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

{{phil:phenix.command_line.guess_molecular_centers}}