Pymol FAQs

Question 1

What is PyMOL-MCP?

Accepted Answer

PyMOL-MCP is a tool that integrates PyMOL with Claude AI, enabling you to control PyMOL using natural language commands. It allows for conversational structural biology, simplifying molecular visualization and analysis.

Question 2

How do I install the PyMOL plugin?

Accepted Answer

In PyMOL, go to Plugin → Plugin Manager, select "Install New Plugin", and choose the `pymol-mcp-socket-plugin/__init__.py` file from the cloned repository.

Question 3

What can I do with PyMOL-MCP?

Accepted Answer

You can use PyMOL-MCP to load and visualize protein structures, color them by secondary structure, highlight active sites, perform structural alignments, calculate distances between residues, and save high-resolution images, all through simple conversational commands.

Question 4

Why isn't Claude connecting to PyMOL?

Accepted Answer

Verify the paths in your Claude configuration file (`claude_desktop_config.json`) are correct and that the PyMOL plugin is actively listening before attempting to connect from Claude. Also, ensure both are running on the same machine.

Question 5

What are the prerequisites for using PyMOL-MCP?

Accepted Answer

You need PyMOL, Claude for Desktop, Python 3.10 or newer, and Git installed on your system. You'll also need to install the required Python packages using pip.

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