Hi, 

I want to use Addh function to add hydrogens and protonate N, C-terminii but I don't understand very well how you detect if a terminus is fake or not.

For example, for the structure 3L4F, I obtain the following log : 

Chain-initial residues that are actual N terminii: MET 586.A, MET 586.B, MET 586.C

Chain-initial residues that are not actual N terminii: GLY 652.D

Chain-final residues that are actual C terminii: LEU 646.A, LEU 646.B

Chain-final residues that are not actual C terminii: ASP 638.C, ARG 758.D

I don't understand why GLY 652.D, ASP638.C and ARG 758.D are not terminii,  can you explain me why and how the algorithm detect that ?

Thank you in advance for your answer.