Calculate Hbonds:Make sure they are on:
  B7: How to show hydrogen bonds.
Hydrogen bonds that involve mainchain atoms can be displayed using two steps of menu selection:

First you need to calculate the hydrogen bonds:

Style ¬ Hydrogen bonds ¬ Calculate

Then make sure they are defined as "on" (this usually is not necessary)

Style ¬ Hydrogen bonds ¬ On

You can vary the thickness of the hbonds:
Style ¬ Hydrogen bonds ¬ 0.25A

Or color them:
Color ¬ Hydrogen bonds ¬ Yellow


  1. The color of the hydrogen bonds are those of the two connecting atoms, i.e. donor and acceptor. Therefore it may be difficult to see them, try making them thicker or change their color.
  2. Note that H-bonds are only displayed between residues in secondary structure (NH-->O=C). To assess H-bonds between a protein and its small molecule ligand, use one of the distance measures to determine if the donor and acceptor are less than 3.2 Å apart and with the correct geometry.