<html> <head> <title> Lesson 10 </title> </head> <h1 align=center> Garlic Tutorial </h1> <h2 align=center> Lesson 10 - The Semitransparent Plane </h2> <hr size="3"> This lesson explains how to control the plane associated with the structure. More precisely, you will learn how to show, hide or move the plane and how to change the plane properties. The plane may be used to divide the structure in two parts, for selection and to model the cellular membrane. <br><br> It might be good idea to read the text about the command <a href="../commands/pla.html"> PLANE </a> before you start with this lesson. <br><br> Step 1 - start garlic (if not started already): <br><br> <font color=RED> garlic <br><br> </font> Step 2 - load some the structure. In this lesson the papain structure is used, but you can use any other structure. <br><br> <font color=RED> load 9PAP.pdb <br><br> </font> Step 3 - make the plane visible: <br><br> <font color=RED> pla <br><br> </font> Now you should see an ellipsa which represents the plane. If you have not rotated the structure before making the plane visible, the ellipsa will be blue. The near edge will be bright, while the far edge will be dark. <br><br> Step 4 - rotate both the structure and the plane about x axis: <br><br> <font color=RED> Hold the [shift] key and press 8 on numeric keypad. <br><br> </font> Note the change of the ellipsa color: now you see another face of the plane. The blue face is treated as the upper side, while the orange-red face is treated as bottom side. <br><br> Step 5 - change the plane radius. <br><br> <font color=RED> pla rad 20 <br><br> </font> Step 6 - Change the plane transparency (make it opaque): <br><br> <font color=RED> pla tra 0 <br><br> </font> Step 7 - select all atoms above the plane: <br><br> <font color=RED> sel above <br><br> </font> Step 8 - change color for the current selection: <br><br> <font color=RED> color cold <br><br> </font> Step 9 - attach movement controls to the plane: <br><br> <font color=RED> mov pla <br><br> </font> Step 10 - rotate the plane, leaving the structure in its current orientation: <br><br> <font color=RED> Use numeric keypad (keys 2, 8, 4 and 6) and modifier keys (shift, alt, control) to rotate the plane. <br><br> </font> Step 11 - attach controls to both structure and plane: <br><br> <font color=RED> mov all <br><br> </font> Step 12 - hide the plane: <br><br> <font color=RED> pla off <br><br> </font> Step 13 - discard the structure: <br><br> <font color=RED> dis all <br><br> </font> <hr size="3"> </html>
