Webb3 nov. 2024 · A Ramachandran plot, also known as a Ramachandran diagram or a Rama plot in the field of biochemistry, was originally developed by Viswanathan Sasisekharan (born in 1993), C. Ramakrishnan and Gopalasamudram Narayana Ramachandran. Ramachandran plot is the plot of angles called psi (ψ) and phi (φ) of the residues (which … Webbdef calc_dihedral(chain, child_res_id): """ calculates the dihedral angles (phi, psi) for residue of index child_res_id in chain returns a tuple of form (phi ... """ Little helper function, calculates the backbone phi and psi torsion angles from the given residues and returns them :param residue: The amino acid residue the torsion ...

Practical course: Calculate phi, psi and omega angles of

http://thegrantlab.org/bio3d_v2/html/torsion.pdb.html Webbphi: a numeric vector of phi angles. psi: a numeric vector of psi angles. acc: a numeric vector of solvent accessibility. sse: a character vector of secondary structure type per residue. hbonds: a 10 or 16 column matrix containing the bridge pair records as well as backbone NH–>O and O–>NH H-bond records. (Only available for dssp topline and bottom line

What is the precise definition of Ramachandran angles?

WebbThe torsion angle is positive when the atom farther away (atom D in the diagram) moves clockwise with respect to the closer atom (atom A in the diagram). The protein backbone can be described in terms of the phi, psi and omega torsion angles of the bonds: The phi angle is the angle around the -N-CA- bond (where 'CA' is the alpha-carbon) Webb# set up two variables for Phi and Psi dihedral angles # these variables will be just monitored to see what happens phi: TORSION ATOMS=5,7,9,15 psi: TORSION ATOMS=7,9,15,17 # creates a CV that measures the RMSD from a reference pdb structure # the RMSD is measured after OPTIMAL alignment with the target structure rmsd: RMSD … topline appliances wall nj