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MCPymol

MCPymol

by chemrich
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Python
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util_rainbow

Idempotent

Colors selected residues in a rainbow gradient from N to C terminus to visualize sequence order and structural progression in PyMOL.

Instructions

Colors residues in rainbow from N to C terminus

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_rainbow"
  }
}

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 declare readOnlyHint=false, destructiveHint=false and idempotentHint=true, so the description is not the sole carrier of the mutation profile. Beyond the purpose statement the description adds no behavioral context: it does not say that existing colors are overwritten, that it only takes effect on visible representations, or how the change persists in the session.

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?

One short sentence with no filler and the essential information front-loaded. It is efficient, though its terseness leaves the reader wanting the missing routing and behavior details.

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 no explanation, and the tool is conceptually simple. However, for a mutation tool with a free-form selection parameter, the definition omits what exactly gets recolored (atoms, cartoons, surfaces) and whether prior colors are lost, leaving real gaps.

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 the single 'selection' parameter is documented in-schema (default 'all', 'What to recolour'). The description adds nothing about selection syntax or scope, so the baseline 3 applies when the schema does the work.

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 names a specific verb ('Colors') and resource ('residues') and specifies the exact scheme ('rainbow from N to C terminus'), which an agent can distinguish from chain-based or element-based coloring siblings. It stops short of naming util_chainbow or spectrum explicitly, so the differentiation is inferable rather than stated.

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 or when-not-to-use guidance, and no alternative is named despite many coloring siblings (util_chainbow, util_color_by_element, spectrum, color). The agent must guess whether this is the right coloring tool and when residue-order rainbow is preferred over chain rainbow.

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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