Author(s)

• mtriage: Pavel Afonine

Purpose

The routine mtriage will evaluate the resolution in a map, compare half-maps, and compare model and map

Usage

How mtriage works:

Examples

Standard run of mtriage:

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

phenix.mtriage emd_8750.map 5w0s.pdb

where emd_8750.map is a map (CCP4, mrc or other related format) and 5w0s.pdb is a model that matches the map

Possible Problems

Specific limitations and problems:

Literature

Additional information

List of all available keywords

• map_file_name = None Map file name
• half_map_file_name_1 = None Half map file name
• half_map_file_name_2 = None Half map file name
• model_file_name = None Model file name
• 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
• radius_smooth = None Mask smoothing radius
• 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
• use_box = True Extract box from map and model and use it for calculations
• 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
• 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
• 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_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
• guiGUI-specific parameter required for output directory
  • output_dir = None