Authors

• Randy J Read, Claudia Millán, Airlie J McCoy, Thomas C Terwilliger

Purpose

The emplace_local tool docks the input model within a sphere of density centered on a defined point in the reconstruction, returning the docked model, a local weighted map, and quality of fit statistics.

How emplace_local works

Ideally, half-maps are provided, then the chosen region of density is analysed for local signal and noise (both of which are resolution and direction-dependent) to define a likelihood target for rotation and translation searches, followed by rigid-body refinement.

If half-maps are unavailable, just a full map can be provided and then the likelihood target is defined by assuming that signal-to-noise drops off isotropically to the stated resolution limit.

The quality of fit can be judged by three factors:

1) whether there is a unique solution;
2) the log-likelihood-gain (LLG) score, which should preferably be greater than 60;
3) the map correlation coefficient to the weighted map used for docking.

The basic inputs are:

model file
two unmasked half-map files (preferred) or full-map file
nominal resolution (optional if half-maps provided, but recommended)
specification of center of search region

Note that the search center can be specified explicitly with the sphere_center keyword (the usual approach) or by translating the search model to the desired search region and not providing a sphere_center keyword.

Standard run of emplace_local

phenix.voyager.emplace_local map1=half1.map map2=half2.map
    d_min=3.3 model_file=model.pdb sphere_center=100,140,170

Literature

• Likelihood-based signal and noise analysis for docking of models into cryo-EM maps. R.J. Read, C. Millán, A.J. McCoy, and T.C. Terwilliger. Acta Cryst. D79, 271-280 (2023).

• Likelihood-based docking of models into cryo-EM maps. C. Millán, A.J. McCoy, T.C. Terwilliger, and R.J. Read. Acta Cryst. D79, 281-289 (2023).

List of all available keywords

• model_file = None Search model file
• sequence_composition = None Optional sequence file with composition for full reconstruction, overrides fixed_scattering_ratio
• map = None Map file for full map (optional, not used if half-maps provided)
• map1 = None Map file for half-map 1 (optional if full map is provided)
• map2 = None Map file for half-map 2 (optional if full map is provided)
• d_min = None Nominal local resolution. Preferred but optional if half-maps provided, required otherwise
• sphere_center = None Centre of sphere for docking
• model_vrms = 1.5 estimated RMSD for model
• fixed_scattering_ratio = 1.5 Estimated scattering ratio between sphere and model
• brute_rotation = False Test all orientations instead of fast rotation function
• refine_scale = False Turn on cell_scale refinement
• output_level = *process concise summary logfile verbose testing Output level from process (minimum output) to testing
• top_files = 5 Maximum number of top docking solutions to save and report
• output
  • fileroot = top_model Manually set file root