Biol 6312

3 April 2018

Lesson 8: More Jmol and HTML files

Download the 3-button template file 2_window_template2018.html

Links to HTML help:

1. Bluegriffon-tutorial (perhaps all you will need is here)
2. Dave Raggett
3. Barebones

Links to Jmol help:

1. Jmol Homepage
2. Scripting Documentation
3. Colors!

Today we will look at the 2 window page and learn a little more about Jmol.

1. Find your jmol_pages folder in the jmol folder. It should also contain a pdb_files folder and a jsmol folder.

2. Move the 2_window_template2018.html file to the jmol_pages folder

3. Open it in BlueGriffon and save it as 2_window_template2.html

4. Load the 1xme.pdb1.gz file in both windows lines 34, and 51

5. If you use a different pdb file, the "ModelKit" part of the lessomn will not work as written.

6. There is no homework assignment associated with this lesson.

7. First part is "Isosurface". Work on the "left" window, the first one.

8. A suface can be an alternative to a simple spacefilling view. Alternatively, the surface can be translucent, so that the wireframe structure can also be seen.

9. First check that the protein is loaded in a wireframe or ball-and-stick view.

Then type "isosurface molecular 1.4"

You may change the surface by changing the number, for example, 0.4 or 2.4

10. To make the surface translucent, type "color isosurface translucent 0.5"

A lower number, e.g, 0.1 is not translucent, whereas a higher number, e.g., 0.9, is almost transparent, only slightly colored.

11. To change the coplor, add a color after the last command. To make it red, simply type "color isosurface translucent 0.5 red"

12. To change to a different color, without a name use [x88cc22] instead of the color name

13. Now we will work on the "ModelKit" function using Jmol.jar

14. Open Jmol.jar from your "jmol" folder

Then open the 1xme.pdb1.gz file from the pdb_files folder

15. Open the Console from the menu at the left, and change the background color of the page, by typing "background white"

16. We are going to mutate the protein by selecting Tyr 486 of chain A and changing it to Cys.

17. Type "select 486:A; display selected; center selected; zoom 500"

18. Now look for the "ModelKit " icon in the menu, just below the "Help"

Click the icon and a popup menu will appear at the upper left of the screen.

14. Click the upper section, and check the "delete atom" box

15. Now, one by one, click on the seven atoms of the Tyr side chain, until only the beta carbon remains. If you make a mistake, the "undo" command might work.

16. Now, go back to the same upper menu, and check the box with ??, just below Br.

In the popup box, type "S". Then return to the menu to check the box again, now it should say S.

17. Return to the menu again and check the box "Drag to Bond"

Click on the beta-carbon and drag it a short distance. A yellow S atom and its Hydrogen should appear.

18. Now save the image: "write image jpg "Cys486.jpg"

19. To save the file for the web page: "write v3000 Cys486.mutant"

20. Now, change the template in Blue Griffon to "load pdb_files/Cys486.mutant"

21. Check the page. Make sure the new file is moved or copied to the pdb_files folder.