xyz mcp for Zed

io.github.mrfentmen/xyz-mcp

XYZ MCP: parse molecules, validate atom counts, elements and coordinates.

client:Zed transport:stdio runtime:npm

Install xyz mcp in Zed

~/.config/zed/settings.json · windows: %APPDATA%\Zed\settings.json

{
  "context_servers": {
    "xyz-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@mrfentmen/xyz-mcp"
      ]
    }
  }
}

Merge this into your existing settings object — do not replace the file. Zed docs