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.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
5P41RR001081-34
Application #
8363632
Study Section
Special Emphasis Panel (ZRG1-BST-D (40))
Project Start
2011-07-01
Project End
2012-06-30
Budget Start
2011-07-01
Budget End
2012-06-30
Support Year
34
Fiscal Year
2011
Total Cost
$27,938
Indirect Cost
Name
University of California San Francisco
Department
Pharmacology
Type
Schools of Pharmacy
DUNS #
094878337
City
San Francisco
State
CA
Country
United States
Zip Code
94143
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