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isomesh

Idempotent

Creates a mesh isosurface from a loaded density map at a chosen contour level, optionally limited to a selection, to visualize regions of interest in PyMOL.

Instructions

Creates a mesh isosurface

Input 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

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed4 schema fields changedv1.5.1
    • addedInput schema / properties / level / description
      Added value: +"Contour level in sigma, e.g. ``1.0`` for 2Fo-Fc density."
    • addedInput schema / properties / map_object / description
      Added value: +"Name of a loaded map (e.g. a CCP4 or DX density map)."
    • addedInput schema / properties / name / description
      Added value: +"Name for the mesh object."
    • addedInput schema / properties / selection / description
      Added value: +"Restrict the mesh to the region around this selection."
  2. First observedv1.2.1

TDQS

C2.8/5.0
Behavior2/5

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

Annotations already declare readOnlyHint=false, idempotentHint=true, destructiveHint=false and openWorldHint=false, so the safety profile is covered. The description adds nothing beyond that: it does not say that a new named object is added to the session, whether re-running with the same name overwrites the existing mesh, or how the mesh relates to the source map.

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 single sentence is front-loaded and free of waste, but it is undersized for a tool with four parameters and a near-duplicate sibling. Brevity here comes at the cost of disambiguation rather than earning its place.

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?

An output schema exists, so return values need not be described, but the description still omits the key context an agent needs: how this differs from 'isosurface', that a map object must be loaded, and that a named object is created in the session. For a mesh-generation tool with a close sibling, this is incomplete.

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% and each parameter is documented in the schema itself (level in sigma, map_object as a loaded map name, selection restricting the region). The description adds no additional meaning, so the baseline 3 applies.

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 gives a specific verb and resource ('Creates a mesh isosurface'), which is enough to know the tool generates contour mesh geometry. It falls short of 5 because it does not distinguish this from the sibling tool 'isosurface', which appears to do something very similar, leaving the agent to guess which to pick.

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 when-to-use guidance, no prerequisite (e.g. a map must already be loaded), and no mention of the 'isosurface' sibling as an alternative. The agent must infer the entire selection context from the name alone.

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