Hi Eric,

Thank you for the quick answer, I tried to use the addcharge command indeed but I think that my HIS residues were still HIS residues for all the histidines and not HID nor HIE.

I expected that one could not do it directly and was prepared to write a script but I did not expected you to write it for me.

Still I thank you as it is much much shorter than what I envisioned.

Best wishes,

Boris TOUZEAU

Le mar. 28 août 2018 à 04:59, Eric Pettersen <pett@cgl.ucsf.edu> a écrit :

Hi Boris,
Well, not directly. If you run the AddCharge tool (or ‘addcharge’ command), which will in turn add hydrogens if any are missing, then the “Amber name” of the residue is computed and put into the ‘amberName’ attribute of each residue. So, if you then run the Python script below (simply by opening it with File→Open or the “open” command), then the regular name of the residue will be overwritten with the amberName attribute and if you then save a PDB file, the residue names will use the Amber convention.

—Eric

Eric Pettersen
UCSF Computer Graphics Lab

On Aug 27, 2018, at 2:00 AM, Boris TOUZEAU <boris.touzeau@gmail.com> wrote:

Hi,

I am Boris TOUZEAU, actually a PhD student at the National Taiwanese University (NTU) based in Taipei.

I had a question about chimera; Is it possible to output pdb files having amber residues naming convention instead of pdb residues naming convention ? I saw it was possible to do it for the atoms (ligands) but I would be more interested to do it for residues.

Best wishes,

Boris TOUZEAU
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