pymol-mcp

PyMOL MCP Integration

Overview

Control PyMOL molecular visualization software directly from Claude using the Model Context Protocol (MCP). Execute PyMOL commands, create visualizations, and perform structural analysis through natural language.

When to Use This Skill

Use this skill when the user wants to:

• Load and visualize protein/molecular structures (PDB, CIF, etc.)
• Create molecular representations (cartoon, surface, sticks, etc.)
• Color molecules by chain, secondary structure, or custom selections
• Perform structural alignments and superpositions
• Measure distances, angles, and dihedrals
• Generate publication-quality images

Prerequisites

Before using PyMOL commands, ensure:

1. PyMOL is running with the socket plugin active
2. The plugin shows "Listening on port 9876"

Run /pymol-skills:setup for installation instructions.

Available MCP Tools

pymol_command

Execute direct PyMOL commands using native syntax.

Examples:

fetch 1ubq              # Load structure from PDB
show cartoon, all       # Display as cartoon
color red, chain A      # Color chain A red
bg_color white          # Set white background
zoom all                # Zoom to fit all

pymol_python_api

Execute PyMOL Python API commands for complex operations.

Examples:

cmd.fetch('1ubq')
cmd.show('cartoon', 'all')
cmd.color('red', 'chain A')
cmd.align('mobile', 'target')
cmd.select('active_site', 'resi 50-100')

Common Workflows

Load and Visualize a Protein

1. Fetch structure: fetch 1ubq
2. Set representation: show cartoon
3. Color by chain: color auto, all
4. Set background: bg_color white

Compare Two Structures

1. Fetch both: fetch 1ubq and fetch 1ubi
2. Align: align 1ubi, 1ubq
3. Color differently: color green, 1ubq and color cyan, 1ubi

Highlight Active Site

1. Select residues: select active, resi 45-50
2. Show as sticks: show sticks, active
3. Color highlight: color yellow, active

Troubleshooting

• Connection refused: Start PyMOL socket plugin before using commands
• Command not recognized: Check PyMOL command syntax
• No output: Some commands don't produce visible output