[Chimera-users] Structure editing: addH

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 10 13:40:56 PDT 2014


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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