<div dir="ltr">Hi Valerie,<div><br></div><div>The functionality you are mentioning is obsolete for some time now. Therefore I would recommend updating to recent Phenix release or nightly, especially for real-space refine.</div><div><br></div><div>If you already have restraints for your ligand, they should be sufficient. If not, you can make them using eLBOW.</div><div><br></div><div>There is a video tutorial about how to find and change parameters in phenix.refine (real-space is very similar): <a href="https://www.youtube.com/watch?v=qB8W_6yuw5k&t=2s">https://www.youtube.com/watch?v=qB8W_6yuw5k&t=2s</a></div><div><br></div><div>Generally, in Phil notation '*' marks selected options.</div><div><br></div><div>Please get back to us if you have more questions.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Mar 27, 2020 at 5:42 AM Valerie Biou <<a href="mailto:valerie.biou@ibpc.fr">valerie.biou@ibpc.fr</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;">Hello<div><br></div><div>I am trying to impose restraints on my lipid ligand during real space refinement. I found the command</div><div><br></div><div><div><font face="Courier">refinement.geometry_restraints.edits.scale_restraints {</font></div><div><font face="Courier"> atom_selection = "resname LLP"</font></div><div><font face="Courier"> scale = 2.5</font></div><div><font face="Courier"> apply_to = *bond *angle dihedral chirality</font></div><div><br></div><div>I have 2 questions</div><div><span style="white-space:pre-wrap"> </span>1) can those lines be called from the GUI and where? if not, how can I insert them in a previous command file?</div><div><span style="white-space:pre-wrap"> </span>2) what do the * stand for? is it to activate or cancel the selection of an item?</div><div>sorry if those questions have been asked before, I can't find the command to browse the bb archive.</div><div><br></div><div>All the best,</div><div><br></div><div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div>Valérie </div></div>
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