[Fwd: Adding residues]

[Dan Thomas Major <>]

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

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• To: modeller_usage <>
• Subject: Adding residues
• From: Dan Thomas Major <>
• Date: Mon, 22 Apr 2002 17:25:36 +0300
• Organization: Bar-Ilan University

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

 
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