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Display of Hydrogen bond

Display of Hydrogen bond is simple.
Action → find → polar contacts → select from menu



Helix is shown in the figure below. (I selected "without solvent".)




Example -Protein-Ligand interface-

I'll show you how to display hydrogen bond between protein and ligand. I use RNase and 3'GMP complex.
  1. Selection of ligand
  2. select gmp, resn 3gp

  3. Display of hydrogen bond
  4. panel of ligand that created
    Action → find → polar contacts → to other atom in object


    Hide → everything
    Show → stick
    Show → cartoon


    Display of water molecule as sphere model ...
    show sphere, resn hoh
    set sphere_scale, 0.2
    Deletion of water molecule ...
    1.click to select water molecule
    2.(all)Hide → Sphere
    3.(sele) Show → Sphere


    Turning of main chain ...
    set cartoon_side_chain_helper, on



    Example -Protein-Protein interface-

    I'll show you how to display hydrogen bond between protein and Protein. I use Nectin-1 homodimer.
    1. Selection of molecule
    2. Select chainA
      select molA, chain A

    3. Display of hydrogen bond
    4. panel of chainA that created
      Action → find → polar contacts → to other atom in object


      See also Interaction interface.