PyMOL-MCP

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Overview

Rosetta Symmetry is a project that integrates PyMOL, a molecular visualization tool, with Claude AI, enabling users to interact with and control PyMOL through natural language commands.

To use Rosetta Symmetry, install the necessary prerequisites, clone the repository, set up the environment, and configure Claude Desktop to connect with PyMOL. Once set up, you can start the connection and use natural language commands to manipulate molecular visualizations.

Two-way communication between Claude AI and PyMOL. - Intelligent command parsing for executing PyMOL commands via natural language. - Control over molecular visualizations, including representations and colors. - Structural analysis capabilities such as measurements and alignments. - Ability to execute arbitrary Python code in PyMOL from Claude.

Conversational control of molecular visualizations in PyMOL.
Performing structural biology analyses through natural language queries.
Enhancing educational experiences in molecular biology and chemistry.

Add to your AI client

Use these steps to connect PyMOL-MCP in Cursor, Claude, VS Code, and other MCP-compatible apps. The same JSON appears in the Use with menu above for one-click copy.

Cursor

Add this to your .cursor/mcp.json file in your project root, then restart Cursor.

.cursor/mcp.json

{
  "mcpServers": {
    "pymol-mcp-vrtejus": {
      "command": "/Users/ammachi/Developer/GitHub/MCP/mcp-rosetta/venv/bin/python",
      "args": [
        "/Users/ammachi/Developer/GitHub/MCP/mcp-rosetta/pymol_mcp_server.py"
      ]
    }
  }
}

Claude Desktop

Add this server entry to the mcpServers object in your Claude Desktop config, then restart the app.

~/Library/Application Support/Claude/claude_desktop_config.json (macOS) or %APPDATA%\Claude\claude_desktop_config.json (Windows)

{
  "mcpServers": {
    "pymol-mcp-vrtejus": {
      "command": "/Users/ammachi/Developer/GitHub/MCP/mcp-rosetta/venv/bin/python",
      "args": [
        "/Users/ammachi/Developer/GitHub/MCP/mcp-rosetta/pymol_mcp_server.py"
      ]
    }
  }
}

Claude Code

Add this to your project's .mcp.json file. Claude Code will detect it automatically.

.mcp.json (project root)

{
  "mcpServers": {
    "pymol-mcp-vrtejus": {
      "command": "/Users/ammachi/Developer/GitHub/MCP/mcp-rosetta/venv/bin/python",
      "args": [
        "/Users/ammachi/Developer/GitHub/MCP/mcp-rosetta/pymol_mcp_server.py"
      ]
    }
  }
}

VS Code (Copilot)

Add this to your .vscode/mcp.json file. Requires the GitHub Copilot extension with MCP support enabled.

.vscode/mcp.json

{
  "servers": {
    "pymol-mcp-vrtejus": {
      "type": "stdio",
      "command": "/Users/ammachi/Developer/GitHub/MCP/mcp-rosetta/venv/bin/python",
      "args": [
        "/Users/ammachi/Developer/GitHub/MCP/mcp-rosetta/pymol_mcp_server.py"
      ]
    }
  }
}

Windsurf

Add this to your Windsurf MCP config file, then restart Windsurf.

~/.codeium/windsurf/mcp_config.json

{
  "mcpServers": {
    "pymol-mcp-vrtejus": {
      "command": "/Users/ammachi/Developer/GitHub/MCP/mcp-rosetta/venv/bin/python",
      "args": [
        "/Users/ammachi/Developer/GitHub/MCP/mcp-rosetta/pymol_mcp_server.py"
      ]
    }
  }
}

Cline

Open Cline settings, navigate to MCP Servers, and add this server configuration.

Cline MCP Settings (via UI)

{
  "mcpServers": {
    "pymol-mcp-vrtejus": {
      "command": "/Users/ammachi/Developer/GitHub/MCP/mcp-rosetta/venv/bin/python",
      "args": [
        "/Users/ammachi/Developer/GitHub/MCP/mcp-rosetta/pymol_mcp_server.py"
      ]
    }
  }
}

FAQ

Can I use Rosetta Symmetry on any operating system?

Yes, as long as you have the prerequisites installed, it can run on macOS, Windows, and other platforms.

What are the prerequisites for using Rosetta Symmetry?

You need PyMOL, Claude for Desktop, Python 3.10 or newer, and Git installed on your system.

Is there a community for support?

Yes, you can join the Bio-MCP Community for troubleshooting and feedback.7:["$","div",null,{"className":"container mx-auto flex flex-col gap-4","children":["$L26","$L27",["$","$L28",null,{"currentProject":{"id":3825,"uuid":"74791205-dfee-41c1-96d6-ce7809328dec","name":"pymol-mcp","title":"PyMOL-MCP","description":"","avatar_url":"","created_at":"2025-03-21T21:19:43.440Z","updated_at":"2025-03-21T21:22:50.185Z","status":"created","author_name":"vrtejus","author_avatar_url":null,"tags":"rosetta-symmetry,molecular-visualization,AI-integration","category":"research-and-data","is_featured":false,"sort":1,"url":"https://github.com/vrtejus/pymol-mcp","target":"_self","content":"$29","summary":"$2a","img_url":null,"type":null,"metadata":null,"user_uuid":"5a26a51e-3742-42e1-b212-2a4947a9dd23","tools":null,"sse_url":null,"sse_provider":null,"sse_params":null,"is_official":false,"server_command":"/Users/ammachi/Developer/GitHub/MCP/mcp-rosetta/venv/bin/python /Users/ammachi/Developer/GitHub/MCP/mcp-rosetta/pymol_mcp_server.py","server_params":"{}","server_config":"{\n \"mcpServers\": {\n \"rosetta-symmetry\": {\n \"command\": \"/Users/ammachi/Developer/GitHub/MCP/mcp-rosetta/venv/bin/python\",\n \"args\": [\n \"/Users/ammachi/Developer/GitHub/MCP/mcp-rosetta/pymol_mcp_server.py\"\n ]\n }\n }\n}","allow_call":false,"is_innovation":false,"is_dxt":false,"dxt_manifest":null,"dxt_file_url":null,"is_audit":false},"randomProjects":[],"currentServerKey":"$undefined"}]]}]

Research and data