Skill

pymol-mcp

Control PyMOL molecular visualization software through natural language. This skill should be used when the user wants to visualize protein structures, create molecular representations, perform structural analysis, or generate publication-quality molecular images using PyMOL.

npx claudepluginhub aeghnnsw/cc-toolkit --plugin pymol-skills

Tool Access

This skill uses the workspace's default tool permissions.

Preview

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.

SKILL.md

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Last CommitMar 23, 2026

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PyMOL MCP Integration

Overview

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:

PyMOL is running with the socket plugin active
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

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

Compare Two Structures

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

Highlight Active Site

Select residues: select active, resi 45-50
Show as sticks: show sticks, active
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