Garlic Tutorial

Lesson 6 - Draw Ramachandran Plot

In this lesson, you will learn how to prepare Ramachandran plot. This plot shows the pairs of dihedral angles phi and psi. You can find more details here .

You can use any protein structure for this lesson. Here we are going to use 1HUC.pdb, retrieved in the previous lesson.

Step 1 - start garlic (if not started already):

garlic

Step 2 - load the structure. You should have the file 1HUC.pdb somewhere in the path searched by garlic (if you defined the environment variable MOL_PATH), or in your current working directory.

loa 1HUC.pdb

Step 3 - prepare Ramachandran plot.

rama

Step 4 - Identify some residues.

Use mouse (pointing device) to identify individual residues. Just move the pointer over the choosen residue symbol and you will see the residue name, serial number and dihedral angles in the output window.

Step 5 - draw Ramachandran plot for glycines.

sel gly
rama sel

Step 6 - return to the main drawing mode. You can either type the command rama off or hit the escape key.

rama off

Step 7 - discard loaded structure:

dis all