rcsb_get_nonpolymer_entity_instances

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

Annotations already declare this as readOnly, idempotent, openWorld, and non-destructive. The description goes beyond these hints by explaining the default return fields (entry/entity/chain identifiers, bound component id, author seq id), how unknown IDs are handled ('returned under not_found'), and the behavior of the 'fields' parameter as a GraphQL selection replacing the default. This is rich behavioral detail that complements the annotations without contradiction.

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: it leads with the primary action in the first sentence, then provides default field context, and ends with a clear Args section. Despite being informative, every sentence earns its place by adding either purpose, parameter meaning, or usage guidance. No waste or 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 that the tool has an output schema (covering return structure) and strong annotations (readOnly, idempotent, openWorld), the description adds exactly the needed context: default fields, error behavior, and how to customize output. It even references rcsb_describe_data_object for further schema discovery, making the description highly complete for an agent to invoke correctly.

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 provides zero descriptions, but the description fully compensates by explaining both parameters: instance_ids is defined as 'entry.asym_id' with an example and error handling, and fields is described as an optional GraphQL selection with an example path and a pointer to a discovery tool. This gives the agent complete semantic understanding of each 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 opens with a specific verb and resource: 'Fetch non-polymer entity instances (individual bound ligands)', backed by a concrete example ('4HHB.E'). This clearly identifies the tool's function and distinguishes it from sibling tools like rcsb_get_nonpolymer_entities, which fetch entity-level data rather than instances.

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 provides clear context for when to use the tool (to retrieve individual ligand instances) and what the default fields return. It also points users to rcsb_describe_data_object for verifying custom field paths, which is helpful guidance. However, it does not explicitly state exclusions or name alternative tools, stopping short of full when/when-not guidance.

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