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> I have to mutate 6 membered ring structure, with 2 Natoms and 4 C atoms. We are talking about modifying a ligand, I take it? > There was no hydrogen atom on the nitrogens. after necessary mutations > i have add a hydrogen atom on one of these N atoms. Using some tool other than Coot, I presume? Or are we talking about the restraints editor? > But due to the diff in bond lengths H is not adding. What did you do to try to add the H? What did you expect to happen? What actually happened? > So i have to slightly change one of the bond lengths to make it single > bond. is there any method to do this with altering or breaking the > whole rong structure. > If we are talking about modifying restraints, then changing the bond length does not change the bond order. I am not convinced that we are talking about Coot. Using the restraints editor is the the recommended way of manipulating chemistry. HTH, Paul.