pymol-mcp

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Hide

hide

Removes a specified representation from view for a chosen molecular selection; use 'everything' to clear all displayed representations.

Instructions

Hide a representation for a selection.

Tool call template

This tool declares no required parameters. Add optional parameters from the input schema as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {},
    "name": "hide"
  }
}

Input Schema

Name	Required	Description	Default
`selection`	No	Selection to hide it for.	all
`representation`	No	Representation to hide (or 'everything').	everything

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Aug 15, 2026

TDQS

C2.9/5.0

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 disclosure burden and largely fails it. It does not say whether hiding is reversible, what 'everything' as a representation means in practice, whether hidden state persists across renders, or whether permissions/selection validity matter.

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?

A single short sentence with no padding and the verb front-loaded. It is efficient, though its brevity contributes to the guidance and behavioral gaps rather than offsetting them.

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?

With only two optional, fully documented parameters, an output schema to describe returns, and default values in the schema, the definition is minimally sufficient to call correctly. It is still thin for a state-mutating view tool with zero annotation coverage, where reversibility and scope of 'everything' would help.

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?

Schema description coverage is 100%, with both parameters documented and defaulted (selection='all', representation='everything'), so the schema does the semantic work. The description adds nothing beyond restating the parameter concepts, which meets the baseline for full coverage.

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?

States a specific verb ('Hide') and resource ('a representation') scoped to a selection, which is unambiguous enough for an agent to act on. It does not explicitly name the sibling 'show' as its inverse, so differentiation relies on the agent inferring the antonym from the name alone.

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 no when-to-use guidance, no prerequisites, and no alternatives. The pairing with 'show' is only inferable from the sibling list, not the definition text, so an agent gets no explicit routing signal.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.