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rcsb_get_branched_entity_instances

Read-onlyIdempotent

Fetch branched entity instances (glycan chains) from PDB using instance IDs. Returns entry, entity, and chain identifiers, with unknown IDs listed under not_found.

Instructions

Fetch branched entity instances (individual glycan chains), e.g. ["5FMB.C"].

Default fields: the entry/entity/chain identifiers.

Args: instance_ids: entry.asym_id (glycan chain), e.g. ["5FMB.C"]. Unknown IDs are returned under "not_found". fields: Optional GraphQL selection replacing the curated default (e.g. "rcsb_branched_entity_instance_container_identifiers.asym_id"); discover/verify paths with rcsb_describe_data_object("branched_entity_instances") (see the server instructions).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
fieldsNo
instance_idsYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior4/5

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

Annotations already cover read-only/idempotent/non-destructive behavior. The description adds valuable behavioral context by noting that unknown IDs are returned under 'not_found' and that default fields are entry/entity/chain identifiers. This goes beyond the annotations without contradicting them.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is compact and front-loaded. The first sentence states the purpose with an example, followed by default fields and clear parameter breakdowns. Every sentence contributes useful information with no redundancy.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool's simplicity, the annotations, and the presence of an output schema, the description adequately covers both parameters, default behavior, error handling, and points to a way to discover field paths. It is complete for selecting and invoking the tool correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The input schema has no descriptions (0% coverage), so the description must carry the full burden. It thoroughly explains instance_ids with format and example, and fields as an optional GraphQL selection with a concrete example and cross-reference to rcsb_describe_data_object. This fully compensates for the schema gap.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description uses the specific verb 'Fetch' with the resource 'branched entity instances', clarifying that these are 'individual glycan chains' and providing a concrete example. This clearly distinguishes it from sibling tools like rcsb_get_branched_entities, which fetches entities 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.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies when to use the tool (for retrieving specific glycan chain instances) through the term 'instances' and the example format. However, it does not explicitly mention alternatives or when not to use it, so it falls short of full guidance.

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

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