<div dir="auto">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><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">tevang3@gmail.com</a>> napsal:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="auto">Hi Eric,<div dir="auto"><br></div><div dir="auto">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"><br></div><div dir="auto">* if alternate locations keep only highest occupancy.</div><div dir="auto">* convert modified residues to standard residues.</div><div dir="auto">* replace incomplete sidechains.</div><div dir="auto"><br></div><div dir="auto"><br></div><div dir="auto">Basically what DockPred does but in python.</div><div dir="auto"><br></div><div dir="auto">Best,</div><div dir="auto">Thomas</div></div><br><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">pett@cgl.ucsf.edu</a>> napsal:<br></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">Hi Thomas,<div><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><br></div><div>setattr a name XX :102.A@OE1</div><div>setattr a name OE1 :102.A@OE2</div><div>setattr a name OE2 :102.A@XX</div><div><br></div><div>Similarly, to rotate the CG-CD bond of that residue:</div><div><br></div><div>rotation 1 :102.A@CD,CG</div><div>rotation 1 180</div><div>~rotation 1</div><div><br></div><div>—Eric<br><div><br><blockquote type="cite"><div>On Mar 28, 2019, at 7:11 AM, Thomas Evangelidis <<a href="mailto:tevang3@gmail.com" rel="noreferrer noreferrer" target="_blank">tevang3@gmail.com</a>> wrote:</div><br class="m_777493216267559648m_-586845445362126228Apple-interchange-newline"><div><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"><div dir="ltr"><div class="gmail_default" style="font-size:large">Hello again!</div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large">@Jaime<br></div><div class="gmail_default" style="font-size:large">Thanks, PyChimera worked great!</div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large">@Eric<br></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></div><div class="gmail_default" style="font-size:large">best,</div><div class="gmail_default" style="font-size:large">Thomas</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr"><br></div></div>--<span class="m_777493216267559648m_-586845445362126228Apple-converted-space"> </span><br><div dir="ltr" class="m_777493216267559648m_-586845445362126228gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><p align="LEFT" style="margin-bottom:0cm"><span><span style="font-family:arial,helvetica,sans-serif"><font size="2">======================================================================</font></span></span></p><p align="LEFT" style="margin-bottom:0cm"><span><span style="font-family:arial,helvetica,sans-serif"><font size="2">Dr Thomas Evangelidis</font></span></span></p><p align="LEFT" style="margin-bottom:0cm"><span style="font-family:arial,helvetica,sans-serif;font-size:small">Research Scientist</span></p><p align="LEFT" style="margin-bottom:0cm"><span style="font-family:arial,helvetica,sans-serif;font-size:small"><a href="https://www.uochb.cz/web/structure/31.html?lang=en" rel="noreferrer noreferrer" target="_blank">IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences</a></span></p><font size="2"><div><font face="arial, helvetica, sans-serif"><div>Prague, Czech Republic</div><div> <span class="m_777493216267559648m_-586845445362126228Apple-converted-space"> </span>& </div></font></div><font face="arial, helvetica, sans-serif"><a href="https://www.ceitec.eu/" rel="noreferrer noreferrer" target="_blank">CEITEC - Central European Institute of Technology</a></font><br><font face="arial, helvetica, sans-serif">Brno, Czech Republic </font></font></div><div><font size="2"><font face="arial, helvetica, sans-serif"><br></font></font></div><div dir="ltr"><p align="LEFT" style="margin-bottom:0cm"><span><span style="font-family:arial,helvetica,sans-serif"><font size="2">email: </font></span></span><a href="mailto:tevang3@gmail.com" style="font-size:small;font-family:arial,helvetica,sans-serif" rel="noreferrer noreferrer" target="_blank">tevang3@gmail.com</a></p><p align="LEFT" style="margin-bottom:0cm"><span><span style="font-family:arial,helvetica,sans-serif"><font size="2">website:<span class="m_777493216267559648m_-586845445362126228Apple-converted-space"> </span><a href="https://sites.google.com/site/thomasevangelidishomepage/" rel="noreferrer noreferrer" target="_blank">https://sites.google.com/site/thomasevangelidishomepage/</a></font></span></span></p><span><br><br></span><div style="margin-bottom:0cm"><br class="m_777493216267559648m_-586845445362126228webkit-block-placeholder"></div></div></div></div></div></div></div></div></div></div></div></div><span 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;float:none;display:inline!important">_______________________________________________</span><br 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"><span 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;float:none;display:inline!important">Chimera-users mailing list:<span class="m_777493216267559648m_-586845445362126228Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" 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" rel="noreferrer noreferrer" target="_blank">Chimera-users@cgl.ucsf.edu</a><br 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"><span 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;float:none;display:inline!important">Manage subscription:<span class="m_777493216267559648m_-586845445362126228Apple-converted-space"> </span></span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" 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" rel="noreferrer noreferrer" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div><br></div></div></blockquote></div>
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