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.