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mahynotch

ChimeraX MCP Server

by mahynotch

measure_buried_area

Calculate the buried solvent-accessible surface area at molecular interfaces between two specified atom sets in protein structures.

Instructions

Measure buried solvent-accessible surface area between two atom sets. Aliases: buried area, interface area, binding interface.

Example: measure_buried_area("#1/A", "#1/B")

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
spec1Yes
spec2Yes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

The description covers what the tool measures but fails to disclose potential behavioral traits such as whether it is read-only, requires an open structure, or has any side effects. Given that no annotations are provided, the description should have compensated by stating these aspects, but it omits them, leaving assumptions to the agent.

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 with two sentences, an alias line, and an example. No redundant information exists, and the key action is front-loaded immediately. Every element is purposeful.

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?

The existence of an output schema reduces the need to explain return values, but the description omits preconditions (e.g., a structure must be open) and constraints (e.g., both selections must be from the same model). It does not mention units or expected output format. The example hints at usage but leaves several contextual 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?

With 0% schema description coverage, the description does not individually describe spec1 and spec2, but it adds meaning by stating 'between two atom sets' and providing an example with '#1/A' and '#1/B', implying they are selection strings. However, it lacks explicit format details or constraints, so it only marginally compensates for the schema gap.

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 explicitly states 'Measure buried solvent-accessible surface area between two atom sets,' which is a specific verb and resource. Aliases like 'interface area' and 'binding interface' further clarify the context. The example demonstrates usage with selection strings, distinguishing it from sibling tools like measure_distance or measure_angle.

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 implies usage for quantifying interfaces via the 'binding interface' alias, but it does not provide explicit guidance on when to use this tool versus alternatives like find_contacts or when not to use it. No conditions or exclusions are stated, leaving the agent to infer context from the aliases.

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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