protein-tools-mcp

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metal_geometry

Analyze metal-binding sites in PDB files: identify coordinating N/O/S ligand atoms, measure distances and angles, fit ideal geometries, and flag bidentate carboxylate chelates.

Instructions

Analyze metal-binding sites in a PDB file.

Finds all atoms of the given metal element (e.g. FE, ZN, MN, MG), lists coordinating ligand atoms (N/O/S donors) with distances and donor types, computes ligand-metal-ligand angles fitted to ideal geometries (octahedral, tetrahedral, ...), and flags bidentate carboxylate chelates.

Input Schema

TableJSON Schema

Name	Required	Default
`pdb_path`	Yes
`metal_element`	No	FE
`cutoff_angstrom`	No

Output Schema

TableJSON Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Oct 20, 2026

TDQS

B3/5.0

Behavior3/5

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

No annotations are provided, so the description carries the full burden. It does disclose the computational behavior (fits angles to ideal geometries, flags bidentate carboxylate chelates), but omits the safety profile, resource cost, and any preconditions; an output schema exists so most return detail is already covered elsewhere.

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?

Front-loads the core action in the first sentence, then enumerates the analysis steps compactly. No filler, though the multi-line formatting is slightly verbose for three parameters.

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

Completeness3/5

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

An output schema exists, so return values need not be explained, and the read-only nature is implied. The remaining gap is the undocumented cutoff_angstrom parameter and lack of routing against sibling metal tools, which is a real omission for an agent.

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

Parameters2/5

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

Schema description coverage is 0%, so the description must compensate. It explains metal_element well with examples (FE, ZN, MN, MG), but says nothing about cutoff_angstrom (the coordination-distance cutoff, default 3) and nothing about the required pdb_path format.

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 ('Analyze') and resource ('metal-binding sites in a PDB file') and elaborates the exact scope: metal atoms, coordinating ligands with distances/donor types, L-M-L angles, and chelate flagging. However, it never distinguishes itself from the very similar sibling 'query_metal_sites' or 'check_metal_params', so an agent cannot route between them from this text alone.

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/when-not-to-use guidance and no mention of alternatives, despite two close siblings (query_metal_sites, check_metal_params). Usage is only implied by the phrase 'in a PDB file'.

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