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seq_cescie_id_5a830e8e

Read-only

Retrieve residue-level sequence conservation data for a specified PDB entry ID and entity ID, with per-residue scores and amino-acid probability distributions.

Instructions

Returns residue-level sequence conservation data for a specified PDB entry ID and PDB entity ID, including per-residue conservation scores and amino-acid probability distributions.

Input Schema

TableJSON 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. Addedv1.1.10

TDQS

B3.2/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false and idempotentHint=false, so the read-only safety profile is covered. The description usefully discloses the return content (per-residue scores and probability distributions), which matters since there is no output schema, but says nothing about failure modes, entity validity, or data volume.

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 opening with the return verb and no filler; the content list is compact. It is slightly dense but every clause carries information.

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?

For a read-only, two-required-parameter retrieval tool with no output schema, the description covers what is retrieved and at what granularity (per residue, per entity). It omits error/edge-case behavior and sibling differentiation, but the core contract is intact.

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% for both parameters, so the schema already defines pdb_id and entity_id fully. The description merely restates them as 'PDB entry ID and PDB entity ID' without adding format, constraint, or validity meaning beyond the schema. Baseline 3 applies.

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 gives a specific verb ('Returns') and resource ('residue-level sequence conservation data') scoped to a PDB entry and entity, plus names the payload (per-residue conservation scores, amino-acid probability distributions). It is clear on its own, but never distinguishes itself from adjacent per-entity retrieval siblings such as sec_struct_ent or var_ent.

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

Usage Guidelines2/5

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

There is no when-to-use guidance, no statement of prerequisites or validity constraints (e.g., whether the entity must exist or be a polymer), and no pointer to alternatives. The agent must infer usage purely from the tool name and description.

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