Download the amino acid cysteine by right clicking on the link and selecting 'Save Target As' option. Save the file to 'My Documents' (or similar) on your computer.
Start the PyMOL program. You should see two windows - we'll refer to the upper one with a white background as the menu window and the lower one with the black background as the main window.
To view the cysteine amino acid, use the File option in the menu window. Click on 'Open', navigate to the directory where you saved your amino acid structure and select the appropriate file name.
Try rotating and moving the molecule with the mouse. To rotate the molecule, click with the left mouse button and move the mouse. To zoom in or out, click with the right mouse button and move the mouse towards or away from you. If there is a middle mouse button, this can be used to move the molecule. To get back to the initial view, click on the reset button on the menu window.
The structure you have displayed is listed at the upper right of the main window. More than one structure can be loaded at the same time, and each will have a separate line and is considered by PyMOL to be a separate object. Objects can be made active or inactive by clicking on the grey bar containing the name.
Each object has a separate set of menus which are accessible by clicking on the letters to the right of the name.
A = Action
S = Show
H = Hide
L = Label
C = Colour
The Action menu provides some options for displaying the molecule in different ways under the preset option. Try for example 'Ball and Stick'. You can also use the Show and Hide menus to display the molecule in different ways, for example lines, sticks, ribbon, spheres, mesh and surface. The show menu makes the various representations visible; the hide menu makes them invisible.If you get lost in what you have done, you can 'hide everything' and then start again!!
Now use the Colour menu to investigate how you can colour the molecule in different ways
You can save a picture by using the File option in the menu window. Select the 'Save Image As' option and save the object in the 'PNG' format.
To identify atoms, display the molecule for example in ball and stick mode, then click on the atom (sphere) you want to identify. The name of the atom should be displayed in the menu window.