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

No annotations are provided, so the description must disclose behavioral traits. It mentions using the ChimeraX 'align' command, but it does not clarify whether this operation modifies the structure (e.g., moves atoms) or is read-only. This ambiguity could lead to unexpected side effects.

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 concise with two sentences, aliases, and an example. It is front-loaded with the core purpose, and every sentence adds necessary information without redundancy.

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 complexity of structural alignment, the description covers the core function but lacks details on side effects (e.g., whether coordinates are moved) and prerequisites. Since an output schema exists, return values are not required, but additional context about behavior would improve completeness.

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 schema has no descriptions for the two string parameters (spec, to_spec). The description adds value by providing an example with format '#1/A' and '#2/A', but it does not explicitly explain what each parameter represents or the expected selection syntax.

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 verb 'align' and resource 'one selection to another', and it reports RMSD. It provides aliases and an example, making the purpose unambiguous. It distinguishes itself from sibling tools like 'measure_distance' or 'find_contacts' which serve different functions.

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 implies usage for structural alignment and RMSD calculation, with an example demonstrating typical input patterns. However, it does not explicitly state when to use this tool versus alternatives or provide exclusions for specific scenarios.

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