<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>Adding ions is in the “Addions” module. Here’s some example code:</div><div class=""><br class=""></div><div class="">from Addions import initiateAddions</div><div class="">from chimera import openModels, replyobj</div><div class="">initiateAddions(openModels.list(), “Cl-“, “neutralize”, replyobj.status)</div><div class=""><br class=""></div><div class="">Now, obviously the above code will only neutralize a positive system since it is adding “Cl-“ ions. Your script would probably need to sum up the total charge of your system in order to know what kind of ion to add…</div><div class=""><br class=""></div><div class="">—Eric<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Mar 31, 2019, at 8:10 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="auto" class="">OK, i found an older post about how to run DockPred from a script. But i cannot find how to add ions in Python. Is there any way to neutralize the system in Python without adding waters?</div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Dne pá 29. 3. 2019 5:28 PM uživatel Thomas Evangelidis <<a href="mailto:tevang3@gmail.com" class="">tevang3@gmail.com</a>> napsal:<br class=""></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="auto" class="">Hi Eric,<div dir="auto" class=""><br class=""></div><div dir="auto" class="">Thanks for the hints, i programmed it to consider also the atom that receives the proton. To make the code complete, namely to generate structures ready for docking or MD, is it possible to do the following in python?</div><div dir="auto" class=""><br class=""></div><div dir="auto" class="">* if alternate locations keep only highest occupancy.</div><div dir="auto" class="">* convert modified residues to standard residues.</div><div dir="auto" class="">* replace incomplete sidechains.</div><div dir="auto" class=""><br class=""></div><div dir="auto" class=""><br class=""></div><div dir="auto" class="">Basically what DockPred does but in python.</div><div dir="auto" class=""><br class=""></div><div dir="auto" class="">Best,</div><div dir="auto" class="">Thomas</div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Dne čt 28. 3. 2019 6:10 PM uživatel Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" target="_blank" rel="noreferrer" class="">pett@cgl.ucsf.edu</a>> napsal:<br class=""></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word;line-break:after-white-space" class="">Hi Thomas,<div class=""><span class="m_777493216267559648m_-586845445362126228Apple-tab-span" style="white-space:pre-wrap"> </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 class=""><br class=""><blockquote type="cite" class=""><div class="">On Mar 28, 2019, at 7:11 AM, Thomas Evangelidis <<a href="mailto:tevang3@gmail.com" rel="noreferrer noreferrer" target="_blank" class="">tevang3@gmail.com</a>> wrote:</div><br class="m_777493216267559648m_-586845445362126228Apple-interchange-newline"><div class=""><div dir="ltr" style="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;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="m_777493216267559648m_-586845445362126228Apple-converted-space"> </span><br class=""><div dir="ltr" class="m_777493216267559648m_-586845445362126228gmail_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 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 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" rel="noreferrer noreferrer" target="_blank" class="">IOCB - 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