Direct-space methods in phase extension and phase determination. I. Low-density elimination

A density-modification procedure for phase extension and refinement is described which replaces all density less than one-fifth of the height of a light-atom peak by zero. Its effectiveness is demonstrated by applications to a small and a medium-size protein structure. With high-resolution data, for the small protein, it is possible to extend and refine from 3 to 1 Å with a mean phase error less than 30°. Successful phase extension from 4 Å is also possible. In general it is shown that phase extension to high resolution gives less error than extension to lower resolution. It has also been shown that for a small protein it is possible to obtain an ab initio solution of the structure by refining from a complete set of random phases for all reflexions.