Keywords: manual

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## Defining loop regions for refinement

By default, the `loopmodel` class selects all `loop' regions in your model for refinement, defined as any insertion in the alignment (i.e., a region of the target where template information is not available). You can override this and select any set of atoms of your choosing by redefining the loopmodel.select_loop_atoms() routine. (This routine should return a `selection` object; see Section 2.2.6 or Section 6.9 for further information.)

This example also demonstrates how to automatically assess each generated loop model.

Example: examples/automodel/model-loop-define.py

      from modeller import *
      from modeller.automodel import *

      log.verbose()
      env = environ()

      env.io.atom_files_directory = './:../atom_files'

      # Create a new class based on 'loopmodel' so that we can redefine
      # select_loop_atoms
      class myloop(loopmodel):
          # This routine picks the residues to be refined by loop modeling
          def select_loop_atoms(self):
              # Two residue ranges (both will be refined simultaneously)
              return selection(self.residue_range('19:', '28:'),
                               self.residue_range('45:', '50:'))

      a = myloop(env,
                 alnfile  = 'alignment.ali',      # alignment filename
                 knowns   = '5fd1',               # codes of the templates
                 sequence = '1fdx',               # code of the target
                 loop_assess_methods=assess.DOPE) # assess each loop with DOPE
      a.starting_model= 1                 # index of the first model
      a.ending_model  = 1                 # index of the last model

      a.loop.starting_model = 1           # First loop model
      a.loop.ending_model   = 2           # Last loop model

      a.make()                            # do modeling and loop refinement