Density modification of cryo-EM maps

Abstract

Density modification uses expectations about features of a map such as a flat solvent and expected distributions of density in the region of the macromolecule to improve individual Fourier terms representing the map. This process transfers information from one part of a map to another and can improve the accuracy of a map. Here the assumptions behind density modification for maps from electron cryomicroscopy are examined and a procedure is presented that allows incorporation of model-based information. Density modification works best in cases where unfiltered, unmasked maps with clear boundaries between macromolecule and solvent are visible and where there is substantial noise in the map, both in the region of the macromolecule and the solvent. It also is most effective if the characteristics of the map are relatively constant within regions of the macromolecule and the solvent. Model-based information can be used to improve density modification, but model bias can in principle occur. Here model bias is reduced by using ensemble models that allow estimation of model uncertainty. A test of model bias is presented suggesting that even if the expected density in a region of a map is specified incorrectly by using an incorrect model, the incorrect expectations do not strongly affect the final map. SynopsisThe prerequisites for density modification of maps from electron cryomicroscopy are examined and a procedure for incorporating model-based information is presented.