First exercise with RasMol

1. Name a Folder with your name and place a copy of RasMol in it. (RasWin for Windows, RasMac for Macintosh).

2. Download a copy of the help file. RasMol
Download the "raw" file. RasWin or RasMol (for Mac). Save it to the same folder. Mac: Hold the control key as you click on the link. This will allow you to download it directly to your folder.

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

4. Find 352 "hits". Now what? Let's "Refine our query" in the pull-down menu.

5. Type in "Dickerson" and select authors.

6. Now find 4 hits. "3cyt" is reduced cytochrome c and "5cyt" is oxidized cytochrome c. Click on "5cyt".

7. You should be here: 5cyt

8. This page shows basic innformation 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 "5cyt.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 5cyt.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, how to save this view for another day?

25. Type: save script 5cyt1.spt

26. Did it work? Type: zap

27. This will clear the current molecule (Up to 5 molecules can be loaded at once.)

28. Type: script 5cyt1.spt

29. The molecule should reappear.