Hi Elaine: At the end of a long journey of ACE/NME capping a fractionated model, I would not leave the impression that I like the way Amber treats the layout of pdb files. With Chimera I had all HETATM capping groups on one side and the ATOM of protein stretches on another side, conserving the residue number they had in the unabridged model. Straightforward to relate to the starting crystallographic work Now, after Amber forced (forced against me) manipulation, the ACE/NMR residues are intermingled with the standard amino acid, all ATOM, and take part to the overall sequential numbering. As the number of atoms in ACE differs from NME, and the stretches are many, headache in relating residue numbers imposed by Amber to residue numbers in the original crystallographic work from which I started. Regards francesco pietra