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util_ss

Color protein atoms by secondary structure type, such as helix, sheet, or loop. Specify a selection to apply coloring only to chosen residues.

Instructions

Colors by secondary structure

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
selectionNoall

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

With no annotations provided, the description carries the full burden. It only states a basic action, omitting details like whether it requires pre-assigned secondary structure, overwrites existing colors, or is non-destructive.

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

Conciseness3/5

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

The description is extremely short (two words), which is concise but insufficiently informative. It front-loads no additional detail beyond the bare minimum, making it under-specified.

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

Completeness2/5

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

Given the tool's purpose and single optional parameter, the description lacks context such as prerequisites, impact on existing colors, or what the output schema contains. It is not complete enough 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.

Parameters2/5

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

Schema description coverage is 0%, but the description adds no information about the 'selection' parameter. It does not explain that the parameter specifies which objects to color, despite its default being 'all'.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose3/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description 'Colors by secondary structure' conveys a verb and criterion, but lacks specificity on what is being colored. It does not differentiate from sibling tools like 'util_color_secondary' or the general 'color' tool.

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?

No guidance is provided on when to use this tool compared to alternatives like 'color' or other utility coloring tools. No conditions or exclusions are stated.

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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