Software extensions to UCSF Chimera for interactive visualization of large molecular assemblies
Software extensions to UCSF Chimera for interactive visualization of large molecular assemblies
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DOI：
10.1016/j.str.2005.01.006
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发表时间：
2005-03-01
期刊：
影响因子：
5.7
通讯作者：
Ferrin, TE
中科院分区：
文献类型：
--
作者：
Goddard, TD;Huang, CC;Ferrin, TE
许多大分子组合的结构，如病毒衣壳和核糖体，已被实验确定为原子分辨率。我们考虑了在大型组件的交互式可视化和分析中出现的四个软件问题：如何有效地表示多定时器，如何制作卡通表示，如何有效地计算接触，以及如何选择子组件。我们描述了我们开发的技术和算法，并给出了使用它们的例子。现有的分子可视化程序可以很好地用于单个蛋白质和核酸分子以及小的复合物。本文提出的方法是作为添加到现有程序或包含在下一代可视化软件中的功能，以允许轻松探索包含数十到数千个大分子的组装。我们的方法是实用的，强调代码的简单性、可靠性和速度。所描述的方法已作为UCSF Chimera （www.cgl.ucsf.edu/ Chimera）分子图形程序的多尺度扩展分发。
Many structures of large molecular assemblies such as virus capsids and ribosomes have been experimentally determined to atomic resolution. We consider four software problems that arise in interactive visualization and analysis of large assemblies:. how to represent multimers efficiently, how to make cartoon representations, how to calculate contacts efficiently, and how to select subassemblies. We describe techniques and algorithms we have developed and give examples of their use. Existing molecular visualization programs work well for single protein and nucleic acid molecules and for small complexes. The methods presented here are proposed as features to add to existing programs or include in next-generation visualization software to allow easy exploration of assemblies containing tens to thousands of macromolecules. Our approach is pragmatic, emphasizing simplicity of code, reliability, and speed. The methods described have been distributed as the Multiscale extension of the UCSF Chimera (www.cgl.ucsf.edu/ chimera) molecular graphics program.