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Providing your own restraints file

To force automodel not to construct restraints at all, but to instead use your own restraints file, simply use the csrfile keyword when creating the automodel class, as in the example below. Note that MODELLER does only rudimentary checking on your restraints file, so you must be careful that it applies correctly to the generated model.

Example: examples/automodel/

# Modeling using a provided restraints file (csrfile)
from modeller import *
from modeller.automodel import *    # Load the automodel class

env = environ()

# directories for input atom files = ['.', '../atom_files']

a = automodel(env,
              alnfile  = 'alignment.ali',     # alignment filename
              knowns   = '5fd1',              # codes of the templates
              sequence = '1fdx',              # code of the target
              csrfile  = 'my.rsr')            # use 'my' restraints file
a.starting_model= 1                 # index of the first model
a.ending_model  = 1                 # index of the last model
                                    # (determines how many models to calculate)
a.make()                            # do homology modeling

Ben Webb 2008-05-05