Section 25.2.1.8.1.2. Masks from atomic coordinates

In some instances, it may be desirable to create masks, either for solvent flattening or NC symmetry averaging, from a set of atomic coordinates. The interactive program MDLMSK can be used for this as it accepts a set of atomic coordinates along with a masking radius, mask number and map region. It then creates a mask file spanning the requested map region such that all grid points within the region that are also within the masking radius of any model atom are assigned the specified mask value, and all other points a solvent mask value. If multiple masks are required, the interactive program MRGMSK can be used to combine separate mask files created by MDLMSK into a single mask file. For NC symmetry averaging purposes, one generally creates mask files separately for each independent molecule, using an average van der Waals radius as the masking radius, and then combines them with MRGMSK. This mask is then edited in the program MAPVIEW (see below) to maintain the outer boundary, but to fill in holes within the molecular interior. This mask can be used directly for NC symmetry averaging. If it is to be used for solvent flattening, then it must first be expanded to correspond to a full unit cell by the program BLDCEL.