[Chimera-users] About Amber residue number renumbering

Francesco Pietra chiendarret at gmail.com
Wed Oct 22 07:34:45 PDT 2008

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.

francesco pietra

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