A Stochastic Hill Climbing Approach for Simultaneous 2D Alignment and Clustering of Cryogenic Electron Microscopy Images  Cyril F. Reboul, Frederic Bonnet, Dominika Elmlund, Hans Elmlund  Structure  Volume 24, Issue 6, Pages 988-996 (June 2016) DOI: 10.1016/j.str.2016.04.006 Copyright © 2016 Terms and Conditions

Figure 1 Results from Simulated Data Analysis (A) Individual particle images from the dataset. (B and C) Comparison of typical SAC solutions obtained with SHC (B) and k-means (C) for a simulated dataset with 50 clusters. The quality of the solution obtained with SHC is excellent, whereas the k-means solution suffers from severe errors due to initial reference bias. (D) Convergence statistics for one of the simulated SHC runs showing average correlation between particles and cluster centers (top), the overlap of the parameter distributions from successive iterations (middle), and the fraction of search space scanned to find an improving configuration (bottom) as functions of iteration number. Structure 2016 24, 988-996DOI: (10.1016/j.str.2016.04.006) Copyright © 2016 Terms and Conditions

Figure 2 Processing of Experimental Cryo-EM Images of Low-Symmetry Particles (A) Three independent EF-G ribosome ab initio 3D reconstructions generated from independent SHC class averages. (B) Evolution of two IP3R class averages throughout the iterative SHC-based clustering and alignment. (C) Ab initio 3D reconstruction of IP3R from reference-free class averages obtained with SHC. (D) Ab initio 3D reconstruction of the Plasmodium falciparum 80S ribosome from reference-free class averages obtained with SHC. (E) Comparison of re-projections of our Pf-rib map (left) with the corresponding SHC class averages (right). (F) Comparison of our ab initio 3D reconstruction of TRPV1 from reference-free class averages obtained with SHC (left) with the published map obtained by reference-based 3D reconstruction (right). The published map was low-pass filtered to 15 Å resolution for comparison. (G) Comparison of re-projections of our TRPV1 map (upper) with the corresponding SHC class averages (lower). reproj, reprojection; cavg, class average. Structure 2016 24, 988-996DOI: (10.1016/j.str.2016.04.006) Copyright © 2016 Terms and Conditions

Figure 3 Processing of Experimental Cryo-EM Images of High-Symmetry Particles, Icosahedral and d7 (A) Top view of the GroEL ab initio 3D reconstruction obtained from SHC class averages. (B) Comparison of re-projections of the GroEl map (left) with the corresponding SHC class averages (right). (C) Side view of the GroEL map in (A). (D) Cut view of the GroEL map with the known atomic model of GroEL fitted. The cutting plane is indicated in (C). (E) View along the 5-fold symmetry axis of the icosahedral BPV 3D reconstruction obtained from SHC class averages. (F) Comparison of re-projections of the BPV map (left) with the corresponding SHC class averages (right). reproj, reprojection; cavg, class average. Structure 2016 24, 988-996DOI: (10.1016/j.str.2016.04.006) Copyright © 2016 Terms and Conditions