run_pml

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

No annotations are provided, so the description carries the full burden. It does disclose the critical requirement (env var) and hints at 'raw' execution, but it does not explicitly warn about potential side effects, lack of safety checks, or that commands may modify the session state irreversibly.

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 extremely concise, consisting of a single sentence plus a requirement note. It front-loads the core purpose and avoids redundancy, making it easy to parse.

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 simplicity (one string parameter) and the presence of an output schema, the description adequately covers the essential opt-in requirement. However, for a raw code-execution tool, it could be more complete by mentioning side effects or typical error behavior, but this is not a critical 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 already provides 100% coverage for the single `command` parameter with a clear description. The tool description adds no additional parameter-level guidance, so the baseline of 3 is appropriate.

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 the action ('Execute') and the resource ('raw PyMOL command-language statements'). The term 'raw' helps distinguish it from more specific tools like run_python or render_image, and it identifies the input language precisely.

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 '[opt-in]' prefix and 'Requires PYMOL_MCP_ALLOW_CODE_EXEC=1' provide clear context on when the tool is available and what prerequisite must be met. However, it does not explicitly mention alternatives or scenarios where this tool should be avoided in favor of higher-level tool-specific commands.

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