Cutting density out of a map with cut_out_density




This routine cuts density out of a map and writes an MTZ file in space group P1 with map coefficients for the cutout density. The density map is calculated from map coefficients supplied as an input MTZ file. The region to be cut out is specified through the center of the region and dimensions in X Y and Z of a box to be cut out (cutout_center=X,Y,Z and cutout_dimensions=a,b,c). Alternatively the region can be specified with a PDB file and optional atom selections, with all points within a specified radius of an atom included, or the region can be specified with a center and the radius of a sphere to include. The density in the region cut out can optionally be offset to have a mean density of zero. The region outside the cut out region always will have a density of zero. The cut out region can be optionally padded with flat density an additional distance beyond the box that is cut out (padding=xx). The resolution of the cutout map can also be specified (the input map will be truncated at the high-resolution limit specified, and the output map will extend to the high-resolution limit.)


The main uses of phenix.cut_out_density are:

Please note: you should not use phenix.cut_out_density to select regions near your model for display purposes. You can create a highly misleading map by displaying only density that is within a small radius of atoms in your model.

How cut_out_density works:

cut_out_density assumes that you are supplying map coefficients and calculates a map. Then it creates a new unit cell in space group P1 with orthogonal axes and dimensions big enough for your cut out region and padding of zero density around it. The density in your map at the center you specify is then centered at the origin in the new map. Then new map coefficients are created and written out.

You can optionally specify the region to be cut out as a box, a sphere, or a region defined by all points within a specified distance of atoms in a PDB file.

You can specify the center of the region to be cut out with its coordinates, or as the centroid of a PDB file that is input.

If you specify an input PDB file, you can use a selection string to select any part of that model (i.e., one domain or one chain) as the region to be cut out or as the center of the cut out region.

If you specify an input PDB file, then the selected atoms from that file will be offset to match the new map and written out.

As a convenience, you can re-transform a PDB file back to the original position in your original model as well.

Output files from cut_out_density

cutout.mtz: An MTZ file with your cut out density in space group P1.

cutout.pdb: A PDB file with your input molecule translated to match the offset used in creating cutout.mtz


Standard run of cut_out_density:

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

phenix.cut_out_density model.pdb map_coeffs.mtz

Preparing density for molecular replacement in Phaser:

The for_phaser=True keyword sets most of the defaults appropriately. You have to provide a PDB file with atoms defining the centers of spheres around which the density should be cut out. Set the cutout_model_radius parameter to define the size of the spheres. If you have a reasonably detailed atomic model, a value of 3. may be appropriate, but you may have a PDB file specifying one big sphere as in this command:

phenix.cut_out_density for_phaser=True cutout_model_radius=15 sphere.pdb map_coeffs.mtz

List of all available keywords