Second exercise with RasMol

1. Get a protein file in pdb format from the Protein Data Bank.
Enter "hemoglobin" in the Search window. Select Full Text Search 
and match exact word.

4. Find about 328 "hits". Now what? Let's "Refine our query" in the pull-down menu.

5. Type in "Perutz" and select authors.

6. Now find 24 hits.. Click on "1bz0" , human Hemoglobin A.

7. You should be here: 1bz0

8. This page shows basic information about this structure.

9. On the left panel are a list of Links. Click on "Download/Display Structure".

10. Scroll down, if necessary to "Download the Structure File"

11. Choose compression: none, file format: PDB. Control-click to download into your RasMol folder.

12. You should find a file there called "1bz0.pdb"

13. Now open RasMol. Look for two windows: graphical(Main window) and command line.
Look under the "Window" menu if they are not visible.

14. Arrange the 2 windows so that the white command line window is in the lower left-hand of the screen. It should be short and wide. Make the graphical window large. Allow a few lines of text in the bottom of the comman line window to be visible.

15. Begin typing "load 1bz0.pdb". Notice that the comman line window will remain in the background while you are typing. As long as you can see what you are typing, it is never necessary to switch back and forth between the windows.

16. After hitting Return, you should see text about the file appear, and the molecule should appear in the graphical window. An online RasMol help file exists, but only for version 2.6. It is largely accurate. You can print out the help manual, but it is not so useful for a beginner.

17. You can change the molecule by using the Display and Colors Menu. Try it out.

18. You can also use the command line, which is extremely powerful once you learn a little.

19. For example, I prefer a white background. (It saves on black ink also). Type: background white (Commmands are always followed by Return).

20. Type: select hem

21. Then select "Spacefill" from the Display menu.

22. Type: select protein

23. Then select "Cartoons" from the Display menu, and "Structure" from the Color menu.

24. Now, paractice saving a script file.

25. Type: save script 1bz0a.spt

26. Did it work? Type: zap

27. Type: script 1bz0a.spt

29. The molecule should reappear.

30. This file has 4 chains: A, B, C, and D. The alpha subunits are A and C. The beta subunits are B and D. To select a chain type: select :a

31. To select both beta chains type: select :b or :d

32. Now type: color cyan

33. Select "Cartoons" from the menu

34. Now type: select :b and 2, 143

35. This should select residues 2 and 143 from the B chain

36. Type: wireframe 100.

37. Now let's look at the pdb file and the script file.

38. Open them using TextEdit or WordPad (?)

Jmol tip:

Using the menu, open the "Console". You can type RasMol type commands here to modify the appearance of the molecule