My colleagues asked me to know if they can use PyMol to quickly find information of salt bridges in their working proteins. It seems there is no simple pymol script to do such purpose (at least I can’t find it).
I tried writing a shell scripts to extract coordinates from all negative (Glu, Asp) and positive (Lys, Arg) charged residues and calculate the distances to know if there are any salt bridges in the protein. Before I finish that coding work, I found that VMD actually provide such analysis tool! Good job VMD!.
Here is a snapshot and using protein EnvZ (PDB code: 1BXD) as an example. The output of analysis is shown in the terminal window.
Definition of salt bridge can be found at Wikipedia.
VMD can be downloaded at VMD official site.