Computational protocol: Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard

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Protocol publication

[…] The purpose of the AutoBuild wizard is to provide a highly automated system for model rebuilding and completion. The wizard design allows the user to specify data files and parameters through an interactive GUI or alternatively through keyworded scripts. The AutoBuild wizard begins with data files with structure-factor amplitudes and uncertainties, along with either experimental phase information or a starting model, typically from molecular replacement. It then carries out cycles of model building and structure refinement alternating with model-based density modification and produces a relatively complete atomic model.The AutoBuild wizard has been designed for ease of use combined with maximal user control, with as many parameters set automatically by the wizard as possible, but maintaining parameters accessible to the user through a GUI and through keyword-based scripts. The wizard uses the input/output routines of the cctbx library (Grosse-Kunstleve et al., 2004) allowing data files of many different formats, so that user data need not be converted to any particular format before using the wizard. Use of the phenix.refine refinement package (Afonine et al., 2005b ) in the AutoBuild wizard allows a high degree of automation of refinement so that neither the user nor the wizard is required to specify parameters for refinement. The phenix.refine package automatically includes a robust bulk-solvent model and automatically places solvent molecules (Afonine et al., 2005a ).The five core modules in the AutoBuild wizard are (i) building a new model into an electron-density map, (ii) rebuilding an existing model, (iii) refinement, (iv) iterative model building beginning from experimental phase information and (v) iterative model building beginning from a model. These five procedures are described in the next sections.The standard procedures available in the AutoBuild wizard that are based on these modules include (1) model building and completion starting from experimental phases, (2) rebuilding a model from scratch, with or without experimental phase information, and (3) rebuilding a model in place, maintaining connectivity and sequence register. In cases where the starting point is a set of experimental phases and structure-factor amplitudes, procedure (1) is normally carried out and the resulting model is then rebuilt with procedure (2). In cases where the starting point is a model (e.g. from molecular replacement) and experimental structure-factor amplitudes, procedure (3) is normally carried out if the starting model differs by less than about 5% in sequence from the desired model; otherwise, procedure (2) is used. […]

Pipeline specifications

Software tools cctbx, PHENIX
Application Protein structure analysis