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 <https://www.uochb.cz/web/structure/31.html?lang=en> Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/> Brno, Czech Republic email: tevang3@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/