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