Get started in 2 minutes

Install, point at your notes, explore. Your half-tagged vault is enough.

1. Install

Terminal
# Homebrew (recommended) $ brew install jshph/enzyme/enzyme
# Or via curl $ curl -fsSL enzyme.garden/install.sh | bash
â–¶ Don't have a markdown vault yet?

Enzyme works on markdown files—readable in any editor, portable across tools, yours forever.

  • → Obsidian — Already markdown. Point Enzyme at your vault.
  • → Kindle/Readwise — Export highlights from Readwise
  • → Voice memos — Transcribe with MacWhisper
  • → PDFs — Convert with docling
  • → Starting fresh — Create a folder, start capturing. Even 20-30 files is enough.

2. Initialize your vault

Navigate to your vault and run enzyme init. Enzyme analyzes your vault structure (recent captures, recurring tags, folder patterns) and builds a graph of how your thinking connects.

Terminal
$ cd ~/path/to/your/vault
$ enzyme init

What happens during init

  • 1 Structure reading — Enzyme scans your tags, links, and folders—including incomplete ones. Your half-finished system is treated as intent, not failure.
  • 2 Graph extraction — Entities and connections are mapped. Long notes become clusters; scattered captures reveal the threads between them.
  • 3 Catalysts surface — Questions, themes, insights emerge from your own words—the threads worth pulling.

This sends excerpts to AI for analysis. Your raw files stay local. See privacy for details. For a deeper look at Slates, Catalysts, and Entities, see the concepts documentation.

Providing your own guide

You can help Enzyme understand your vault by providing a guide — a short description of how you organize your thinking. This is especially useful for vaults with lots of structure, or if you want to steer the analysis toward certain areas.

Terminal
# Pipe a guide file
$ cat VAULT_GUIDE.md | enzyme init

# Or pass it directly
$ enzyme init --guide VAULT_GUIDE.md
â–¶ What to include in a vault guide

Write it however feels natural. A few sentences about:

  • Folder purposes — "inbox/ is quick captures, garden/ has evergreen notes"
  • Key tags — "I use #to-review for things I want to revisit"
  • Important people or concepts — wikilinks you reference often
  • What matters most — areas you want Enzyme to know about

This isn't a template. Just jot down how you think about your notes. Enzyme uses it as soft guidance, not strict requirements.

See example vault guides on GitHub →

3. Explore

Use Enzyme as an MCP server in Claude Code or any agentic coding tool.

Terminal
# Add Enzyme to Claude Code
$ claude mcp add enzyme --scope project enzyme-mcp

Try asking:

  • > hey what do you have going on in my vault today?
  • > help me come up with 10 writing prompts based on my thoughts on travel and paradox
  • > help me with wording in a product brief based on my Readwise annotations that describe my ideas about storytelling

Explore with voice

Want to wander through your thinking conversationally, from your phone, with voice? Push your graph to Enzyme's servers, then connect Claude.ai.

Terminal
$ enzyme push
→ Your connector URL: https://mcp.enzyme.garden/vault/abc123

Connect to Claude.ai

  1. 1. Go to Claude.ai → Settings → Connectors
  2. 2. Click Add custom connector, name it "Enzyme", paste your URL
  3. 3. Click Connect to authenticate
  4. 4. Under Configure → Tool permissions, set to "Always allow"

Now open Claude on your phone. Tap the voice button. Ask: "What have I been circling back to lately?"

Shared vaults

Using a vault that syncs with collaborators—via Obsidian Sync, iCloud, Dropbox, or git? Enzyme works on top of whatever sync you already use. You manage the markdown, we understand it.

We're collecting patterns for team workflows before writing the full guide.

Tell us how you collaborate

Quick reference

Command What it does
enzyme init Analyze vault, build graph, find your threads
enzyme push Sync to cloud for mobile/voice access
enzyme push --clear Delete cloud data

Questions

What formats work? ▼

Markdown files (.md), Obsidian vaults, and any folder of plain text. Apple Notes support is coming soon.

This is intentional. Markdown is the simplest thing that works—readable in any editor, portable across tools, durable across decades. No database, no proprietary sync, no lock-in. Your Readwise highlights, your quick captures, your evergreen notes—all just text files in folders.

For PDFs and other documents, use docling to convert to markdown first.

Do I need to organize first? ▼

No. Incomplete systems still remember. Your half-finished tags, your links that go nowhere—Enzyme treats them as intent, not failure. Even scattered captures reveal the threads between them. That's enough.

What gets sent to the cloud? ▼

During enzyme init, excerpts are sent to AI for analysis. Your raw files stay on your device.

If you run enzyme push, catalysts (distilled questions and insights) are synced to our servers for remote access. You can delete this data anytime with enzyme push --clear.

Go deeper

Inspect your slate
enzyme slate | jq '.slate_entities[] | .entity'

See what entities Enzyme found, check activity levels, explore catalysts
Understand catalysts

Questions tuned to what's latent in each cluster. They help you recognize which threads are yours—not by matching words, but by speaking to the same question.
Vault guide templates

Shell scripts to help describe your vault structure before running init