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EMDB Image Processing and Structural Analysis: Tools and Guidelines

Explore EMDB for image processing and structural analysis, including additional MSD items. Develop descriptors for 2D crystals, filaments, and individual structures. Archive particle positions and box sizes. Obtain subset particles with orientation info. Enforce symmetry and archive structural data with necessary details.

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EMDB Image Processing and Structural Analysis: Tools and Guidelines

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  1. Suggestions for EMDB:Image Processing; Structural analysis; additional MSD itemsTim Baker and Vijay Reddy

  2. EM Image Processing em_2d_singleparticle_selection em_euler_anlge_distrubution em_3d_reconstruction **Note: Develop similar descriptors for 2d crystals, filaments and Individual structures For each scanned micrograph, positions of the particles selected and box size need to be archived (non mandatory). Subset of the chosen particles will have orientation information, ie., 3 angular parameters with the proper definitions.

  3. EM Structure Analysis em_3d_fitting em_3d_fitting_list

  4. Additional MSD data items Map Description filedata_typenum_row  num_col num_secspacing_row spacing_col spacing_secorigin_row origin_col origin_sec minimum maximum average std display_threshold (mandatory)enforced_symmetry Data set descriptions2D crystal:a_length b_length c_length (delete) thickness (add)alpha beta gamm (delete)plane_groupdetailsstructure_factors (delete) lattice lines (add) Icosahedron: (delete) (**no separate section for icosahedron, to be included under single particle)num_digital_imagesnum_singleparticlest_numbereuler_angle_distributiondetails (Replace Helix with) Filament:delta_phidelta_zdyad hand (delete)axial_symmetrydetails Helix selection rule layer_lines (not mandatory) num_asymmetric_units (add)Single particle:num_digital_images (delete) num_micrographs (add) num_single_particles (add) Point group Symmetry (PGS) T_number {if PGS is icosahedral} details (delete)local_symmetry_details (add) num_asymmetric_units (add) euler_angle_distribution (delete) Supplemental materialslice_col slice_row slice_secmask_setfigure_set

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