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save_file

Save molecular selections or entire sessions to files such as PDB, PSE, PNG, or MOL2. The output format is determined by the file extension.

Instructions

Save a selection/session to a file (format from extension).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pathYesOutput path; extension sets format (.pdb, .pse, .png, .mol2, ...).
stateNoState to save (-1 = current, 0 = all).
selectionNoSelection to save.all

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior2/5

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

With no annotations provided, the description carries the full burden of disclosing behavior. It states the basic save operation and format-from-extension, but does not mention side effects like overwriting files, permissions, or any nuanced behavior related to the selection or state parameters.

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 a single, clear sentence that is front-loaded with the core action. It omits unnecessary words and effectively conveys the essential purpose and format mechanism.

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?

The description provides a minimal but adequate overview for a fairly simple tool. It leaves some ambiguity about what 'session' means and whether files overwrite, but given the output schema and comprehensive parameter descriptions, it offers enough context to understand the tool's basic function.

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%, so the schema already documents all parameters. The description adds only a minor clarification that the extension determines format, which is also stated in the schema. Thus it meets the baseline but does not significantly enhance understanding beyond the schema.

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 identifies the action (save) and the target (a selection/session to a file), and notes that the format is inferred from the extension. While it does not explicitly differentiate from siblings like render_image, the mention of selection/session makes its scope distinct enough.

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 for when to use this tool versus alternatives, such as render_image for images or load_structure for reading files. There is no mention of exclusions or specific use cases, leaving the agent to infer usage solely from the tool name and description.

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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