occupancy_view

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

The description discloses the visual behavior ('Alternates at q<1 are visually de-emphasised in proportion') and clarifies the semantic meaning, but with no annotations it carries full burden. It does not mention that the tool overwrites B-factors or that restore_bfactors may be needed, even though the schema hints at this via preserve_bfactors.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is front-loaded with the primary action in the first sentence and uses later paragraphs to clarify a common misinterpretation. While the third paragraph is somewhat verbose, each sentence contributes to preventing misuse, and the structure is logical.

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

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

Given the nuance of the occupancy concept, the description provides strong conceptual completeness and an output schema exists to cover return values. It is adequate for an agent to select and invoke the tool, though it omits the B-factor overwriting side effect that the parameter schema hints at.

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

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

Schema description coverage is 100% for both parameters, and the description does not add meaning beyond what the schema already provides. The parameter descriptions in the schema are sufficient, so the baseline score of 3 is appropriate.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Does the description clearly state what the tool does and how it differs from similar tools?

The description opens with a specific verb phrase 'Colour and scale a structure by per-atom crystallographic occupancy' and clearly distinguishes the tool's scope from sibling views like altloc_view by explaining what the occupancy means and what it does not mean. The resource and action are unambiguous.

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

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

The description provides clear contextual guidance by explicitly contrasting crystallographic occupancy with particle occupancy, stating 'this tool never reports the other sense.' It implies when to use the tool (for crystallographic occupancy) without naming specific alternative tools, but the context is strong enough to guide selection.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.