Map improvement (cryo-EM)


Cryo-EM maps can be improved by methods such as sharpening/blurring and density modification.

Sharpening can reveal the high-resolution details concealed in the cryo-EM map. Often, 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. We note that sharpening (and blurring) modify the amplitudes of Fourier coefficients and leave the phases unchanged.

Density modification can be used to improve a cryo-EM map by adjusting 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 adjusted surface area (default) or kurtosis. 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 applying this to the entire map; however, other options are available.

The program phenix.resolve_cryo_em performs density modification of a 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.resolve_cryo_em: Click here

Common issues

Related programs