Density Restraints
For the structure refinement we need to compute the forces on the atoms that move them into the density. We derive forces by comparing the target density with a density that is computed from the coordinates of the model, the model density. The goal is to minimize the difference between the target and the model density:
Target density, Model density, Difference density.
Since experimental density map often contain a significant amount of noise, we compute a stochastic gradient that is more robust than an analytical gradient. For this a set of map_probe_n (see parameter file) vectors are randomly chosen from within a given search radius (map_probe_sig) around each atom. The obtained vectors are weighted by the difference density at this point and then averaged. This averaged vector is used to move the atom.