[Chimera-users] Protonation of selected atoms ?

Eric Pettersen pett at cgl.ucsf.edu
Wed Nov 27 11:18:58 PST 2013


Hi Marek,
	You can do this with Build Structure.  With the nitrogens selected, go to that tool's "Modify Structure" tab and do the following:

1) Change element to N
2) Change geometry to tetrahedral if it isn't already
3) Change bonds to 4
4) Change "Residue Name" option to "Leave unchanged"
5) Click Apply

Normally using Build Structure would be suboptimal since hydrogen placement would not consider H-bonding interactions, but for protonating tertiary amines that consideration is moot.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

On Nov 27, 2013, at 7:24 AM, "Marek Maly" <marek.maly at ujep.cz> 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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