Keywords: manual

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## model.make_chains() -- Fetch sequences from PDB file

`make_chains(file, structure_types='structure', minimal_resolution=99.0, minimal_chain_length=30, max_nonstdres=10, chop_nonstd_termini=True, minimal_stdres=30, alignment_format='PIR')`

> This command fetches the sequences of the various chains found in the PDB file that has been read into memory (see model.read()).

> The sequence of every chain that matches the input criteria is written out to separate files.

> structure_types refers to the experimental method used to determine the structure. The following types are recognized: 'structureX' for x-ray, 'structureN' for NMR and 'structureM' for model, 'structureE' for electron microscopy, 'structureF' for fiber diffraction, 'structureU' for neutron diffraction, 'structure' for any structure.

> minimal_resolution refers to the cut-off value of the experimental resolution of the structure. Structures with resolutions larger than this threshold are not processed.

> minimal_chain_length refers to the lower limit of the chain length. Chains whose lengths are smaller than this value are not processed.

> max_nonstdres sets the maximum limit of non-standard residues that is tolerated.

> chop_nonstd_termini removes the non-standard residues found at the termini of the chains.

> minimal_stdres sets the minimum number of standard residues that are required to process the chain. Chains that don't have at least this number of standard residues are not written out.

> alignment_format specifies the format of the output file; see alignment.write().

Example: examples/commands/make_chains.py

      # Example for: model.make_chains()

      # This will read a PDB file (segment), and write out all of its chains
      # satisfying the listed conditions into separate alignment files in the
      # PIR format.

      from modeller import *

      env = environ()
      mdl = model(env, file='../atom_files/pdb1lzd.ent')
      mdl.make_chains(file='1lzd', minimal_chain_length=30, minimal_resolution=2.0,
                      minimal_stdres=30, chop_nonstd_termini=True,
                      structure_types='structureN structureX',
                      alignment_format='PIR')

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