Structure Settings
Open Structure > Structure Settings… (or search for it in the command palette, Ctrl+K) to change how every structure in the current document is drawn. A change applies to the whole document as soon as you make it. The dialog can be dragged out of the way while you watch the canvas, and Done closes it.
These are document defaults. To restyle one bond or one atom, use the Bond Styling or Object Properties panel; a per-object value always wins over the default set here.
Ctrl+Z undoes changes made in the dialog. A slider drag is one undo step however far it travels, and changes made less than half a second apart are grouped into one step.
Presets
The Preset dropdown at the top switches between Traditional, Compact and Textbook, plus any custom presets you have saved. Choosing a preset rewrites the settings in one step and leaves your element color scheme alone. When your settings no longer match a named preset, the dropdown reads Custom. A new document starts from the preset you used last, or Traditional if you have never chosen one. Structure Presets lists what each preset contains.
The defaults in the tables below are the Traditional values. Where the other built-in presets differ in a way you would notice, the table says so.
Bonds
Defaults for bonds.
| Setting | What it does | Range (default) |
|---|---|---|
| Line Cap | Shape of bond ends | Butt or Round (Butt; Round in Compact and Textbook) |
| Bond Length | Length of newly drawn bonds | 15-80 px (40; 28 in Compact) |
| Thickness | Bond line width | 0.5-4 px (1.5) |
| Color by Element | Colors each half of a bond by its atom’s element color | Checkbox (off) |
| Gradient Width | Width of the blend zone where the two colors meet on an element-colored bond | 0-50% (16%) |
| Double Bond Offset | Gap between the lines of a double bond | 1-5 px (2.5) |
| Triple Bond Offset | Gap between the lines of a triple bond | 2-6 px (3) |
| Wedge Max Width | Width of the wide end of a wedge | 1.5-4 px (2.5) |
| Hash Line Count | Number of lines in a hashed wedge | 5-11 (7) |
| Wavy Amplitude | Height of the waves in a wavy bond | 1-5 px (2.5) |
| Crossing Padding | Gap left where one bond passes behind another | 0-10 px (1) |
| Display Mode (Aromatic Display) | How aromatic rings are drawn | Kekulé or Circle (Kekulé; Circle in Textbook) |
If some bonds carry their own element-coloring override, switching Color by Element opens an “Individual Settings Found” prompt. Preserve Settings keeps those per-bond overrides, Reset All to Auto clears them so every bond follows the new value, and Cancel leaves everything as it was. The reset is a single undo step however many bonds it touches.
With Color by Element on, a bond into a condensed label such as OCH3, NH2 or SO3H takes the color of the atom it attaches to, for example the O of OCH3.
Atoms
| Setting | What it does | Default |
|---|---|---|
| Show Carbon Labels | Writes “C” on every carbon instead of leaving vertices bare | Off |
| Show Implicit Hydrogens | Writes implicit hydrogens into atom labels | Off |
| Label Font | Typeface for atom labels: Arial (default), Times New Roman, Helvetica, Georgia, Courier New, plus fonts you have added | Arial |
| Color Scheme > Preset | Element palette: Simple, Black & White, CPK (Jmol), Colorblind Safe, WCAG AA or Publication | Your last-used scheme |
Next to Label Font, the + button opens the font import dialog and the × button removes the selected font you added (built-in fonts cannot be removed); see Fonts. Under the color scheme, Save Current… stores your colors as a named scheme and Delete removes a saved one (it is disabled for built-in schemes). Edit Element Colors… opens the Color Scheme Editor. Color Schemes covers both.
Electrons
The tab has one block for lone pairs and a matching block for radicals.
| Setting | What it does | Range (default) |
|---|---|---|
| Visible | Shows or hides all lone pairs (or radicals) in the document | Checkbox (on) |
| Representation | Drawing style for each electron pair or unpaired electron | Dots, Lines or Lobes (Dots) |
| Size | Dot size or line thickness | 0.5-4 px (1.5; 1.2 in Compact) |
| Dot Spacing | Gap between the two dots of a pair (lone pairs only) | 1-5 px (2) |
| Distance | Distance from the atom | 1-12 px (5) |
| Color Mode | Color source: the bond color, the atom’s element color, or Custom Color | Bond, Element or Custom (Element) |
| Custom Color | Color used when Color Mode is Custom | Black |
Charges
Defaults for charges.
| Setting | What it does | Range (default) |
|---|---|---|
| Style | Plain superscript sign, or a sign inside a circle | Superscript or Circle (Superscript) |
| Size | Scale relative to the atom label. The readout says px, but the value is a factor. | 0.5-1.5 (0.85; 1 in Compact) |
| Default Position | Where charges sit around the label | Auto, Top Right, Top Left, Top Center, Bottom Right, Bottom Left, Bottom Center (Auto) |
| Fine Tune X / Fine Tune Y | Small nudge applied to every charge | -3 to 3 px (0) |
Geometry
| Setting | What it does | Range (default) |
|---|---|---|
| Default Bond Length | The same setting as Bond Length on the Bonds tab; changing one moves the other | 15-80 px (40) |
| Label Clearance | Gap bonds leave around an atom label | 1-8 px (3; 1.3 in Compact, 2.1 in Textbook) |
| Arrow Length (Dative Bond Arrow) | Length of the arrowhead on a dative bond | 3-12 px (6) |
| Arrow Width (Dative Bond Arrow) | Width of that arrowhead | 1.5-5 px (2.5) |
Projections
Defaults for new projections. Existing projections keep their own values.
Fischer Projection Defaults
| Setting | Range (default) |
|---|---|
| Vertical Spacing | 10-80 px (40) |
| Arm Length | 10-80 px (40) |
| Crossing Style | Break or Continuous (Continuous) |
| Show Center Labels | Checkbox (off) |
| Show R/S Labels | Checkbox (on) |
Newman Projection Defaults
| Setting | Range (default) |
|---|---|
| Circle Radius | 8-50 px (25) |
| Bond Length | 10-60 px (40) |
| Show Center Dot | Checkbox (off) |
| Show Dihedral Angle | Checkbox (off) |
| Show Conformation Label | Checkbox (on) |
| Back Bond Style | Truncated or Full (Truncated) |
Orbitals
Lobe clipping and phase colors for the orbital tool.
| Setting | What it does | Range (default) |
|---|---|---|
| Clip at Label | Stops lobes short of atom labels | Checkbox (on) |
| Clip Padding | Extra space between a lobe and the label it stops at; negative values let the lobe overlap the label | -2 to 8 (1.5) |
| Truncate at Intersections | Ends lobe outlines where same-atom lobes cross. Applies to outlined lobes only; tilted orbitals are drawn untruncated. | Checkbox (on) |
| Phase Colors | Color (blue / red) phase lobes, or Monochrome (B/W print): positive lobes shaded gray, negative lobes open | Color (blue / red) |
Truncate at Intersections is the control for lobes that overlap on the same atom.
Structure menu shortcuts
Several items under Structure > Display switch the same document settings as this dialog, so you can flip them without opening it. The check mark in the menu and the control in the dialog always agree.
| Structure > Display item | Same setting as |
|---|---|
| Aromatic Display: Kekulé / Circle | Bonds > Display Mode |
| Show Lone Pairs | Electrons > Lone Pairs > Visible |
| Show Radicals | Electrons > Radicals > Visible |
| Bond Colors by Element | Bonds > Color by Element (the menu toggle does not show the Individual Settings Found prompt) |
| Show Carbon Labels | Atoms > Show Carbon Labels |
| Show Implicit Hydrogens | Atoms > Show Implicit Hydrogens |
| Auto-Clear Orbitals from Labels | Orbitals > Clip at Label |
Two more document display settings live only in the Structure menu. Show Orbitals (on by default) shows or hides every orbital lobe, and Show Validation Warnings (on by default in all three presets) controls the validation markers on the canvas. The Structure Menu reference lists every item.