← Algorithms · Continuous density (DENSS)

Continuous density (DENSS)

Purpose. Instead of discrete beads, reconstruct a continuous electron-density map on a voxel grid. This can capture hollow or low-density regions more naturally than a uniform bead DAM, at the cost of a heavier computation and a different set of ambiguities.

Engine. DENSS (Grant protocol). GNOM supplies D_max only; DENSS fits I(q) from the staged profile rather than reusing the full GNOM transform as the density prior.

What autosaxs adds (protocol glue).

1. pilot — one reconstruction for a quick look (default in liveview).
2. average — many independent maps (n_maps), alignment, FSC resolution estimate, and an averaged density.
3. refined — refine starting from the averaged map.
4. Builds a voxel-wise σ map across the aligned ensemble so the 3D view can color / opacity-code variability, not only mean density.

Choose denss mode (slow / fast / membrane) for the underlying DENSS algorithm; choose protocol stage (pilot / average / refined) for how much ensemble work to invest.

← Ab initio DAM · Algorithms index