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ebi-pdbe-chains_ent_chains_id_entity_id_200017f6

Read-only

Retrieve chain-level annotations for a PDB entity, including polymer chains, residue ranges, per-residue validation data, best chain ID, and author chain identifiers.

Instructions

Returns detailed chain-level annotations for a specified PDB Entity ID, including all of their polymer chains, their residue ranges, and per-residue validation information, along with metadata such as Best Chain ID and author-provided chain identifiers (Obs: chainId in additionalData response refers to struct_asym_id not the author-provided auth_asym_id).

Input Schema

NameRequiredDescriptionDefault
pdb_idYes4-character PDB id code. title: Pdb Id description: 4-character PDB id code.
entity_idYesEntity id (molecule number in mmcif-speak). type: string pattern: ^[0-9]+$ title: Entity Id description: Entity id (molecule number in mmcif-speak).

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv2.0.1

TDQS

A3.7/5.0
Behavior4/5

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

Annotations already cover the safety profile (readOnlyHint=true, destructiveHint=false), so the description adds genuine context: it discloses the response contents and flags an important interpretation trap, that chainId in additionalData is struct_asym_id rather than auth_asym_id. That identifier-semantics warning is real behavioral value beyond structured fields, though idempotency and error behavior are not addressed.

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

Conciseness4/5

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

A single front-loaded sentence states the return payload first, then appends the chainId caveat where it is most relevant. It is dense but every clause carries information; only the parenthetical could be split out for readability.

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

Completeness4/5

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

There is no output schema, so the description carries the burden of describing returns, and it does so with reasonable specificity (chains, residue ranges, validation, metadata, identifier caveat). Missing are failure modes and whether the result is nested per-chain, but for a two-parameter read tool this is close to complete.

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

Parameters3/5

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

Schema description coverage is 100%, with both pdb_id and entity_id documented in the schema, so the baseline is 3. The description restates that the tool keys on a PDB Entity ID but adds no format, range, or edge-case detail (e.g., what happens with an entity that has no polymer chains) beyond what the schema supplies.

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

Purpose4/5

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

The description uses a specific verb and resource ('Returns detailed chain-level annotations for a specified PDB Entity ID') and enumerates the payload (polymer chains, residue ranges, per-residue validation, Best Chain ID, author chain identifiers). This clearly distinguishes it in kind from entity-level siblings like sec_struct or bind_sites, though it never names or contrasts any of them.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

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

Usage is only implied by the stated scope: an agent can infer it applies when it needs chain-level rather than entity-level or residue-level data. There is no explicit when-to-use statement, no prerequisites, and no routing guidance versus the many other 'ent_*' entity tools.

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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