Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure
Fig 5
Exhaustive search rigid body fitting to an experimental HS-AFM image of actin filament.
(A) The stage plane estimated from the background regions of experimental AFM image. (B) The AFM image after the correction of stage position. (C) The reference image used in the rigid-body fitting. It is taken from the lower left rectangular region of the image in B. (D) The pseudo-AFM image generated by the best estimation with the cosine similarity score with the 3 nm/16 degree probe that shows the best score. (E) The absolute value of difference between C and D. (F) The resulting actin filament structure model on top of the reference AFM image. In (A-F), the color map is given in nm unit. In (D) and (F), the orientation of the generated actin filament model is indicated by (+) and (-) labels. (G-I) The cost values of the best fit using varying probe shape. From left to right, the result using the cosine similarity (G), the pixel-RMSD (H), and the correlation coefficient (I) are plotted. In (G-I), the marker color and shape represent the probe angle and three consecutive markers have the same probe radius. (J, K) The results of finer-grid search of probe angle with radius 3.0, using the cosine similarity score (J) and the pixel-RMSD score (K).