Hi All, I used JLigand to form a covalent bond between ligand, Benzoate and residue Ser and followed the tutorial in the JLigand website and refined it. How shall I know that a covalent bond is existing now? It does not show in coot as a bond. Also although i had inserted the line with Link befor ethe Cryst1 in my i/p pdb file, the o/p file does not have any line specifying the link. The Benzoate also shows up as a different chain (like if I were to add it without creating a bond). Does that mean the for some reason the bond did not form?
Thank you, Subhangi
