MULTI-SCALE VISUALIZATION OF LARGE MOLECULAR COMPLEXES

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 我们正在开发加州大学旧金山分校嵌合体分子的软件扩展 建模包(用于交互的http://www.cgl.ucsf.edu/chimera) 大分子组装的可视化和分析 病毒和核糖体。这些扩展有助于研究原子 从原子细节到各种尺度的分辨率模型 二级结构(螺旋和片状)，到三级结构 (蛋白质和核酸折叠)，到四级结构(包装 形成组件的大分子)。虽然许多计算机程序 允许对小范围的蛋白质或核酸进行反复探索 大分子，没有一种能很好地与30个或更多的组装在一起 分子。已知的病毒颗粒结构由数百个 数以千计的分子，特别难用来研究 现有软件。 我们开发的软件侧重于四元结构层面。 基本功能封装在多尺度模型工具中。 它允许将分子表示为简单的表面，从而整体显示 分子形状。这种抽象对于具有以下特性的系统是必需的 数百个分子。应用对称性是另一项基本能力。 大约250个病毒衣壳结构中的大多数都有二十面体 对称性。仅指定非对称单位(衣壳的1/60) 在原子坐标文件中。我们能够利用对称性 显示整个衣壳，同时只创建原子的副本 显示非对称单位时需要的坐标 不同的风格和颜色。这对病毒衣壳很重要 它可以包含数百万个原子。除了抽象之外 表示和对称处理，这是 大型装配正在导航到相关部件。为 例如，病毒衣壳可能有两层，每层由数百人组成 蛋白质的含量。需要一种机制来隐藏外层，以便 内层是可以研究的。病毒衣壳等亚组分 在蛋白质数据库文件中，通常不会对层进行注释，因此 用户可以自行定义这些部件。我们的多尺度 扩展模块允许使用用户定义的部件导航到部件 分子群。 多尺度模型工具的详细信息发表在Goddard TD上， 黄春春，费林。UCSF嵌合体的软件扩展 大分子组装的交互式可视化。结构 (Camb)。2005年3月；13(3)：473-82。 过去几年增加的更多高级功能包括高效的 计算分子间原子接触的算法 组件，显示晶体单位细胞的能力， 能够删除组件，能够显示透明表面 与其他分子显示方式相结合，并能够 导出用于制作动画的3维模型。 这些功能已用于为病毒粒子创建图像 资源管理器网站(http://viperdb.scripps.edu/)适用于所有已知 二十面体病毒衣壳结构。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We are developing software extensions to the UCSF Chimera molecular modeling package (http://www.cgl.ucsf.edu/chimera) for interactive visualization and analysis of large molecular assemblies such as viruses and ribosomes. These extensions facilitate studying atomic resolution models over a range of scales from atomic detail, to secondary structure (helices and sheets), to tertiary structure (protein and nucleic acid folds), to quaternary structure (packing of macromolecules to form an assembly). While many computer programs permit interative exploration of small sets of protein or nucleic acid macromolecules, none work well with assemblies of 30 or more molecules. Known virus particle structures are composed of hundreds to thousands of molecules and are particularly difficult to study with existing software. The software we've developed focus on the quaternary structure level. The basic capabilities are encapsulated in the Multiscale Models tool. It allows representing molecules as simple surfaces that show overall molecular shape. This abstraction is needed for systems having hundreds of molecules. Applying symmetry is another basic capability. Most of the approximately 250 virus capsid structure have icosahedral symmetry. Only the asymmetric unit (1/60 of the capsid) is specified in atomic coordinate files. We are able to use the symmetry to display the entire capsid while only creating copies of the atomic coordinates when they are needed for displaying asymmetric units with differing styles and colorings. This is important for virus capsids which can contain millions atoms. In addition to abstract representations and symmetry handling, another challenge posed by large assemblies is in navigating to relevant subassemblies. For example, a virus capsid may have two layers each comprised of hundreds of proteins. A mechanism is needed to hide the outer layer so that the inner layer can be studied. Subassemblies such as virus capsid layers are in general not annotated in the Protein Databank files so defining these subassemblies is left to the user. Our multiscale extension permits navigating to subassemblies using user-defined molecule groupings. Details of the Multiscale Models tool were published in Goddard TD, Huang CC, Ferrin TE. Software extensions to UCSF chimera for interactive visualization of large molecular assemblies. Structure (Camb). 2005 Mar;13(3):473-82. More advanced capabilites added in past years include an efficient algorithm for calculating atomic contacts between molecular components, the ability to show crystallographic unit cells, the ability to delete components, the ability to show transparent surfaces in combination with other molecular display styles, and ability to export 3 dimensional models for making animations. These capabilities have been used to create images for Virus Particle Explorer web site (http://viperdb.scripps.edu/) for all known icosahedral virus capsid structures.