Editing Practical Pymol for Beginners (section)

==Getting started: explore a protein==
PyMOL is great for casual visualization of biological molecules. In this example, a PDB file describing a protein is loaded and its style and color are tweaked.

[[Image:Kchannel-rainbow.png|thumb|right|The end result will look something like this]]
[[Image:Mouse-3view.png|thumb|right|Default buttons for viewing with a 3-button mouse]]
# Obtain a PDB coordinates file for your favorite protein. (The [http://www.pdb.org/ RCSB Protein Data Bank] is a public structure repository containing over 40,000 protein structures in PDB format available for download, not a bad place to look.) For this example, we're using the potassium channel from ''Streptomyces Lividans'' ([http://www.pdb.org/pdb/files/1bl8.pdb 1BL8]).
#* or just type, <source lang="python">fetch 1bl8</source> and you can skip the next step (see [[Fetch]] command), as PyMOL will open the file for you.
# Open the PDB file using '''File''' => '''Open...''' from the menu bar. The protein's structure will appear, probably rendered as simple bonding lines. 
# The right side of the Viewer shows the loaded PDB as an object, as well as its command buttons. Each button contains a submenu with more options. Click '''S''', then '''cartoon''' to show the protein's secondary structure in popular cartoon form. 
#* Notice that the lines view is still visible on top of the cartoon view. To hide the lines, click '''H''' then '''lines'''. 
# To change the color of each protein chain (as defined in the coordinate file), click '''C''' then select '''chainbows''' from the '''by chain''' menu. "Chainbows" colors residues in each protein chain as a rainbow that begins with blue and ends with red.
#* Another common coloring method assigns a single color to each chain. Click '''C''' then select '''by chain''' from the '''by chain''' menu.
# Click and drag the protein to change the view. A list of mouse buttons is below the object control panel. 
#*Rota: Rotate
#*Move: Translate object along an axis
#*MoveZ: aka Zoom
#*Sele: Select
#*Slab:
#*Cent:
#*PkAt:

=== Related Commands ===
[[Load]], [[Fetch]], [[Color]], [[Show]], [[Show_as]], [[Cartoon]], [[Lines]], [[Rotate]], [[Select]], [[Center]]