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remove

DestructiveIdempotent

Permanently deletes atoms matching a selection in PyMOL instead of merely hiding them. Use hide when you only need to conceal atoms without removing them from the structure.

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

NameRequiredDescriptionDefault
selectionYesAtoms to delete permanently. To hide them instead, use hide.

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changedv1.5.1
    • addedInput schema / properties / selection / description
      Added value: +"Atoms to delete permanently. To hide them instead, use hide."
  2. First observedv1.2.1

TDQS

A3.6/5.0
Behavior3/5

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

Annotations already declare destructiveHint=true, idempotentHint=true and readOnlyHint=false, so the safety profile is covered structurally. The description's added value is the emphasis on permanence and non-hiding, but it never says what happens to the containing object, whether the change is undoable, or whether the selection must be non-empty.

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

Conciseness4/5

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

Three short sentences, front-loaded with the core action and consequence. The middle sentence ('This deletes atoms; it does not just hide them') partially duplicates the following redirect to hide, but the redundancy is defensible given the destructiveness.

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 one-parameter destructive tool with full annotation coverage and an output schema, the description supplies enough to act correctly. Remaining gaps are minor: interaction with sibling removal tools and any object-level side effects.

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?

With a single parameter at 100% schema description coverage, the schema already explains 'selection'. The description's restatement ('atoms matching the selection') adds no syntax guidance such as selection-expression format, so baseline 3 applies.

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?

The description gives a specific verb and resource ('Permanently removes the atoms matching the selection'), which is far more precise than the bare name 'remove'. It distinguishes itself from the sibling 'hide' but does not address how it differs from 'delete' or 'extract', which are also plausible candidates for an agent choosing a removal tool.

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?

It explicitly names the alternative for the non-destructive case ('To hide instead, use hide'), which is exactly the disambiguation an agent needs. It stops short of stating prerequisites or how it relates to other removal siblings like delete/extract.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.