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system

Execute a shell command on the machine running PyMOL to manage system tasks directly from your workflow.

Instructions

Executes a system command

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
commandYesShell command to run on the machine PyMOL is running on.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior1/5

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

There are no annotations, so the description bears the full burden of behavioral disclosure. It merely says 'Executes a system command' without mentioning potential side effects, security risks, lack of sandboxing, working directory behavior, or error handling. For a tool that can run arbitrary shell commands, this is a critical omission.

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?

The description is extremely concise: one sentence, front-loaded, with no wasted words. It is appropriately sized for a simple tool with only one parameter, though the lack of crucial safety details reduces the value of its brevity.

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

Completeness2/5

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

Despite having only one parameter and no nested objects, the tool's nature as a system command executor makes context critical. The description fails to explain what the command output looks like (stdout/stderr/exit code), whether there are any restrictions, or how errors are handled. Even with a simple schema, this is incomplete for a high-risk operation.

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?

The schema already provides 100% coverage for the single parameter 'command' with a description ('Shell command to run on the machine PyMOL is running on.'). The tool description adds no extra meaning beyond this. The baseline of 3 applies because 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?

The description clearly states the verb 'Executes' and the resource 'a system command', making the tool's basic function obvious. However, it does not differentiate this from the sibling tool 'execute_pymol_command', which may overlap in function. This is a clear purpose but with no sibling differentiation.

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 guidance is provided on when to use this tool instead of alternatives. The sibling 'execute_pymol_command' could be confused with this one, but the description gives no criteria for choosing between them. Usage context is completely absent.

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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