[Chimera-users] Protonation of selected atoms ?

[Elaine Meng]

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.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#deletion>
Best,
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 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