Editing Bondpack (section)

== HydroBond ==
HydroBond visualizes all potential polar contacts between protein and ligand molecules within a user-specified distance.<br>  
The underlying function is based on the different atom types, such as hydrogen bond acceptor and donor atoms,<br>
and thus it is required to have hydrogen atoms present in the structure. <br>
If your structure file doesn't contain hydrogen atoms already, you can add them directly in PyMOL as shown in the image below.<br><br>
[[File:add_hydrogens.png]]
<br><br>HydroBond is related to PyMOLs "[A]->find->polar contacts" command, however,<br>
it doesn't consider geometry criteria and angle thresholds,<br> but is rather based on atom types.<br> 
When you select HydroBond from the "Plugin" menu, you will be prompted to enter the name of the protein object,<br>
the ligand object, and a distance cutoff as shown in the figure below.<br>
If HydroBond was able to detect hydrogen bond and acceptor atoms within the<br>
specified distance, potential interactions will be visualized as yellow dashed lines.<br><br>
[[File:hydrobond_action.png]]
<br><br>