pymol-mcp

by wjgoarxiv

Overview Schema Source Related Servers Discussions Admin

Python

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Get Selection Info

get_selection_info

Summarize a molecular selection by reporting atom count, chains, and residue names present.

Instructions

Summarize a selection: atom count, chains, and residue names present.

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": "get_selection_info"
  }
}

Input Schema

Name	Required	Description	Default
`selection`	No	Selection expression to summarize.	all

Output Schema

Name	Required	Description	Default
No arguments

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Aug 15, 2026

TDQS

B3.2/5.0

Behavior3/5

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

No annotations are supplied, so the description carries the burden; it does signal a read-only summarization operation and enumerates what the summary reports. It does not say what happens if the selection expression is invalid or matches nothing, nor whether a selection must already exist, which leaves gaps for a no-annotation tool.

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?

One front-loaded sentence with no wasted wording; the key output fields are listed inline. It is appropriately sized for a simple inspection tool, though the terse phrasing leaves almost no room for supporting context.

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?

An output schema exists, so return values need not be re-explained, and the tool is only one optional parameter deep. Still, the definition omits error/precondition behavior and routing guidance that would make it complete for an agent choosing among many structure-inspection siblings.

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 coverage is 100% and the single parameter is documented as a 'Selection expression' with a default of 'all'. The description adds no syntax or format detail beyond the schema, which is the expected baseline when the schema does the heavy lifting.

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 ('Summarize') and resource ('a selection') plus the concrete contents of the summary (atom count, chains, residue names). This distinguishes it reasonably from action-oriented siblings like select or run_pml, though it does not explicitly contrast with get_object_info.

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 when-to-use guidance and no named alternatives. An agent must infer from the name that this is the way to inspect a selection rather than, say, calling select or get_object_info first.

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