Rosetta Context

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)

- 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.)

- 37 element typessupported (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(withSpan),Reweight,ScoreFunction
- Reports unrecognized elements so you know what needs manual work

- get_rosetta_helpnow accepts any topic: movers by name ("FastRelax"), concepts ("constraints", "docking"), or score functions ("ref2015") -- auto-fetches live docs from rosettacommons.org
- search_rosetta_web_docsfallback: when DuckDuckGo is rate-limited, probes direct Rosetta docs URLs
- get_cached_docsauto-caches: no need to callcache_cli_docsfirst
- Expanded static help for score_functions, movers, filters, xml, and parameters

- pyrosetta_score: newper_residueoption returns per-residue energy breakdown
- scorefxnparameternow works (was ignored in v1.1.8)
- Proper error messages for missing files instead of silent{}

- validate_xml: newvalidate_against_schemaoption checks element names against the Rosetta XSD schema (catches typos likeFastRleax)

- tools/callresponses now use correct{ content: [{ type: "text", text }] }format
- Tool errors returnisError: true(not JSON-RPC errors)
- Standard JSON-RPC error codes (-32601, -32700, -32603)
- Removed falseresourcescapability advertisement

- User input no longer interpolated into Python code (uses env vars / stdin)
- Temp files written toos.tmpdir()(not module directory)

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

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 includescorefxn,repeats,cartesian,disable_design,MoveMapconfiguration...

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.

# 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).

{ "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" } } } }

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

<ROSETTASCRIPTS> <SCOREFXNS> <ScoreFunction name="ref" weights="ref2015"/> </SCOREFXNS> <RESIDUE_SELECTORS> <Chain name="chainA" chains="A"/> </RESIDUE_SELECTORS> <MOVERS> <FastRelax name="relax" scorefxn="ref" repeats="5" cartesian="true"/> </MOVERS> <PROTOCOLS> <Add mover="relax"/> </PROTOCOLS> </ROSETTASCRIPTS>

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

- 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_scriptsfails: VerifyROSETTA_BINpoints to a valid binary. Try"$ROSETTA_BIN" -help.
- PyRosetta tools say "not available": Install viapip install pyrosetta-installerthen 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_helpreturns "No detailed help": Try the exact Rosetta class name (e.g., "FastRelax" not "relax"). The tool resolves common aliases but may miss unusual names.

# 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']]"

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

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