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isomesh

Generate a mesh isosurface from a density map at a specified contour level, optionally restricted to a selection, to visualize electron density.

Instructions

Creates a mesh isosurface

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
nameYesName for the mesh object.
levelYesContour level in sigma, e.g. ``1.0`` for 2Fo-Fc density.
selectionNoRestrict the mesh to the region around this selection.all
map_objectYesName of a loaded map (e.g. a CCP4 or DX density map).

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
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 behavioral disclosure. It only states the action without revealing side effects, dependencies (e.g., a loaded map object), or the meaning of the 'level' parameter in sigma. This leaves significant gaps for safe invocation.

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

Conciseness3/5

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

The description is a single short sentence, which is concise and front-loaded. However, it is under-specified for a tool with four parameters and a sibling that could be confused with it, resulting in a balance between brevity and adequacy.

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?

Given the tool's complexity and the presence of a closely related sibling 'isosurface', the description is incomplete. It does not explain what a mesh isosurface is, when to use it over 'isosurface', or any workflow context such as requiring a prior loaded map. The output schema exists but the description fails to provide sufficient context for a new agent.

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 parameters are already well-documented in the schema. The description adds no additional meaning beyond the schema, keeping it at the baseline.

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 uses the specific verb 'Creates' and names the resource 'mesh isosurface', which clarifies the basic purpose. However, it does not differentiate this tool from the sibling 'isosurface' tool, which could be a similar operation, so it lacks sibling distinction.

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?

There is no guidance on when to use this tool versus alternatives. No mention of prerequisites, such as requiring a loaded map, or when a mesh isosurface is preferable to a regular isosurface. The description provides no context for selection.

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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