Regions of a pair of stereo micrographs. Stereo pairs of minicircles used for reconstruction are indicated with negative color frames.

All the reconstructed shapes of DNA are aligned by superposition of their principal axes of inertia. The upper and lower views differ by a rotation of 90° around the horizontal axis: (a) all the 31 CAP minicircles (blue), (b) all the 95 minicircles and (c) all the 64 TATA minicircles (red).

Normalized histograms (i.e. probability density) of the shape-distance values between any two TATA minicircles reconstructed shapes (red), any two CAP shapes (blue) and between one TATA shape and one CAP shape (green).

Stereo images of the cluster 7–15. Images are presented in ‘side by side’ stereo mode.

The sequences of the studied minicircles. The differences between the two sequences are highlighted in red.

Probability density function of curvature in reconstructed TATA and CAP minicircles (the corresponding profiles are red and blue, respectively). The function is approximated by a normalized histogram counting curvature values within intervals of 0.03 nm⁻¹.

Estimation of the error of reconstruction. (a) The same DNA minicircle is shown from two different angles. In the right image, the sample is rotated by 30° around the vertical axis with respect to the left image. (b) Two reconstructions from the stereo-pair in (a) starting from two different user initializations. The shape-distance between the two reconstructions is 0.89 nm. (c) Error values, i.e. shape-distances between two reconstructions of each of six stereo-pairs. To allow comparison with shape-distances between different data, the error values are expressed with the color code of Figure 7.

(Upper panel) The shape-distance matrix after clustering. Each line of the figure contains information about one minicircle reconstructed shape: the sequence type (first column), the shape-distance between the shape and a perfect circle (second column), between the shape and an ellipse (third column), and between the shape and every other reconstructed shape in the set (matrix). Shape-distance values are represented by colors with scale in nanometers shown on the right. (Lower panel) Different views of the clusters are produced by successive rotations of 45° around the horizontal axis. The indices of the minicircles shown are indicated with the brackets below the matrix. TATA (resp. CAP) minicircles are colored in red (resp. blue).