This chapter describes experimental phasing methods as implemented in SHELX. After introducing fundamental concepts underlying all experimental phasing approaches, the methods used by SHELXC/D/E are described in greater detail, such as dual-space direct methods, Patterson seeding and density modification with the sphere of influence algorithm. Intensity differences from data for experimental phasing can also be used for the generation and usage of difference maps with ANODE for validation and phasing purposes. A short section describes how molecular replacement can be combined with experimental phasing methods. The second half covers practical challenges, such as prerequisites for successful experimental phasing, evaluation of potential solutions, and what to do if substructure search or density modification fails. It is also shown how auto-tracing in SHELXE can improve automation and how it ties in with automatic model building after phasing.
Thorn, A. (2017). Experimental phasing: Substructure solution and density modification as implemented in SHELX. In Methods in Molecular Biology (Vol. 1607, pp. 357–376). Humana Press Inc. https://doi.org/10.1007/978-1-4939-7000-1_15