[Chimera-users] Add Hydrogens - non standard residue - protonation state

Hi There, Can anybody please suggest me how to use 'setattr' (or any other function) to assign a protonation state for an atom in a non-standard residue. I have a ligand and I am using a python script to add hydrogens and charge to the ligand molecule using chimera no-gui. I see that chimera adds an extra hydrogen to a nitrogen atom in the ligand and assigns a charge of +1 to the molecule. Removing this hydrogen using GUI is simple but not practical for large set of molecules. So, it would be helpful if somebody suggest me a command-line to set specific protonation states for atoms (in non-standard residue). Thanks and Best Regards, Subha