Rosetta MCP Server

Author: Ariel J. Ben-Sasson

A Model Context Protocol (MCP) server that lets Cursor (or any MCP client) work with Rosetta, PyRosetta, and Biotite: run RosettaScripts, validate XML protocols, translate between Rosetta and Biotite, score structures, and query documentation -- all from your AI coding assistant.

What's new in v1.3.0 (vs v1.1.8 on npm)

New: Biotite integration

• `rosetta_to_biotite` -- Find the Biotite equivalent of any Rosetta function with working example code (21 mappings covering structure I/O, SASA, RMSD, superimposition, secondary structure, contacts, hydrogen bonds, B-factors, angles, and more)
• `biotite_to_rosetta` -- Reverse lookup: find the Rosetta equivalent of a Biotite function
• `translate_rosetta_script_to_biotite` -- Translate entire RosettaScripts XML or PyRosetta code to Biotite Python. Design/optimization operations are flagged as Rosetta-only.
• Fuzzy search with keyword aliases ("contacts", "binding energy", "surface area", "align", etc.)

Improved: XML to PyRosetta translator

• 37 element types supported (was 6): 11 movers, 9 filters, 10 selectors, 7 task operations
• Full attribute handling: `repeats`, `disable_design`, `cartesian`, `tolerance`, `threshold`, `distance`, and more
• Child element support: `MoveMap` (with `Span`), `Reweight`, `ScoreFunction`
• Reports unrecognized elements so you know what needs manual work

Improved: Help and documentation

• `get_rosetta_help` now accepts any topic: movers by name ("FastRelax"), concepts ("constraints", "docking"), or score functions ("ref2015") -- auto-fetches live docs from rosettacommons.org
• `search_rosetta_web_docs` fallback: when DuckDuckGo is rate-limited, probes direct Rosetta docs URLs
• `get_cached_docs` auto-caches: no need to call `cache_cli_docs` first
• Expanded static help for score_functions, movers, filters, xml, and parameters

Improved: Scoring

• `pyrosetta_score`: new `per_residue` option returns per-residue energy breakdown
• `scorefxn` parameter now works (was ignored in v1.1.8)
• Proper error messages for missing files instead of silent `{}`

Improved: Validation

• `validate_xml`: new `validate_against_schema` option checks element names against the Rosetta XSD schema (catches typos like `FastRleax`)

MCP spec compliance fixes

• `tools/call` responses now use correct `{ content: [{ type: "text", text }] }` format
• Tool errors return `isError: true` (not JSON-RPC errors)
• Standard JSON-RPC error codes (-32601, -32700, -32603)
• Removed false `resources` capability advertisement

Security fixes

• User input no longer interpolated into Python code (uses env vars / stdin)
• Temp files written to `os.tmpdir()` (not module directory)

Cleanup

• Removed 3 redundant tools: `list_functions` (merged into `get_rosetta_info`), `search_pyrosetta_wheels`, `cache_cli_docs` (auto-cache in `get_cached_docs`)
• Removed hardcoded personal paths
• Fixed shadowed variables, async anti-patterns, dead code
• 18 tools (was 21), all with improved agent-oriented descriptions

Example: asking a naive question

This is what makes the MCP server powerful -- an AI agent can answer domain questions by calling the right tools automatically:

User asks in Cursor: *"How do I relax my protein and what's the Biotite equivalent?"*

The agent calls two MCP tools behind the scenes:

1. `get_rosetta_help("FastRelax")` returns 6000+ chars of live documentation:

> FastRelax performs all-atom relaxation using the FastRelax protocol. Parameters include `scorefxn`, `repeats`, `cartesian`, `disable_design`, `MoveMap` configuration...

2. `rosetta_to_biotite("FastRelax")` returns:

{
  "found": true,
  "results": [{
    "rosetta": { "name": "FastRelax", "example": ["relax = FastRelax()", "relax.set_scorefxn(get_score_function('ref2015'))", "relax.apply(pose)"] },
    "biotite": null,
    "equivalence": "none_from_biotite",
    "notes": "Biotite does NOT perform structure optimization. These are Rosetta-specific capabilities."
  }]
}

The agent synthesizes: *"FastRelax is Rosetta's all-atom relaxation protocol. Here's how to use it... Note: Biotite is analysis-only and has no equivalent -- you need PyRosetta for structure optimization."*

Without the MCP, the agent would guess from training data and likely get parameter names or API signatures wrong.

What you get (18 tools)

Discovery & Help

Documentation

Execution & Scoring

Translation

Validation & Schema

Environment

Quick start

1. Install from npm

npm install -g rosetta-mcp-server

2. Set up Python environment

# Create a venv with PyRosetta and Biotite
uv venv ~/.venvs/rosetta-mcp
~/.venvs/rosetta-mcp/bin/pip install pyrosetta-installer biotite
~/.venvs/rosetta-mcp/bin/python -c "import pyrosetta_installer as I; I.install_pyrosetta()"

Or skip this step -- PyRosetta auto-installs on first use (takes 10-30 min).

3. Configure your MCP client

Cursor (`~/.cursor/mcp.json`):

{
  "mcpServers": {
    "rosetta": {
      "command": "rosetta-mcp-server",
      "args": [],
      "env": {
        "ROSETTA_BIN": "/path/to/rosetta_scripts.default.macosclangrelease",
        "PYTHON_BIN": "/path/to/.venvs/rosetta-mcp/bin/python"
      }
    }
  }
}

Claude Desktop (`~/Library/Application Support/Claude/claude_desktop_config.json`):

{
  "mcpServers": {
    "rosetta": {
      "command": "rosetta-mcp-server",
      "env": {
        "ROSETTA_BIN": "/path/to/rosetta_scripts.default.macosclangrelease",
        "PYTHON_BIN": "/path/to/.venvs/rosetta-mcp/bin/python"
      }
    }
  }
}

Environment variables:

4. Restart your editor

Open Settings -> MCP. The "rosetta" server should appear green with 18 tools.

XML to PyRosetta translation example

Input XML:

// Code block

Generated PyRosetta code:

import pyrosetta
from pyrosetta import pose_from_pdb
from pyrosetta.rosetta.core.scoring import get_score_function
from pyrosetta.rosetta.core.select.residue_selector import *
from pyrosetta.rosetta.protocols.relax import *

pyrosetta.init("-mute all")

pose = pose_from_pdb("your_protein.pdb")

# Residue Selectors
chainSelector = ChainSelector()
chainSelector.set_chain_strings("A")

# Movers
fastRelax = FastRelax()
fastRelax.set_scorefxn(get_score_function("ref"))
fastRelax.set_default_repeats(5)
fastRelax.cartesian(True)

sfxn = get_score_function("ref2015")

# Apply movers
fastRelax.apply(pose)

pose.dump_pdb("output.pdb")
score = pose.energies().total_energy()
print(f"Final score: {score}")

Rosetta Biotite mapping coverage

Troubleshooting

• Server shows red in Cursor: Restart Cursor. Use absolute path in config (e.g., `/opt/homebrew/bin/rosetta-mcp-server`). Ensure Node 14+ and Python 3.8+.
• `run_rosetta_scripts` fails: Verify `ROSETTA_BIN` points to a valid binary. Try `"$ROSETTA_BIN" -help`.
• PyRosetta tools say "not available": Install via `pip install pyrosetta-installer` then run the installer, or let the MCP server auto-install on first use.
• Biotite tools return no results: Install Biotite in the same Python env: `pip install biotite`
• `get_rosetta_help` returns "No detailed help": Try the exact Rosetta class name (e.g., "FastRelax" not "relax"). The tool resolves common aliases but may miss unusual names.

Verify from the command line

# Check version
echo '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2024-11-05"}}' | rosetta-mcp-server 2>/dev/null | python3 -c "import sys,json; print(json.loads(sys.stdin.readline())['result']['serverInfo'])"

# List all tools
echo '{"jsonrpc":"2.0","id":1,"method":"tools/list","params":{}}' | rosetta-mcp-server 2>/dev/null | python3 -c "import sys,json; [print(t['name']) for t in json.loads(sys.stdin.readline())['result']['tools']]"

Development

rosetta-mcp-server/
├── rosetta_mcp_wrapper.js   # Node MCP server (protocol + all 18 tools)
├── rosetta_mcp_server.py    # Python helper (static Rosetta data)
├── install_pyrosetta.js     # Standalone PyRosetta installer
├── package.json             # npm package config
└── README.md

License and attribution

• MIT for this repository
• Rosetta/PyRosetta: see RosettaCommons licenses; commercial use requires the appropriate license
• Biotite: BSD 3-Clause license