We applied the signed distance function (SDF) for representing the depths of atoms in a macromolecule. The calculations of SDF values were performed on grid points in a rectangular box that accommodates the macromolecule. The depth for an atom inside the molecule was then obtained as a result of tri-linear interpolation of SDF values at the nearest grid points surrounding the atom. Theoretical concept and computational development performed by Wendy Chen.
Adepth allows you to :
- 1) Calculate accurately the depth of any atom within a macromolecular structure
- 2) Provide an extrusion (skin) of a macromolecular structure
- 3) Generate of pseudo-2D convolution map, highlighting the effect of AFM tips on single molecules