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Hydrogen-Bond Visualization

Clavis can display the water hydrogen-bond network as a frame-aware scene overlay. The network is used by cage and ring workflows and can also be inspected directly alongside atoms, cages, and CHILL+ classification.

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Controls

  • Press H or use SHOW H-BONDS to toggle the network.
  • Adjust the distance cutoff in the analysis controls.
  • Adjust line width and opacity in the visualization controls.
  • Use WRAP PBC when you want periodic-boundary-crossing geometry wrapped into the visible box.
The default distance cutoff is 3.5 Å (0.35 nm). Treat it as a starting point and choose criteria appropriate for the water model, pressure, temperature, and analysis convention used in your study.

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With CHILL+

CHILL+ and H-bonds are composable. Running CHILL+ builds the current-frame H-bond data needed by its result controls instead of clearing the H-bond overlay. Changing the H-bond cutoff refreshes the network without disabling CHILL+ class colors or its classified-water network. These overlays answer different questions:

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Trajectories and Export

On supported native GROMACS frame changes, Clavis refreshes H-bond geometry for the selected frame and preserves the user’s visibility intent. Standard and path-traced multi-frame exports prepare the active TRACE cage and H-bond overlays frame by frame. If a frame cannot be prepared, the export stops instead of silently reusing stale geometry. HTR ring and occupied-guest overlays do not currently have the same safe multi-frame refresh path. Hide those overlays before starting a multi-frame export when the app requests it.