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XtalView/Xfit——一个用于处理原子坐标和电子密度的通用程序。

XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density.

作者信息

McRee D E

机构信息

Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA.

出版信息

J Struct Biol. 1999 Apr-May;125(2-3):156-65. doi: 10.1006/jsbi.1999.4094.

Abstract

Xfit is a model-building and map viewing program in XtalView that is used by the structural biology community including researchers in the fields of crystallography, molecular modeling, and electron microscopy. Among its distinguishing features are built-in fast Fourier transforms that allow users flexibility in map calculations including the creation of OMIT maps and the updating of structure factors to reflect model changes from within the program. Written in C and using the freely available XView toolkit, it is highly portable to almost any X-windows based workstation including Intel-based LINUX systems. Its user interface is designed to aid in facile model-building and contains a semiautomated fitting system that allows the user to interactively and rapidly build chain de novo into an electron density map. The program is highly optimized to allow such features as interactive contour levels and map calculations to be completed within a few seconds. Features in the latest version including phase-combination, solvent-flattening, automated water addition, and small-probe dot contact surfaces, as well as basic design features, are discussed.

摘要

Xfit是XtalView中的一个模型构建和地图查看程序,被结构生物学界所使用,包括晶体学、分子建模和电子显微镜领域的研究人员。其显著特点包括内置快速傅里叶变换,这使得用户在地图计算方面具有灵活性,包括创建省略地图以及更新结构因子以反映程序内部模型的变化。它用C语言编写并使用免费的XView工具包,几乎可以高度移植到任何基于X窗口的工作站,包括基于英特尔的LINUX系统。其用户界面旨在辅助轻松进行模型构建,并且包含一个半自动拟合系统,允许用户以交互方式快速将链从头构建到电子密度图中。该程序经过高度优化,能够在几秒钟内完成诸如交互式轮廓级别和地图计算等功能。讨论了最新版本中的功能,包括相位组合、溶剂扁平化、自动加水和小探针点接触表面,以及基本设计功能。

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