Ramachandran Matrix [1]

The Ramachandran matrix tabulates backbone \(\varphi\) and \(\psi\) dihedral angles for amino-acid and alternative amino-acid backbones, which are defined by the four consecutive backbone atoms \(N-C_\alpha-C-N\).

../_images/08ramachandran-explain.png

Definition

Definition of the backbone dihedral angles \(\varphi\) and \(\psi\):

\[\begin{split}\varphi &= \angle ~ C_{i}-N_{i+1}-C_\alpha{i+2}-C_{i+3} \\ \psi &= \angle ~ N_{i+1}-C_\alpha{i+2}-C_{i+3}-N_{i+4}\end{split}\]

Command line

-Ramachandran
--Ramachandran
Calculate the Ramachandran matrix. Optionally provide an output filename.
Default: AARamachandran.csv

Example

MakroLyzer -xyz peptide.xyz -Ramachandran

Angles are rounded to integers and shifted by +180 to map to 0-359 degrees. Below we show an example Ramachandran plot for hemoglobin.

../_images/08ramachandran.png

Output

Each frame is written as a separate matrix file named <base>_frame<idx>.csv. Each file is a 360x360 CSV matrix where rows are \(\phi\) (0-359) and columns are \(\psi\) (0-359).