ENHANCE CHIMERA'S ANIMATION AND PHYSICAL MODELING CAPABILITIES

增强 Chimera 的动画和物理建模能力

• 批准号: 8363632
• 负责人: THOMAS E FERRIN
• 金额: $ 2.79万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-07-01 至 2012-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8363632
• 关键词: Amino Acids; Architecture; Automobile Driving; Binding Sites; Cell physiology; Chimera organism; Clip; Communication; Education; Exhibits; Funding; General Population; Grant; Imagery; Informatics; Intelligence; Modeling; Molecular Conformation; Motion; National Center for Research Resources; Plastics; Play; Principal Investigator; Printing; Process; Proteins; Publications; RNA; Research; Research Infrastructure; Research Personnel; Resources; Ribosomes; Scientist; Source; Specific qualifier value; Students; Techniques; Technology; Time; TimeLine; To specify; Transfer RNA; Translation Process Protein; United States National Institutes of Health; Vertebral column; animation; base; biocomputing; cost; improved; molecular assembly/self assembly; molecular dynamics; movie; physical model; polypeptide; tool

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.

该子项目是利用资源的众多研究子项目之一 由 NIH/NCRR 资助的中心拨款提供。子项目的主要支持 并且子项目的主要研究者可能是由其他来源提供的， 包括其他 NIH 来源。 子项目可能列出的总成本 代表子项目使用的中心基础设施的估计数量， NCRR 赠款不直接向子项目或子项目工作人员提供资金。 我们计划增强 Chimera 的动画能力，并探索使用物理模型来改善科学假设和研究成果的交流。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展示他们对动态分子和细胞过程的发现。该项目的第二个方面将利用三维打印技术制作分子组装体的多件塑料模型，以促进假设的讨论 以及关于研究人员或学生小组的架构和功能的发现。 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追踪骨架，或根据正常模式分析驱动蛋白质运动。通过在图形时间轴动画编辑器中构建更多智能，可以提高易用性。例如，录制分子构象之间变形的动画目前除了 Chimera 的电影录制器之外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。在图形编辑器中构建更多智能将实现故事板风格的电影合成，其中指定一系列“关键帧”（场景快照）并使用适当的技术（变形、淡入淡出、剪辑、摄像机运动）自动插值。关键帧和故事板也可以成为向专业科学动画师传达动画科学原理的重要工具，从而顺利地从研究人员生成的动画过渡到适合公众或教育的更专业、更具视觉吸引力的动画。 我们还计划启用商业动画包中称为“绑定”的概念。绑定意味着为分子组件的各个部分定义允许的铰链和滑动运动，以将刚性模型转变为铰接模型。例如，研究表明，动力学在 RNA 到蛋白质的翻译过程中发挥着关键作用，在 Chimera 中实施装配将允许核糖体模型在大亚基和小亚基之间表现出必要的“棘轮”运动，从而说明 tRNA 如何当每个新氨基酸添加到多肽中时，分子从 A（氨酰基）前进到 P（肽基）再到 E（出口）结合位点。