<html> <head> <title> Lesson 2 </title> </head> <h1 align=center> Garlic Tutorial </h1> <h2 align=center> Lesson 2 - Load a Small Structure </h2> <hr size="3"> In this lesson, you will learn how to load a PDB file and how to move the structure. <br><br> Step 1 - start garlic (if not started already): <br><br> <font color=RED> garlic <br><br> </font> Step 2 - load tryptophan (it should be included in the source package). This command should be executed at garlic prompt: <br><br> <font color=RED> loa trp.pdb <br><br> </font> Step 3 - how to use the pointing device (mouse): <br><br> <font color=RED> Move the mouse pointer over atoms and bonds and read the text which appears in the output window (bottom right corner). Note that half of each bond is assigned to each of two atoms involved in bond formation. <br><br> </font> Step 4 - use garlic controls (i.e. the keys on numeric keypad) to rotate the structure (just a single amino acid): <br><br> <font color=RED> First play for a while with keys 4 and 6, then with 2 and 8, and finally with 7 and 9. Try the same while holding shift (alone), control (alone), alt and shift (simultaneously) and control and shift (simultaneously). Do not try control-alt combinations, unless you are very experienced with unix and X. <br><br> </font> Step 5 - use garlic controls (numeric keypad) to translate the structure: <br><br> <font color=RED> PC keyboard: use /, *, -, +, 5 and 0. <br> Terminal keyboard: use PF2, PF3, -, comma, 5 and 0. <br> Repeat while holding modifier keys (alone or in combination). <br><br> </font> Step 6 - move the structure to the screen center again: <br><br> <font color=RED> pos 0 0 0 <br><br> </font> Step 7 - rotate and translate the structure using commands instead of controls. Try the following set of commands: <br><br> <font color=RED> rot x 90 <br> tra x 4 <br> tra y -4 <br> tra z -50 <br> rot y 180 <br><br> </font> Step 8 - move the color surfaces. As your structure is very small, be sure to hold the control key while pressing functions keys: <br><br> <font color=RED> Hold control key and press F1. <br> Hold control key and press F4. <br> Note that color is changing. <br> Hold control key and play with F1, F2, F3 and F4 for a while. <br><br> </font> Step 9 - move the slab surfaces. As your structure is very small, be sure to hold the control key: <br><br> <font color=RED> Hold control key and 3 (numeric keypad). Repeat until some atoms and bonds disappear. <br> Hold control key and play with 1, 3, decimal separator (next to 0) and enter for a while. Note that (in control window) visible atoms are red and invisible atoms are dark cyan. <br><br> </font> Step 10 - discard loaded structure: <br><br> <font color=RED> dis all <br><br> </font> <hr size="3"> </html>
