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
Hello-
I just wanted to make sure the below script looks correct for telling modeller to make a certain proline (in my case, residue 10) in the cis-conformation.
I've seen a few ways of either doing it directly (as below) or making a constraint file after the fact (or before?).
I tried to use the below script, and I'm not sure if it's doing it correctly (so I wanted to check to see if the script was OK).
Thanks for your input, Doug Kojetin
################################################## model-cis.top ################################################## INCLUDE SET ALNFILE = 'beta4_1be9_align.ali' SET KNOWNS = '1be9' SET SEQUENCE = 'beta4' SET STARTING_MODEL = 10 SET ENDING_MODEL = 15
CALL ROUTINE = 'model'
SUBROUTINE ROUTINE = 'special_restraints' CALL ROUTINE = 'cispeptide', ATOM_IDS1 = 'O:10' 'C:10' 'N:11' 'CA:11',; ATOM_IDS2 = 'CA:10' 'C:10' 'N:11' 'CA:11' RETURN END_SUBROUTINE
-
Dan Thomas Major -
Douglas Kojetin