Using SwissPDB Viewer

1.  Open SwissPDB.  The splash screen at startup can be disabled under "Preferences/ General..."  Remember where you saved the protein lipase?  Click "File", then "Open PDB," and select the molecule that you want.  It can be helpful to rename the PDB ID to include the name of the enzyme/molecule.  (Ours is 1R4Z in case you forgot)

2.  From here, many effects can be applied.  To make the molecule 3D, press Ctrl+3 twice.  Right now we will only discuss displaying your protein with ribbons (this is a quick tutorial!).  Click "Window...Control Panel" to bring up the Control Panel.

3. Now hold "shift" and click in the columns that are headed "show," "side," and "ribn."  This will turn off the individual atoms view and bring up the ribbons.

4. To change the color of the ribbon, first click the black down arrow beside "col" (currently says "B S" for Backbone+Sidechain) and click "Ribbon."

5. Next hold shift and click any box under "col."  This will color the whole molecule the same color.

6.  Many PDB files come with designations of secondary structure (look at the letters to the left of the amino acids).  To color each motif separately, click and drag to select the appropriate amino acids.  It can be painstaking, but the end result is usually great! For now though:

7. Adjust the model using the rotation button.  When you are satisfied, press the "center" button.

8. Now click "File/Save/PovRay 3.5 Scene."  You probably have Pov-Ray 3.6, but that's okay.

9. You're ready to use Pov-Ray!  If you like the molecule the way it is, then just Save "Image."

10.  Please note that this is a very basic intro to SwissPDB aimed at quickly getting you oriented.  For a more extensive tutorial consider visiting Gale Rhodes' impressive guide:

http://www.usm.maine.edu/~rhodes/SPVTut/

On to Pov-Ray Tutorial