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Topic 3 Bernard Heymann

Topic 3 Bernard Heymann. Methods to generate maps. Single/multiple particle analysis Single reference analysis Multiple reference analysis Filament processing Classical helical reconstruction Single particle analysis 2D crystallography Classical 2D crystallography

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Topic 3 Bernard Heymann

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  1. Topic 3Bernard Heymann

  2. Methods to generate maps • Single/multiple particle analysis • Single reference analysis • Multiple reference analysis • Filament processing • Classical helical reconstruction • Single particle analysis • 2D crystallography • Classical 2D crystallography • Single particle analysis • Tomography • 3D single particle analysis

  3. Map interpretation • Segmentation • Thresholding (watershed) • Clustering • Region selection and extraction • Modeling • Building atomic structures • Fitting atomic structures as rigid bodies • Building arbitrary structures • Points • Lines • Surfaces • Movies: Structural dynamics

  4. Modeling: Quality of fitting • Measures of goodness-of-fit • Reciprocal space R-factor • Correlation coefficient between map and density generated from an atomic structure • Good geometry when fitting flexible structures • Cross-validation • Reciprocal space Rfree-factor • Correlation coefficient calculated from a resolution shell not used in fitting

  5. Model and map archiving • The map must conform to the 3DEM standard conventions • Proposed conventions: Heymann, Chagoyen and Belnap (2005) JSB 151, 196 - 207. • The atomic structures must have origins and orientations coinciding with those of the map • The atomic structure should be deposited in the PDB with links to the EMDB • The map should be deposited in the EMDB with links to the PDB • The metadata associated with the project should be included in both databases (as close to a 1-1 mapping as possible)

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