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MCPymol

MCPymol

by chemrich
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Python
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util_color_secondary

Idempotent

Colors secondary structure elements in PyMOL to visually distinguish helices, sheets, and loops within a selected region or the entire structure.

Instructions

Colors secondary structure elements

Tool call template

This tool declares no required parameters. Add optional parameters from the input schema as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {},
    "name": "util_color_secondary"
  }
}

Input Schema

NameRequiredDescriptionDefault
selectionNoWhat to recolour. Defaults to everything.all

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changedv1.5.1
    • addedInput schema / properties / selection / description
      Added value: +"What to recolour. Defaults to everything."
  2. First observedv1.2.1

TDQS

C2.9/5.0
Behavior2/5

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

Annotations already state that the tool is not read-only, is idempotent, and is non-destructive, so the safety profile is covered. The description adds no further behavioral context about what recoloring entails, whether existing colors are replaced, or what color scheme is applied.

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?

The description is a single, front-loaded sentence with no wasted wording. It is concise, though its terseness leaves important context unstated rather than being overly verbose.

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?

The tool is simple with one optional parameter, annotations, and an output schema, so the description does not need to explain return values. However, in a crowded family of coloring utilities, it should say more about when this specific secondary-structure coloring tool is appropriate.

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%, so the single selection parameter is already fully documented as 'What to recolour. Defaults to everything.' The description adds no meaning beyond that baseline, which is acceptable given complete schema coverage.

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 and resource: coloring secondary structure elements. This distinguishes it reasonably from siblings like util_color_by_element, though it does not explicitly name an alternative or clarify the color scheme used.

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 guidance on when to use this tool versus the many other coloring tools such as util_color_by_element, color, spectrum, or util_rainbow. The agent must infer the appropriate context from the tool name alone.

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

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