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A. Phi and Psi angles using graphical interface To calculate the dihedral angles of proteins, you need: (i) to identify the backbone residues of the protein. In the selection box of VMD (Graphical Representations > Selected Atoms), type "protein and backbone". 1. What do you observe? Which part of the amino acids is missing? (ii) You will need to know which atoms are involved in the phi and psi angles: phi: C' i-1 -N i -Ca i -C' i psi: N i -Ca i -C' i -N i+1 2. Calculating the phi angle of residue 7 a. For the phi angle: 2 residues: residue i-1 and residue i. For example, to calculate the phi angle of residue i=7, we need both residue 6 and residue 7. b. In the VMD selection box, type: "protein and backbone and resid 6 7". c. Zoom in until you see the atoms well. You will see atoms of different color. (N=blue, C=cyan, O=red). (Switch to CPK Drawing Method to see the atoms and bonds.) d. Once you have identified the 4 atoms involved in the phi angle of residue 7, click in VMD Main window on Mouse->Label->Dihedrals. e. The selection requires you to click 4 atoms consecutively in the right order. f. The result displayed will be the value of the dihedral angle phi:

          A. Phi and Psi angles using graphical interface

To calculate the dihedral angles of proteins, you need:

(i) to identify the backbone residues of the protein.

In the selection box of VMD (Graphical Representations > Selected Atoms), type "protein and backbone".

1. What do you observe? Which part of the amino acids is missing?

(ii) You will need to know which atoms are involved in the phi and psi angles:

phi: C' i-1 -N i -Ca i -C' i
psi: N i -Ca i -C' i -N i+1

2. Calculating the phi angle of residue 7
a. For the phi angle: 2 residues: residue i-1 and residue i. For example, to calculate the phi angle of residue i=7, we need both residue 6 and residue 7.
b. In the VMD selection box, type: "protein and backbone and resid 6 7".
c. Zoom in until you see the atoms well. You will see atoms of different color. (N=blue, C=cyan, O=red). (Switch to CPK Drawing Method to see the atoms and bonds.)
d. Once you have identified the 4 atoms involved in the phi angle of residue 7, click in VMD Main window on Mouse->Label->Dihedrals.
e. The selection requires you to click 4 atoms consecutively in the right order.
f. The result displayed will be the value of the dihedral angle phi:

A. Phi and Psi angles using graphical interface

To calculate the dihedral angles of proteins, you need:

(i) to identify the backbone residues of the protein.

In the selection box of VMD (Graphical Representations > Selected Atoms), type "protein and backbone".

1. What do you observe? Which part of the amino acids is missing?

(ii) You will need to know which atoms are involved in the phi and psi angles:

phi: C' i-1 -N i -Ca i -C' i
psi: N i -Ca i -C' i -N i+1

2. Calculating the phi angle of residue 7
a. For the phi angle: 2 residues: residue i-1 and residue i. For example, to calculate the phi angle of residue i=7, we need both residue 6 and residue 7.
b. In the VMD selection box, type: "protein and backbone and resid 6 7".
c. Zoom in until you see the atoms well. You will see atoms of different color. (N=blue, C=cyan, O=red). (Switch to CPK Drawing Method to see the atoms and bonds.)
d. Once you have identified the 4 atoms involved in the phi angle of residue 7, click in VMD Main window on Mouse->Label->Dihedrals.
e. The selection requires you to click 4 atoms consecutively in the right order.
f. The result displayed will be the value of the dihedral angle phi:

Added by Raul J.

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