I want to calculate all the three dihedral angles in a residue.
calc_dihedral(atom1, atom2, atom3, atom4) of Biopython requires vector coordinates of four atoms as arguments and returns an output of a single value. I'm not sure which of the three angles output represents.
Please suggest which atoms in the residue are required to calculate which angle and in what order the atom coordinates should be given in the function as arguments.
We need backbone atoms only N,CA,C. so for the protein chain we get N,CA,C,N,CA,C,N,CA,C,N,CA,C.
we need to define them in plane, to find out the angle we need two planes (plane1: C,N,CA)(plane2: N,CA,C). we neglect the N,CA for first residue. Consider the bolded atoms only. so you submit the bolded atoms (3 atoms of one residue and 4th atom from the second residue.) I dont know about omega.
Which atoms are required by Biopython's calc_dihedral() to calculate all 3 dihedral angles?