Open AccessIterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard
Author(s) -
Terwilliger Thomas C.,
GrosseKunstleve Ralf W.,
Afonine Pavel V.,
Moriarty Nigel W.,
Zwart Peter H.,
Hung LiWei,
Read Randy J.,
Adams Paul D.
Publication year - 2008
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s090744490705024x
Subject(s) - wizard , computer science , ranging , factor (programming language) , model building , resolution (logic) , set (abstract data type) , algorithm , programming language , physics , telecommunications , quantum mechanics , world wide web
The PHENIX AutoBuild wizard is a highly automated tool for iterative model building, structure refinement and density modification using RESOLVE model building, RESOLVE statistical density modification and phenix.refine structure refinement. Recent advances in the AutoBuild wizard and phenix.refine include automated detection and application of NCS from models as they are built, extensive model‐completion algorithms and automated solvent‐molecule picking. Model‐completion algorithms in the AutoBuild wizard include loop building, crossovers between chains in different models of a structure and side‐chain optimization. The AutoBuild wizard has been applied to a set of 48 structures at resolutions ranging from 1.1 to 3.2 Å, resulting in a mean R factor of 0.24 and a mean free R factor of 0.29. The R factor of the final model is dependent on the quality of the starting electron density and is relatively independent of resolution.