I need help. Can some one tell me a way to find out whether 2 molecules are connected by covalent linkage or not. Say for example in pdb files we have ligand and protein molecules and I wish to know a way to find out if the ligand is connected to the protein via a covalent bond or not, The problem is I cannot use covalent radius values for specific bonds as the resolution is not good in pdb.
I wonder how does the program in pymol does that. I would be very grateful if someone could tell me a way out. Please help.