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intra_rms

Read-onlyIdempotent

Calculates RMSD between states of a selected PyMOL object to compare conformational differences across states.

Instructions

Calculates RMSD between states within an object

Input Schema

NameRequiredDescriptionDefault
selectionYesObject whose states to compare.

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: +"Object whose states to compare."
  2. First observedv1.2.1

TDQS

B3.3/5.0
Behavior2/5

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

The annotations already establish that the operation is read-only, idempotent, non-destructive, and closed-world. Beyond those fields, the description does not clarify whether fitting or superposition is performed, which states are included, or whether a multi-state object is required.

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 single sentence is front-loaded, direct, and contains no unnecessary wording. Its brevity is appropriate even though additional operational guidance would improve other dimensions.

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?

For a simple one-parameter calculation with an output schema and comprehensive safety annotations, the description is minimally sufficient for invocation. However, important RMSD semantics—especially fitting behavior and state coverage—remain unspecified, as does its relationship to nearby sibling tools.

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%, and the required selection parameter is already documented as the object whose states should be compared. The description adds no further selection syntax, state-handling details, or examples, so the baseline score 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 operation and scope: calculating RMSD between states within one object. It does not explicitly differentiate the tool from related siblings such as rms_cur or intra_fit.

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 wording implies use for comparing multiple states of a single object. It provides no explicit prerequisites, when-not guidance, or conditions for choosing another RMSD or fitting tool.

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