Given a set of atomic coordinates, MKMASK builds a mask of the 3-D unit cell which represents the atom sites as spheres of a given radius. The solvent region of the unit cell is indicated in the mask by zero values while non-solvent regions are depicted by non-zero values. This mask is output to an unformatted binary file and can then be used by APMASK to carry out a solvent flattening procedure.

Cell dimensions, crystallographic symmetry information and the atomic coordinates for the unit cell to be masked are supplied by an input bdf. The layout and orientation of the desired mask can also be provided by the bdf from records 21, 22 (described in the FOURR write-up). Otherwise, the user can describe the mask using the layout line.

NOTE: When the mask is used by APMASK for solvent flattening of a corresponding density map, the layout and orientation of the density map and the mask must be identical.

Reads input archive bdf to be modified

Writes modified output archive bdf

MKMASK sum

layout do ac la 50 50 70 1 1 1

param *4 2 2 2

In this example, the layout for the mask is not taken from the input bdf as is the cell dimensions, symmetry and atomic coordinates. Instead, the layout line specifies that x will follow down the mask grid, y will progress across the grid and z will run layer to layer in the grid. The grid dimension will be x=50, y=50 and z=50 units, all incrementing by 1 unit. In the process of building the mask, any atom sites falling within 2 Angstroms outside the unit cell boundaries will be symmetrically mapped into the mask grid. Values of the mask will refect a count of the number of overlapping atom sites at each grid location within the molecule region. The map will contain zeros in the non-molecule (solvent) region.