Figure 1.

Overview of Guided Ligand Replacement (GLR) as implemented in Phenix. Core routines are outlined by short dashes. Inputs are outlined by long dashes. The top box lists input related to the target structure: (i) the apo model into which the ligand is to be placed (e.g. molecular-replacement solution), (ii) structure factors in order to generate an electron-density map for real-space refinement and (iii) ligand specification. The right box lists ways in which the structure of the reference protein–ligand complex can be obtained: (i) provide it directly, (ii) provide a directory of protein–ligand complexes to be searched, (iii) poll the Chemical Component Dictionary through the RCSB web service and (iv) a user-written query to another structural database (e.g. a proprietary database in the pharmaceutical industry). The functionality outlined by double lines is part of the Phenix distribution.