bone_prune [Id 2 atoms]
This command attempts to create a tentative CA trace. It modifies the connectivity of all atoms linking the 2 identified atoms, to more closely resemble a CA trace. The two end-point atoms are kept, as are all atoms containing a branch. Connections from/to other atoms are removed if the distance to the last tentative CA atom is less than 3.8 Å. When an atom is found to be more than 3.8Å from the last tentative CA, it is shifted to make a more exact separation. Any remaining short separations between tentative CA atoms are flagged in an object called WARN.