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execute_pymol_command

Run raw PyMOL CLI commands for operations not covered by dedicated tools, including custom settings and scripts.

Instructions

Executes a raw PyMOL command string (PyMOL CLI syntax). PREFER the dedicated tools when one exists — show, color, select, distance, ligand_view, interface_view, etc. They have better defaults, do compound setup in one call, and produce cleaner results. Reach for this tool only when no other tool covers what you need (e.g. set ray_shadow, 0, bg_color grey20, multi-statement scripts). Note: this accepts the PyMOL cmd.do mini-language, not Python.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
commandYesA PyMOL CLI command, e.g. `set ray_shadow, 0`. Not Python.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

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

With no annotations, the description carries the full burden of behavioral disclosure. It adds useful context about the PyMOL 'cmd.do' mini-language and explicitly says 'not Python', preventing misuse. It also hints at lower-level behavior via 'raw' and 'better defaults'. However, it does not explicitly mention potential side effects or error behavior, which keeps it from a 5.

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, front-loaded with the core purpose, followed by usage guidance and a technical note. Every sentence serves a purpose with no redundant filler.

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?

For a single-parameter raw execution tool, the description is exceptionally complete: it states the operation, gives conditional guidance with examples, and clarifies language syntax. The output schema exists, so return-value details are not needed. It fully covers how an agent should decide to use this tool.

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%, and the schema already describes the parameter with an example and the Python exclusion. The tool description adds multi-statement script mention as a usage hint, but it does not materially extend parameter semantics beyond what the schema provides, so the baseline 3 applies.

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 uses a specific verb+resource construction ('Executes a raw PyMOL command string') and is clear about the tool's role as a fallback, distinguishing it from the dedicated sibling tools (show, color, select, etc.) with explicit examples.

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

Usage Guidelines5/5

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

The description explicitly tells the agent to 'PREFER the dedicated tools' and provides concrete when-to-use and when-not-to-use scenarios, including examples like `set ray_shadow, 0` and multi-statement scripts. It clearly excludes common cases and names 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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