Object Properties Panel
The Object Properties panel is the right-side dock labeled “Properties”. It appears whenever you select atoms, bonds, lone pairs, radicals, or orbitals, and gives you per-object overrides for everything from label color to radical dot spacing. Changes apply only to the selected objects; document-wide defaults live in the Structure Settings dialog. Bond controls (thickness, wedge settings, aromatic display, and more) have their own page: Bond Styling.
Opening and closing the panel
The panel opens automatically when you select an object with the Select tool and hides when the selection empties. You can also press P to open it while atoms, bonds, lone pairs, or radicals are selected; with nothing selected, P sets the active element to phosphorus instead.
The chevron in the panel header collapses it to a slim strip; click the header to expand it again. Both the panel collapse state and each section’s collapse state persist across sessions.
If a projection (Fischer, Newman, chair, and so on) is selected, the Projection Properties panel takes precedence and this panel stays hidden.
Shared behaviors
- Double-click any slider to reset it. This clears the per-object override and the object falls back to the document default.
- Mixed selections show “Mixed”. When selected objects have different values for a control, the value reads “Mixed” (checkboxes show an indeterminate state). Editing the control applies your new value to every selected object at once.
- Only sections relevant to the current selection are visible; each section header collapses independently.
Atom Label
Shown when any atom is selected.
| Control | What it does |
|---|---|
| Color | Overrides the label color (reset button returns to the scheme’s element color) |
| Show label | Toggles label visibility for the atom |
| Size | Font size, 8 to 32 px (default 14) |
| Weight | Font weight; the list only offers weights the current font actually renders distinctly |
| Clearance | Gap between the label and its bond ends, 0 to 8 (default 2.1) |
| Halo | Knockout padding around the label, 0 to 10 (default 2.1) |
| Aux Pos | Position of auxiliary text such as implicit H: Auto, Left, Right, Above, or Below |
About the halo: when a bond from a different molecule or layer passes behind a label, Molkit draws a canvas-colored rectangle behind the label so the foreign bond does not strike through the text. The Halo slider sets how far that mask extends past the label edges; 0 disables it. The slider only appears when a foreign bond actually runs close enough to a selected label to matter.
The Aux Pos row likewise only appears when the atom has auxiliary text to position.
Lone Pairs
Shown when lone pairs are selected (attached to atoms or as standalone annotations). See Lone Pairs for how to place them.
| Control | What it does |
|---|---|
| Style | Dots, Lines, or Lobes |
| Size | Dot or lobe size, 0.5 to 4 (default 1.5) |
| Spacing | Distance between the two dots (default 2) |
| Distance | How far the pair sits from the atom label (default 5) |
| Color | Standard, Element Color, or Custom; Custom adds a swatch plus a per-dot option for coloring each dot individually |
Standalone lone-pair annotations additionally expose Angle (0 to 360 degrees) and Opacity controls; atom-attached pairs hide these.
Radicals
Shown when radicals are selected. Controls mirror the Lone Pairs section (Style, Size, Spacing, Distance, Color with per-dot option) plus a Radial slider that nudges the dot toward or away from the atom in small steps. Spacing applies to biradicals. Standalone radical annotations also get Angle and Opacity. See Radicals.
Charges
Shown when a selected atom carries a formal charge.
| Control | What it does |
|---|---|
| Position | Auto or one of six fixed positions around the label; “Custom” appears (disabled) after you drag the charge manually |
| Style | Superscript or Circle, or inherit the global style |
| Color | Charge color with reset |
| Size | Scale factor 0.5 to 1.5 (default 0.85) |
Picking a named position clears any manual drag offset. See Charges.
Stereo Labels
Shown for selected atoms when stereo labels are enabled. The Label field is a free-text combo box with common descriptors (R, S, r, s, RS, E, Z, M, P, re, si) in the dropdown. Once a label is set, a style sub-section appears with Position (Auto plus eight placements), Color with reset, and Size (0.3 to 1.5, default 0.65). See Stereo Labels.
Atom Numbering
Shown for selected atoms when atom numbering is enabled. Enter a number (0 to 999) or clear it with the X button. Once a number is set, the style sub-section offers Position, Color with reset, Size (0.3 to 1.5, default 0.6), and a Font dropdown (Default, Arial, Times, Courier, Georgia, Verdana). See Atom Numbering.
Orbitals
Selecting an orbital reveals the largest section in the panel: roughly 25 controls covering orbital type (s, p, hybrids, d orbitals, pi overlap), label, lobe shape and dimensions, angle and tilt, fill mode, render layer, opacity, phase colors, stroke, and a Delete Orbital button. The Orbital tool page covers each control in detail.