claudemol: PyMOL Skills for Claude Code

claudemol is a collection of specialized skills for Claude Code to interact usefully with pymol-open-sourcee. To talk to pymol it depends on a lightweight python library, pymol-agent-bridge.

It theoretically empowers Claude Code (or other agents) to do stuff in pymol. Pymol is a very versatile tool and the contents here are biased towards the subset of things with which I'm acquainted. Basically all of the skills here have been generated by coding agents. I've made an effort both to test them myself and to build tests for them, but use at your own risk. And please feel free to leave issues or contributions!

🛠️ Installation

1. Install the Plugin

In Claude Code, install the plugin

/plugin marketplace add ANaka/claudemol
/plugin install claudemol-skills

2. Run Setup

Ask Claude to run /pymol-setup. It will do the following:

1. Install pymol-agent-bridge — the Python library that connects your agent to PyMOL over a local socket. Recommend doing this in a virtual environment using uv, conda, poetry, venv, etc.
2. Add a pymol plugin to you ~/.pymolrc — puts a socket in PyMOL so it can hear your agent.
3. Verify the connection — confirms your agent can send commands to PyMOL

If you don't have pymol-open-source it can also help you install it.

Pairs well with protein-design-skills.

🧬 Available Skills

The plugin includes specialized skills for common structural biology workflows:

Visualization & Analysis

• pymol-fundamentals - Basic visualization, selections, coloring
• protein-structure-basics - Secondary structure, B-factor, representations
• binding-site-visualization - Protein-ligand interactions
• structure-alignment-analysis - Comparing and aligning structures
• antibody-visualization - CDR loops, epitopes, Fab structures
• publication-figures - High-quality figure export
• movie-creation - Animations and rotations
• miscellaneous - Additional patterns and utility commands
• pymol-setup - Guided configuration and troubleshooting

Protein Design

• rfd3 - RFdiffusion3 interactive config builder
• rfdiffusion-viz - RFdiffusion output inspection, trajectories, scaffold QC
• proteinmpnn-viz - ProteinMPNN/LigandMPNN sequence design visualization
• alphafold-validation - AlphaFold/ESMFold pLDDT coloring, self-consistency RMSD
• design-interface-analysis - Interface contacts, BSA, hotspots, H-bonds
• design-comparison - Batch ranking, before/after overlay, iteration tracking
• la-proteina-viz - La-Proteina config building, generation, and output visualization
• proteina-complexa-viz - Proteina-Complexa binder/ligand/AME pipeline setup and visualization

Design skills compose together for complete workflows:

RFdiffusion:          rfd3 → rfdiffusion-viz → proteinmpnn-viz → alphafold-validation → design-interface-analysis
La-Proteina:          la-proteina-viz → alphafold-validation → design-comparison
Proteina-Complexa:    proteina-complexa-viz → alphafold-validation → design-interface-analysis
Batch QC:             alphafold-validation + design-comparison

🙏 Acknowledgments

This project was originally forked from pymol-mcp by vrtejus and rewritten as a CLI tool pymol-agent-bridge. Also inspired by ChatMol. And of course, huge acknowledgement to the very wonderful PyMOL.

📜 License

MIT License - see LICENSE file for details.