Configuration & Studio on Mol* Linker Wiki

Scene Settings

Mon, 01 Jan 0001 00:00:00 +0000

The Global Scene Settings panel controls the overall look of the Mol* viewer, independent of any particular molecule.

Canvas Background Color#

Sets the viewer background. Click the color swatch to open a color picker, or type a hex value directly (e.g. #111111 for dark mode).

The default is white (#ffffff). If you want a dark background without changing anything else, use the built-in Dark Mode Canvas preset from the popup.

Molecular Targets

Mon, 01 Jan 0001 00:00:00 +0000

The Global Target Configurations panel lets you set the default visual style for each class of molecule. Each target is a collapsible card.

Available Targets#

Target	Selector	Default Representation	Default Color
Proteins	`protein`	Cartoon	Chain ID
Nucleic Acids (DNA/RNA)	`nucleic`	Cartoon	Chain ID
Ligands & Small Molecules	`ligand`	Ball & Stick	Element symbol
Carbohydrates & Glycans	`branched`	Ball & Stick	Element symbol
Lipids	`lipid`	Ball & Stick	Element symbol
Single Ions	`ion`	Ball & Stick	Element symbol
Water / Solvent	`water`	Hidden (Off)	—
All Atoms	`all`	Ball & Stick	Element symbol

The all target is a catch-all that applies to every atom in the structure. It is useful as a fallback representation but is hidden by default. Enable it only when you want a uniform style applied across the entire structure regardless of molecule type.

Custom Rules

Mon, 01 Jan 0001 00:00:00 +0000

Custom rules let you target specific chains, residues, or atoms and apply a color override or a completely separate representation on top of (or instead of) the global target settings.

Click + Add New Rule at the bottom of the Custom Highlighting Rules panel to create one.

Rule Types#

Highlight (color overlay)#

Overlays a color on the existing representation without adding new geometry. Use this to call attention to a residue range or chain while keeping the surrounding context intact.