changing either moves both.
- Label Clearance: 1-8 px (2.1), the gap bonds leave around atom labels.
- Dative Bond Arrow: two sliders, Arrow Length 3-12 px (6) and Arrow Width 1.5-5 px (2.5).
Projections
Defaults for new projections, split into two groups:
- Fischer: Vertical Spacing 10-80 px (40), Arm Length 10-80 px (40), Crossing Style Break / Continuous (Continuous), Show Center Labels (off), Show R/S Labels (on).
- Newman: Circle Radius 8-50 px (25), Bond Length 10-60 px (40), Show Center Dot (off), Show Dihedral Angle (off), Show Conformation Label (on), Back Bond Style Truncated / Full (Truncated).
Orbitals
Lobe clipping for the orbital tool:
- Clip at Label (on): lobes stop short of atom labels.
- Clip at Sibling Lobes (on): lobes clip against other lobes on the same atom.
- Clip Padding: -2 to 8 (1.5), extra space around each clipped edge; negative values let lobes encroach.
- Truncate at Intersections (on): ends lobe outlines cleanly where same-atom siblings cross. Outline mode only; tilted orbitals fall back to untruncated. This is an alternative to Clip at Sibling Lobes, so avoid running both on the same drawing.