Jmol Training Session Part V: Adding H Bonds and Struts

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 . . . .

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

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

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

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

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

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>

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

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.

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

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 #1408 2.586 2.724 -14.31 [GLY]83:B.CA #1691 4.741 -20.706 5.2530003 Type the following commands to delete the strut: After Type – select atomno=1408 or atomno=1691 Connect strut delete

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

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!