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spectrum

Color molecular selections by per-atom properties like B-factor. Choose a palette and expression to map values to colors for visualization.

Instructions

Color a selection along a spectrum of a per-atom expression (e.g. B-factor).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
paletteNoColor palette, e.g. 'rainbow', 'blue_white_red'.rainbow
selectionNoSelection to color.all
expressionNoPer-atom expression to color by, e.g. 'b', 'count', 'resi'.count

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 full burden for behavioral disclosure. It only states the basic action and gives an example expression; it does not mention what happens to existing colors, whether the operation is reversible, or what output is produced. This is a significant gap for a mutating visualization 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, focused sentence with no redundant wording. It is front-loaded with the action and includes a helpful example. Every word earns its place.

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

Completeness4/5

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

For a simple coloring tool with a fully described schema and output schema, the description provides sufficient context. It clarifies the intended use through the per-atom expression example, and the sibling context shows where it fits. It only lacks explicit exclusion guidance, but the overall picture is 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%, so the baseline is 3. The description adds an example expression ('B-factor') but does not elaborate on palette or selection semantics beyond what the schema already provides. It neither compensates nor detracts.

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?

Description uses a specific verb ('Color') and clearly identifies the resource ('a selection') and the distinguishing mechanism ('along a spectrum of a per-atom expression'). The example 'B-factor' adds context and differentiates this from the sibling 'color' tool, which likely applies a solid color.

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

Usage Guidelines3/5

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

The description implies usage for coloring by a continuous property (e.g., B-factor) but provides no explicit when-to-use vs alternatives. It does not name the sibling 'color' tool or state when not to use spectrum, so guidance is only implicit.

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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