Object Properties Panel
Select an oxygen atom in ethanol and a panel opens on the right, titled “Atom · Oxygen”. This is the Object Properties panel. It appears whenever you select atoms, bonds, lone pairs, radicals or orbitals, and its title names what you picked: “Bonds ×3” for three bonds, “Objects ×5” for a mixed selection. Changes made here apply only to the selected objects. Document-wide defaults live in the Structure Settings dialog, and the bond controls 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. The per-object override is cleared and the object falls back to the document default.
When the selected objects disagree on a value, the control reads “Mixed” and checkboxes show an indeterminate state. Editing the control applies the new value to every selected object at once.
Only the sections that apply to the current selection are visible, and 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 offers only the weights the current font 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 |
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, and 0 turns it off. The slider appears only when a foreign bond runs close enough to a selected label to matter.
The Aux Pos row likewise only appears when the atom has auxiliary text to position.
Molecule
Select one whole molecule (drag a box around all of water, for example) and a MOLECULE section appears below Atom Label with a Show net dipole (μ) checkbox. Tick it to draw the dipole arrow; Color, Head size, Thickness and a Position ⟲ Reset button then appear for styling it. A partial selection, or one that spans two molecules, hides the section. Dipole explains how the arrow is computed.
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.
This section has no field for the charge value itself. To change the value, click the charge sign on the canvas with the Select or Charge tool. That opens a separate Charge panel whose Charge field accepts text such as +, -, 2+, 3-, or ++, and whose dropdown lists +, −, 2+, 2−, 3+, and 3−. A charge of 0 displays nothing, and the field ignores 0, 0+, and 0-. To make an atom neutral again, click its charge with the Eraser.
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.
Orbital Picture
Shown when the selection touches an orbital picture, and, while the hybridization tools are on, whenever atoms are selected.
The section starts with a Preset list and Save as… / Delete buttons for presets of your own, followed by the picture’s controls: Draw, Joined by, Far side, Pi system, Far lobes, Style, Ink (Colour or B & W), Spacing (Automatic, As drawn, Cozy, Roomy), Letter, Names, Pairs and Lock. Build draws a picture (it reads Redraw once there is one) and Remove takes it away. A note under the buttons says when there is no picture yet, when several pictures with different settings are selected (a change then applies to all of them), and when the orbital names do not fit at the current bond length.
Each control is explained on Orbital Pictures.
Orbitals
Selecting an orbital reveals the largest section in the panel. It covers orbital type (s, p, hybrids, d orbitals, pi overlap), label, lobe shape (Rounded, Petal, Teardrop, Egg, Ellipse) and dimensions, angle, Out of page (0 to 45 degrees), fill mode, render layer, opacity, phase colors, stroke, and a Delete Orbital button. The Orbital tool page covers the main controls.
Some rows appear only for certain selections:
| Row | Shown for | What it does |
|---|---|---|
| Round tip | Teardrop and Egg lobes | Rounds off the point, 0 (sharp) to 1 |
| At letter | Lobes other than s and dz² | Default, Start at its edge, Lines stop at it, or Run through it |
| Lock | Items an orbital picture drew | Keep when the picture is redrawn |
| Joined by | A selected bridge | Ribbon, Single line, or Dashed line for that pi bond |
A selected bridge or shared pair takes its shape from the orbitals it joins, so the type, angle and cloud sliders are hidden for it.
For the color swatches and reset buttons shared with the other panels, see Common Controls.