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
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):
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.
Step 3 - prepare Ramachandran plot.
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.
Step 6 - return to the main drawing mode. You can either type the command
rama off or hit the escape key.
Step 7 - discard loaded structure: