Second Computer Lab:

Examine a PDB file, save and open a script file, save and open an image file.

1. Open the application "TextEdit" from the Dock

4. Under "File" choose "Open", (or type ⌘ + O)

5. Go to the Desktop to find :1xme.pdb1 (If not found, you will need to download it again. See last week.)

6. These files can be rather large. They have an introductory section, called the "header" that includes reference material, amino acid sequence for the polypeptide, list of secondary structures, and list of chains and non-protein molecules. Finally, there is one line for each atom in the structure. Widen your window, if necessary, so that it can contain each line. This information identifies the atoms (carbon, nitrogen, ..) the amino acid, its number, the chain, and the xyz coordinates. The spacing of the information is critical for Jmol to read the file correctly. Sometimes it will be useful to look at such a file to find out how to select atoms properly, i.e. what number. You can also modify these files by deleting multiple chains or water molecules.

7. After looking at the file, quit TextEdit (without saving any changes).

8. Now open the application Jmol, as last week: open the unnamed folder in the Dock, and "double-click" Jmol.jar. Or, under the Apple menu at the upper left, go to Recent items->Documents->Jmol.jar

9. Here is another way to open a pdb file. In the console type:

load /users/proteins/desktop/1xme.pdb1

10. Now change the view of this molecule:

11. Select all; wireframe off, cpk 100%;

12. Now make it more or less 'shiny'

13. Type: set specpower 20

14. Now a trick. To change this setting, use the "up arrow". You will see the previous command. Just edit the number to 60. (You can access all of your previous commands using the up and down arrows.

15. Type: select tyr

16. Type: color magenta

17. To select an individual residue, just type the number. If there is more than one chain, you will need to identify that also. Type: 286:a

18. (Without identifying the chain, it is possible that you might also select water number 286, as well as residue 286 in chains b or c.)

19. Type: color chartreuse

20. (Or choose another color.)

21. Other ways to set the color: [a,b,c] where a,b,c are numbers from 0 to 255

22. Or [xABCDEF] where ABCDEF are 6 hexadecimal digits 0-9 and A-F

23. Try a few colors. In both cases, if all the digits are the same, you get shades of gray.

24. Again select 286:a

25. To see through something, type: color translucent white

26. How to save your molecule as is looks right now?

27. Type: write script /users/proteins/documents/1xme001.spt

29. The last part is the name of the file. It contains the pdb file number 1xme, a script number 001 in case you make different versions , and an extension .spt to indicate that this is a Jmol script file. Actually, you can call it anything, but I have found it advantageous to have a method for naming files.

30. The phrase " /users/proteins/documents "determines where the file is saved. Now check your documents folder to see if the file is there.

31. If the file is there, go back to the Jmol console and close the file. This can be done by typing: zap

32. Now retrieve the file by typing: script /users/proteins/documents/1xme001.spt

33. If you see the molecule again, you have been successful. Later, a script file can be used to make a web page with a Jmol molecule.

34. How to get an image for printing or displaying in another document file?

35. First make your image window as large as can be. This will increase the quality of the image you export (I think!). Grab the lower right corner.

36. Under the "File" menu, select "Export" "Export Image or Script"

37. You have the choice of "JPEG", "PNG", "PPM" or "SPT" The last is another way to save a script file. The first two are common image formats (PPM is less common).

38. Choose "JPEG" and quality 90. Change the destination to "Desktop" and the name to "1xme001.jpg

39. Now find the saved file. If you "double-click" it, it should open in "Preview"

40. From "Preview" it can be saved in many different formats.

41. Quit "Preview" and open "Word", the blue W in the Dock.

42. Open a new document, and from the "Insert" menu, choose "Picture" -> from file. Find your file on the Desktop and insert it. Save your word document. Another trick I use is to insert the figure into a Table with 2 cells. The other cell can contain the caption.