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wjgoarxiv

vmd-hydrate-mcp

by wjgoarxiv

set_representation

Customize the visual style, color, and material of molecular representations using VMD atom selections.

Instructions

Set the visual representation of a loaded molecule (e.g. style=NewCartoon, Licorice, VDW, Lines; color=Name, ResType, Beta; selection is a VMD atom-selection string like "water" or "name CA").

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
colorNoName
molidYes
styleNoVDW
materialNoOpaque
selectionNoall
Behavior2/5

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

No annotations are provided, so the description carries the full burden. It fails to disclose behavioral traits such as whether the tool overwrites existing representations, whether it modifies the original molecule state, or any side effects like resetting other representation settings. The description focuses on acceptable values rather than behavior.

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 a single sentence that efficiently communicates the core action and provides illustrative examples. It is front-loaded with the purpose, and the parenthetical examples are concise but informative. No redundant information.

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 has 5 parameters, no annotations, and no output schema, the description leaves gaps. It does not explain what the tool returns (if anything), what constitutes a valid 'molid', or the exact effect on the molecular visualization. For an AI agent to use it correctly without prior VMD knowledge, more context is needed.

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 adds meaning for style, color, and selection by listing common values and explaining that selection is a VMD atom-selection string. However, it does not describe the 'molid' parameter (required) or the 'material' parameter (optional). The defaults are in the schema, but the description could be more complete.

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 states the tool sets the visual representation of a loaded molecule and provides specific examples of style, color, and selection values. It distinguishes from sibling tools like 'add_representation' and 'clear_representations' by implying a single representation is set, but could be more explicit about how it differs from adding a new representation.

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?

The description gives examples of valid values for parameters but does not specify when to use this tool versus alternatives like 'add_representation'. No guidance on prerequisites, such as requiring the molecule to already be loaded, or what happens if the tool is called on an invalid molecule ID.

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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