Finding and analyzing difference map peaks

Overview

Configuration

Output

List of all find_peaks_holes keywords

Overview

phenix.find_peaks_holes is a utility for identifying points of interest in difference maps, typically at the end of refinement. It will calculate an mFo-DFc map and locate peaks and holes, plus anomalous map peaks (if anomalous data are provided) and flagging of waters with suspiciously high mFo-DFc values. This information may be used to improve the model, especially in the addition of solvent and small ions.

Configuration

The program requires only a PDB file and data (including R-free flags). The default options should be sufficient for most cases, although for very large structures or especially noisy maps, you may find it helpful to increase the sigma cutoff.

By default, peaks which overlap with the input atoms (within a cutoff distance) will not be included. If you want to find all peaks, set the minimum peak-model distance to zero. Additional options are available by clicking the "Peak search" button.

On the command line, the minimal input is simply the paths to your model and data files (column labels may need to be specified if the choice is ambiguous). Running the program without arguments will print out a summary of available options, which are also listed below.

Output

A summary tab will appear at the end of the run with peak counts, plus output files and buttons to view them. By default the program will write a PDB file containing up to five "chains", all with atoms labeled UNK:

• A: mFo-DFc peaks (positive).
• B: mFo-DFc holes (negative)
• C: anomalous map peaks
• D: waters in mFo-DFc peaks
• E: waters in anomalous peaks

The program will also write the 2mFo-DFc, mFo-DFc, and anomalous (if available) maps. Additional tabs will display each type of result in a list; clicking these items will recenter the view in Coot and/or PyMOL on the selected point.

List of all find_peaks_holes keywords

------------------------------------------------------------------------------- 
Legend: black bold - scope names
        black - parameter names
        red - parameter values
        blue - parameter help
        blue bold - scope help
        Parameter values:
          * means selected parameter (where multiple choices are available)
          False is No
          True is Yes
          None means not provided, not predefined, or left up to the program
          "%3d" is a Python style formatting descriptor
------------------------------------------------------------------------------- 
map_cutoff= 3.0
anom_map_cutoff= 3.0
wavelength= None Optional parameter, if defined this will cause all atoms to
            be treated as anomalous scatterers using the standard Sasaki table
            to obtain theoretical fp and fpp values. Only really useful if the
            Phaser LLG map is being used for the anomalous map.
filter_peaks_by_2fofc= None If this is set, peaks outside 2mFo-DFc density at
                       the cutoff will be discarded. (This does not apply to
                       the analysis of solvent atoms.) Holes will not be
                       changed.
use_phaser_if_available= True If True, and Phaser is installed and configured,
                         an anomalous LLG map will be used in place of the
                         simple anomalous difference map. The wavelength
                         should be specified for this to be maximally useful.
write_pdb= True
write_maps= True
output_file_prefix= peaks_holes
job_title= None Job title in PHENIX GUI, not used on command line
input
   sequence= None
   skip_twin_detection= False
   scattering_table= wk1995 it1992 *n_gaussian neutron
   xray_data Scope of X-ray data and free-R flags
      file_name= None
      labels= None
      high_resolution= None
      low_resolution= None
      outliers_rejection= True Remove basic wilson outliers , extreme wilson
                          outliers , and beamstop shadow outliers
      french_wilson_scale= True
      sigma_fobs_rejection_criterion= None
      sigma_iobs_rejection_criterion= None
      ignore_all_zeros= True
      force_anomalous_flag_to_be_equal_to= None
      french_wilson
         max_bins= 60 Maximum number of resolution bins
         min_bin_size= 40 Minimum number of reflections per bin
      r_free_flags
         file_name= None This is normally the same as the file containing Fobs
                    and is usually selected automatically.
         label= None
         test_flag_value= None This value is usually selected automatically -
                          do not change unless you really know what you're
                          doing!
         ignore_r_free_flags= False Use all reflections in refinement (work
                              and test)
         disable_suitability_test= False
         ignore_pdb_hexdigest= False If True, disables safety check based on
                               MD5 hexdigests stored in PDB files produced by
                               previous runs.
         generate= False Generate R-free flags (if not available in input
                   files)
         fraction= 0.1
         max_free= 2000
         lattice_symmetry_max_delta= 5
         use_lattice_symmetry= True
         use_dataman_shells= False Used to avoid biasing of the test set by
                             certain types of non-crystallographic symmetry.
         n_shells= 20
   pdb
      file_name= None Model file(s) name (PDB)
   monomers
      file_name= None Monomer file(s) name (CIF)
find_peaks
   use_sigma_scaled_maps= True Default is sigma scaled map, map in absolute
                          scale is used otherwise.
   resolution_factor= 1./4.
   max_number_of_peaks= None
   map_next_to_model
      min_model_peak_dist= 1.8
      max_model_peak_dist= 6.0
      min_peak_peak_dist= 1.8
      use_hydrogens= False
   peak_search
      peak_search_level= 1
      max_peaks= 0
      interpolate= True
      min_distance_sym_equiv= None
      general_positions_only= False
      min_cross_distance= 1.8
      min_cubicle_edge= 5