occupancy_view

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

Annotations already declare the safety profile (readOnlyHint=false, idempotentHint=true, destructiveHint=false), and the description usefully explains the visual mapping — a half-occupied conformer appears "half-there." However, the actual write behavior (overwriting B-factors, and the linkage to restore_bfactors) appears only in the schema parameter text, not the description, so the mutation is under-disclosed for a non-read-only tool.

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?

Structure is sound: the action comes first, then the visual consequence, then the semantic disambiguation. The final paragraph is longer than strictly necessary to make its point, but every sentence is doing real work rather than padding.

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?

For a two-parameter view tool with an output schema and full schema coverage, the definition is close to complete on the conceptual side. The only meaningful omission is the B-factor overwrite side effect and how to undo it, which matters for an agent chaining this with restore_bfactors.

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%, with both obj_name and preserve_bfactors fully documented including the default and its purpose. The description adds nothing about either parameter, which is acceptable given the schema carries that load, but warrants only the baseline score.

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 opening states a specific verb and resource: "Colour and scale a structure by per-atom crystallographic occupancy (q)." It then pins the exact sense of the measure, which is the thing most likely to be confused with sibling views such as qscore_view or bfactor_view.

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 gives a scope exclusion (it never reports the particle-fraction sense of occupancy), which is a form of when-not guidance, but it never names an alternative tool or states the conditions under which an agent should pick this view over altloc_view or bfactor_view. Usage is implied rather than directed.

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