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load_structure

Load a structure from a local file path into PyMOL for analysis, using BFS multimer heuristic to group interacting chains. Replace or add to the current session.

Instructions

Loads a structure from a local file path and applies the BFS multimer heuristic.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
replaceNoClear the session first, so this is the only structure loaded. Pass False to add to what is already loaded — which is how you get two structures into one session for superposition_view.
obj_nameYesName for the object in PyMOL
file_pathYesPath to the structure file (PDB, MMCIF, etc.)
multimer_cutoffNoDistance (A) between chains to keep them in the same multimer. Default 8.0A is suitable for most functional assemblies.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

No annotations are provided, so the description carries full behavioral burden. It mentions the BFS multimer heuristic but fails to disclose that the default behavior (replace=true) clears the session before loading, which is a significant side effect. It also omits the option to add structures without clearing (replace=false).

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, front-loaded sentence that directly states the tool's core function and unique heuristic. Every word earns its place, and there is no redundancy or unnecessary detail.

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?

While an output schema exists and the input schema is rich, the description lacks guidance on important contextual nuances such as the replace parameter's effect on the session and how to intentionally load multiple structures. It is adequate for a simple load operation but leaves some context to be inferred from the schema.

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 baseline is 3. The description itself adds no parameter-level detail beyond what the schema already provides, so it earns the baseline score without further compensation.

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 a specific action ('Loads a structure') and a resource ('from a local file path'), and adds a distinguishing detail ('applies the BFS multimer heuristic'). This separates it from siblings like fetch_structure (remote) and load_session (session file).

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

Usage Guidelines3/5

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

The phrase 'local file path' implies when to use this tool, but there is no explicit comparison to alternatives like fetch_structure or load_session, nor any 'when not to use' guidance. The usage context is implied rather than explicitly stated.

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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