Constructing a DNA strand with a ligand — MMTK User Guide 2.7.7 documentation

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# Constructing a DNA strand with a ligand

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    # Create a nucleotide chain with a ligand from a PDB file.
    #

    from MMTK import *
    from MMTK.PDB import PDBConfiguration
    from MMTK.NucleicAcids import NucleotideChain
    from MMTK.Visualization import view

    # Load the PDB entry 110d. It contains a single DNA strand with a
    # ligand (daunomycin).
    configuration = PDBConfiguration('110d.pdb')

    # Construct the nucleotide chain object. This also constructs positions
    # for the missing hydrogens, using geometrical criteria.
    chain = configuration.createNucleotideChains()[0]

    # Construct the ligand. There is no definition of it in the database,
    # so it can only be constructed as a collection of atoms. The second
    # argument of createMolecules() is set to one in order to allow
    # this use of an unknown residue.
    ligand = configuration.createMolecules(['DM1'], 1)

    # Put everyting in a universe and show it graphically.
    universe = InfiniteUniverse()
    universe.addObject(chain)
    universe.addObject(ligand)

    view(universe)

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