使用PHENIX自动构建向导进行迭代模型构建、结构优化和密度修正。
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard.
作者信息
Terwilliger Thomas C, Grosse-Kunstleve Ralf W, Afonine Pavel V, Moriarty Nigel W, Zwart Peter H, Hung Li Wei, Read Randy J, Adams Paul D
机构信息
Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA.
出版信息
Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):61-9. doi: 10.1107/S090744490705024X. Epub 2007 Dec 5.
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 A, 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.
PHENIX自动构建向导是一种高度自动化的工具，用于使用RESOLVE模型构建、RESOLVE统计密度修正和phenix.refine结构精修进行迭代模型构建、结构精修和密度修正。自动构建向导和phenix.refine的最新进展包括在构建模型时自动检测和应用来自模型的非晶体学对称性（NCS）、广泛的模型完成算法和自动溶剂分子拾取。自动构建向导中的模型完成算法包括环构建、结构不同模型中链之间的交叉以及侧链优化。自动构建向导已应用于一组分辨率在1.1至3.2埃之间的48个结构，最终平均R因子为0.24，平均自由R因子为0.29。最终模型的R因子取决于起始电子密度的质量，并且相对独立于分辨率。
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