Author

• Randy J Read

Purpose

The reduce_cryoem_resolution tool constructs a realistic set of lower-resolution maps by adding random noise to the half-maps. Noise is added as a function of resolution of the Fourier terms so that the resulting half-map FSC curve looks typical of an experimental map at that resolution.

How reduce_cryoem_resolution works

A study of hundreds of FSC curves from maps in the EMDB at different resolutions showed that these FSC curves could be approximated very well with a simple functional form that depends only on the nominal resolution of the map. To reduce the resolution to match the generic curve requires evaluating the signal to noise ratio from the input half-maps, than adding resolution-dependent random noise to produce the desired FSC curve. To avoid including any information beyond the target resolution, the Fourier terms are filtered at the target resolution, where the half-map FSC is 0.143. The two half-maps and the corresponding averaged full map are produced, in addition to an optional plot showing half-map FSC curves for the original and reduced-resolution maps.

Running reduce_cryoem_resolution

This can be controlled by an input script using the phil syntax, either on the command line or in a phil file. The command to take two half-maps and limit a starting resolution of 3A to 4A, while producing the FSC plot, looks like this:

phenix.reduce_cryoEM_resolution hm1.mrc hm2.mrc d_min=3.0 target_d_min=4.0 plot=True

Note that the starting d_min is optional, but is useful if you want to compare the maps over their full resolution ranges.

It is recommended to start with half-maps when they are available, but it is also possible to reduce the resolution of a single full map. Here it is assumed that the map is close to perfect at the new resolution limit.

phenix.reduce_cryoEM_resolution full.mrc target_d_min=4.0

List of all available keywords

• d_min = None Nominal resolution of input map(s) (Angstroms). Optional to see initial FSC
• target_d_min = None Desired high-resolution limit (Angstroms)
• mute = False Flag to mute standard output
• map_model
  • full_map = None Input full map file
  • half_map = None Input half map files
• output_files
  • output_dir = "." Directory where output files will be written
  • file_root = "reduced_resolution" Filename root for resulting output map file(s)
  • plot = False Flag to make and save FSC plot