<html> <head> <title> Lesson 5 </title> </head> <h1 align=center> Garlic Tutorial </h1> <h2 align=center> Lesson 5 - How to Select Atoms </h2> <hr size="3"> In this lesson, you will learn how to select atoms. The command select (or whatever command plays this role) is one of the most important commands in every molecular visualization program. <br><br> For this lesson, you will need a true protein structure, not just a single amino acid as in previous lessons. <br><br> Step 1 - obtain the protein structure: <br><br> <font color=RED> Use you web browser to access <a href="http://www.rcsb.org/pdb"> The Protein Data Bank (www.rcsb.org) </a> . <br> Type 1HUC into the small search field. Start the search and wait for the answer. <br> Choose the option "Download/Display File". <br> Finally, choose file format "PDB", compression "none" in the section "Download the Structure File" and wait. <br><br> </font> Step 2 - start garlic (if necessary): <br><br> <font color=RED> garlic <br><br> </font> Step 3 - 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 4 - draw backbone, to simplify the picture: <br><br> <font color=RED> bac <br><br> </font> Step 5 - use different colors for different chains: <br><br> <font color=RED> col chain <br><br> </font> Step 6 - select chain A, draw balls and sticks and change color scheme to CPK: <br><br> <font color=RED> sel a/*/*/* <br> bac off <br> bon 4 <br> ato bal <br> col cpk <br><br> </font> Step 7 - redefine the internal system origin (the rotation center) and move chain A to the screen center: <br><br> <font color=RED> cen <br> pos 0 0 0 <br><br> </font> Step 8 - restrict the selection to aliphatic amino acids and change color to yellow (chain A): <br><br> <font color=RED> res ali <br> col yellow <br><br> </font> Step 9 - select all, make it visible, show only backbone but reduce the backbone thickness: <br><br> <font color=RED> sel * <br> sho <br> bac 3 <br><br> </font> Step 10 - hide side chains: <br><br> Step 10 - select cysteine residues, but only for chains A and C; make them visible, use spacefill style: <br><br> <font color=RED> sel a,c/*/cys/* <br> show <br> ato spa <br><br> </font> Step 11 - discard loaded structure: <br><br> <font color=RED> dis all <br><br> </font> <hr size="3"> </html>
