Hi Thomas,
The same atom name will always receive the proton (as noted on the addh help page).  Your two options are to swap the atom names, or use the “rotate” command to rotate the appropriate bond by 180°.  For example, to swap the names of OE1 and OE2 in GLU 102 of chain A:

setattr a name XX :102.A@OE1
setattr a name OE1 :102.A@OE2
setattr a name OE2 :102.A@XX

Similarly, to rotate the CG-CD bond of that residue:

rotation 1 :102.A@CD,CG
rotation 1 180
~rotation 1

—Eric

On Mar 28, 2019, at 7:11 AM, Thomas Evangelidis <tevang3@gmail.com> wrote:

Hello again!

@Jaime
Thanks, PyChimera worked great!

@Eric
I wrote a script and posted it to a new thread to avoid confusion with this one. However, I just spotted a flaw. Is it possible to control to which oxygen of the carboxylate the proton is added? Ideally, I want to get both alternative protonations. If not then to flip the resulting carboxylic group by 180 degrees. Could you give me some hints, please?

best,
Thomas


-- 

======================================================================

Dr Thomas Evangelidis

Research Scientist

IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences

Prague, Czech Republic
  & 
CEITEC - Central European Institute of Technology
Brno, Czech Republic 

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