Author(s)

• mtriage: Pavel Afonine, Billy Poon (GUI)

Purpose

The routine mtriage will evaluate the resolution in a map, compare half-maps, and provide some basic statistics about the map

Usage

How mtriage works:

Possible inputs to mtriage are:

• one full map;
• one full map and two half-maps;
• one full map and a file with atomic model;
• one full map, a file with atomic model and two half-maps.

If only one map is provided, mtriage will calculte some basic map stitistics (min, max, mean, standard deviation), show histogram of map values and calculate resolution estimate d99.

If two half-maps are given in addition to the full map, then FSC curve between the two half-maps will be calculated as well as resolution estimate d_FSC(0.143).

If an atomic model is provided then two sets of statistics will be calculated: using original and masked maps. The soft mask is calculated using the atomic model as described in citation below. Also, some model-based resolution estimates will be calculated, such as d_model and d_FSC_model as well as map-model FSC curve.

Model file can be in PDB or mmCIF formats. Map file is expected to be CCP4, mrc or other related format.

Guide to resolution estimates:

• d_FSC - highest resolution at which the experimental data are confident. Obtained from FSC curve calculated using two half-maps and taken at FSC=0.143.
• d99 - resolution cutoff beyond which Fourier map coefficients are negligeably small. Calculated form the map.
• d_model - resolution cutoff at which the model map is the most similar to the target (experimental) map. Requires map and model. For d_model to be meaningful, model is expected to fit the map as good as possible.
• d_FSC_model - resolution cutoff up to which the model and map Fourier coefficients are similar.

Refer to Table 2 in article below for more details about interpretation of various resolution estimates.

Examples

Standard run of mtriage:

Running mtriage is easy. From the command-line you can type:

phenix.mtriage map.mrc
phenix.mtriage map.mrc half_map_1.map half_map_2.map
phenix.mtriage map.mrc model.pdb
phenix.mtriage map.mrc model.pdb half_map_1.map half_map_2.map

Possible Problems

All inputs maps are expected to be on the same grid, the program will stop otherwise. Box information (aka unit cell CRYST1 in PDB files, for example) must match across all inputs.

Specific limitations and problems:

Reference

• New tools for the analysis and validation of cryo-EM maps and atomic models. P.V. Afonine, B.P. Klaholz, N.W. Moriarty, B.K. Poon, O.V. Sobolev, T.C. Terwilliger, P.D. Adams, and A. Urzhumtsev. Acta Cryst. D74, 814-840 (2018).

Additional information

List of all available keywords

• scattering_table = wk1995 it1992 n_gaussian neutron *electron Scattering table (X-ray, neutron or electron)
• resolution = None Map resolution (d_FSC)
• mask_maps = None Mask out region outside molecule
• auto_mask_if_no_model = True If mask_maps is set and no model is present, mask based on density
• auto_mask_if_model = False If mask_maps is set and model is present, mask based on density
• radius_smooth = None Mask smoothing radius
• radius_smooth_ratio = 2 If mask smoothing radius is not specified it will be radius_smooth_ratio times the resolution
• n_bins = None Number of bins for FSC curves. Suggested number is 5000. Alternative is default (None) which gives bins of width 100.
• nproc = 1 Number of processors to use
• show_time = False Show individual run times for each step
• include_curves = True Keep FSC curves
• include_mask = True Keep mask
• wrapping = None You can ignore the wrapping information from map files and set it
• fsc_model_plot_file_name_prefix = fsc_model
• fsc_half_maps_file_name_prefix = fsc_half_maps
• write_mask_file = True
• mask_file_name = mask.ccp4
• soft_mask = True Use soft mask when running box_map_before_analysis. Reduces artifacts from boxing.
• box_map_before_analysis = False You can box the map (cut out box a little bigger than supplied model) before any analysis if you want. This will make the analysis faster, but it can introduce masking artifacts. Artifacts reduced with soft_mask = True. Requires a model. If model is similar in size or bigger than the map this will extend the map around the model using data from the opposite part of the map.
• ignore_symmetry_conflicts = False You can ignore the symmetry information (CRYST1) from coordinate files. This may be necessary if your model has been placed in a box with box_map for example.
• job_title = None Job title in PHENIX GUI, not used on command line
• map_model
  • full_map = None Input full map file
  • half_map = None Input half map files
  • model = None Input model file
• compute
  • map_counts = True Compute map counts
  • fsc_curve_model = True Compute model-map CC in reciprocal space: FSC(model map, data map)
  • d_fsc_half_map_05 = False Compute d_half_map (FSC=0.5)
  • d_fsc_model_05 = True Compute d_fsc_model (FSC=0.5)
  • d_fsc_model_0 = True Compute d_fsc_model (FSC=0)
  • d_fsc_model_0143 = True Compute d_fsc_model (FSC=0.143)
  • d_model = True Resolution estimate using model and map
  • d_model_b0 = True Resolution estimate using model and map, assumin all atoms B=0
  • d99 = True Resolution estimate d99
• output
  • write_fsc_as_xml = True Exports FSC curve (half maps) in XML format for EMDB
• guiGUI-specific parameter required for output directory
  • output_dir = None