Something like this may be useful:
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 1
DEFINE_STRING VARIABLES = LOOP_CSRFILE LOOP_INI_MODEL # no idea why this is
needed
SET SEQUENCE = 'model_loop2' # root name of the new models
SET LOOP_MODEL = 'model_loop1.pdb' # initial model of the target, must
already exist
SET ATOM_FILES_DIRECTORY = './'
SET LOOP_STARTING_MODEL= 1 # index of the first loop model
SET LOOP_ENDING_MODEL = 20 # index of the last loop model
# (determines how many models to
calculate)
SET LOOP_MD_LEVEL = 'refine_3' # the loop refinement method, see
instructions for details
SET RAND_SEED = -21840
SET PDB_EXT = '.pdb'
CALL ROUTINE = 'loop'
# Cluster the models:
CALL ROUTINE = 'cluster', ID1 = STARTING_MODEL, ID2 = ENDING_MODEL
# This routine picks model residues that need to be refined (necessary):
SUBROUTINE ROUTINE = 'select_loop_atoms'
PICK_ATOMS SELECTION_SEGMENT = '135:' '138:', SELECTION_STATUS = 'initialize'
RETURN
END_SUBROUTINE
At 03:27 AM 5/5/2004, you wrote:
Dear Modeller users,
I am looking for a simple MODELLER top-script that allows to remodel an
already existing loop of a protein while leaving the rest of the molecule
unchanged, that is, the input would be a single PDB file and a residue range.
The idea is to generate a number of different conformations of that
loop and
to evaluate them against X-ray crystallographic data (I am trying to model a
loop that is only barely visible in a low resolution dataset).
Thank you very much in advance,
Kind regards,
Karsten Suhre, IGS-CNRS, Marseille, France.
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