From pymol-skills
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.
How this skill is triggered — by the user, by Claude, or both
Slash command
/pymol-skills:pymol-mcpThe summary Claude sees in its skill listing — used to decide when to auto-load this skill
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.
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.
Use this skill when the user wants to:
Before using PyMOL commands, ensure:
Run /pymol-skills:setup for installation instructions.
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
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')
fetch 1ubqshow cartooncolor auto, allbg_color whitefetch 1ubq and fetch 1ubialign 1ubi, 1ubqcolor green, 1ubq and color cyan, 1ubiselect active, resi 45-50show sticks, activecolor yellow, activenpx claudepluginhub aeghnnsw/cc-toolkit --plugin pymol-skillsRun and analyze molecular dynamics simulations using OpenMM and MDAnalysis. Covers system setup, energy minimization, production MD, and trajectory analysis for structural biology.
Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis — setting up protein and small-molecule systems, assigning force fields, running energy minimization and production MD, and analyzing trajectories (RMSD, RMSF, contact maps, free energy surfaces).