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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