Goddard Thomas D, Huang Conrad C, Ferrin Thomas E
Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA.
Structure. 2005 Mar;13(3):473-82. doi: 10.1016/j.str.2005.01.006.
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.
许多大分子聚集体的结构，如病毒衣壳和核糖体，已经通过实验确定到了原子分辨率。我们考虑在大型聚集体的交互式可视化和分析中出现的四个软件问题：如何高效地表示多聚体，如何制作卡通表示，如何高效地计算接触，以及如何选择子聚集体。我们描述了我们开发的技术和算法，并给出了它们的使用示例。现有的分子可视化程序对于单个蛋白质和核酸分子以及小复合物运行良好。这里提出的方法作为现有程序的功能添加或包含在下一代可视化软件中，以便于探索包含数十到数千个大分子的聚集体。我们的方法是务实的，强调代码的简单性、可靠性和速度。所描述的方法已作为加州大学旧金山分校（UCSF）Chimera（www.cgl.ucsf.edu/chimera）分子图形程序的多尺度扩展进行了分发。
