ARP⧸wARP and Automatic Interpretation of Protein Electron Density Maps

Abstract

Publisher Summary This chapter presents phase improvement, coupled with automated map interpretation and model building, as one unified process within the framework of the automated refinement procedure (ARP/wARP) software suite. ARP/wARP is an experimental hypothesis-generating and testing procedure for placing atoms in the most likely places (according to density) and using graph-searching combined with geometric comparisons against expected stereochemical parameters to determine the most likely mainchain fragments. ARP/wARP is a software suite (copyrighted by the European Molecular Biology Laboratory) based on the paradigm of viewing model building and refinement as one unified procedure for optimizing phase estimates. The current version ARP/wARP 6.0, released in July 2002, works with density recognition-driven procedures for placing and removing atoms and therefore is limited to diffraction data extending to about 2.5 A. The iterative cycles of density modeling by the placement of atoms, unrestrained refinement of their parameters, automated model building, and restrained refinement of the hybrid model provide a powerful means of phase refinement.