Map manipulations (cryo-EM)


For crystallography, maps are improved by manipulating the phase information, while the diffraction intensities (or amplitudes) remain unchanged. In contrast, cryo-EM maps are improved by methods such as sharpening and blurring, which typically modify the amplitudes of Fourier coefficients and leave the phases unchanged.

Cryo-EM maps can appear smooth and can lack a high level of detail (contrast) because high-resolution amplitudes of corresponding Fourier map coefficients decay from causes such as radiation damage, sample movement, sample heterogeneity, and errors in the reconstruction procedure. However, sharpening can reveal the high-resolution details concealed in the cryo-EM map.

Density modification can also be used to adjust the Fourier coefficients to better agree with both the original map and the expected features. This improvement relies on two ideas: (1) the Fourier coefficients representing the map are uncorrelated, and (2) some features in a map region are known in advance.


The program phenix.auto_sharpen performs map sharpening by optimizing the detail and connectivity of a cryo-EM map. It tests several resolution-dependent functions and outputs the one with maximal clarity, based on kurtosis (default) or adjusted surface area criteria. The program works best on maps with 4.5 Å or better resolution. At lower resolutions, it may be unable to distinguish variations in the quality of the map as the sharpening is varied. Typically, optimal sharpening is determined by examining a box cut out of the map, and then applied to the entire map; however, other options are available.

The program phenix.combine_focused_maps creates a weighted composition map from a set of locally focused maps and associated models, where each part of each map is weighted by its correlation with the corresponding model. The maps do not have to be superimposed or even have the same gridding or size.

The program phenix.resolve_cryo_em performs density modification of cryo-EM map using two unmasked half-maps, the FSC-based resolution, and a sequence file specifying the contents of the map. You can also supply a model, which will be randomized, refined, and used in model-based density modification. You normally access the program's functionality by running the ResolveCryoEM tool in the Phenix GUI.

How to use phenix.auto_sharpen: Click here

How to use phenix.combine_focused_maps: Click here

How to use phenix.resolve_cryo_em: Click here

Common issues

Related programs