Editing Biochemistry student intro (section)

== Background ==
This tutorial is designed to give you a basic working knowledge of making pretty and informative pictures of protein structures using PyMOL. <br>
This tutorial does not cover all the functions of PyMol, but tries to focus on the most important ones. <br>
A great resource for more advanced use is this wiki and the large number of good tutorials found online, which can be accessed via google.<br>
 
When you open PyMOL you will see two windows opening.<br>
The upper window entitled '''PyMOL Tcl/Tk GUI''' controls the general settings and functionalities of the program while the lower one entitled '''PyMOL viewer''',
contains the settings that are related to the current display of the molecule. <br>
Each of these two windows contain a command line, where we can enter commands into the program. <br>
One can, however, get really far without ever having to worry about writing any commands.
 
First, we will need to load a structure file into the program. Protein structures are deposited at [[www.pdb.org]]<br>
There are several ways to open this file:<br>
Either we can download the file from PDB and save it to our computer.<br>
We can then open the PDB file (if you have it on the harddisk) using the menu '''File > Open'''.<br>
or we can write: '''fetch''' followed by the PDB id in either of the two command lines. Ex: '''fetch 1LEV''' <br>
The Viewer window should now contain the PDB file displayed with lines.
 
In the right hand side of the viewer window there is a selection menu that currently contains two lines:<br>
'''all''' and the four character name of the PDB file, ex. '''1lev'''.<br>
Later on we will make new selections that will appear in this menu.<br>
Each of the two lines have 5 buttons labeled '''A''' (Actions), '''S''' (Show), '''H''' (Hide), '''L''' (Label), '''C''' (Color).<br>
Press these buttons to see the options available in each menu.
 
'''Hide the line representation'''. Press '''H > everything''' in the '''all''' line. This will remove the line representation of the molecule.<br>
'''Visualize the molecule in the cartoon representation''' by selecting '''S > cartoon'''.<br>
Try also to show the molecule as ribbon, sticks or surface to get a feeling for the different representations.<br>
The cartoon option gives us the best overview of the overall structure, so hide the other representations and show the protein only in cartoon mode.<br>
Color everything white selecting '''C > grey > white'''.
 
Ok, now we are going to try to move the molecule around.
<br>Try to move the mouse around while pressing the left mouse button. This will rotate the molecule.<br>
Try to move it around holding the middle button (moves the view) or the right button (zooms in and out).<br>
If you have a one or two button mouse you can change the mode in the '''Mouse''' menu in the Tcl/Tk GUI window. <br>
The box in the lower right corner will show how to move and rotate the molecule in this case.