Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
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DOI：
10.1107/s2059798319011471
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发表时间：
2019-10-01
影响因子：
2.2
通讯作者：
Adams, Paul D.
中科院分区：
文献类型：
--
作者：
Liebschner, Dorothee;Afonine, Pavel V.;Adams, Paul D.
衍射(X射线、中子和电子)和电子冷冻显微镜是确定三维大分子结构的有力手段，这对于了解生物过程和开发新的治疗疾病的方法是必要的。这些技术的整体结构-解决方案工作流程相似，但存在细微差别，因为简化的实验数据的属性不同。因此，应为每种方法量身定制用于确定结构的软件工具。Phenix是一个用于确定大分子结构的综合软件包，可以处理这些技术中的任何一种数据。与Phenix一起执行的任务包括数据质量评估、地图改进、模型建立、验证/重建/改进周期和沉积。每个工具都迎合实验数据的类型。Phenix的设计强调在可能的情况下程序的自动化，以最大限度地减少重复和耗时的手动任务，而选择默认参数是为了鼓励最佳实践。图形用户界面提供了对Phenix的许多命令行功能的访问，并简化了程序之间的转换、项目跟踪和以前任务的重新运行。
Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.