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mahynotch

ChimeraX MCP Server

by mahynotch

show_hydrophobicity_surface

Calculate and display molecular lipophilicity potential on a surface, highlighting hydrophobic regions in dark goldenrod and hydrophilic in dark cyan.

Instructions

Calculate and display Molecular Lipophilicity Potential on the surface. Dark cyan = hydrophilic, dark goldenrod = hydrophobic. Aliases: hydrophobicity, lipophilicity, MLP, hydrophobic surface.

Example: show_hydrophobicity_surface("#1")

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
specNo#1

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

With no annotations, the description carries full burden. It explains the visualization result (colors) but does not disclose side effects (e.g., whether it replaces existing surfaces), performance impact, or required permissions.

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 (three lines) and includes aliases and an example. It front-loads the purpose and color mapping, with no filler words.

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 output schema exists (so return format is not needed), the description is adequate for a simple visualization tool. However, it lacks detail on whether the surface is additive or replaces previous surfaces, and could better integrate with the sibling context.

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 coverage is 0% for the 'spec' parameter. The description includes an example usage with '#1' but does not explain the parameter's format, allowed values, or meaning beyond a vague selection specifier.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool calculates and displays Molecular Lipophilicity Potential on the surface, with specific color meanings. It distinguishes from sibling tools like show_electrostatic_surface by the property displayed, but does not explicitly contrast them.

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 like show_electrostatic_surface or show_surface. Only an example is provided, but no context on appropriate scenarios or prerequisites.

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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