I have a problem with  the __loop.top.  When I try to run it with the following 'selected atoms':

SUBROUTINE ROUTINE = 'select_loop_atoms'
  READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUENCE, ADD_SEQUENCE = off
  SET SELECTION_STATUS = 'INITIALIZE'
  SET SELECTION_MODE = 'ATOM'
  SET SELECTION_SEARCH = 'SEGMENT'
  SET SELECTION_FROM = 'ALL'
  SET GAP_EXTENSION = 2 2 # gaps are extended for two residues in both
                          # directions to get loops (insertions & deletions)
  PICK_ATOMS SELECTION_SEGMENT = 'LOOPS'
  RETURN
END_SUBROUTINE

it seems to select all the atoms in the model (that's what I see when it does UNBUILD_MODEL, because all the coordinates are put to -999).

I don`t understand why it does it, because it should only choose atoms aligned with gaps  +/- 2 ( insertions or deletions).  Do I have wrong ideas?

If not, what's the best way to choose atoms in the  __loop.top? ( I would like to do it automatically, not by choosing every time the segment).

Thanks in advance.