LUT (grayscale) 3D plot of SP-D (two arms of a dodecamer)

easy to see the CRD, the N terminus where two trimers join in the center (looks like a blue lake) (peaks are “valleys” here so I need to do something about that). The peaks at the junction of the collagen-like domains and the N termini are the next highest (lowest here) peaks (orange).

 

Simpleton inversion (shadows are important in graphics) makes these peaks.