Still working on the peak height, width, valley measurements on surfactant protein D dodecamer grayscale values using AFM images. Just thought this was an interesting way to show both the signal processing divisions for peaks, as well as the more subjective estimation (also from peak counts of image and signal processing peak numbers) division into sections. N peak center, either side, glycosylation peak(s), next is a long lumpy section (dark green), a reasonably consistent tiny low peak (pink), and a broader peak before the presumed neck coiled section (white), the likely neck domain (yellow) and the CRD (orange). These measurements are taken from the N term outwards in two directions to the respective CRD of hexamers. Two hexamers are measured separately, though mirrored and identical (theoretically) in all for trimeric arms.
This particular ridge plot is from molecule 80 (my designation number, as collected mostly from images found in Arroyo et al), and light gray lines along the plot lengths for each of the two hexamers are the divisions found by octave’s ipeak.m program using M80 as the amplitude and smoothing settings (unbiased). These come close in this randomly selected image to fitting the 15 peak per hexamer consensus found previously. Color divisions are mine (educated bias), made to approximate the 15 peak per hexamer findings as well as my observations on the AFM images.
An obvious deviation is the unusually tall (bright) peak on the left side of the top hexamer at the domain of the CRD, and just as unusual is the low (less bright peak) on the left side of the bottom hexamer. In other respects this molecjule (number 80) is very close to the means found for the first four dodecamers posted on this site.