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