ebi-pdbe-compare_structures

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

Beyond the readOnly/openWorld/non-destructive annotations, the description discloses a crucial negative capability: the viewer applies PDBe's transforms and no additional fitting, RMSD, per-residue displacement or inferred binding sites are computed. That prevents an agent from promising analyses the tool does not perform, and the opt-in behavior of ligands/annotations is also spelled out.

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?

Four sentences, front-loaded with purpose then prerequisites then behavioral caveats, with no filler. The middle sentence about opt-in data and workspace controls is slightly dense but every clause carries actionable information.

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?

For an 8-parameter comparison tool with no output schema, the description covers inputs, prerequisites, what is rendered (PDBe/SIFTS correspondence, CSV export) and what is explicitly not computed. The only minor omission is guidance on what the returned correspondence structure looks like, though the CSV export mention partially covers output expectations.

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?

With 75% schema coverage the schema already documents chain IDs, segment_index and the two booleans; the description still adds meaning by framing include_ligands/include_annotations as opt-in supplied data and uniprot_accession/segment as conditionally required when mappings or segments are ambiguous. It does not add format or case-sensitivity detail beyond what the schema carries.

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 first sentence states a specific verb and resource ('Compare two protein label chains') and names the exact mechanism ('PDBe's precomputed superposition matrices and SIFTS residue correspondence'), which distinguishes it from neighboring tools like comp_intx_proteins or comp_similarity that operate on ligands or interactions rather than chain superposition.

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?

Prerequisites are stated plainly: a shared UniProt accession and a PDBe segment covering both chains, with the note that the aligned proteins are opened first and ligands/annotations must be opted into. It stops short of naming a sibling alternative or an explicit 'do not use this for X' exclusion, so it lands at a strong 4 rather than 5.

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