Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure
Fig 2
Twin-experiments for a molecular model of dynein.
(A) One of the reference AFM images in the twin-experiment, with the 1 nm/10 degree probe. (B) The image generated from the predicted structure with the cosine similarity. (C) One of the reference AFM images with the 3 nm/20 degree probe. (D) The image generated from the predicted structure with the cosine similarity. The color bar shows the height in nm (shared by all of the images here). (E-L) The results of twin-experiment with the reference image generated by the 1 nm/10 degree probe. Results of 10 replicated runs are overlaid; each run uses different reference AFM images with independent noise. The row corresponds to the cost function. The leftmost 4 panels (E, G, I, K) show the lowest scores of images. The next 4 panels (F, H, J, L) show the structure-RMSD of the structures with the lowest score. Red vertical dashed lines show the ground-truth probe shape. Results from two probe angles, 10 degree in red and 20 degree in blue, are plotted in parallel. Solid lines connect the representative results from one reference AFM image. (M-T) The results of twin-experiment with the reference image generated by 3 nm/20 degree probe, shown in the same way as E-L. The cyan vertical dashed lines show the ground-truth probe shape.