Skip to main content
Glama
mahynotch

ChimeraX MCP Server

by mahynotch

select_near

Selects all atoms within a specified distance (Angstroms) of a given selection for structural analysis.

Instructions

Select all atoms within N Angstroms of a selection. Aliases: select nearby, zone, within distance.

Example: select_near("/A:501", 5.0)

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
specYes
distanceYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

No annotations are provided, so the description bears full responsibility for behavioral disclosure. It does not explain whether the tool modifies the current selection, creates a new named selection, or what side effects occur. The term 'select' is ambiguous.

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 short and includes aliases and an example, which is useful. However, the example adds value, and there is no superfluous text.

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?

Given that an output schema exists (reported in context), the description is incomplete as it does not indicate what the tool returns (e.g., a confirmation, number of atoms selected). For a relatively simple tool, the description leaves significant gaps in understanding tool behavior.

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 has no descriptions for parameters (0% coverage). The description provides an example but does not explain the format of the 'spec' parameter (e.g., what constitutes a valid selection string) or the units/detail for 'distance'. The example hints but is insufficient.

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?

Description clearly states the tool selects atoms within a distance of a selection, with aliases and a concrete example. This distinguishes it from sibling selection tools like select_atoms or select_chain.

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. The description lists aliases but does not provide context about when to choose this tool over other selection methods (e.g., select_atoms, invert_selection).

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

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/mahynotch/chimerax-mcp'

If you have feedback or need assistance with the MCP directory API, please join our Discord server