In the following, user input is written in boldface. Current molecule has not been loaded. Notice the error in the last line. It was trying to find a second residue in the zone called end . Lsq definition defaults are taken.
Least squares match by explicit definition of atoms.
3 names in A implies a zone and an atom name. Defining 2 names in A implies a zone and CA atoms. Defining 1 name in A implies the CA of that residue. The B molecule requires just the start residue. A blank line terminates input.