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Finding NCS from density in a map with find_ncs_from_density

Author(s)
Purpose
Usage
How find_ncs_from_density works:
Output files from find_ncs_from_density
Examples
Standard run of find_ncs_from_density:
Possible Problems
Specific limitations and problems:
Literature
Additional information
List of all find_ncs_from_density keywords

Author(s)

  • find_ncs_from_density: Tom Terwilliger

Purpose

find_ncs_from_density is a tool to identify NCS relationships directly from an electron density map specified with a map coefficients file. It writes out the NCS operators in a format that can be read by find_ncs and by the PHENIX wizards. Usually find_ncs_from_density is used through find_ncs (phenix.find_ncs contains find_ncs_from_density).

Usage

How find_ncs_from_density works:

  • The find_ncs_from_density algorithm first identifies potential locations of centers of macromolecules in the density map by finding maxima of the local RMS density using phenix.guess_molecular_centers.
  • Then it cuts out a sphere of density centered at a trial center and carries out an FFT-based rotation-translation search to find all occurrences of similar density in the asymmetric unit of your map.
  • The region over which NCS-related correlation is high is identified and the operators are written out as a "find_ncs.ncs_spec" file that can be read by the phenix wizards and a "find_ncs.phenix_refine" file that can be read by phenix.refine.
  • You can run the algorithm as a whole or you can run each part separately with phenix.guess_molecular_centers and phenix.find_ncs_from_density.
  • 
    
    
    

    Output files from find_ncs_from_density

    find_ncs_from_density.ncs_spec: A formatted file that can be read by phenix.find_ncs and the PHENIX wizards that specifies the NCS operators. temp_dir/ncs_avg_map_coeffs.mtz: This is an mtz file with just one averaged NCS region written out in space group P1.

    Examples

    Standard run of find_ncs_from_density:

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

    phenix.find_ncs_from_density  map_coeffs.mtz 
    

    Possible Problems

    If your molecule is large, you may wish to increase the radius used for NCS identification (density_radius) and the peak separation (peak_separation). If your molecule has pseudo-symmetry you may also want to increase these parameters.

    If you know how many NCS copies are present, you may wish to specifying that with ncs_copies_max.

    Specific limitations and problems:

    Literature

    Additional information

    List of all find_ncs_from_density 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
    ------------------------------------------------------------------------------- 
    find_ncs_from_density
       input_files
          mtz_in= None MTZ file with coefficients for a map
          labin= "" Labin line for MTZ file with map coefficients. This is
                 optional if find_ncs_from_density can guess the correct
                 coefficients for FP PHI and FOM. Otherwise specify: LABIN FP=myFP
                 PHIB=myPHI FOM=myFOM where myFP is your column label for FP
          center_pdb_in= None Optional PDB file with list of centers of density to
                         be used as search model
          density_mtz_in= None MTZ file with coefficients for density around
                          center defined by first atom in center_pdb_in (required)
                          NOTE: Must be in space group p1 with identical cell to
                          mtz_in
          density_labin= "" Labin line for MTZ file density_mtz_in. This is
                         optional if find_ncs_from_density can guess the correct
                         coefficients for FP PHI and FOM. Otherwise specify: LABIN
                         FP=myFP PHIB=myPHI FOM=myFOM where myFP is your column
                         label for FP
       output_files
          centers_pdb_out= guess_molecular_centers.pdb Output PDB file with coords
                           of centers
          log= find_ncs_from_density.log Output log file
          ncs_spec_file= 'find_ncs_from_density.ncs_spec' NCS specification file
                         with all NCS information
          params_out= find_ncs_from_density_params.eff Parameters file to rerun
                      find_ncs_from_density
       directories
          temp_dir= "temp_dir" Temporary work directory
          output_dir= "" Output directory where files are to be written
       density_search
          density_radius= 10. Radius for density to be cut out and compared
          peak_separation= 15 Minimum distance between centers. Use about
                           1.5*density_radius
          density_peaks= 20 Number of NCS-related peaks of density to output
          delta_phi= 20 Angular spacing of search
          ncs_copies_max= None Maximum number of NCS copies to look for
          min_ratio_to_top_cc= 0.75 Peaks will be kept up to ncs_copies_max, or
                               min_ratio_to_top_cc * best cc, whichever comes
                               first
          minimum_ncs_cc= 0.40 Overall NCS CC at full resolution must be at least
                          this high
          dump_ncs_density= False You can dump 1 mtz file for each possible NCS
                            copy so that you can see if the NCS is real Each file
                            has the local map transformed to the orientation and
                            position of copy 1 so they should all superimpose
       find_centers
          smoothing_radius= 10. Radius for smoothing squared density to find
                            centers Choose a smaller value to get more center
                            guesses
          n_center_find= None Target number of centers to find Smoothing radius
                         will be varied from 2 to 2*smoothing_radius and the value
                         giving the number of peaks closest to n_center_find will
                         be used
          n_center_use= 1 Number of locations to consider as molecular centers in
                        density search
       crystal_info
          resolution= 4. High-resolution limit for map calculation It is useful to
                      cut the resolution at 3-5 A If you use higher resolution,
                      use a finer delta_phi
          solvent_fraction= 0.5 solvent fraction
       control
          verbose= True Verbose output
          debug= False Debugging output
          raise_sorry= False Raise sorry if problems
          dry_run= False Just read in and check parameter names
          resolve_command_list= None You can supply any resolve command here NOTE:
                                for command-line usage you need to enclose the
                                whole set of commands in double quotes (")
                                and each individual command in single quotes (')
                                like this: resolve_command_list="'no_build'
                                'b_overall 23' "