Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard [0.03%]
利用PHENIX AutoBuild 向导进行迭代建模、结构优化和密度修正
Thomas C Terwilliger,Ralf W Grosse-Kunstleve,Pavel V Afonine et al.
Thomas C Terwilliger et al.
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...
Serge X Cohen,Marouane Ben Jelloul,Fei Long et al.
Serge X Cohen et al.
Automatic iterative model (re-)building, as implemented in ARP/wARP and its new control system flex-wARP, is particularly well suited to follow structure solution by molecular replacement. More than 100 molecular-replacement solutions autom...
Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis [0.03%]
基于模态分析处理分子替代及结晶学优化中的结构变体问题
Marc Delarue
Marc Delarue
Normal-mode analysis (NMA) can be used to generate multiple structural variants of a given template model, thereby increasing the chance of finding the molecular-replacement solution. Here, it is shown that it is also possible to directly r...
Model preparation in MOLREP and examples of model improvement using X-ray data [0.03%]
MOLREP中的模型准备及利用X射线数据改善模型的例子
Andrey A Lebedev,Alexei A Vagin,Garib N Murshudov
Andrey A Lebedev
The success of molecular replacement is critically dependent on the quality of the search model. Several model-preparation procedures are integrated in the molecular-replacement program MOLREP. These include model modification on the basis ...
Geoffrey J Barton
Geoffrey J Barton
This article focuses on the key step of obtaining the best possible sequence alignment of the Query (the protein you are interested in) to the Target (a protein of known three-dimensional structure) in order to build a molecular model for m...
Eleanor Dodson
Eleanor Dodson
This review addresses the essential questions to consider when attempting to phase a new crystal structure using molecular replacement. Sequence matching can suggest whether there is a suitable three-dimensional model available, but it is a...
Stefano Trapani,Jorge Navaza
Stefano Trapani
An account is given of the latest developments of the AMoRe package: new rotational search algorithms, exploitation of noncrystallographic symmetry, generation and use of ensemble models and interactive graphical molecular replacement.
Philip Evans,Airlie McCoy
Philip Evans
Molecular replacement is fundamentally a simple trial-and-error method of solving crystal structures when a suitable related model is available. The underlying simplicity of the method is often obscured by the mathematical trickery required...
Mariusz Jaskolski,Miroslaw Gilski,Zbigniew Dauter et al.
Mariusz Jaskolski et al.
Experimental determination of optimal root-mean-square deviations of macromolecular bond lengths and angles from their restrained ideal values [0.03%]
实验确定限制理想值的大分子键长和键角的最佳均方根偏差数值上限
Ian J Tickle
Ian J Tickle
A number of inconsistencies are apparent in the recent research paper by Jaskolski et al. [(2007), Acta Cryst. D63, 611-620] concerning their recommendations for the values of the magnitude and resolution-dependence of the root-mean-square ...