In this tutorial, we will show you how to use the Interactive Ramachandran Plot SAMSON extension.
The Ramachandran plot is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure.
For this tutorial, you can open any protein you like. We will be using 1YRF. You can use the Protein Data Bank Downloader to fetch molecules from RCSB Protein Data Bank.
Once you loaded a protein, open the Ramachandran Plot app (Apps menu > Biology > Ramachandran plot ) and click on update to obtain a plot like this one:
The white regions represent the energetically unfavoured conformations, and the yellow regions – the favored ones. There are four tabs to represent different categories of residues: the glycine and the proline that take specific conformations, the pre-proline residues are the ones just before a proline in the amino acid chain, which generally means every other type of residue.
Here, all the residues are well placed. To visualize one particular residue let’s click on it (here with the proline):
The residue become selected in the viewport and the status bar displays information about the dihedral angles of the residue:
If you drag and drop the residue on this window, the dihedral angles are updated in the viewport, and the protein moves. This is an undoable action so if you’re not satisfied with the result, just press Ctrl+Z. The other way also works. Lock the window of the Ramachandran plot and select the twister editor . Then play with the protein and see what happens to the plot.
A small challenge to finish, reload 1yrf, compute the 10 first normal modes (see the tutorial on Calculating non-linear normal modes to learn how to use the NMA Lite SAMSON Extension), put the scaling factor to 1, and the first mode completely to the left like this:
Then try to adjust all modes so that all the residues are in a favored configuration in the Ramachandran Plot.
If you have any questions or feedback, please use the SAMSON forum.