Pintilie, G. D., Zhang, J., Goddard, T. D., Chiu, W. & Gossard, D. C. Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions.
The fitting of structures into density maps can then be formulated as a point matching problem, which has been solved by exhaustive or heuristic search methods (Birmanns and Wriggers, 2007; Wriggers et al., 1999).
By means of this theory, Owen claimed he could coherently explain both the deep resemblance of forms in their internal anatomy, emphasized by Geoffroy St. Hilaire, and also the close fitting of structure and function to the organism's "conditions of existence," the point emphasized by Cuvier.
The Chimera 'Fit in Map' option was used for rigid-body fitting of crystal structures and to generate all surface renderings included in the figures (Pettersen et al., 2004).
Trabuco, L. G., Villa, E., Mitra, K., Frank, J. & Schulten, K. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.
Trabuco, L.G., Villa, E., Mitra, K., Frank, J. & Schulten, K. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.
NORMA: normal mode fitting of crystal structures into EM densities using URO and NMA, presented at the EMBO Practical Course on Combination of Electron Microscopy and X-ray Crystallography in Structure Determination, Gif s/Yvette, France, 2005.
The fitting of hDmc1 structures allowed us to analyse the location of the conserved amino acid residues that are involved either in DNA-binding or ATPase catalytic activity.
Such modification (that is often used in fitting of atomic structures into EM maps) requires knowledge of the target resolution, the experimental determination of which is susceptible to inaccuracies, especially in low resolution studies [38].
The obtained 3D EM maps of the ssDNA-hDmc1 nucleoprotein filaments, combined with fitting of atomic structures of the hDmc1 domains, allow us to outline for the first time the principles of the internal architecture of the hDmc1-ssDNA nucleoprotein filament that are most relevant to the presinaptic complex formation in the recombination process.
MDFF is a popular method to carry out flexible fitting of atomic structures into EM maps.
