<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Thomas,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>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:</div><div class=""><br class=""></div><div class="">setattr a name XX :102.A@OE1</div><div class="">setattr a name OE1 :102.A@OE2</div><div class="">setattr a name OE2 :102.A@XX</div><div class=""><br class=""></div><div class="">Similarly, to rotate the CG-CD bond of that residue:</div><div class=""><br class=""></div><div class="">rotation 1 :102.A@CD,CG</div><div class="">rotation 1 180</div><div class="">~rotation 1</div><div class=""><br class=""></div><div class="">—Eric<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Mar 28, 2019, at 7:11 AM, Thomas Evangelidis <<a href="mailto:tevang3@gmail.com" class="">tevang3@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><div dir="ltr" class=""><div class="gmail_default" style="font-size: large;">Hello again!</div><div class="gmail_default" style="font-size: large;"><br class=""></div><div class="gmail_default" style="font-size: large;">@Jaime<br class=""></div><div class="gmail_default" style="font-size: large;">Thanks, PyChimera worked great!</div><div class="gmail_default" style="font-size: large;"><br class=""></div><div class="gmail_default" style="font-size: large;">@Eric<br class=""></div><div class="gmail_default" style="font-size: large;">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?</div><div class="gmail_default" style="font-size: large;"><br class=""></div><div class="gmail_default" style="font-size: large;">best,</div><div class="gmail_default" style="font-size: large;">Thomas</div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr"><br class=""></div></div>--<span class="Apple-converted-space"> </span><br class=""><div dir="ltr" class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><p align="LEFT" style="margin-bottom: 0cm;" class=""><span style="" class=""><span style="font-family: arial, helvetica, sans-serif;" class=""><font size="2" class="">======================================================================</font></span></span></p><p align="LEFT" style="margin-bottom: 0cm;" class=""><span style="" class=""><span style="font-family: arial, helvetica, sans-serif;" class=""><font size="2" class="">Dr Thomas Evangelidis</font></span></span></p><p align="LEFT" style="margin-bottom: 0cm;" class=""><span style="font-family: arial, helvetica, sans-serif; font-size: small;" class="">Research Scientist</span></p><p align="LEFT" style="margin-bottom: 0cm;" class=""><span style="font-family: arial, helvetica, sans-serif; font-size: small;" class=""><a href="https://www.uochb.cz/web/structure/31.html?lang=en" target="_blank" class="">IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences</a></span></p><font size="2" class=""><div class=""><font face="arial, helvetica, sans-serif" class=""><div class="">Prague, Czech Republic</div><div class=""> <span class="Apple-converted-space"> </span>& </div></font></div><font face="arial, helvetica, sans-serif" class=""><a href="https://www.ceitec.eu/" target="_blank" class="">CEITEC - Central European Institute of Technology</a></font><br class=""><font face="arial, helvetica, sans-serif" class="">Brno, Czech Republic </font></font></div><div class=""><font size="2" class=""><font face="arial, helvetica, sans-serif" class=""><br class=""></font></font></div><div dir="ltr" class=""><p align="LEFT" style="margin-bottom: 0cm;" class=""><span style="" class=""><span style="font-family: arial, helvetica, sans-serif;" class=""><font size="2" class="">email: </font></span></span><a href="mailto:tevang3@gmail.com" target="_blank" style="font-size: small; font-family: arial, helvetica, sans-serif;" class="">tevang3@gmail.com</a></p><p align="LEFT" style="margin-bottom: 0cm;" class=""><span style="" class=""><span style="font-family: arial, helvetica, sans-serif;" class=""><font size="2" class="">website:<span class="Apple-converted-space"> </span><a href="https://sites.google.com/site/thomasevangelidishomepage/" target="_blank" class="">https://sites.google.com/site/thomasevangelidishomepage/</a></font></span></span></p><span style="" class=""><br class=""><br class=""></span><div style="margin-bottom: 0cm;" class=""><br class="webkit-block-placeholder"></div></div></div></div></div></div></div></div></div></div></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; 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