Thu Apr 16 11:20:20 PDT 2009
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 look at models of an alpha helix.


 1) script d1

    model peptide planes and sidechains as separate
    rigid bodies connected by hinge joints.

    set spring constant for hinge joints.

    add spring potential btw residue sidechains.


 2) script d2

    model peptide planes and sidechains as separate
    rigid bodies connected by hinge joints.

    set spring constant for hinge joints.

    add spring potential btw residue sidechains.

    add spring potential btw backbone hydrogen bonds.

        note that peptide   domains have oxygens
                  sidechain domains have nitrogens

        residue 783 atom O  ----- residue 787 atom N

     
 3) script d3

    model peptide planes and sidechains as separate
    rigid bodies connected by hinge joints.

    use multibody command with hinge joints.

    creates 95 rigid bodies.


 4) script d4

    model peptide planes and sidechains as separate
    rigid bodies connected by hinge joints.

    use multibody command with ball joints.

    creates 95 rigid bodies.