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## Refining an existing PDB file

All of the loop modeling classes can also be used to refine a region of an existing PDB file, without comparative modeling, as in the example below. Note that it is necessary in this case to redefine the loopmodel.select_loop_atoms() routine, as no alignment is available for automatic loop detection.

Example: examples/automodel/loop.py

      # Loop refinement of an existing model
      from modeller import *
      from modeller.automodel import *

      log.verbose()
      env = environ()

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

      # Create a new class based on 'loopmodel' so that we can redefine
      # select_loop_atoms (necessary)
      class myloop(loopmodel):
          # This routine picks the residues to be refined by loop modeling
          def select_loop_atoms(self):
              # One loop from residue 19 to 28 inclusive
              return selection(self.residue_range('19:', '28:'))

      m = myloop(env,
                 inimodel='1fdx.B99990001.pdb', # initial model of the target
                 sequence='1fdx')               # code of the target

      m.loop.starting_model= 20           # index of the first loop model
      m.loop.ending_model  = 23           # index of the last loop model
      m.loop.md_level = refine.very_fast  # loop refinement method

      m.make()