INCLUDING CHIMERA IN THE NRAMM AUTOMATED ELECTRON MICROSCOPY PIPELINE

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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. This collaborative project develops the software to use Chimera visualization capabilities within the NRAMM Automated Processing Pipeline (Appion) for electron microscope single particle reconstructions. The Appion pipeline produces 3-dimensional density maps of large molecular assemblies such as viruses, ribosomes, proteasomes and other molecular machinery in the cell which has sufficiently uniform structure to allow averaging many specimens. The pipeline aims to bring this experimental technique to researchers who are not experts in this experimental methods. This is the central goal of the National Resource for Automated Molecular Microscopy, a Biomedical Technology Research Resource directed by Bridget Carragher. The visualization component of the pipeline is handled by the Chimera package developed by the RBVI. The effort to incorporated Chimera in the pipeline involves code that automatically produces standard views of pipeline generated data sets residing in a database. A more advanced capability to include Chimera sessions within the pipeline database that allow users to quickly open their data in Chimera in useful standard views (coloring, slicing, thresholding, filtering, ...) as a starting point for more specialized analysis is also planned.