show_hydrophobicity_surface · ChimeraX MCP Server MCP

WHAT IT DOES

What show_hydrophobicity_surface does on ChimeraX MCP Server

AI agents invoke show_hydrophobicity_surface to trigger actions in ChimeraX MCP Server. What it does depends on the arguments the agent supplies, and its effects often reach beyond the immediate call — builds kicked off, notifications sent, workflows started.

WHY IT NEEDS A POLICY

Why show_hydrophobicity_surface needs a policy

This tool performs a computation (calculates MLP) and triggers a visualization rendering operation in ChimeraX. It runs an analysis and display pipeline rather than simply reading existing data or writing persistent data. The effects are session-state changes in the running ChimeraX application, which is consistent with Execute.

From the tool's definition Calculate and display Molecular Lipophilicity Potential on the surface

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

show_hydrophobicity_surface Rate-limited

show_hydrophobicity_surface stays usable, but rate-capped — a runaway agent can't fire it dozens of times a minute. Everything else on the server is denied unless you say otherwise.

View as policy code

policy.json

{
  "version": "1",
  "default": "deny",
  "tools": {
    "show_hydrophobicity_surface": {
      "limits": [
        {
          "counter": "show_hydrophobicity_surface_rate",
          "window": "minute",
          "max": 10,
          "scope": "grant"
        }
      ]
    }
  }
}

RATE-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 show_hydrophobicity_surface

What does the show_hydrophobicity_surface tool do? +

Calculate and display Molecular Lipophilicity Potential on the surface. It is categorised as a Execute tool in the ChimeraX MCP Server MCP Server, which means it can trigger actions or run processes. Use rate limits and argument validation.

How do I enforce a policy on show_hydrophobicity_surface? +

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

show_hydrophobicity_surface is a Execute tool with high risk. Execute tools should be rate-limited and have argument validation enabled.

Can I rate-limit show_hydrophobicity_surface? +

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

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

show_hydrophobicity_surface 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.