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util_color_by_element

Idempotent

Colors atoms by chemical element in PyMOL to visually distinguish elements, with an optional selection that defaults to the entire structure.

Instructions

Colors atoms by their element

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 destructiveHint=false, idempotentHint=true, and readOnlyHint=false, so the mutation-but-safe profile is covered. The description adds no behavioral context beyond that: it does not say that existing colors are overwritten, which element-to-color scheme is applied, or how atoms with unknown elements are handled.

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?

A single short sentence with no filler, and the key criterion (by element) is front-loaded. It is efficient but underspecified rather than padded.

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, an output schema, and rich annotations, so little is required. Still, the description omits the observable side effects (recolor-and-overwrite) that an agent would want before calling a non-read-only tool.

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% and the single optional 'selection' parameter is documented in the schema with its default explained. The description adds no extra meaning about the parameter, so the baseline of 3 applies.

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 states a specific verb and effect ('Colors atoms') plus the criterion ('by their element'), which distinguishes it from the chain/rainbow/spectrum siblings. It falls short of a 5 only because it 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 mention of prerequisites, and no reference to alternative coloring tools such as color, util_color_secondary, or util_cbc. The agent must infer the choice purely from sibling names.

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