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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.

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Common Layer Workflows

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Adding Layers

  1. Upload the primary structure file with UPLOAD STRUCTURE.
  2. Open the LAYERS tab.
  3. Use ADD LAYER to load another supported structure file.
  4. 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.

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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.

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Per-Layer Settings

Each layer can carry its own visual settings: When a layer contains multiple residue names, Clavis also creates Residue Channels inside the selected layer settings. These channels are generated from the loaded structure or native GROMACS .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.

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Residue channels with CHILL+

CHILL+ classification and class filtering belong to the cage-forming water network, not to every residue in the layer. Non-water residue changes are presentation-only: hiding SDS, NA, a guest, or a material channel does not clear CHILL+ colors or its network. Those residues also remain eligible for their own atom and bond sizing while CHILL+ is active. Changing or hiding the water channel is different because it changes the analyzed water set. In that case, Clavis refreshes the current-frame classification when possible or reports that the displayed frame no longer matches the analysis.

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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.

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Tips

  • Name files clearly before upload so layer labels stay meaningful in the panel.
  • Keep the water layer selected before running TRACE, HTR, 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 guest visibility.