Fig. 2: Ensemble representation of cryo-EM models.

a Depiction of structure ensemble (orange), along with the map (transparent grey); a plot of the CCC of each individual model in the ensemble is shown (blue horizontal lines from y axis), as well as the ensemble map (red). b depiction of a single-model map (green), experimental map, and our computed ensemble map at contour level 0.02. c Differences in the ensemble for different residues, for the ensemble of the Methionine Transporter (PDB ID: 7MC0, EMDB ID: 23752): for residue R71 (left) the ensemble is more widespread, and the side-chain density is more spread out into two peaks, each populated by parts of the ensemble. For high-resolution portions of the map shown on the right side, for example, R117 and Y114, the ensemble is highly constrained, and the side-chain density is well-defined. d SMOCf plot (shown in orange) and RMSFe (shown in blue) for each structure in the ensemble for the Faba bean necrotic stunt virus (PDB ID: 6S44, EMDB ID: 10097, map resolution 3.3 Å); the RMSF and SMOCf score are clearly anticorrelated.