[Chimera-users] Chimera: Amber to PDB

Boris TOUZEAU boris.touzeau at gmail.com
Mon Aug 27 17:58:46 PDT 2018

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 at 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 at 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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