Map improvement (cryo-EM)

Why

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.

How

The program phenix.map_sharpening 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.map_sharpening: Click here

How to use phenix.resolve_cryo_em: Click here

Common issues

• phenix.map_sharpening doesn't work for map_box-produced maps: map_sharpening should not be used on maps produced with the exact-unique option of map_box. These maps are closely masked around the density of a single molecular, so much of the map is set to zero. Therefore, the map is missing noise information and auto-sharpen doesn't work properly.
• phenix.resolve_cryo_em doesn't work well: Poor results could be due to using masked half-maps, having non-uniform solvent noise, or getting interference from having very prominent density away from the macromolecule. The program can also crash if you have limited memory and are using multiple processors. See phenix.resolve_cryo_em for ways to address these issues.

Related programs

• phenix.map_symmetry: This tool finds internal symmetries in a map, allowing the map to be reduced to the repeating unit.
• phenix.map_box: This tool cuts out a box from a larger map. It is used to extract the unique part of a map.
• phenix.combine_focused_maps: This tool 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.