<div dir="ltr"><div dir="ltr">Hi Błażej,<div><br></div></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">I have a ligand that I built into the polder map and I want to tell the <br>
software "do not change the positions in space of these atoms". How can <br>
I do that?<br></blockquote><div>You can use reference_coordinate_restraints scope which is intended to keep the model in place. Note that they are restraints, so some deviation can still occur. Check available parameters here: <a href="https://phenix-online.org/documentation/reference/refinement.html">https://phenix-online.org/documentation/reference/refinement.html</a> , but you will need</div><div>enabled = True</div><div>selection = "your atom selection"</div><div>check <a href="https://phenix-online.org/documentation/reference/atom_selections.html">https://phenix-online.org/documentation/reference/atom_selections.html</a> for selection syntax.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Also, side question: why there are three different(?) versions of <br>
command line phenix.refine for every phenix installation? What is the <br>
difference between them?<br>
<br>
REMARK 6 I followed the online guide for "Refinement at high resolution" <br>
on my 1,2~1,3A structure and the results were surprisingly nice, I'd say <br>
potentially even better than usually used parameters in GUI (5 cycles <br>
both).<br>
<br>
Kind regards,<br>
Blazej<br>
<br>
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