add_hydrogen · ChimeraX MCP Server MCP: Risk & Policy

WHAT IT DOES

What add_hydrogen does on ChimeraX MCP Server

AI agents use add_hydrogen to create or update resources in ChimeraX MCP Server — usually the action step of a workflow, after the agent has gathered context. Every call changes real data in your ChimeraX MCP Server environment.

WHY IT NEEDS A POLICY

Why add_hydrogen needs a policy

The tool modifies the protein structure by adding hydrogen atoms, which is a reversible write operation. It does not delete data (which would be Destructive), execute arbitrary code (Execute), or involve financial transactions.

From the tool's definition Tool name 'add_hydrogen' and description 'Add hydrogens to the structure' indicate modification of molecular structure data. This is a reversible structural alteration (hydrogens can be removed), not an irreversible deletion.

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

add_hydrogen Rate-limited

add_hydrogen stays usable, but capped — an agent stuck in a loop can't make hundreds of changes a minute. Everything else on the server is denied unless you say otherwise.

View as policy code

policy.json

{
  "version": "1",
  "default": "deny",
  "tools": {
    "add_hydrogen": {
      "limits": [
        {
          "counter": "add_hydrogen_rate",
          "window": "minute",
          "max": 30,
          "scope": "grant"
        }
      ]
    }
  }
}

LIMIT THIS TOOL →

Instant setup, no code required.

PolicyLayer is an MCP gateway: every tool call is checked against your rule before it reaches ChimeraX MCP Server, so you can run agents against it safely.

FAQ

Questions about add_hydrogen

What does the add_hydrogen tool do? +

Add hydrogens to the structure. It is categorised as a Write tool in the ChimeraX MCP Server MCP Server, which means it can create or modify data. Consider rate limits to prevent runaway writes.

How do I enforce a policy on add_hydrogen? +

Register the ChimeraX MCP Server MCP server in PolicyLayer and add a rule for add_hydrogen: allow, deny, rate-limit, or require approval. Point your MCP client at the PolicyLayer proxy URL and the rule is enforced on every call, before it reaches ChimeraX MCP Server. Nothing to install.

What risk level is add_hydrogen? +

add_hydrogen is a Write tool with medium risk. Write tools should be rate-limited to prevent accidental bulk modifications.

Can I rate-limit add_hydrogen? +

Yes. Add a rate_limit block to the add_hydrogen rule in your PolicyLayer policy. For example, setting max: 10 and window: 60 limits the tool to 10 calls per minute. Rate limits are tracked per agent session and reset automatically.

How do I block add_hydrogen completely? +

Set action: deny in the PolicyLayer policy for add_hydrogen. The AI agent will receive a policy violation error and cannot call the tool. You can also include a reason field to explain why the tool is blocked.

What MCP server provides add_hydrogen? +

add_hydrogen is provided by the ChimeraX MCP Server MCP server (mahynotch/chimerax-mcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.