rosetta-mcp-server — Claude Code MCP server: what it does
An MCP server that lets your coding assistant run RosettaScripts protocols, score protein structures, and map code between PyRosetta and Biotite.
claude mcp add --env ROSETTA_BIN=<ROSETTA_BIN> --env PYTHON_BIN=<PYTHON_BIN> --env MCP_DEBUG=<MCP_DEBUG> --transport stdio rosetta-mcp-server -- npx -y rosetta-mcp-serverWhat rosetta-mcp-server does
The server exposes 18 tools to the agent. They cover live help on movers and score functions pulled from rosettacommons.org, XML validation against the Rosetta schema, and execution of a protocol on a PDB file. A translator converts RosettaScripts XML into PyRosetta Python across 37 element types, handling attributes such as repeats, cartesian and threshold plus child elements like MoveMap and Reweight. Anything it cannot map gets listed so you know where to step in.
Biotite support works as a two-way lookup table for function equivalents, with examples, and can rewrite a whole script. Ask about design or structure optimisation and you get a plain answer: Biotite does not do that, you need PyRosetta. There are also checks for the environment: Python version, installed packages, whether PyRosetta is present, where the rosetta_scripts binary lives, and an installer for PyRosetta itself.
It will not run on a bare machine. You need a Python environment with PyRosetta and the Rosetta binary path in ROSETTA_BIN. The built-in installer takes 10-30 minutes, so do not start it right before a deadline.
What it helps with
- run a RosettaScripts protocol on a PDB from the chat
- convert a RosettaScripts XML into PyRosetta code
- find the Biotite counterpart of a Rosetta call
- catch a misspelled XML element before running
- get per-residue energy numbers for a structure
Example prompts for the agent
- How do I relax a protein with PyRosetta, and is there a Biotite equivalent?
- Validate
protocol.xmland list the elements you could not map - Run
rosetta_scriptsonmodel.pdband show per-residue energies
How to install rosetta-mcp-server
Platform CLI
claude mcp add --env ROSETTA_BIN=<ROSETTA_BIN> --env PYTHON_BIN=<PYTHON_BIN> --env MCP_DEBUG=<MCP_DEBUG> --transport stdio rosetta-mcp-server -- npx -y rosetta-mcp-serverReplace <…> with your own values
Platform CLI
codex mcp add rosetta-mcp-server --env ROSETTA_BIN=<ROSETTA_BIN> --env PYTHON_BIN=<PYTHON_BIN> --env MCP_DEBUG=<MCP_DEBUG> -- npx -y rosetta-mcp-serverReplace <…> with your own values
Config file
{
"mcpServers": {
"rosetta-mcp-server": {
"command": "npx",
"args": [
"-y",
"rosetta-mcp-server"
],
"env": {
"ROSETTA_BIN": "<ROSETTA_BIN>",
"PYTHON_BIN": "<PYTHON_BIN>",
"MCP_DEBUG": "<MCP_DEBUG>"
}
}
}
}Replace <…> with your own values
Config file
{
"servers": {
"rosetta-mcp-server": {
"type": "stdio",
"command": "npx",
"args": [
"-y",
"rosetta-mcp-server"
],
"env": {
"ROSETTA_BIN": "<ROSETTA_BIN>",
"PYTHON_BIN": "<PYTHON_BIN>",
"MCP_DEBUG": "<MCP_DEBUG>"
}
}
}
}Replace <…> with your own values
Platform CLI
gemini mcp add -e ROSETTA_BIN=<ROSETTA_BIN> -e PYTHON_BIN=<PYTHON_BIN> -e MCP_DEBUG=<MCP_DEBUG> rosetta-mcp-server npx -y rosetta-mcp-serverReplace <…> with your own values
Step by step, with commands for each platform: How to add an MCP server to Claude Code, Codex, Cursor, VS Code, Gemini CLI and more
Questions about rosetta-mcp-server
How do I install rosetta-mcp-server in Claude Code?
Run claude mcp add rosetta-mcp-server -- npx -y rosetta-mcp-server. To pass paths and debug flags, use `claude mcp add --env ROSETTA_BIN=<ROSETTA_BIN> --env PYTHON_BIN=<PYTHON_BIN> --env MCP_DEBUG=<MCP_DEBUG> --transport stdio rosetta-mcp-server -- npx -y rosetta-mcp-server`.
What does rosetta-mcp-server do?
It gives the assistant tools for Rosetta work: documentation lookup, XML protocol runs, structure scoring, schema validation, and translation of code to and from Biotite.
Do I need PyRosetta installed already?
For scoring and protocol runs, yes. The server can install PyRosetta for you, which takes 10-30 minutes, and the rosetta_scripts path goes into ROSETTA_BIN.
