Dear colleagues and friends, I notice that during "Tools -> Dockprep" and "Tools -> addH" steps Chimera sometimes will automatically add hydrogens to the positions considered necessary by the program itself. However, these positions do not always really have these hydrogens imposed on them. One situation is when I added hydrogen to the molecule containing nitrogen with lone-pair electrons, Chimera added hydrogen to the position of this lone-pair. One other situation is in the disulfide bond. It seems that Chimera can not recognize the disulfide bond, so hydrogen is added to each of the thiol group, which is obviously inappropriate. I'm wondering what causes these situations and how users can prevent them happening. Any help is appreciated. If you coincidently encountered with similar situation, I'm glad to hear your story as well~ Happy new year and best wishes to your research! Sincerely yours CHIU,YEUNG