<html> <head> <title> Lesson 6 </title> </head> <h1 align=center> Garlic Tutorial </h1> <h2 align=center> Lesson 6 - Draw Ramachandran Plot </h2> <hr size="3"> 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 <a href="../commands/ram.html"> here </a> . <br><br> You can use any protein structure for this lesson. Here we are going to use 1HUC.pdb, retrieved in the previous lesson. <br><br> Step 1 - start garlic (if not started already): <br><br> <font color=RED> garlic <br><br> </font> 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. <br><br> <font color=RED> loa 1HUC.pdb <br><br> </font> Step 3 - prepare Ramachandran plot. <br><br> <font color=RED> rama <br><br> </font> Step 4 - Identify some residues. <br><br> <font color=RED> 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. <br><br> </font> Step 5 - draw Ramachandran plot for glycines. <br><br> <font color=RED> sel gly <br> rama sel <br><br> </font> Step 6 - return to the main drawing mode. You can either type the command rama off or hit the escape key. <br><br> <font color=RED> rama off <br><br> </font> Step 7 - discard loaded structure: <br><br> <font color=RED> dis all <br><br> </font> <hr size="3"> </html>
