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select

Assign a name to a PyMOL selection expression for easy reuse in later commands.

Instructions

Creates (or replaces) a named selection for later reuse.

Args: name: Identifier you'll refer to later (e.g. active_site). selection: PyMOL selection expression to assign to that name.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
nameYes
selectionYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

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

Given no annotations, description discloses creation/replacement behavior and mentions 'for later reuse', suggesting persistence. Could be more explicit about replacement overwriting existing selections.

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?

Extremely concise: two sentences then parameter list. No wasted words, front-loaded with main purpose.

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?

Covers purpose and parameters adequately for a simple tool with output schema. Could mention that it operates in the current PyMOL session.

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

Parameters4/5

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

Adds meaningful explanation for both parameters beyond the schema titles: name is an identifier with example, selection is a PyMOL expression. Compensates for low schema 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?

Clear verb 'creates (or replaces)' and resource 'named selection'. Purpose is specific, but no explicit differentiation from sibling tools like 'deselect' or 'show'.

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?

Implies usage for naming selections for later reuse, but no explicit guidance on when to use vs alternatives or prerequisites.

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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