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jonathan6620

PyMOL-MCP

by jonathan6620

list_commands

Lists available PyMOL commands with descriptions. Use optional filter to find specific commands and their parameter details for correct syntax.

Instructions

Lists the PyMOL commands parse_and_execute accepts.

Without filter, returns every command name with a one-line description. With filter (a substring matched against names and descriptions), returns full detail for the matches: the exact regex the input must satisfy, plus each parameter's name, whether it is required, its default, and its allowed values. Use it to confirm syntax before calling parse_and_execute.

Examples: filter="color" for the colouring commands, filter="cartoon" for cartoon-related ones, filter="fetch" for the exact fetch signature.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
filterNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

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

Describes output differences with/without filter: without filter returns one-line descriptions, with filter returns full detail (regex, params). No annotations, so description must stand alone; it adequately discloses behavior.

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?

Three concise sentences: purpose, behavior clarification, and examples. No redundant information, well-organized.

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?

Complete for a documentation tool with one optional parameter. Output schema exists for return details. Covers what tool does, parameter usage, and use case. No missing critical information.

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

Parameters5/5

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

Schema only provides name and default; description adds that filter is a substring match against names and descriptions, and its presence triggers detailed output. Fully clarifies parameter meaning and effect.

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?

Clearly states it lists PyMOL commands accepted by parse_and_execute, with distinct behaviors for with/without filter. Distinguishes from sibling tools list_instances and parse_and_execute.

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?

Explicitly explains when to use filter (for full detail on matches) vs without (list all). Suggests use case: 'confirm syntax before calling parse_and_execute'. Lacks explicit when-not-to-use alternatives.

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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