Rosetta Symmetry MCP server

The MCP server implements the Model Context Protocol (MCP) to facilitate seamless interaction between models and their context. This server allows you to define paths for Rosetta scripts, manage PDB files, and output directories while ensuring proper integration with Rosetta binary and database resources.

Environment Setup

Before using the MCP server, you'll need to set up your environment variables to point to your local Rosetta installation and relevant directories:

# Define Rosetta script path
export ROSETTA_SCRIPT_PATH="/path/to/mcp-rosetta/make_symmdef_file.pl"

# Define directories for PDB files and output
export PDB_DIR="/path/to/mcp-rosetta/pdb_files"
export OUTPUT_DIR="/path/to/mcp-rosetta/pdb_output_files"

# Set Rosetta binary and database paths
export ROSETTA_BIN_PATH=/path/to/rosetta-binary/main/source/bin
export ROSETTA_DB_PATH=/path/to/rosetta-binary/main/database

Configuration

Customizing Paths

Replace the example paths above with your actual file system locations. For example:

# Example for a user named 'john'
export ROSETTA_SCRIPT_PATH="/home/john/mcp-rosetta/make_symmdef_file.pl"
export PDB_DIR="/home/john/mcp-rosetta/pdb_files"
export OUTPUT_DIR="/home/john/mcp-rosetta/pdb_output_files"

Verifying Your Setup

To verify that your environment variables are set correctly, you can run:

echo $ROSETTA_SCRIPT_PATH
echo $PDB_DIR
echo $OUTPUT_DIR
echo $ROSETTA_BIN_PATH
echo $ROSETTA_DB_PATH

Using the MCP Server

Running Basic Operations

After setting up your environment, you can execute Rosetta commands through the MCP server. For example:

# Example of running a Rosetta script
$ROSETTA_BIN_PATH/rosetta_scripts.default.linuxgccrelease \
  -database $ROSETTA_DB_PATH \
  -in:file:s $PDB_DIR/your_protein.pdb \
  -out:file:o $OUTPUT_DIR/results.pdb

Working with PDB Files

Place your PDB files in the directory specified by $PDB_DIR to make them accessible to the MCP server:

# Copy a PDB file to your PDB directory
cp /path/to/your/protein.pdb $PDB_DIR/

Output files will be generated in the directory specified by $OUTPUT_DIR.

How to install this MCP server

For Claude Code

To add this MCP server to Claude Code, run this command in your terminal:

claude mcp add-json "mcp-rosetta" '{"command":"perl","args":["${env:ROSETTA_SCRIPT_PATH}"]}'

See the official Claude Code MCP documentation for more details.

For Cursor

There are two ways to add an MCP server to Cursor. The most common way is to add the server globally in the ~/.cursor/mcp.json file so that it is available in all of your projects.

If you only need the server in a single project, you can add it to the project instead by creating or adding it to the .cursor/mcp.json file.

Adding an MCP server to Cursor globally

To add a global MCP server go to Cursor Settings > Tools & Integrations and click "New MCP Server".

When you click that button the ~/.cursor/mcp.json file will be opened and you can add your server like this:

{
    "mcpServers": {
        "mcp-rosetta": {
            "command": "perl",
            "args": [
                "${env:ROSETTA_SCRIPT_PATH}"
            ]
        }
    }
}

Adding an MCP server to a project

To add an MCP server to a project you can create a new .cursor/mcp.json file or add it to the existing one. This will look exactly the same as the global MCP server example above.

How to use the MCP server

Once the server is installed, you might need to head back to Settings > MCP and click the refresh button.

The Cursor agent will then be able to see the available tools the added MCP server has available and will call them when it needs to.

You can also explicitly ask the agent to use the tool by mentioning the tool name and describing what the function does.

For Claude Desktop

To add this MCP server to Claude Desktop:

1. Find your configuration file:

• macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
• Windows: %APPDATA%\Claude\claude_desktop_config.json
• Linux: ~/.config/Claude/claude_desktop_config.json

2. Add this to your configuration file:

{
    "mcpServers": {
        "mcp-rosetta": {
            "command": "perl",
            "args": [
                "${env:ROSETTA_SCRIPT_PATH}"
            ]
        }
    }
}

3. Restart Claude Desktop for the changes to take effect