ENHANCE CHIMERA'S ANIMATION AND PHYSICAL MODELING CAPABILITIES

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 而子项目的主要调查员可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 我们计划提高奇美拉的动画能力，并探索使用物理模型来改善科学假设和研究结果的交流。新的动画工具将使科学家能够在针对其他研究人员或学生的出版物和演示文稿中说明他们对动态分子和细胞过程的发现。本计画第二方面将利用三维打印技术制作分子集合体的多件塑胶模型，以方便假说的讨论 以及在研究人员或学生的小团体中关于组件的结构和功能的发现。 其他命令可以执行随时间变化的效果，例如按顺序快速突出显示蛋白质残基以直观地跟踪主链，或基于正常模式分析驱动蛋白质运动。增加易用性将来自于在图形时间轴动画编辑器中构建更多的智能。例如，记录分子构象之间的变形动画目前需要使用一个单独的变形工具，除了奇美拉的电影记录器。通过允许用户直接在动画编辑器中指定起始和结束构象，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。在图形编辑器中构建更多的智能将使电影合成的故事板风格成为可能，其中指定了一系列“关键帧”（场景快照），并使用适当的技术（变形、淡入淡出、剪辑、相机运动）自动插入。关键帧和故事板也可以是将动画的科学原理传达给专业科学动画师的重要工具，使研究人员生成的动画顺利过渡到更专业，视觉上吸引人的动画适合公众或教育。 我们还计划启用一个概念，从商业动画包称为“索具。“操纵意味着定义允许的铰链和滑动运动的分子组装件，把一个刚性的模型变成一个铰接的。例如，已经表明，动力学在RNA至蛋白质的翻译过程中起着关键作用，并且在嵌合体中实施操纵将允许核糖体模型在大小亚基之间表现出必要的“棘轮”运动，从而说明当每个新氨基酸被添加到多肽中时，tRNA分子如何从A（氨酰基）前进到P（肽基）再到E（出口）结合位点。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. 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.