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mahynotch

ChimeraX MCP Server

by mahynotch

zoom_to

Center the camera view on a specified molecular selection, such as a residue or chain, to focus on areas of interest in protein structures.

Instructions

Zoom the camera to center on a selection. Aliases: focus, center on, look at, zoom in.

Example: zoom_to("/A:501")

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
specYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

No annotations are present, so the description must disclose behavioral traits. It does not mention side effects, requirements (like a valid selection), or what happens if the spec is invalid. The output schema exists but is not referenced. Minimal disclosure beyond the action.

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 description is concise with two sentences plus aliases and an example. No filler, easy to parse. Slightly more structure (e.g., separate sections) could improve scannability, but it is efficient.

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 the output schema exists, return values are covered. However, the description lacks prerequisites (e.g., a selection must exist), scope (single vs multiple selections), and error behavior. The example helps but leaves gaps in completeness.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The schema has 0% description coverage for the single parameter 'spec'. The description adds context via an example 'zoom_to("/A:501")', implying spec is a selection string, but does not explain format, valid values, or constraints. The schema only states type string.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the verb (Zoom) and resource (camera to center on a selection), and provides aliases (focus, center on, look at, zoom in) which further clarify the purpose. It distinguishes from sibling tools like reset_view or spin by specifying a precise action.

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 guidance on when to use this tool versus alternatives. No explicit context, prerequisites (e.g., having a selection), or when-not conditions are mentioned. Only an example is provided.

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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