BIOL 6312: Proteins

Spring 2018

Lesson 2: February 6

1. Download the Jmol application at Direct download of the latest here. Download java here if needed.

2. Look for this file, wherever your downloads appear:

3. Double-click it to expand the file, into a folder. You may move the folder to a convenient place. (Desktop, Applications folder, etc) or leave it in the Downloads folder

4. You may rename the folder "jmol". In any case I will refer to it as the "jmol" folder.

5. Open the "jmol" folder and make new folders called "pdb_files" and "jmol_pages"

6. Find the "1xme.pdb1.gz" file (or download again) and copy or move it to the "pdb_files" folder.

7. Find the file, and expand it into a folder by double-clicking it.

8. Move the new "jsmol" folder into the "jmol_pages" folder (look for the jsmol.htm page in the jsmol folder and open it in Firefox to explore jmol capabilities)

9. Find the file "Jmol.jar" file in the jmol folder. Double click this icon. You might not allowed to open the file. (On a Mac hold the "control" key down while opening.)

10. Drag the window to the left side of your screen, if necessary. You can make the window larger or smaller by dragging the lower right corner. Probably you should expand it to the bottom of your screen.

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

12. Move this window to the upper right of your screen, and make it more narrow, if necessary, so that you can see both windows at the same time. (they can overlap a little.)

How to visualize a protein:

12. One way: at the upper left, under the Jmol "File" menu, click "Open"

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

14. Now you should see the "1xme.pdb1.gz" file. Select it and click "Open".

15. Now you should see the protein appear in the window, probably in a "ball-and-stick" rendering with CPK colors and a black background.

Note: You can also load a molecule directly from the PDB, from the "File" menu, Get PDB, then type "1xme". Or, type "load=1xme". Or to use your downloaded file, type "load pdb_files/1xme.pdb1.gz". To reload in a different way, type "zap" to clear the screen.

16. In the Script window, type: "background white" (after typing commands you must hit the enter key"

17. When you hit enter/return, the black should turn to white. (This is important if you want to print the image of your molecule. I tend to prefer the white background in any case.)

18. Now let's learn how to save the file. We will not change the pdb file. We must save a new file called a script file.

19. Type: "write script jmol_pages/1xme_1.spt"

20. This creates a file called "1xme_1.spt" in the "jmol_pages" folder. This works because the jmol_pages folder is in the jmol folder.

21. When doing a project it is helpful to name your files systematically, so you can tell what they are. Now let's see if it worked.

22. In the console type "zap". When you hit return the molecule should disappear, screen is now black.

23. To bring the molecule back, type in the console: "script jmol_pages/1xme_1.spt"

24. When you hit return the molecule should reappear. If the screen is white, you know you are successful.

25. You can also save an image file, such as in "jpg" or "png" format, which is more useful for general purposes.

26. AN image file can be created under the File menu, choose "Export", then "Export Image". At the right, change the Image Type to PNG.

27. I prefer to type the command. For example, a better quality image can be saved.

28. To get a better quality image you can designate the size. Type "write image 2000 2000 "1xme2.jpg"

29. Now open the two images to compare. Zoom them a couple times and you can see that the first image will become jagged.

30. This will function as a normal jpg file, but it also serves as a script file. You can type "load pdb_files/1xme2.jpg" or "load 1xme2.jpg" (depending upon where the file is stored). You can even drag and drop the file onto the jmol window.

31. Next time we will learn how to change details of the image of the molecule. The basic idea is to "select" the protein, or some of its amino acids, or some of its atoms. Then change their view.

32. For some examples: Type the following

33. "select hem"

34. "cpk"

35. This makes one heme spacefilling, in cpk colors (oxygen is red, nitrogen is blue, carbon is gray)

36. Individual commands can be separated by a semicolon ;

37. "select has; cpk"

38. "select cu; color green; cpk"

39. "select cua; color cyan; cpk"

40. "select protein; color yellow"

41. "select :a; color group"

Comments/questions: email me

Copyright 2018, Steven B. Vik, Southern Methodist University

Last modified February 6, 2018