protein-tools-mcp

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rmsf_peaks

Extract flexible residues and atoms from a GROMACS RMSF .xvg file by finding top-N values and contiguous segments above mean plus one standard deviation.

Instructions

Extract the most flexible residues/atoms from a GROMACS RMSF .xvg file: top-N highest values and contiguous flexible segments (above mean + 1 stdev).

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "xvg_path": "<xvg_path>"
    },
    "name": "rmsf_peaks"
  }
}

Input Schema

Name	Required	Description	Default
`top_n`	No
`xvg_path`	Yes

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Oct 20, 2026

TDQS

A4/5.0

Behavior3/5

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

No annotations exist, so the description carries the full behavioral burden. It usefully discloses the computation criteria (top-N, mean + 1 stdev) and the required input format, but says nothing about failure modes for malformed/non-RMSF files, whether it is a read-only analysis, or units/atom selection semantics.

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?

A single front-loaded sentence delivering purpose, input type, and selection criteria with no filler; the parenthetical scoping is terse and informative.

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?

An output schema exists, so return structure need not be explained. For a two-parameter analysis tool the description covers what it extracts and how, leaving only edge-case/error behavior and default handling unstated.

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

Parameters4/5

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

With 0% schema description coverage, the prose does compensate: it clarifies that xvg_path must be a GROMACS RMSF .xvg file and that top_n controls the 'top-N highest values' cutoff. It stops short of stating the default (10) or whether top_n=0 means all, but adds real meaning beyond the bare schema titles.

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?

States a specific verb (Extract), a specific resource (most flexible residues/atoms), and even the selection algorithm (top-N plus contiguous segments above mean + 1 stdev). This clearly separates it from generic siblings like xvg_summary, rmsd_summary, and plot_xvg.

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 implied by the 'GROMACS RMSF .xvg' input and the flexible-residue extraction goal, but the description never states when to prefer this over xvg_summary or plot_xvg, nor any prerequisites (e.g. the file must actually be an RMSF profile).

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