v4.1Torsions
Swiss-PdbViewer allows to alter the torsions angles of amino-acids and hetero-atoms, as well as the backbone omega, phi and psi angles.
To initiate a torsion, simply click on the torsion tool located at the
top of the display window. You will be prompted to select a group, which
is readily made by clicking on any amino-acid or hetero-group atom.
Acting on amino-acids:
If you picked an atobelonging to an amino-acid, the "torsion tool" will allow you to rotate sidechains atoms downstream a specfic bond. A real-time evaluation of clashes and hydrogen bonds is performed. The procedure is very easy: first click on the tool, then pick any atom belonging to the amino-acid you want to modify. A number of little arrows will appear below and at the right of the toriosn tool icon. Arrows located below the torsion icon will let you move the phi and psi backbone torsion angles of the residue (note that you can also use the Ramachandran plot to do it). By default, the C-terminal part of the protein will move, but you can let the N-terminal part of the protein move by removing the checkmark of the last item of the Tool menu.
If the amino-acids has a long sidechain with freely rotratable bonds, you can alter it with the arrows that appear at the right of the torsion tool icon. From top to bottom, you will affect the chi-1 to chi-5 torsion angles. When you're over with a torsion, click once again on the torsion tool and accept (or discard) your modifications. If you accept, atoms names will be updated accordingly to the IUPAC nomenclature, if needed.
Note: For those who prefer to use the keyboard instead of clicking on an arrow, any sidechain bond can be rotated by holding down a key from "1" to "5" while clicking and moving the mouse from left-to right. Key "1" will rotate the CA-CB bond, key "2" the CB-CD bond and so on. Phi or Psi angle by holding down the "9" or "0" key respectively.
Acting on Hetero-Atoms groups (ligands):
You can also alter rotatable bonds of substrates, which is useful to refine the position of a substrate, for example during electron density map fitting. Simply click on the torsion tool, and pick two atoms. The first one will define the "fixed point", while the second one will be used to define the rotation axis. All atoms downstream the second one will move around the bond defined by the two atoms you picked. Here again, clashes and H-bonds will be updated in real tiome during the torsion. You might want to enable the display of H-bond length from the display menu to have a numeric feedback. Once you're finished with the torsion, click once again on the torsion tool icon and accept or discard it.