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util_ss

Color molecular structures by secondary structure to highlight alpha helices, beta sheets, and loops for visual analysis.

Instructions

Colors by secondary structure

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
selectionNoWhat to recolour. Defaults to everything.all

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

With no annotations, the description carries the full burden of behavioral disclosure. It does not explain what 'recolour' entails, whether existing colors are overwritten, or if the operation is reversible. The parameter description clarifies the selection scope but not the visual or side effects.

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 concise and front-loaded, with no wasted words. It efficiently states the core action, though it could be more informative without becoming 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?

Given the tool's simplicity (one parameter, no annotations), the description is minimally sufficient for understanding the basic function. However, it omits contextual details like whether a structure must be loaded or what color scheme is used, making it only partially complete.

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% because the only parameter 'selection' has a description: 'What to recolour. Defaults to everything.' The tool description adds no further parameter context, so it relies on the schema. This meets the baseline for full 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 'Colors by secondary structure' specifies a clear action (colors) and resource (secondary structure), making it easy to infer the tool's purpose. It is terse but sufficient, though it does not explicitly distinguish itself from the similarly named sibling 'util_color_secondary'.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines1/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides no guidance on when to use this tool instead of alternatives like 'color', 'spectrum', or 'util_color_secondary'. It lacks any context about typical use cases, requirements, or exclusions.

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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