BIOL 6312: Proteins
Spring 2018

Lesson 4: February 20

1. Find the file "Jmol.jar" file in the jmol folder. Double click this icon.

2. Drag the window to the left side of the screen. If necessary, make the window larger by dragging the lower right corner.

3. Go to the "File" menu at the upper left of the Jmol window, and click on "Console". You should see a new window.

4. Move this window to the upper right of your screen, so that you can see both windows at the same time.

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

6. Look for the "pdb_files" folder and open it.

7. Now you should see the "1xme.pdb1.gz" file. Open it. (Or drag and drop an image file you previously saced, to load the 1xme pdb file a different way.)

8. Now you should see the protein appear in the window, in a "cartoon" or ribbons rendering.

9. Let's try to look at the environment of the heme (Hem)

10. Type: "cartoon off;wireframe 100;color cpk"

11. Now select the heme by typing: "select hem;center selected"

12. Now type: "display selected" . You should see only the heme. To make it larger, type: "zoom 300" (that's 3x). Or use the mouse to zoom.

13. To see its environment, select the nearby atoms by typing: "select within (5.0, hem)"

That selects any atoms within 5 Å of any atoms in hem. Instead of hem you could use a single atom(70:a.ca) the alpha carbon of residue 70 in chain a), or amino acid (70:a), or chain (:a). If you change the 5 to 3, you will get only those atoms in direct contact with the heme.

14. To see the nearby atoms, type: "display selected"

15. You should see some wireframe fragments that surround the heme. If you see cartoon, type: "cartoon off;wireframe 100; color cpk". What residues ligate the Fe of the heme? Carbon atoms are colored gray. Those are hydrophobic contacts. At one end of the heme there are two carboxyl groups. Let's study those

16. Find the red oxygens in the carboxyl groups of the heme. Double click one and then click a nearby blue nitrogen. This will measure the distance. There are quite a few in the 3 Å range, indicating ion pairing or hydrogen bonding.

17. There are also 2 water molecules in that region. If you can't see them, type: "select water; cpk"

18. You can also make measurements to the water molecules. Water molecule 834 makes hbonds to both of the carboxyl groups.

19. You can add hydrogens several ways. Type: "calculate hydrogens". In a second or two, many hydrogens will appear. Type again (or use the up arrow): "select within(5.0, hem)" Then type "wireframe 100"

20. For better placement of the hydrogens, before you load the protein, type: "set pdbAddHydrogens TRUE".

Type this:

zap; set pdbAddHydrogens TRUE; (then load the file again)
cartoon off;wireframe 100;color cpk;
select hem;center selected; zoom 300; display selected

21. Go back to the heme view: Type: "select within(5.0, hem);display selected" Make sure that the heme is properly sized and placed. If necessary, type: "cartoons off;wireframe 100;color cpk"

22. To see hydrogen bonds: Type "calculate hbonds". To see them better, type "hbonds 50". To color them, type "color hbonds magenta". It does place some hbonds to sidechains, as well as to backbone.

23. Now type: "zap; set pdbAddHydrogens FALSE" and reload the protein 1xme as before

24. Now resize the protein with the mouse, and move it to a new position so that the long dimension is vertical. Center it with the mouse (Shift key down, and double click but don't release the mouse)

25. Type: "show orientation" . (Or it can be done through the popup Jmol menu) It should start with moveto /...

26. Copy the text from moveto until just before the #OR.

27. Now move the protein around and change its size.

28. Paste the moveto text into the console, and press return. One thing to play with is the length of time, that is the first number in the text, by default it is 1.0 (seconds) You can increase this to make a slower change, or make it 0 to change instantly. You can also change the zoom. It is the first number after /* zoom, translation */ . For example, try 30

29. Now let's learn how to label atoms. Select the other heme by Typing: "select has;display selected; center selected; zoom 200; select all; wireframe only; wireframe 100; color cpk"

30. Click on the Fe atom to learn its atom number. It is #6033

31. Now select it. Type: "select atomno=6033" Updated Jmol: type "select @6033"

32. Now type: "label "Fe"", where 'Fe' is the text you want to show.

33. To change the position of the label type "set labeloffset 20 5" This moves the label along the x and y axes.

34. Type: "font label 30" to make it larger. "color label cyan" to make it cyan. "font label 30 serif bold". serif can be replaced by "sanserif" or "monospaced". bold can be replaced by "italic" or "plain". Now type "labels off"

35. Now let's label an amino acid. Type "select within(5.0, @6033); display selected". This heme has an oxygen and Cu on one side, and a Histidine on the other side of the Fe.

36. Click on the Nitrogen nearest the heme Fe to learn its number. (It is #3008 in His 384). Type "select @3008; label His 384;font label 40 serif bold"

That is a good way to label. If you simply select His384 and type label, it will put a label on each atom.

37. Now try to move the label: "set labeloffset 50 5".

38. change the 50 and the 5 to move the label. You can use negative numbers. When you are done, type "labels off".

39. Type "select within (5.0, has); display selected"

40. If you see lots of water, type "wireframe only; wireframe 100; color cpk"

41. To show a single hbond, determine the two atom numbers, type something like this "draw hbond1 line width 0.4 color white (@1908)(@1867)"

42. Try "spin on". THat's the default, around the y axis.

43. Try "spin x 10". Then "spin off"