Keywords: manual

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## model.patch() -- patch MODEL topology

`patch(residue_type, residues)`

> This command uses a CHARMM patching residue to patch the topology of the MODEL. CHARMM patch rules are observed.

> residue_type is the type of the patching residue (`PRES` entry in the topology library), such as `'DISU'`, `'NTER'`, `'CTER'`, etc. You do not have to apply explicitly the N- and C-terminal patches to protein chains because the `'NTER'` and `'CTER'` patches are applied automatically to the appropriate residue types at the termini of each chain at the end of each model.generate_topology() command.

> residues should be one or more `residue` objects to be patched. The first residue is the patched residue 1, the second residue is the patched residue 2, etc; for example, the `'DISU'` patching residue has two patched Cys residues while the `'ACE'` patching residue has only one patched residue. The order of the residue identifiers here has to match the definition of the patching residue in the topology library.

> It is not allowed to patch an already patched residue. Since the N- and C-terminal residues of each chain are automatically patched with the `'NTER'` and `'CTER'` patching residues, respectively, a user who wants to patch the N- or C-terminal residues with other patches, should turn the default patching off before executing model.generate_topology(). This is achieved by setting patch_default = `False`.

Example: examples/commands/patch.py

      # Example for: model.patch(), topology(), parameters.read()

      # This will define a CYS-CYS disulfide bond between residues 3 and 22.

      from modeller import *
      from modeller.scripts import complete_pdb

      env = environ()
      env.io.atom_files_directory = '../atom_files'
      env.libs.topology.read(file='$(LIB)/top_heav.lib')
      env.libs.parameters.read(file='$(LIB)/par.lib')

      # Create the disulfide bond:
      def patches(mdl):
          mdl.patch(residue_type='DISU', residues=(mdl.residues['3:'],
                                                   mdl.residues['22:']))
      # Read the sequence:
      code = '1fas'
      mdl = complete_pdb(env, code, special_patches=patches)

      # Create the stereochemical restraints
      sel = selection(mdl)
      mdl.restraints.make(sel, restraint_type='stereo', spline_on_site=False)

      # Calculate the energy to test the disulfide:
      sel.energy()

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