Skip to main content
Glama
mahynotch

ChimeraX MCP Server

by mahynotch

show_sticks

Display stick representation for molecular structures, highlighting bond geometry for specified selections.

Instructions

Show stick representation for a selection. Aliases: sticks, ball and stick, show bonds.

Example: show_sticks("/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 provided, so the description must carry the full burden. It only states 'show stick representation' with an example, failing to disclose behavioral traits such as whether it modifies state, what happens on invalid input, or any prerequisites. This is insufficient for a tool with no structural safety signals.

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 description is extremely concise—one short sentence plus aliases and an example—with no extraneous information. Every part is relevant and front-loaded.

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 tool has one parameter and an output schema exists, the description is mostly adequate for a simple visualization command. However, it lacks details about the effect of the tool, how it interacts with other display modes, or what the output contains. This is minimally complete but leaves gaps.

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 sole parameter 'spec' has a schema description coverage of 0%. The description adds an example '/A:501' which clarifies that 'spec' is likely a selection string, but no further meaning beyond the schema is provided. With low schema coverage, the description partially compensates but could be more explicit.

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 'Show stick representation for a selection,' with an explicit verb and resource. It provides aliases and an example, distinguishing it from sibling tools like show_cartoon or show_surface.

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 description includes an example command but does not specify when to use this tool versus alternatives like show_cartoon or show_surface. The usage context is implied through the example and the tool name, but no explicit when/when-not guidance is given.

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