select_chain · ChimeraX MCP Server MCP: Risk & Policy

WHAT IT DOES

What select_chain does on ChimeraX MCP Server

AI agents use select_chain 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_chain needs a policy

An AI agent can call select_chain 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.

Risk signalsBulk/mass operation — affects multiple targets

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

select_chain Rate-limited

select_chain 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_chain": {
      "limits": [
        {
          "counter": "select_chain_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_chain

What does the select_chain tool do? +

Select an entire chain. 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_chain? +

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

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

Can I rate-limit select_chain? +

Yes. Add a rate_limit block to the select_chain 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_chain completely? +

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

select_chain 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.