Input
Unsharpened, unfiltered cryo-EM half-map.
Matching unsharpened, unfiltered cryo-EM half-map.
Output
Input
Unsharpened, unfiltered cryo-EM half-map.
Matching unsharpened, unfiltered cryo-EM half-map.
Output
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
C1until symmetry-specific runtime checks are added.
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