ENHANCE CHIMERA'S ANIMATION AND PHYSICAL MODELING CAPABILITIES

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。 我们计划增强奇美拉的动画能力，并探索使用物理模型来改善科学假设和研究结果的交流。新的动画工具将允许科学家在针对其他研究人员或学生的出版物和演示中展示他们对动态分子和细胞过程的发现。这个项目的第二个方面将使用三维打印技术来制作分子组装的多件塑料模型，以便于讨论假说 以及在一小群研究人员或学生中发现关于组件的结构和功能。 其他命令可以执行时变效果，例如按顺序快速突出显示蛋白质残基以直观地跟踪主干，或基于正常模式分析驱动蛋白质运动。通过在图形时间线动画编辑器中内置更多智能功能，将提高易用性。例如，除了Chimera的电影录像机外，记录分子构象之间的变形动画目前还需要使用单独的变形工具。通过允许用户直接在动画编辑器中指定开始和结束构象，可以简化此过程。然后，编辑器将自动使用单独的变形计算工具。在图形编辑器中内置更多的智能将启用电影构图的故事板风格，其中指定并使用适当的技术(变形、淡入淡出、剪辑、相机运动)自动内插一系列“关键帧”(场景快照)。关键帧和故事板也可以是向专业科学动画师传达动画的科学原理的重要工具，使研究人员生成的动画顺利过渡到更专业、更具视觉吸引力的适合普通公众或教育的动画。 我们还计划启用商业动画包中的一个概念，称为“装备”。操纵意味着为分子组装的片段定义允许的铰链和滑动运动，以将刚性模型转变为铰接式模型。例如，已证明动力学在RNA到蛋白质的翻译过程中起着关键作用，在嵌合体中实施操纵将使核糖体模型能够在大亚基和小亚基之间显示必要的“棘轮”运动，从而说明当每个新的氨基酸添加到多肽中时，tRNA分子是如何从A(氨基酰基)到P(肽)到E(出口)结合部位的。

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 plan to enhance Chimera's animation capabilities and to explore the use of physical models to improve the communication of scientific hypotheses and research results. The new animation tools will allow scientists to illustrate their discoveries of dynamic molecular and cellular processes in publications and presentations aimed at other researchers or students. The second aspect of this project will use three-dimensional printing technology to make multi-piece plastic models of molecular assemblies to facilitate discussion of hypotheses and discoveries regarding the architecture and function of the assemblies among small groups of researchers or students. Additional commands can perform time-varying effects such as quickly highlighting protein residues in sequential order to visually trace the backbone, or driving protein motion based on normal mode analysis. Increased ease of use will come from building more intelligence into the graphical timeline animation editor. For example, recording an animation of morphing between molecular conformations currently requires use of a separate morphing tool in addition to Chimera's movie recorder. This process could be simplified by allowing users to specify starting and ending conformations directly in the animation editor. The editor would then automatically use the separate morph calculation tool. Building more intelligence into the graphical editor will enable a storyboard style of movie composition where a sequence of "keyframes" (scene snapshots) is specified and automatically interpolated using appropriate techniques (morphing, fading, clipping, camera motion). Keyframes and storyboards can also be important tools for communicating the scientific rationale for an animation to a professional scientific animator, smoothing the transition from researcher-generated animations to more professional, visually appealing animations appropriate for the general public or education. We also plan to enable use of a concept from commercial animation packages called "rigging." Rigging means defining allowed hinge and glide motions for pieces of a molecular assembly to turn a rigid model into an articulated one. For example, it has been shown that dynamics plays a critical roll in the RNA-to-protein translation process and implementing rigging within Chimera would allow a ribosome model to exhibit the necessary "ratcheting" motion between large and small subunits and thus illustrate how tRNA molecules advance from A (aminoacyl) to the P (peptidyl) to the E (exit) binding sites as each new amino acid is added to the polypeptide.