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util_color_secondary

Color secondary structure elements in a protein model to highlight helices, sheets, and loops. Accepts an optional selection parameter to target specific chains or residues.

Instructions

Colors secondary structure elements

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
selectionNoall

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior1/5

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

With no annotations, the description must disclose behavioral traits. It only states the action, not whether existing colors are overridden, whether a default color scheme is used, or how the selection parameter affects behavior. No behavioral insights are given.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness2/5

Is the description appropriately sized, front-loaded, and free of redundancy?

While short, the description is under-specified. It consists of three words, which is too terse to be helpful. Conciseness is valued, but not at the expense of essential information.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness1/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool's purpose and the presence of a single parameter, the description should at minimum mention the parameter's role and default behavior. It fails to do so, leaving the definition incomplete for an agent to use correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters1/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description should explain the 'selection' parameter. It does not, leaving the agent to infer meaning from the parameter name alone, which is insufficient for correct usage.

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 clearly states the verb 'colors' and the resource 'secondary structure elements', making the purpose evident. However, it lacks specificity about which secondary structures (helix, sheet, loop) or how colors are assigned, preventing a higher score.

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?

No usage guidelines are provided. The description does not indicate when to use this tool instead of alternatives like 'color', 'util_ss', or 'util_rainbow', leaving the agent without decision support.

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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