First Computer Lab: the Protein DataBank (PDB) and Jmol (the application)

1. Click "Safari" in the Dock, lower left of the screen.

2. Find the Bookmarks Bar near the top of the screen. Click "PDB" at the far left.

3. First take a look at "Molecule of the Month". Click on the molecule to enter this tutorial. They have archived these monthly summaries.

4. In the search box at the top of the page type "1xme". That is a protein databank file name. It is not case-sensitive.

5. Click "Site Search" (Make sure that 'PDB ID or keyword' is checked, not 'Author')

6. The file for this structure will appear. Now click the "Biology and Chemistry" tab at the top. There is much useful information here.

7. Scroll down a bit. It tells you that there are 3 chains in this molecule, and they are called A, B, and C.

8. Below that it tells you that there are several ligands or prosthetic groups. Importantly for us, it tells the ID. For HAS, a heme group, click on "View" to see more about it.

9. Scroll down. There is a Jmol window. Now go back one page. (Do not close the window).

10. Look for "Download Files" at the left. Click the triangle to open the list of options.

11. I usually take the last one: "Biological Unit Coordinates". Click this one and a PDB file will download to your desktop

12. Find it on your Desktop. It will be named 1XME.pdb1 (Now quit Safari- or Hide it, or minimize it.)

13. Now open Jmol. Look for the unnamed folder in the dock, at the lower right of your screen. Click this folder.

14. Find the file "Jmol.jar". It will be easier in 'list' view. Double click this icon.

15. Make the window larger by dragging the lower left corner so that it fills about two-thirds of the screen.

16. At the upper left, under the Jmol "File" menu, click "Open"

17. In the upper right of this panel look for the house icon and click it. (That is your 'home' folder.)

18. Now double click "Desktop". It should be at the top of the list.

19. Now you should see the "axme.pdb1" file. Double click it.

20. Now you should see it appear in the window, in a ball-and-stick rendering.

21. Now go to the "File" menu again, and click on "Script". You should see a new window, comparable to the "Console" in the web-based Jmol.

22. Move this window to the upper right of your screen.

23. Now click the "Help" box. Move this to the lower right corner of your screen, expanding its size to fill the screen.

24. Back to the molecule: In the Script window, type: background white

25. When you hit return, the black should turn to white. (This is essential if you want to print your molecule)

26. Type: select all; wireframe off; spacefill off; cartoons

Note: the commands can be separated by a semi-colon, or each can be followed by a return.

27. Type: color chain

28. If these colors do not please you, try: select :a; color blue

29. To make the N-terminus blue and C-terrminus red: select :c; color group

30. Now lets find a heme group: select HAS; spacefill

31. Make it spin: spin y 5

32. Continue exploring, or to close this molecule: zap