冷冻电镜密度图可视化软件VAT4M

VAT4M: Visualization Software for CryoEM Density Map

基于冷冻电镜三维密度图的特征分析,研究开发了冷冻电镜密度图可视化软件VAT4M(Visual Analysis Tools for Macro-Molecule Map and Model),实现了对三维冷冻电镜密度图的可视化分析,其主要功能包括密度图和分子模型的可视化、密度图的分割和晶体结构在密度图中的匹配。在可视化方面,在实现等值面可视化方法的同时还实现了体绘制可视化模式。对于结构分析,VAT4M提供了自动分割工具,和所见即所得的分割浏览器。同时,VAT4M还提供了极值吸收法与梯度法相结合的自动匹配方法,而且,对于具有对称性的密度图,可根据一个亚基的匹配结果,迅速得到其准原子模型。最后给出了若干应用实例。实验表明,本平台对冷冻电镜密度数据具有良好的可视与分析功能。

The visualization software VAT4M （ Visual Analysis Tools for Macro-Molecule Map and Model） is discussed, which is developed for analyzing density map from CryoEM （Cryo-electronic microscope）. Its main functions include the visualization of density maps and crystal structures, the segmentation of density maps, and the structure fitting of density maps and crystal structures. It supports volume rendering and isosurface for the visualization of density maps, the automatic segmentation tool, and the convenient explorer of segmentation results. Moreover, the extreme absorption algorithm and the gradient method are proposed for automatic structure fitting. When the density map is symmetric, the pseudo-atomic structure of density map can be quickly obtained according to the fitted result of one sub-structure. Finally, three examples are discussed, which demonstrates the efficiency of this software.