ASIR: an automatic procedure for determining solvent structure in protein crystallography

A procedure for automating the determination of solvent positions in a protein crystal structure refinement has been developed (ASIR: automatic solvent inclusion and refinement). In contrast to previously published computer programs which predict probable solvent structure in proteins, this procedure simulates as fully as possible the conventional manual process of determining solvent structure in protein crystallography. ASIR also features a method for tracking all solvent and unexplained difference electron-density peaks during refinement. A definition for equivalent water molecules in homologous proteins is also discussed, clarifying an ambiguity in the current literature. Five test cases are presented. They demonstrate that this automatic procedure can perform comparably to a strict conventional manual approach, while significantly reducing the time required to complete protein structure refinement.