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mahynotch

ChimeraX MCP Server

by mahynotch

save_structure

Save a molecular model to PDB, mmCIF, or mol2 file for export or download.

Instructions

Save a model to PDB, mmCIF, or mol2 file. Aliases: export, write structure, download.

Example: save_structure("/tmp/model.pdb", "#1")

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pathYes
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 exist, and the description fails to disclose behavioral traits such as whether it overwrites existing files, required permissions, or handling of invalid paths or model IDs. The example shows basic usage but lacks behavioral context.

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 a clear purpose, an aliases line, and an example. It front-loads the main action. Minor improvement could organize information more structuredly, but overall efficient.

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 tool saves to multiple file formats with a path and model selection, and has no annotations, the description lacks details on file format selection (implicit from extension?), output, error cases, and behavioral constraints. The existence of an output schema (not shown) doesn't fully compensate for these gaps.

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%, meaning the input schema provides no parameter explanations. The description mentions 'model' and 'path' via example but does not explain the path format, allowed extensions, or the meaning of model_id beyond a default. This is inadequate for two parameters.

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 tool saves a model to PDB, mmCIF, or mol2 files, with aliases and an example. This verb-resource combination distinguishes it from sibling tools like open_structure or minimize_energy.

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 explicit guidance on when to use this tool versus alternatives. It provides aliases but no when-not or context for choosing between saves or other operations.

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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