Guess location of molecular centers in a map with guess_molecular_centers

Author(s)

Purpose

Usage

How guess_molecular_centers works:

Output files from guess_molecular_centers

Examples

Standard run of guess_molecular_centers:

Possible Problems

Specific limitations and problems:

Literature

Additional information

List of all guess_molecular_centers keywords

Author(s)

• guess_molecular_centers: Tom Terwilliger

Purpose

guess_molecular_centers is a tool to identify potential locations of molecules in an electron density map.

Usage

How guess_molecular_centers works:

guess_molecular_centers identifies centers of macromolecules in the density map by finding local maxima of the local RMS density. You can specify the radius of the sphere used to estimate local RMS density.

Output files from guess_molecular_centers

guess_molecular_centers.pdb: A PDB file with pseudo-atoms marking the locations of centers of your molecule(s)

Examples

Standard run of guess_molecular_centers:

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

phenix.guess_molecular_centers  map_coeffs.mtz 

Possible Problems

If your molecule is large, you may wish to increase the radius used for smoothing (smoothing_radius). If you cannot find the centers you want, you can try looking for more by increasing n_centers_find.

Specific limitations and problems:

Literature

Additional information

List of all guess_molecular_centers 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
------------------------------------------------------------------------------- 
guess_molecular_centers
   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 guess_molecular_centers 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
      pdb_out= guess_molecular_centers.pdb Output PDB file
      log= guess_molecular_centers.log Output log file
      params_out= guess_molecular_centers_params.eff Parameters file to rerun
                  guess_molecular_centers
   directories
      temp_dir= "temp_dir" Optional temporary work directory
      output_dir= "" Output directory where files are to be written
   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
   crystal_info
      resolution= 0. high-resolution limit for map calculation
      solvent_fraction= 0.5 solvent fraction
   control
      verbose= True Verbose output
      raise_sorry= False Raise sorry if problems
      debug= False Debugging output
      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' "