I am trying to visualize a protein-ligand complex of a metalloprotein using Pymol.
The ligand and certain amino acids are coordinated with the metal ions in the binding site.The binding site also have some water molecules which are also making interactions with amino acids and the metal ions. But using Pymol i am not able to visualize the coordinated bonds.
When I am visualizing the binding site of this protein using Pymol, the water molecules are showing multiple hydrogen bonds (6 hydrogen bonds), which is not correct according to the valency of oxygen.

Please help me


Prija Ponnan
Research Student
Department of Chemistry
University of Delhi
Delhi-110007, India
Canadian Commonwealth Scholarship Program Scholar
College of Pharmacy and Nutrition
University of Saskatchewan