pdb mcp for Zed

io.github.mrfentmen/pdb-mcp

RCSB PDB: search 230k+ structures, read chains, ligands, formulas and citations — keyless.

client:Zed transport:stdio runtime:npm

Install pdb mcp in Zed

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

{
  "context_servers": {
    "pdb-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "pdb-mcp"
      ]
    }
  }
}

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