> ## Documentation Index
> Fetch the complete documentation index at: https://docs.claviscage.app/llms.txt
> Use this file to discover all available pages before exploring further.

# Hydrogen-Bond Visualization

> Inspect the frame-aware water hydrogen-bond network with periodic boundaries

# 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.

## 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.

## 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:

| Overlay            | Meaning                                                                   |
| ------------------ | ------------------------------------------------------------------------- |
| **H-bonds**        | Water–water interactions that satisfy the active geometric criteria       |
| **CHILL+ network** | O–O neighbor edges associated with the displayed CHILL+ structure classes |
| **TRACE cages**    | Closed cage topology detected from the water network                      |

## 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.

## Related Guides

* [CHILL+ Classification](/analysis/chill-plus)
* [HTR Analysis](/analysis/htr)
* [Exporting Data](/getting-started/export)