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util_color_secondary

Color secondary structure elements in PyMOL to highlight helices, sheets, and loops. Specify a selection to recolor only parts of the structure.

Instructions

Colors secondary structure elements

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 only says 'Colors secondary structure elements' without explaining whether existing colors are overwritten, if it is reversible, or what specific color scheme is applied. This is significant under-specification for a mutation-like tool.

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

Conciseness5/5

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

The description is a single, front-loaded sentence with no wasted words. It directly conveys the core purpose without redundancy.

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?

Despite a simple schema and output schema, the description lacks essential context about the tool's behavior and place among many sibling color utilities. It provides no information on output, side effects, or typical scenarios, which is inadequate for an agent to confidently select and invoke it.

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?

The schema already describes the only parameter (`selection`) with a default and explanation ('What to recolour. Defaults to everything.'). The tool description adds no additional parameter semantics, so the baseline of 3 applies given 100% schema coverage.

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

Purpose5/5

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

The description 'Colors secondary structure elements' clearly states the action (colors) and the target (secondary structure elements), distinguishing it from sibling color utilities like `color` or `util_rainbow`. It is specific and unambiguous.

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 versus alternatives such as `color`, `spectrum`, or other `util_color_*` functions. The description does not mention any exclusions, prerequisites, or recommended use cases.

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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