Author(s)

• local_resolution: Tom Terwilliger

Purpose

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

Examples

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.

Literature

Additional information

List of all available keywords

• job_title = None Job title in PHENIX GUI, not used on command line
• input_files
  • map_model
    • full_map = None Input full map file
    • half_map = None Input half map files
    • model = None Input model file
• output
  • local_resolution_map = default Local resolution map file name
  • adjust_local_resolution_coloring = False Adjust local resolution coloring based on limits of resolution. Default is to use a standard coloring scheme.
  • full_map = default Full map file name. Same as input full map if supplied, otherwise result of default run of local_aniso_sharpen on half maps
  • overwrite = True Overwrite files with same names
  • file_name = None Not used
  • filename = None Not used
  • serial = None Not used
• local_resolution
  • method = boxes *fft Method for local resolution. Boxes means calculate resolution in boxes and display smoothed values. FFT means use FFT-based method to estimate resolution in one step
  • n_bins = None Number of bins for analyses
  • n_bins_default_boxes = 2000 Default bins for boxes method
  • n_bins_default_fft = 20 Default bins for fft method
  • min_bin_width = 20 Minimum number of Fourier coefficients per bin. Overrides value of n_bins.
  • max_resolution_ratio = 10 Maximum resolution as ratio to minimum. Maximum resolution will be truncated at this value
  • n_boxes = None Number of boxes
  • box_size_grid_units = None Size of core region of boxes (not including region where mask is applied, in grid units
  • smoothing_radius_ratio = 1 Ratio of smoothing radius to resolution (FFT only)
• crystal_info
  • resolution = None Nominal resolution of map
• control
  • multiprocessing = *multiprocessing sge lsf pbs condor pbspro slurm Choices are multiprocessing (single machine) or queuing systems Not implemented
  • queue_run_command = None run command for queue jobs. For example qsub. Not implemented
  • nproc = 1 Number of processors to use. NOTE: by default multiple processors will only be used in the map-to-model step (this is because multiprocessing requires writing out nproc sets of huge files and it can be very slow with distributed queues.). You can override this with force_nproc = True.
• guiGUI-specific parameter required for output directory
  • output_dir = None