Skip to main content
Glama
mahynotch

ChimeraX MCP Server

by mahynotch

minimize_energy

Run energy minimization to optimize a model's geometry, reducing steric clashes and strain. Accepts steps and model ID as parameters.

Instructions

Run energy minimization on a model. Aliases: relax, optimize geometry, energy minimize.

Example: minimize_energy(100, "#1")

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
stepsNo
model_idNo#1

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 carries full burden. It only says 'run energy minimization' without disclosing behavioral traits like destructiveness, reversibility, or required permissions. Minimal transparency.

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 very short and to the point, with aliases and an example. It is front-loaded and lacks fluff, but does not include structured details like parameter descriptions.

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 the simplicity of the tool but with an output schema, the description does not mention return values, prerequisites (e.g., model must be loaded), or effects on the model state, leaving context incomplete.

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 description coverage is 0%, so description must compensate. The example hints at parameter order and values but does not explain what 'steps' or 'model_id' mean or their roles, providing minimal extra semantics.

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 'Run energy minimization on a model' with aliases and an example, making the verb and resource specific and distinct from sibling tools like 'open_structure' or 'get_sequence'.

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 only states what it does, not the context or prerequisites (e.g., model must be open) or when not to use it.

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