[Chimera-users] Structure editing: addH
wagner at mail.sysu.edu.cn
Thu Apr 10 19:27:38 PDT 2014
You could also try using Avogadro, which allows protonation according to a user defined pH:
----- 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:
> 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
> (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
> open pubchem:543977
> I hope this helps,
> 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
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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