Creating a local resolution map with local_resolution



The routine local_resolution is a tool for creating a local resolution map showing the local resolution of a cryo-EM map and having the same gridding as the cryo-EM map

Usage and how local_resolution works:

Local resolution is calculated in small boxes cut out from the cryo-EM map, where the density near the edges of each box is masked so that it gradually diminishes to zero at the edges. Then the values of local resolution are smoothed and placed at grid points of a full-size map matching the original map.

The local resolution map can be used to color a map in display programs such as ChimeraX. In ChimeraX you can simply load in your original map and the local resolution map and then specify:

color sample #1 map #2 palette rainbow

to color map #1 based on the resolution values in map #2.

Procedure used by local_resolution

The basic inputs to local_resolution are:

Two unmasked half-maps

Optional inputs are:

nominal resolution


Standard run of local_resolution:

You can use local_resolution to get the local resolution in a cryo-EM map:

phenix.local_resolution half_map_A.mrc half_map_B.mrc

Possible Problems

If the half-maps are not actually independent the procedure will not work well

Specific limitations and problems:

If you have a very large map, this procedure can be really slow. If your map is large but is mostly empty, it may be helpful to run map_box to select just the region of your two half-maps where your molecule is located before running local_resolution.


Additional information

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