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Layer Management

Layers let you group atoms and apply independent visual settings to each group. This is useful for highlighting specific regions, guest molecules, or cage-forming waters.

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Creating Layers

  1. Open the LAYERS tab in the right panel
  2. Click Add Layer
  3. Name the layer (e.g., “Guest Molecules”, “Interface Waters”)

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Assigning Atoms to Layers

  1. Switch to Select mode by pressing S
  2. Click or drag-select atoms in the 3D view
  3. Use Ctrl/Cmd + A to select all, or I to invert selection
  4. In the LAYERS panel, click the target layer to assign selected atoms

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Per-Layer Settings

Each layer has independent visual settings that override global settings for its atoms:
SettingDescription
VisibleShow or hide all atoms in the layer
Atom ColorOverride the default element color
Atom SizeScale atom radius for this layer
OpacityLayer-specific transparency
Per-layer settings take priority over global visual settings. When a layer is selected, changes in the VISUAL tab apply only to that layer.

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Layer Priority

When an atom belongs to multiple layers, the settings from the most recently assigned layer take effect. The per-atom layerSettings property stores the active override.

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Tips

  • Use layers to dim background water while highlighting cage-forming molecules
  • Create a “Guest” layer with larger atom sizes to make guest molecules stand out
  • Temporarily hide layers to focus on specific structural features