LocScale

Physics-informed local sharpening for cryo-EM density maps.

Input

Map input

Half Map 1

Unsharpened, unfiltered cryo-EM half-map.

Half Map 2

Matching unsharpened, unfiltered cryo-EM half-map.

CPU processes

Resolution cutoff (A)

Window size (pixels)

FDR threshold

FDR window size

Averaging filter size

FDR pre-filter (A)

Mask threshold

EMmerNet batch size

EMmerNet cube size

EMmerNet stride

Low-context EMmerNet model

Filter input maps

Apply FSC filter

60 credits

Output

Configure inputs to begin

Set options on the left, then click “Submit job”.

What is LocScale?

LocScale performs local density scaling for cryo-EM maps. It sharpens map regions according to local signal and reference information rather than applying one global B-factor across the whole volume.

ProteinIQ runs LocScale on uploaded MRC/MAP files and returns the sharpened map plus the processing log and generated map files. The first release focuses on the standard LocScale command for local sharpening with half-map or full-map inputs. Feature-enhanced maps, coordinate-model refinement, hybrid model completion, MPI runs, and PDF reports are tracked for future support.

Inputs

Input	Description
Half Map 1	First unsharpened, unfiltered half-map in MRC or MAP format.
Half Map 2	Second matching unsharpened, unfiltered half-map.
Cryo-EM Map	Full unsharpened map for datasets without half-maps.
Mask	Optional MRC/MAP mask. LocScale estimates an FDR mask when this is omitted.
Reference Map	Optional MRC/MAP model map used directly as the LocScale reference.

Half-map input is recommended when available because LocScale can use the pair for FSC-based resolution estimation.

Settings

The default settings match LocScale defaults for local sharpening: one CPU process, FDR threshold 0.01, averaging filter size 3, EMmerNet batch size 8, cube size 32, stride 16, and no input filtering. Optional resolution, window-size, FDR-window, FDR pre-filter, mask-threshold, and reference-map-resolution fields are passed to the corresponding LocScale command-line options only when set.

Outputs

LocScale returns a primary sharpened MRC map. ProteinIQ also returns the LocScale log and generated processing files such as FDR masks or local-scaling diagnostic maps when LocScale writes them.

Open the returned MRC files in ChimeraX, Coot, or another cryo-EM map viewer for inspection.

Limitations

Inputs should be unsharpened and unfiltered. Pre-sharpened maps can produce misleading artifacts.
Coordinate-model and hybrid LocScale modes require additional REFMAC/CCP4 runtime support and are not enabled in this release.
Feature-enhanced maps and pVDDT confidence maps are not enabled in this release.
Point-group symmetry options are held at the LocScale default of C1 until symmetry-specific runtime checks are added.

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