# viz-protein-structure

`station__observatory__viz-protein-structure` · external (needs EXECUTION_BACKEND_URL configured) · domain `observatory` · pv-relevance `non-pv`

contact map, hydrogen bonds, radius of gyration, and aggregate metrics.

> **Note:** This tool routes through an external execution backend. If `EXECUTION_BACKEND_URL` is unset on the server, calls return JSON-RPC error `-32603 "Tool execution backend not configured"`. Tools with `backend: native` execute in-process and are always callable.

## Agent metadata

- `idempotent`: unknown
- `read_only`: unknown
- `expected_latency_ms`: unknown (not yet contract-tested)
- `cost_tokens_estimate`: unknown

## Input schema

- `contact_threshold` *number* — Distance threshold for contact map (CA–CA, default 8.0 Å).
- `hbond_cutoff` *number* — Distance cutoff for backbone H-bond detection (default 3.5 Å).
- `molecule_json` *string* (required) — JSON-serialized `nexcore_viz::molecular::Molecule`.

## Example call

```json
POST /api/mcp
Content-Type: application/json

{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "station__observatory__viz-protein-structure",
    "arguments": {
      "molecule_json": ""
    }
  }
}
```

## Related

- [/tools](/tools) — all 3062 tools
- [/tools/observatory__viz-protein-structure](/tools/observatory__viz-protein-structure) — HTML page
- [/tools/observatory__viz-protein-structure/json](/tools/observatory__viz-protein-structure/json) — JSON form (agent-friendly)
- [/api/mcp](/api/mcp) — endpoint
- [/AGENTS.md](/AGENTS.md) — agent guide