Help

Troubleshooting

Common issues and how to fix them.
View as Markdown

Server not showing up

After editing ~/.cursor/mcp.json, you need to reload:

Cmd+Shift+P → Developer: Reload Window

For Claude Desktop, fully quit and reopen the app.

A missing comma or bracket will silently break the config. Paste your mcp.json into jsonlint.com to validate.

Common mistakes:

  • Trailing comma after the last entry
  • Missing closing brace }
  • Using single quotes instead of double quotes

If you used the one-line installer, verify the binary is in place:

$ls ~/.atoms/atoms-mcp

If not, re-run the installer:

$curl -fsSL https://raw.githubusercontent.com/smallest-inc/mcp-server/main/install.sh | bash

The npm method requires Node.js 18+. Check with:

$node --version

If not installed, download from nodejs.org, or use the one-line installer instead (no Node.js needed).

API key errors

Your ATOMS_API_KEY is either incorrect or has been revoked.

1

Go to the Atoms Console

Open console.smallest.ai → API Keys

2

Create a new key

Click Create API Key and copy it.

3

Update your config

Replace the old key in ~/.cursor/mcp.json or claude_desktop_config.json.

4

Reload

Reload Cursor (Cmd+Shift+P → Reload Window) or restart Claude Desktop.

Your API key is valid but isn’t linked to an organization. This usually means the account was just created. Ask your team admin to add you to the org.

Tools not being called

In Cursor, make sure you’re in Agent mode (not Ask mode). Ask mode is read-only and won’t trigger tools.

If the AI still doesn’t pick up the tools, be more explicit:

Use the atoms MCP to list my agents

Calls not going through

When using make_call, check these:

RequirementExample
Phone number in E.164 format+14155551234 (with + and country code)
Agent exists and is not archivedCheck with List all my agents
Org has a phone number assignedCheck with List all phone numbers

Still stuck?

Reach out to the Atoms team on your internal Slack channel or email support@smallest.ai.