The complete question: "I have been using the rs_fit utility in version 5.9.1. It works well for all atoms per residue, which seems to be a default. However I have failed to run the rsfit_mc and rsfit_sc. In the manual it stands that "the user is free to decide which atoms in each residue contribute to the the rsfit. Any suggestions? I am not to familiar with O, so I am happy if anyone can give a detailed answer. When selecting residue zone, the program does not like the rs_fit 16 243, e.g. It works only when clikking at the fist and last atom in zone."

You have to read in a file defining which atoms to use, e.g.:

  O > read odat/rsfit_mc.o
  O > rs_fit mol res1 res2

Notice that the zone definition should include the name of the molecule.