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mahynotch

ChimeraX MCP Server

by mahynotch

name_selection

Save the current selection as a named bookmark for reuse in subsequent commands. Preserve key regions like binding sites to streamline molecular visualization tasks.

Instructions

Save current selection under a reusable name. Aliases: save selection, bookmark, name zone.

Example: name_selection("binding_site")

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
nameYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

With no annotations, the description carries full burden but only states the basic function; it does not disclose if overwriting occurs, persistence, or behavior with empty selection.

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?

Extremely brief with two short sentences and an example; no wasted words, though it could expand on key details without losing efficiency.

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 tool with one parameter and an output schema, the description covers the core action but lacks details on edge cases and behavior, making it minimally adequate.

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?

Schema coverage is 0%, and the description only provides an example ('binding_site') without explaining the parameter's role, constraints, or uniqueness requirements.

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 states the verb 'Save' and the resource 'current selection' under a reusable name, clearly distinguishing it from sibling tools which involve selection but not naming.

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?

No guidance on when to use this tool versus alternatives like select_atoms; no exclusions or context for using it, 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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