> 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
> 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.