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Visualization Controls

Clavis provides interactive 3D controls for atoms, cages, rings, H-bonds, guests, layers, and publication-oriented rendering.

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Camera Controls

Normal-size sessions save camera position and OrbitControls target in browser session recovery, so refresh/navigation restores the view angle as well as settings.

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Mobile Layout

On phone-size screens, the app prioritizes the 3D scene and places the control panel underneath it. Header actions collapse to icon buttons, tabs scroll horizontally, and the panel remains independently scrollable. This avoids the previous mobile pattern where menus and controls could visually overlap the active scene. On desktop, the left control panel uses a resizable desktop sidebar so repeated VIEW, ANALYZE, RESULTS, LAYERS, and RENDER work can claim more room without changing the mobile stacked layout.

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Atom Display

Use the VIEW tab to adjust atom size, bond width, opacity, color mode, and rendering style. Atoms can be shown as ball-and-stick, ball-only, stick-only, or hidden depending on the selected render mode.

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Cage and Ring Display

Toggle cage visibility with the C key or the cage controls. HTR ring and TRACE cage overlays can be filtered independently. Detected cage types use stable colors, including: See the Cage Types Reference for the full notation table.

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CHILL+ Display

Running CHILL+ recolors classified water oxygens and draws their O–O neighbor network. Use the result panel to isolate hydrate, ice, interfacial, or liquid classes and to adjust network width, opacity, and color. CHILL+ owns only the classified water presentation. Non-water residue channels remain visible and keep their own atom size, bond size, opacity, color, and render style. Toggling a residue such as SDS or NA does not disable CHILL+; hiding or changing the cage-forming water channel can make the current classification inapplicable and triggers truthful refresh guidance. See CHILL+ Classification for trajectory refresh and time-series behavior.

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Occupied Guest Highlights

When occupancy data is available, enable HIGHLIGHT OCCUPIED GUESTS to emphasize guest molecules assigned to detected cages. The control is independent from cage wireframe visibility, so you can hide cages while keeping occupied guests visible. Guest controls include:
  • Size scaling for guest atoms and guest bonds
  • Per-cage-type filtering, such as 5^12 or 5^12·6^2
  • Algorithm-owned occupied-cage filtering; native GRADE does not provide a crystal-structure bucket
  • Single-atom guest halo rendering and multi-atom guest ball-and-stick rendering
  • Neon halo/bond styling for cleaner contrast than the earlier warm highlight palette

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Hydrogen Bonds and PBC Box

  • Press H to show or hide H-bonds
  • Press B to show or hide the periodic boundary condition box
  • Press X to toggle the axes helper
H-bonds can remain visible with CHILL+ colors and its classified-water network. On supported trajectory frame changes, Clavis refreshes the H-bond geometry while preserving the visibility setting. See Hydrogen-Bond Visualization.

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Selection Tools

Use VIEW or SELECT mouse mode to switch between camera navigation and atom selection. Selection supports atom/residue units, click selection, box selection, and common shortcuts such as clear/invert/select all.