Providing your own restraints file
Keywords: manual

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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/model-myrsr.py

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

      log.verbose()
      env = environ()

      # directories for input atom files
      env.io.atom_files_directory = './:../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