[Chimera-users] Protonation of selected atoms ?

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 27 09:56:19 PST 2013

Hi Marek,
Sorry, the hydrogens are added to the whole model. The whole structure is used to calculate the hydrogen locations (hydrogens from different parts may sterically clash or H-bond with one another).  However, you can delete all the hydrogens you don't want after addition.
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 27, 2013, at 7:24 AM, Marek Maly wrote:

> Dear all,
> I would like to protonate just several nitrogen atoms
> (tertiary amines) of my hyperbranched polymer.
> I tried Structure "Editing -> Add hydrogens"
> but it protonised all my tertiary amines in the structure
> ignoring the fact that only few of them were selected and considered for
> protonation.
> So is there any way how to protonate only selected N atoms ?
> If not would be a good idea to add this possibility into Add Hydrogens
> panel (function).
> Thank you,
>    Best wishes,
>        Marek

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