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extract

Idempotent

Move selected atoms into a new PyMOL object, removing them from the original structure for focused analysis.

Instructions

Extracts a selection to a new object

Input Schema

NameRequiredDescriptionDefault
nameYesName for the new object.
selectionNoAtoms to move into it. Unlike create, these are *removed* from the original object.all

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changedv1.5.1
    • addedInput schema / properties / name / description
      Added value: +"Name for the new object."
    • addedInput schema / properties / selection / description
      Added value: +"Atoms to move into it. Unlike create, these are *removed* from the original object."
  2. First observedv1.2.1

TDQS

C2.8/5.0
Behavior1/5

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

The definition states that selected atoms are 'removed from the original object,' which is a destructive modification of the source object. The annotations declare destructiveHint=false, directly contradicting that behavior. The description also does not clarify reversibility or permissions, leaving the agent with a misleading safety signal.

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?

The main description is a single front-loaded sentence with no wasted wording. It is concise, though its brevity leaves important behavioral nuance to the schema rather than stating it directly.

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?

The tool has an output schema, complete parameter descriptions, and annotations, so not everything must be repeated in the one-line description. However, the critical fact that the source object loses atoms is only in the schema, and the annotations' destructiveHint=false creates a conflicting picture. The definition is usable but not fully coherent without careful cross-reading.

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 schema already documents both parameters well. The schema's selection description adds useful meaning by saying atoms are moved and removed from the original, unlike create. The main description itself contributes no additional parameter semantics, so the baseline of 3 is appropriate.

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 states a specific verb and result: 'Extracts a selection to a new object.' This is clear enough to understand the operation. It does not distinguish itself from the sibling 'create' tool in the main description, though the schema parameter text later contrasts them.

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?

The description gives no explicit when-to-use or when-not-to-use guidance, and it does not identify alternatives such as 'create' or 'clip' as choices. The schema's selection text notes 'Unlike create,' but only in passing and not as actionable routing guidance.

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