We report several tools for 3DEM structure identification and model-based refinement developed by our research group and implemented in our in-house software package, VolRover. For viral density maps with icosahedral symmetry, we segment the capsid, polymeric and monomeric subunits using segmentation techniques based on symmetry detection and fast marching. For large biomolecules without symmetry information, we use a multi-seeded fast-marching method to segment meaningful substructures. In either case, we subject the resulting segmented subunit to secondary structure detection when the EM resolution is sufficiently high, and rigid-body fitting when the corresponding crystal structure is available. Secondary structure elements are identified by our volume- and boundary-based skeletonization methods as well as a new method, currently in development, based on solving the grassfire flow equation. For rigid-body fitting, we use a translational fast Fourier based scheme. We apply our segmentation, secondary structure elements identification, and rigid-body fitting techniques to the PSB 2011 cryo-EM modeling challenge data, and compare our results to those submitted from other research groups. The comparisons show that our software is capable of segmenting relatively accurate subunits from a viral or protein assembly, and that the high segmentation quality leads in turn to high-quality results of secondary structure elements identification and rigid-body fitting.
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