[Chimera-users] Structure editing: addH

Christian Wagner wagner at mail.sysu.edu.cn
Thu Apr 10 19:27:38 PDT 2014

Hi George, 

You could also try using Avogadro, which allows protonation according to a user defined pH: 

Best regards, 
Chris Wagner 
----- Original Message -----

> From: "Elaine Meng" <meng at cgl.ucsf.edu>
> To: "George Tzotzos" <gtzotzos at me.com>
> Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Sent: Friday, April 11, 2014 4:40:56 AM
> Subject: Re: [Chimera-users] Structure editing: addH

> Hi George,
> Chimera tries to make the protonation reasonable for near-neutral pH,
> so in general carboxylates would not be protonated. However, if you
> want to force protonation of such groups, it can be done by changing
> the atom type of one of the oxygens first.

> Choosing menu item "Actions… Labels… IDATM Type" shows the atom
> types, which are described here:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/idatm.html>

> Type "O2-" is not going to get protonated. You could change one of
> the carboxylate oxygens to type O3, which would be protonated. For
> example, select (Ctrl-click) the oxygen you want to become
> protonated, then change the type with command:

> setattr a idatmType O3 sel

> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
> (you would have to re-label for the label to change, but the type has
> changed)… then add hydrogens. Having one oxygen with type O3 and the
> other with type O2- is inconsistent, so you could change the other
> to type O2, but it isn't necessary if all you care about is the
> protonation state.

> Another possibility is to just get this compound from Pub3D, which
> already has carboxyl groups protonated, e.g. with the Chimera
> command:

> open pubchem:543977

> <http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=543977>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco

> On Apr 10, 2014, at 11:14 AM, George Tzotzos <gtzotzos at me.com> wrote:

> > Hi everybody,
> > I’ve been trying to add hydrogens to a ligand (7-octenoic acid)
> > obtained from docking. Hydrogens are added but not on the carboxyl
> > group.
> > I’m attaching the ligand.pdb for easy reference.
> > I’d appreciate any suggestions regarding this behavior
> > Best regards
> > George

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