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Script file

The script file contains commands for MODELLER, in the TOP language (Chapter 4). A sample script file model-default.top to produce one model of sequence 1fdx from the known structure of 5fd1 and from the alignment between the two sequences is


# Homology modelling by the MODELLER TOP routine 'model'.

INCLUDE                             # Include the predefined TOP routines

SET OUTPUT_CONTROL = 1 1 1 1 1      # uncomment to produce a large log file
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               # index of the first model 
SET ENDING_MODEL  = 1               # index of the last model
                                    # (determines how many models to calculate)

CALL ROUTINE = 'model'              # do homology modelling

See Section 3.2 for information on the model script and its arguments.



Bozidar BJ Jerkovic 2001-12-21