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mahynotch

ChimeraX MCP Server

by mahynotch

show_surface

Display molecular surfaces of proteins or molecules with adjustable opacity for visual analysis.

Instructions

Show molecular surface. Aliases: surface, display surface, solvent-accessible surface.

Example: show_surface("#1", 0.7)

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
specNoall
opacityNo

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 behavioral transparency burden. It only says 'show' without disclosing effects, reversibility, or system impact. The example hints at parameters but lacks comprehensive 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 very concise with one sentence, aliases, and an example. It communicates the core action efficiently, though the example could be formatted more clearly.

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?

Despite having an output schema, the description lacks context on what to expect as output, prerequisites, or constraints. For a tool with two parameters, more detail is needed to be complete.

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 has 0% description coverage. The description adds minimal meaning via the example (spec='#1', opacity=0.7), but does not explain spec format, valid opacity range, or defaults beyond schema.

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's function: 'Show molecular surface.' The aliases and example reinforce this, distinguishing it from sibling surface tools like show_electrostatic_surface and show_hydrophobicity_surface by not specifying a surface type.

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 like show_electrostatic_surface. The example shows basic usage but does not clarify contexts 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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