chimerax_run

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations provided, the description carries the full burden and does well by warning about arbitrary command execution including Python via 'runscript' and shell commands via 'shell', plus stating the return type. It does not elaborate on other potential side effects or state changes, but the security warning is valuable and goes beyond a basic read/write hint.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is compact and well-structured: a one-sentence purpose, a clear preference statement, a critical security note, and an Args/Returns block. Every sentence earns its place, with no redundancy or filler.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool's generic nature and the presence of an output schema, the description covers the core aspects: purpose, usage preference, security, parameter, and return value. It lacks explicit mention of prerequisites like a running ChimeraX session, but given sibling tools include chimerax_start and chimerax_status, this is a minor gap.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The input schema has zero parameter descriptions, but the tool description compensates thoroughly by explaining the 'command' parameter as 'The ChimeraX command to execute' with two illustrative examples. This adds essential meaning beyond the bare schema for the single string parameter.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states 'Execute a ChimeraX command through the MCP-managed REST connection' and provides concrete examples like 'open 1a0s' and 'color red'. This specific verb+resource combination distinguishes it from sibling tools that target narrower operations such as chimerax_open or chimerax_screenshot.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description explicitly says 'Prefer this tool over shelling out to ChimeraX for routine commands', offering clear usage context. However, it does not mention when to avoid this tool in favor of dedicated sibling tools (e.g., using chimerax_open for opening structures) or that a running session may be required, so exclusions are missing.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.