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outliers_val_outliers_all_id_b2720a4a

Read-only

Retrieve all MolProbity geometric and model-data outliers for a PDB ID, grouped by category with involved atoms/residues and per-residue outlier types.

Instructions

Lists all geometric and model–data outliers detected by MolProbity, grouped by category (e.g., clashes, sidechains, RSRZ, bond/angle outliers, RNA suite/pucker, chirality, planes, symmetry clashes). Atoms or residues involved in each outlier are reported using unit-id notation The types_of_outliers section summarizes, per residue, which types of outliers it participates in.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pdb_idYes4-character PDB id code. title: Pdb Id description: 4-character PDB id code.

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv1.1.10

TDQS

A3.5/5.0
Behavior3/5

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

Annotations declare readOnlyHint=true, destructiveHint=false, and idempotentHint=false. The description adds context about output structure (unit-id notation, types_of_outliers section) but does not disclose behavior beyond what annotations cover, such as result size or pagination. For a read-only listing tool, the annotations already carry the safety profile; the description adds modest value.

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?

Two sentences, front-loaded with the primary purpose, followed by output format detail. Some redundancy in the category enumeration, but overall efficient and well-structured.

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?

Given no output schema exists, the description helpfully explains the return structure (unit-id notation, types_of_outliers section). This compensates for the absent output schema. It is nearly complete for a read-only listing tool with a single documented parameter.

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 coverage is 100% and there is a single parameter (pdb_id) fully documented in the schema. The description adds no parameter-specific information, which is the baseline expectation when the schema does the heavy lifting.

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?

States a specific verb and resource: lists all geometric and model-data outliers from MolProbity, grouped by category. The enumerated categories (clashes, sidechains, RSRZ, etc.) make the scope concrete. Sibling tools are entirely different structural queries, but the description does not explicitly distinguish from them — though none of the siblings appear to overlap this function, so minimal differentiation is needed.

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?

No explicit when-to-use or when-not-to-use guidance. Usage is implied by the name and single required parameter (a PDB id). No alternatives are named, though none of the sibling tools serve the same outlier-listing purpose, so the risk of misuse is low.

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