Oct 16, 2008

Hydrogen Bonds

Hydrogen bonds interconnect the turns on a helix and the backbones of a sheet. They also stabilize DNA and RNA. Here is the rundown on how to display hydrogen bonds in a typical fashion.
1. Go to File--> Browse Commands
2. Click PMV --> select 'hbondCommands', click 'Load Selected Module'

3. Select "backbone" under 'Atom' in 'Select From String'

4. Go to Edit--> Hydrogens--> Add
5. Select 'Polar Only' and hit OK

6. Go to Hydrogen Bonds--> Build--> Click "Select Parms and Build"
Click OK on the dialog that pops up.

7. Goto Hydrogen Bonds--> Display --> Cylinders
8. Click 'Set anchors', donors: N, acceptors C, and change the color if you wish as well.
In the Show Hydrogen Bonds as Cylinders dialog you can adjust the radii and length of the bonds as well as toggle them on and off by clicking the individual bonds in the table on top.


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