Layer Management
Layers let you load multiple supported structure files into the same scene and control how each group appears. This is especially useful when cage-forming waters, guest molecules, and material slabs come from separate exports.
Common Layer Workflows
| Workflow | How to use layers |
|---|
| Water + guest occupancy | Upload the water/cage-forming file first, then add a guest structure layer. Run TRACE/GRADE on the water layer; visible non-water guest residues in other layers are collected as cross-layer guests. |
| Compare structures | Add reference and candidate structures as separate layers, then toggle visibility or adjust opacity. |
| Presentation styling | Keep background waters dim while highlighting selected guest, interface, or cage-adjacent molecules. |
Adding Layers
- Upload the primary structure file with UPLOAD STRUCTURE.
- Open the LAYERS tab.
- Use ADD LAYER to load another supported structure file.
- Toggle each layer’s visibility or select which layer should drive analysis.
On mobile, the scene appears above the control panel and the LAYERS tab is part of the horizontally scrollable tab strip.
Selecting the Analysis Layer
Cage, ring, GRADE, F3/F4, and occupancy analysis should run on the layer that contains cage-forming waters. If you click a guest-only layer for analysis, Clavis keeps or asks for a valid water layer rather than treating guest atoms as the hydrate water network.
For occupancy workflows:
- The selected analysis layer supplies the water network and cage geometry.
- Visible non-water guest residues from other layers are treated as candidate cross-layer guests, while metal/slab and geologic residues remain material categories.
- Cross-layer guests contribute to occupancy metrics, while their atoms remain visible through their own layer styling.
Per-Layer Settings
Each layer can carry its own visual settings:
| Setting | Description |
|---|
| Visible | Show or hide all atoms in the layer |
| Atom Color | Override default element coloring for that layer |
| Atom Size | Scale atom radius for the layer |
| Opacity | Make a layer solid, translucent, or dimmed |
.tpr topology metadata, so mixed systems can expose water, guest, metal/slab, and material residues without manual residue-name entry.
Residue channels can override the parent layer for:
- Visibility
- Atom scale
- Stick width
- Atom and stick opacity
- Color mode
- Render style
Layer-level settings remain the fallback for residues without an explicit override. Normal-size scene recovery preserves residue-channel overrides together with the rest of the layer session.
Per-layer styling is separate from analysis overlays such as cage wireframes and occupied guest highlights. You can hide cage wires while keeping occupied guest highlights visible, or dim a guest layer while still using it for occupancy assignment.
Session Recovery
Normal-size multi-layer scenes can recover from session-local browser storage after refresh or a quick navigation away from the app. Recovery includes layer visibility, settings, selected analysis layer, overlays, and camera view. Large streaming trajectories intentionally skip this recovery path because browser storage is not suitable for very large coordinate payloads.
Tips
- Name files clearly before upload so layer labels stay meaningful in the panel.
- Keep the water layer selected before running TRACE or GRADE.
- Hide or lower opacity on dense water layers when inspecting guest positions.
- Use occupied guest filters in the results/overlay controls when you need per-cage-type or structure-type guest visibility.
