The complete question: "I need to rebuild a loop ( ~6 residues ) in my model. Is there an efficient way to do it without going through bones ? It is too difficult to move_zone all 6 residues together, and when I try to move_zone one residue at a time, I end up with really messy geometry."
Use move_atom to put your CAs into the density; run lego_loop to see what the database has to say; select the best loop (not necessarily the top one ! use a difference map); run lego_auto_mc (i don't know if this is really necessary, but it doesn't hurt) and then lego_auto_sc. Finally, lego_side_ch to put in the correct rotamers, mo_zo one residue at a time, tor_res and what have you. See the tutorial chapter 8.2 to 8.5 for more info and examples.
Pete Dunten (already using O 5.10) added: "I'd use baton instead of move_ca, as you will keep the Ca-to-Ca distance right at 3.8 A (if you place it each time with rotations and avoid translations). You don't need a skeleton. Try baton_mode 2ry, then baton_build. Lego_auto_m is automatic after you accept the new positions with 'yes'. Then proceed as Gerard outlined. Whatever you do, don't try Lego_meets_Godzilla or Lego_meets_TRex, as these are only for Daniel to play with."