Rosetta MCP Server

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:

<ROSETTASCRIPTS>

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

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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')"

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']"

Development

rosetta-mcp-server/

├── rosetta_mcp_wrapper.js # Node MCP server (protocol + all 18 tools) ├── rosetta_mcp_server.py # Python helper (static Rosetta data)