protein-tools-mcp

Overview Schema Source Related Servers Discussions Admin

plot_xvg

Plot every series from a GROMACS .xvg file against column 0 into a PNG, decimating large datasets to 5000 points, and return the output path.

Instructions

Plot every series of a GROMACS .xvg file against column 0 into a PNG (large series are decimated to <=5000 points). Returns the output path.

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": "plot_xvg"
  }
}

Input Schema

Name	Required	Description	Default
`title`	No
`out_png`	No
`xvg_path`	Yes
`y_from_zero`	No

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Oct 20, 2026

TDQS

B3.1/5.0

Behavior3/5

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

With no annotations, the description carries the full behavioral burden. It does disclose one genuinely useful trait beyond the schema: large series are decimated to <=5000 points, i.e. the plot is downsampled. However, it omits where the PNG is written when out_png is left empty, what happens on malformed or multi-column data, and any error behavior.

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?

Two tight sentences with the core action front-loaded and the decimation caveat and return value following immediately. No filler and nothing redundant.

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 the description need not explain the returned path, and it still does so helpfully. But for a mutation-free plotting tool with four undocumented parameters and no annotations, it leaves meaningful gaps around output location defaults and the y_from_zero/title parameters.

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% across 4 parameters, so the description must compensate. It only obliquely covers out_png ('into a PNG') and says nothing about the default output path, what 'title' controls, or what y_from_zero does to the y-axis, leaving three of four parameters semantically unexplained.

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 ('Plot every series of a GROMACS .xvg file against column 0 into a PNG'), plus the output artifact, so an agent knows exactly what the tool produces. It implicitly separates itself from siblings like xvg_summary and compare_plot by describing a raw plotting operation, but never names or contrasts those alternatives explicitly.

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 (e.g., the file must be a valid .xvg with numeric columns), and no routing to alternatives such as xvg_summary for textual output or compare_plot for multi-run overlays. Usage is only inferable from the verb 'plot'.

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