[Chimera-users] Protonation of selected atoms ?

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 27 10:01:30 PST 2013

Let me rephrase that: obviously hydrogens don't H-bond with one another, but the placement of one hydrogen affects how a nearby hydrogen should be placed within a network of H-bonding functional groups.

On Nov 27, 2013, at 9:56 AM, Elaine Meng wrote:

> 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
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