BIOL 6312: Proteins
Spring 2018

Lesson 5: March 6

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. If not, type: "select all;cartoon only"

9. Shiny appearance can be set by "set specpower 80" where 80 can be any number betwoon 0 and 100.

10. Or another command is : "set ambientpercent 50" where 50 is any number between 0 and 100

11. See this link:

12. How to vary the look of the cartoon: type "set hermitelevel -3"

13. See this link:

14. Hermite level can be 0 to 8. A negative value makes the cartoon stay thick while moving (but not while spin is on)

15. You can also change the shape of the ribbon by typing: "set ribbonaspectratio 20"

16. For ribbon aspect ratio, 16 is default. Higher numbers make a flatter ribbon, lower numbers a thicker ribbon.

17. To make a ribbon that stays thick while spin is on, type: "set cartoonfancy on"

18. Another lighting control is zshade, to highlight the front of the molecule. Type: "set zshade on; set zshadepower 1" You can use 2 or 3 also.

19. Now change to spacefilling, by typing: "select all and not water; cpk only"

20. You can use the slab and depth commands to control what you see.

21. To see the hemes better, type "select hem or has;color cpk"

22. With the slab on, rotate the protein around

23. Now type: " slab 40; depth 40;slab on" to see a thin slice

24. Link to surfaces in Jmol


Comments/questions: email me

Copyright 2018, Steven B. Vik, Southern Methodist University

Last modified Tuesday, March 6, 2018