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@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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