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local_resolution_view

Color a density map's isosurface by local-resolution values instead of a single global number. Validates voxel grids and converts breakpoints to the correct sigma scale.

Instructions

Colour a map's isosurface by a local-resolution volume instead of by chain.

A single global resolution number misrepresents almost every map: a rigid core at 2.5 Å and a flexible periphery at 5 Å live in the same volume, and one isosurface invites the reader to believe all of it is equally real.

Two things make this harder than it looks, and both are handled. The volumes must share a voxel grid — colouring one map by another samples it at the first map's coordinates, so a mismatch in extent, spacing, origin or axis order draws colour from the wrong place and renders smooth, plausible and wrong. This tool refuses and names what differs. And PyMOL normalises maps on load, so ramp breakpoints given in Ångström must be converted to sigma against the RESOLUTION map's own header — a different sigma scale from the contour level, which comes from the density map's. Every breakpoint is reported in both units.

Local resolution is an estimate. Estimators disagree with each other on the same map, and the value at a voxel depends on the window and the mask as much as on the data.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
nameNoSurface object name (defaults to "<map_obj>_localres")
carveNoCarve radius in Ångström; ignored without a selection
levelNoContour level for the isosurface. If omitted, 1.5 sigma is used.
unitsNoUnits of `level` only: "sigma" or "absolute". Ramp breakpoints are always in Ångström.sigma
breaksNoAscending resolution breakpoints in Ångström. Defaults to the resolution map's own observed range.
map_objYesThe density volume to draw, loaded through the load_map tool
paletteNoOne PyMOL colour per breakpoint. Defaults to blue (best) through red (worst).
res_objYesA local-resolution volume (values in Ångström), loaded through the load_map tool
ramp_nameNoRamp object name (defaults to "<res_obj>_ramp")
selectionNoRestrict the surface to a carve around this PyMOL selection
validate_onlyNoRun the grid check and report, creating nothing

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior5/5

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 proactively reveals two hidden complexities: grid mismatches are checked and reported, and Ångström breakpoints are converted to sigma relative to the resolution map's header. It also cautions that local-resolution estimates are inherently uncertain, giving the agent crucial expectations about reliability.

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

Conciseness4/5

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

The description is front-loaded with a concise one-sentence summary followed by necessary technical caveats. It is somewhat verbose, especially the illustrative analogy about a rigid core versus flexible periphery, but the added details are substantive and not mere padding.

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

Completeness5/5

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

Given the tool's complexity (11 parameters, no annotations) and the presence of an output schema, the description covers the essential non-obvious failure modes: voxel-grid compatibility, sigma conversion, and the uncertainty of local-resolution estimates. It leaves return-value documentation to the output schema, which is appropriate, and gives an agent enough context to use the tool safely and interpret results.

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

Parameters4/5

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

The input schema already covers all 11 parameters, so the baseline is 3. The description adds valuable semantic context beyond the schema by explaining the relationship between `map_obj` and `res_obj` grid requirements, and by clarifying how `level`, `units`, and `breaks` relate to sigma scales in the two maps. This helps an agent reason about parameter interactions without repeating every field.

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 opening sentence states a precise action and target: 'Colour a map's isosurface by a local-resolution volume instead of by chain.' This clearly identifies the tool's function and differentiates it from generic isosurface or chain-based coloring, making the purpose unmistakable.

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

Usage Guidelines4/5

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

The description gives strong contextual guidance by explaining why a global resolution number is misleading and when local-resolution coloring is valuable. It does not explicitly name alternative tools or list 'when not to use' exclusions, but the intended use case is clear enough for an agent to choose correctly.

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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