select_atoms · ChimeraX MCP Server MCP: Risk & Policy

WHAT IT DOES

What select_atoms does on ChimeraX MCP Server

AI agents use select_atoms 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 select_atoms needs a policy

An AI agent can call select_atoms faster than any human can review — one bad instruction and it creates or modifies resources in ChimeraX MCP Server by the hundred, each call as confident as the last.

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

select_atoms Rate-limited

select_atoms 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": {
    "select_atoms": {
      "limits": [
        {
          "counter": "select_atoms_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 select_atoms

What does the select_atoms tool do? +

Select atoms/residues by ChimeraX specifier string. 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 select_atoms? +

Register the ChimeraX MCP Server MCP server in PolicyLayer and add a rule for select_atoms: 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 select_atoms? +

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

Can I rate-limit select_atoms? +

Yes. Add a rate_limit block to the select_atoms 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 select_atoms completely? +

Set action: deny in the PolicyLayer policy for select_atoms. 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 select_atoms? +

select_atoms 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.