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remove

Delete atoms matching a selection to permanently remove them from the molecular structure. Use this to clean up or modify protein models.

Instructions

Permanently removes the atoms matching the selection.

This deletes atoms; it does not just hide them. To hide instead, use :func:hide.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
selectionYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

No annotations provided; description bears full burden. States destructive nature ('permanently removes', 'deletes atoms'), but does not mention side effects or reversibility.

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?

Two sentences, zero waste, front-loaded with core action, then additional context in second sentence.

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

Completeness3/5

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

Given an output schema and moderate sibling complexity, description covers main action and one alternative but lacks mention of irreversibility or impact on other objects.

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 has 0% description coverage; description adds 'the atoms matching the selection' clarifying the 'selection' parameter's role. Adds value but minimal.

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?

Clearly states 'permanently removes atoms matching selection', uses specific verb 'removes' and resource 'atoms'. Distinguishes from 'hide' but not from sibling 'delete', which may cause ambiguity.

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

Usage Guidelines4/5

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

Explicitly says 'To hide instead, use hide' providing a clear when-not scenario. However, no guidance on when to use versus other deletion-like tools.

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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