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jonathan6620

PyMOL-MCP

by jonathan6620

list_instances

Lists running PyMOL instances and their loaded objects to identify which window corresponds to each port.

Instructions

Lists the running PyMOL instances and what each has loaded.

Each PyMOL claims its own port, so several can run at once. Pass a port as instance to parse_and_execute to drive that specific one. Use this when a command reports the choice is ambiguous, or when the user refers to a particular window.

The loaded object names are what distinguish one window from another; a port number on its own identifies nothing to a human.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

No annotations are provided, so the description bears full responsibility. It explains that each PyMOL claims its own port and that loaded object names distinguish windows, implying a read-only operation. However, it does not explicitly confirm read-only behavior or mention any safety aspects.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is three sentences long, begins with the primary purpose, and efficiently conveys key usage details. Every sentence adds value without redundancy.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the absence of parameters and the presence of an output schema, the description comprehensively covers purpose, usage context, and relationship to sibling tools. It explains how to interpret the results (loaded object names vs. port numbers) and when to use this tool.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The tool has no parameters, and the description does not need to explain them. It adds context about the returned information (port numbers and loaded object names), which is helpful for understanding the output. Baseline for 0 parameters is 4.

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 that the tool lists running PyMOL instances and their loaded objects. It distinguishes itself from sibling tools 'list_commands' and 'parse_and_execute' by specifying its unique output and usage context.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description explicitly indicates when to use the tool (when a command reports ambiguity or the user refers to a particular window) and references the alternative 'parse_and_execute' for driving a specific instance. However, it does not explicitly state when not to use it.

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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