I want to add missing residues to a pdb file using modeller without changing existing coordinates.
I try select the wanted residues with the select_atoms subroutine, but it seems to me that it changes the coordinates of other residues as well, not just the ones selected.
Thanks,
Dan

Below is the top file:

##############################################################################
# Modeller script to add missing residues in rhodopsin X-ray structure #
##############################################################################

SET OUTPUT_CONTROL = 1 1 1 1 1

INCLUDE                              # Include the predefined TOP routines
READ_ALIGNMENT FILE = '1HZX-1HZX.ali', ALIGN_CODES = '1HZXA' '1HZXA2'
SET ALNFILE = '1HZX-1HZX.ali'      # alignment filename
SET KNOWNS   = '1HZXA'               # codes of the templates
SET SEQUENCE = '1HZXA2'               # code of the target
SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files
DESCRIBE

##############################################################################
# Thorough homology modelling by the MODELLER TOP routine 'model'.
# Initial model read from file and not from template
SET OUTPUT = 'LONG'
SET STARTING_MODEL = 1
SET ENDING_MODEL = 1
###############
# Do modeling #
###############
CALL ROUTINE = 'very_fast' # prepare for extremely fast optimization
CALL ROUTINE = 'model' # do homology modelling
##############################################################################

##############################################################################
# Select missing loop coordinates for modelling
SUBROUTINE ROUTINE = 'select_atoms'
    # Missing segment 235-241
    PICK_ATOMS SELECTION_SEGMENT = '236:' '240:', SELECTION_SEARCH = 'segment',;
    SELECTION_STATUS = 'initialize'
    # Missing segment 330-334
    PICK_ATOMS SELECTION_SEGMENT = '331:' '333:', SELECTION_STATUS = 'add'
    RETURN
END_SUBROUTINE
##############################################################################

-- 
Dan Thomas Major (at Dr. B. Fischer's lab)
Bar-Ilan University 
Ramat-Gan, Israel
Phone: 972-3-5317785
Fax:   972-3-5348730