Additional bonds to heteroatoms may have to be manually added using the bond command. See the pymol wiki for how to select atoms to link with the bond command. You will have to show sticks to see the bond. Waters are usually visualized as spheres, and you may want to modify their vdw radius to 0.5-1.0 A to make them small enough.
On Apr 18, 2011 5:48 PM, "Prija Ponnan" <firstname.lastname@example.org
> I am trying to visualize a protein-ligand complex of a metalloprotein using
> 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