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.

Literature

• Finding non-crystallographic symmetry in density maps of macromolecular structures. T.C. Terwilliger. J Struct Funct Genomics 14, 91-5 (2013).

List of all available keywords

• 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
    • target_output_format = *None pdb mmcif Desired output format (if possible). Choices are None ( try to use input format), pdb, mmcif. If output model does not fit in pdb format, mmcif will be used. Default is pdb.
    • 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_centers = 1 Report up to n_centers centers
    • 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' "