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intra_fit

Fits all states of a PyMOL object onto its first state for structural comparison.

Instructions

Fits all states within an object

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
selectionYesObject whose states to fit onto its first state.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior1/5

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

The description provides no behavioral disclosure beyond the bare statement 'Fits all states within an object'. It does not mention that fitting modifies coordinates, whether the operation is reversible, or what side effects occur. Since no annotations are provided, the description carries the full burden and fails to disclose these traits.

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

Conciseness3/5

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

The description is a single, front-loaded sentence, which is efficient, but it under-specifies the tool's behavior. It avoids verbosity but lacks crucial details, making it only minimally adequate.

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

Completeness2/5

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

The tool has a simple schema with one well-described parameter and an output schema, but the description does not explain what the output is, what the tool does to the states, or any side effects. For a fitting operation that modifies state coordinates, this is incomplete without annotations.

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?

The tool description contains no parameter information, but the input schema has 100% coverage with a clear description for 'selection' ('Object whose states to fit onto its first state.'). The baseline of 3 applies because the schema fully documents the parameter.

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 uses a specific verb ('fits') and specifies the resource ('all states within an object'). The schema parameter description clarifies that states are fit onto the first state, which distinguishes it from sibling tools like 'intra_rms' (measurement) and 'morph_states' (interpolation). However, it could explicitly mention superposition or alignment for even greater clarity.

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

Usage Guidelines1/5

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

No guidance is given on when to use this tool versus alternatives such as 'align', 'super', or 'intra_rms'. There are no prerequisites (e.g., the object must have multiple states) or exclusions mentioned.

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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