<html> <head> <title> Lesson 3 </title> </head> <h1 align=center> Garlic Tutorial </h1> <h2 align=center> Lesson 3 - Playing with Two Structures </h2> <hr size="3"> In this lesson, you will learn how to work with two or more structures. The original source package contains two PDB files: trp.pdb and phe.pdb. Each contains a single amino acid: trp.pdb = tryptophan, phe.pdb = phenylalanine. In this lesson, tryptophan will be colored blue, while phenylalanine will be colored red. Note the role of the command cat (catch). <br><br> Step 1 - start garlic (if necessary): <br><br> <font color=RED> garlic <br><br> </font> Step 2 - load trypthophan: <br><br> <font color=RED> loa trp.pdb <br><br> </font> Step 3 - change TRP color to blue: <br><br> <font color=RED> col blue <br><br> </font> Step 4 - load phenylalanine: <br><br> <font color=RED> loa phe.pdb <br><br> </font> Step 5 - change PHE color to red: <br><br> <font color=RED> col red <br><br> </font> Two structures will be distinguished by color and by the identifier: tryptophan is treated as structure number 1, and phenylalanine is treated as structure number 2. Two structures are now overlapping. <br> Step 6 - move tryptophan to the left: <br><br> <font color=RED> cat 1 <br> pos -5 0 0 <br><br> </font> Step 7 - move phenylalanine to the right: <br><br> <font color=RED> cat 2 <br> pos 5 0 0 <br><br> </font> Step 8 etc. - use the command cat (catch) to rotate structures one by one: <br><br> <font color=RED> Use cat 1 and cat 2 to catch and rotate structures, one by one. <br> Translate both structures to the position where they will be overlapped, but do not use keyword pos! <br><br> </font> When finished, discard loaded structures: <br><br> <font color=RED> dis all </font> <hr size="3"> </html>