1. Jmol Training Session Part V: Adding H Bonds and Struts

2. Finishing Touches: H Bonds
In some models you will want to display the hydrogen bonds (particularly in the beta sheets)
Since there are no sheets in this model, you will not need to display the hbonds.
NOTE: Hydrogen bonds are not typically displayed in the alpha helices.
Here’s why

3. Finishing Touches: H Bonds
To add hydrogen bonds to beta sheets:
Type – select <area> and sheets
Type – calculate hbonds

4. Finishing Touches: H Bonds
To give the hbonds weight:
Type – hbonds 1.0

5. Finishing Touches: H Bonds
To solidify the hbonds:
Type – set hbonds solid

6. Finishing Touches: H Bonds
To set the hbonds to the backbone:
Type – set hbonds backbone

7. Finishing Touches: H Bonds
To color hydrogen bonds:
Type – color hbonds <color>
What’s up with the hbond arrangement?

8. Finishing Touches: Struts
In some models you will need to stabilize the model or connect a
ligand to the model. To do this you will need to add struts.
To add struts
Type – select :b
Type – calculate struts
Type – struts 1.0
Type – color struts <color>

9. Finishing Touches: Connect a Ligand
To connect a ligand
Type – set picking strut
Hover where you would like the strut
Click to get a “cross” and release
Move the mouse to the connection point and click
Try to keep your struts under .9nm

10. Finishing Touches: Connect a Ligand
To give the strut weight and color:
Type – strut 1.0
Type – color strut lemonchiffon
Depending on the size of the ligand a general rule of thumb is to secure it with three struts.

11. Finishing Touches: More Struts
If you create a strut that you don’t ultimately want in the model – you can delete it. One way to delete the unwanted strut is to hit the up arrow until you get to the strut added line.
Type – (space) delete
1 new bonds; 0 modified
$ strut 1.0
$ color strut lemonchiffon
$ connect ({1423}) ({1716})STRUTS delete

12. Finishing Touches: More Struts
Before
A second way to get rid of a strut is to click on the ends of the strut to identify the atom numbers.
SER]44:B.CA #
[GLY]83:B.CA #
Type the following commands to delete the strut:
After
Type – select atomno=1408 or atomno=1691
Connect strut delete

13. Finishing Touches: More Struts
To turn off “set picking struts”:
Type – set picking ident

14. Your Fifth Assignment!
Your mission for the weekend is to design a model of the phenylalanine hydroxylase .
Your model will be based on pdb file: 1J8U
When you feel like throwing your computer out of the window – remember we are here for you OR
Yell JMOOOOOOOOOL!
You’ll feel better!
JMOOOOOOOOOL!