query_pdb_structure

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

With no annotations, the description fully carries the behavioral burden. It goes beyond a simple read operation by explaining how to interpret output fields (e.g., chain types, numbering gaps, structural breaks) and their practical implications (e.g., ligand chains cannot be relaxed with built-in presets). This is rich useful context, though it doesn't explicitly state that the tool is non-mutating, which is implied by 'Inspect'.

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 well-structured with headings (WHEN TO USE, WORKFLOW POSITION, OUTPUT — WHAT TO CHECK) and bullet points. It is longer than average, but each section earns its place by explaining workflow and output interpretation. The main purpose is front-loaded in the first sentence.

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?

Despite having an output schema, the description adds substantial interpretive value that the schema alone would not provide (e.g., what a structural break coinciding with a numbering gap means). It covers the tool's role in the workflow and gives the agent enough context to act on the results. For a query tool with this complexity, it is complete.

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?

Schema coverage is 100%: both input_pdb and notes have clear descriptions. The tool description does not add parameter-specific details beyond the schema, but none are needed since the schema already documents the parameters well. Baseline 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 opens with a specific verb and resource: 'Inspect a PDB file and return a detailed chain-level summary.' This clearly distinguishes it from sibling tools like fix_pdb_structure or relax_pdb_structure, which modify rather than inspect. The tool's role is unmistakable.

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?

Explicit guidance is provided: 'Always call this FIRST before any fixing or relaxation' and 'Step 1 of every session.' It also advises re-running after split_pdb for per-component details. This directly tells the agent when to use this tool versus alternatives, and even names alternatives in context.

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