Keywords: manual

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## iterative_structural_align() -- obtain the best structural alignment

`iterative_structural_align(aln)`

> Given an initial alignment of two or more structures, this will run alignment.salign() in an iterative fashion, exploring a range of suitable parameter values, to determine the best structural alignment, as detailed in [Madhusudhan et al., 2009].

Example: examples/salign/salign_iterative.py

      # Illustrates the SALIGN iterative multiple structure alignment
      from modeller import *
      import modeller.salign

      log.none()
      env = environ()
      env.io.atom_files_directory = ['.', '../atom_files']

      aln = alignment(env)
      for (code, chain) in (('1is4', 'A'), ('1uld', 'D'), ('1ulf', 'B'),
                            ('1ulg', 'B'), ('1is5', 'A')):
          mdl = model(env, file=code, model_segment=('FIRST:'+chain, 'LAST:'+chain))
          aln.append_model(mdl, atom_files=code, align_codes=code+chain)

      modeller.salign.iterative_structural_align(aln)

      aln.write(file='1is3A-it.pap', alignment_format='PAP')
      aln.write(file='1is3A-it.ali', alignment_format='PIR')