Script for modeling of loops

The new loop optimization method relies on a scoring function and optimization schedule adapted for loop modeling [Fiser et al., 2000]. The corresponding TOP routine is called when you set DO_LOOPS to 1. Unless you re-define routine select_loop_atoms, all regions around gaps in the alignment, whether they are insertions or deletions, will be optimized thoroughly after the usual modeling procedure is finished. The loop optimization relies on a new scoring function adapted for loop modeling.

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Example:

# Homology modelling by the MODELLER TOP routine 'model'.
#
# This can be ran with run_clustor model-loop.top, too.
#
# In addition to the standard overall homology modeling, at the end, this 
# routine also calls the thorough loop optimization routine, which generates
# by default 25 loop models for each *.B9999???? model. The default
# loop selection (regions around gaps) can be changed by re-defining 
# routine select_loop_atoms.

INCLUDE                             # Include the predefined TOP routines

 SET OUTPUT_CONTROL = 1 1 1 1 0

SET ALNFILE  = 'alignment.ali'      # alignment filename
SET KNOWNS   = '5fd1'               # codes of the templates
SET SEQUENCE = '1fdx'               # code of the target
SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files
# SET STARTING_MODEL= 1
# SET ENDING_MODEL  = 1
                                    # (determines how many models to calculate)

SET DO_LOOPS = 1                    # do loops extensively
SET LOOP_STARTING_MODEL = 1
SET LOOP_ENDING_MODEL = 4
SET LOOP_MD_LEVEL = 'refine_1'
SET MD_LEVEL = 'nothing'

CALL ROUTINE = 'model'              # do homology modelling