Conventions and workflows for using Situs.
Conventions and workflows for using Situs.
复制标题
DOI：
10.1107/s0907444911049791
复制
发表时间：
2012-04
期刊：
影响因子：
--
通讯作者：
Wriggers W
中科院分区：
文献类型：
--
作者：
Wriggers W
综述了多尺度建模软件SUTUS的最新进展。描述了在处理来自电子显微镜、断层摄影术或小角X射线散射的生物物理数据时遇到的典型工作流程和约定。SITUS是一个模块化程序包，用于对来自电子显微镜、断层扫描或小角X射线散射的原子分辨率结构和低分辨率生物物理数据进行多尺度建模。本文概述了SITURS包的最新发展，重点介绍了对实际应用很重要的工作流程和约定。程序的模块化设计促进了bash外壳中的脚本编写，允许以超出开发人员原始意图的创造性方式组合特定的程序。描述了几种启用脚本的功能，例如数据类型的灵活转换、对称约束的使用或创建二维投影图像。在这种工作流程中，低分辨率生物物理地图的处理不仅遵循基本原则，而且往往依赖于隐含的惯例。回顾和总结了与地图格式、分辨率、相关函数和特征检测相关的SITUS约定。讨论了SITUS工作流与CCP4约定和程序的兼容性。
Recent developments of the Situs software suite for multi-scale modeling are reviewed. Typical workflows and conventions encountered during processing of biophysical data from electron microscopy, tomography or small-angle X-ray scattering are described. Situs is a modular program package for the multi-scale modeling of atomic resolution structures and low-resolution biophysical data from electron microscopy, tomography or small-angle X-ray scattering. This article provides an overview of recent developments in the Situs package, with an emphasis on workflows and conventions that are important for practical applications. The modular design of the programs facilitates scripting in the bash shell that allows specific programs to be combined in creative ways that go beyond the original intent of the developers. Several scripting-enabled functionalities, such as flexible transformations of data type, the use of symmetry constraints or the creation of two-dimensional projection images, are described. The processing of low-resolution biophysical maps in such workflows follows not only first principles but often relies on implicit conventions. Situs conventions related to map formats, resolution, correlation functions and feature detection are reviewed and summarized. The compatibility of the Situs workflow with CCP4 conventions and programs is discussed.