Nanome Plugin for Claude Code

A Claude Code plugin for creating Nanome molecular visualization workspaces. Load structures from RCSB PDB, AlphaFold, PubChem, ChEMBL, SWISS-MODEL, and COD, organize them into scenes with custom visualizations, and get a shareable workspace URL.

What You Get

• nanome:nanome-auth -- Opens your browser to create an API key at mara.nanome.ai/settings and saves it automatically. No manual config needed.
• nanome:nanome-workspace -- High-level workspace builder. Describe what you want to visualize and it resolves structures, builds a scene with sensible defaults, and delivers a shareable workspace URL. Creates one focused scene by default; ask for multiple if needed.

Installation

claude --plugin-dir /path/to/nanome-plugin

Use /reload-plugins inside a session to pick up changes without restarting.

Requirements

• Python 3 and curl (for API calls and config management)
• A Nanome account (free to create)

Quick Start

Just ask Claude to create a workspace:

Create a Nanome workspace with PDB 1IEP

If you're not authenticated, the plugin will automatically open your browser and walk you through login. After that, the workspace is built and you get a URL like:

https://mara.nanome.ai/workspaces/abc123-...

Authentication

The plugin handles auth automatically. When no valid API key is found, the nanome-auth skill:

1. Opens your browser to mara.nanome.ai/settings
2. You log in, go to the System tab, and click Create under API Keys
3. The key is auto-copied to your clipboard
4. Paste it back in Claude -- it's saved to ~/.nanome/config.json

API keys are long-lived, so you rarely need to re-authenticate. To set up auth manually or re-authenticate, tell Claude:

set up nanome auth

Manual configuration

If you prefer to set up auth manually, create ~/.nanome/config.json:

{
  "api_base": "https://workspaces.nanome.ai",
  "token": "your-api-key-here"
}

Environment variables NANOME_API_BASE and NANOME_TOKEN override the config file.

Plugin Structure

nanome-plugin/
  .claude-plugin/
    plugin.json            # Plugin manifest
  skills/
    nanome-auth/
      SKILL.md             # Authentication skill
    nanome-workspace/
      SKILL.md             # Workspace creation skill
  README.md

Supported Structure Databases

Database	Identifier	Example
RCSB PDB	4-char PDB code	1HVR, 6LU7, 5CEO
AlphaFold	UniProt accession	P00533, Q9Y6K9
PubChem	CID number	2244 (aspirin)
ChEMBL	ChEMBL ID	CHEMBL25
SWISS-MODEL	UniProt accession	P00533

Visualization Capabilities

The workspace skill supports these visualization types:

• Ribbon/Cartoon -- secondary structure visualization
• Ball-and-stick -- atomic detail with bonds
• Molecular surface -- solvent-accessible surface with adjustable opacity
• Wire -- minimal bond representation
• Van der Waals -- space-filling spheres
• Residue labels -- text annotations
• Interactions -- hydrogen bonds, hydrophobic contacts, salt bridges, pi-stacking, and more

Coloring options include element type, chain, B-factor, secondary structure, residue type, and custom uniform colors.

License

MIT