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Visualization Controls

Clavis provides extensive options for customizing the 3D visualization of your hydrate structures.

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Atom Display

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Size

Adjust the atom radius using the slider in the VISUAL tab. Atoms are rendered as spheres with element-specific default colors.

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Color Modes

• Element colors: Default CPK coloring (O = red, H = white, C = gray, etc.)
• Per-layer override: Each layer can define its own atom color scheme

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Opacity

Atom opacity can be adjusted from fully transparent (0) to fully opaque (1). Useful for seeing through outer layers to view internal cage structures.

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Cage Display

Toggle cage visibility with the C key or the cage toggle in the toolbar.

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Cage Rendering

Detected cages are rendered as translucent polyhedra. Each cage type has a distinct color: See the Cage Types Reference for the full color table.

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Cage Opacity

Cage transparency can be adjusted independently from atom opacity in the visual settings panel.

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Hydrogen Bonds

Toggle H-bond display with the H key. H-bonds are drawn as dashed lines between donor-acceptor pairs.

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PBC Box

Press B to show or hide the periodic boundary condition (PBC) box. The box represents the simulation cell boundaries.

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Axes

Press X to toggle the coordinate axes indicator showing the X (red), Y (green), and Z (blue) directions.

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Camera Controls