Single particle analysis is an increasingly important technique for determining intermediate resolution structures of molecules and macromolecules. The overall aim of this program project is to make single particle reconstructions routine at substantially higher resolution than currently possible, and extending the resolution of certain projects to near-atomic resolution. In addition, by integrating the new package, SPARX, with x-ray crystallographic software, the process of combining x-ray and EM information will be greatly facilitated. Reconstructions at the proposed routine resolution of 8-12 Angstroms have been performed on a few particles with existing software, but only with months or years of human effort. Human time is the primary limiting factor preventing such reconstructions from becoming routine. Existing software typically requires substantial human involvement at every stage of the reconstruction. For this program project to succeed, a powerful framework for automation of the computational aspects of the project must be developed. Currently available software does not fulfill our requirements; therefore the primary focus of this project is the development of a new software system for single particle analysis that leverages existing code and our experience in software development for single particle image reconstruction and X-ray crystallography. SPARX will utilize code from EMAN, an existing single particle reconstruction suite, and other sources, and will be built around the framework provided by PHENIX, a new x-ray crystallographic software suite being developed at LBNL. This package will be fully object oriented, and fully parallelized for use on Linux clusters as well as supercomputers. It will contain a graphical user interface both for performing reconstructions, and modifying existing or designing new reconstruction algorithms.
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