Connect Your AI
Atlas connects to any AI tool that supports the Model Context Protocol (MCP). You build the model once, every tool gets structured context about your actual business.
Generate your API key
- In Atlas, click your email → Settings → API Keys
- Click + New App, name it (e.g., "Claude MCP")
- Click + New Key on your app
- Set: JWT Token, Full Access, Production, 90-day expiration
- Click Generate Token
This token is only shown once. Don't close this screen until you've pasted the config.
Click Copy Config. It copies the full MCP JSON with your token embedded.
Connect your tool
- Claude Desktop →
- Claude Code →
- Other MCP Clients →. Cursor, Windsurf, ChatGPT
What you get
Your AI gets access to 47 tools:
- Atlas, Points, Paths, Views, Folders: full CRUD on your data
- Analytics: PageRank, centrality, neighborhoods
- Graph Algorithms: communities, shortest path, similarity
- Cypher Queries: custom queries against your atlas
- Validation & Ontology: check types, browse the ontology
Token scopes
Full Access is recommended. For fine-grained control:
| Scope | What it allows |
|---|---|
read:atlases | View atlases |
write:atlases | Create/update atlases |
read:points, read:paths | View Points and Paths |
write:points, write:paths | Create/update Points and Paths |
delete:points, delete:paths | Remove Points and Paths |
use:llm | AI features (Navigator, extraction) |
use:embeddings | Semantic search |
Token management
- Expiration: tokens expire after the period you set (recommended: 90 days). Expired tokens return
401 Unauthorized. - Revoking: revoke anytime from Settings → API Keys. Takes effect immediately.
- Security: never commit tokens to git. Never share publicly. Rotate every 90 days.
Environment variables
| Variable | Required | Default | Description |
|---|---|---|---|
GRAPHITE_ACCESS_TOKEN | Yes | — | Your JWT token |
GRAPHITE_API_URL | No | https://graphiteatlas.com | API base URL |
Troubleshooting
"Could not load app settings: Unexpected non-whitespace character after JSON"
The config file has two separate { } blocks. JSON only allows one top-level object.
Open the file and look near the bottom — you'll see a second { starting a new block. You need to merge the "mcpServers" key inside the first object, not paste it after. See the merge example on the Claude Desktop setup page.
"Server disconnected" or "spawn npx ENOENT"
Node.js is not installed, or was just installed and needs a computer restart for the PATH to update.
Install from nodejs.org (LTS version), restart your computer, then try again.
Windows only: if Node is installed but this error persists, replace "command" and "args" in your config with:
"command": "cmd",
"args": ["/c", "npx", "-y", "@graphite-atlas/mcp-server"],
"Unauthorized" / 401
Token expired or revoked. Generate a new one in Settings → API Keys, update GRAPHITE_ACCESS_TOKEN in the config file, save, fully quit your AI tool, and reopen it.
"GRAPHITE_ACCESS_TOKEN required"
Config didn't paste correctly. Re-copy from Settings → API Keys using the Copy Config button.
"403 Forbidden"
Token doesn't have the required scope. Generate a new token with Full Access permissions.
Tools don't appear / AI doesn't see Atlas
You closed the window but didn't fully quit the app. On Mac: Cmd+Q or Claude menu → Quit. On Windows: system tray icon → Quit.
Still stuck? [email protected]