<div dir="ltr">Thanks, Oleg.<div><br></div><div>1 or 2 degrees work. Actually, it is in the FAQ of phenix refinement. Here is the page in case anyone else like to do similar restraint.</div><div><br></div><div><a href="http://www.phenix-online.org/documentation/faqs/refine.html#targets-and-restraints">http://www.phenix-online.org/documentation/faqs/refine.html#targets-and-restraints</a><br></div><div><br></div><div><p style="color:rgb(0,0,0);font-family:Verdana,Helvetica,Arial,sans-serif;font-size:14px"><strong>I want my ligand geometry to be absolutely perfect with no deviation from the target value(s). Can I just set the sigmas to zero or an extremely low value?</strong></p><p style="color:rgb(0,0,0);font-family:Verdana,Helvetica,Arial,sans-serif;font-size:14px">You cannot set the sigma to zero because the weight on the restraints is equal to 1/sigma^2. A very low value will not crash, but it will almost certainly confuse the minimizer and result in a sub-optimal structure, because those restraints will dominate the target and gradients, forcing the minimizer to take inappropriately large steps.</p><p style="color:rgb(0,0,0);font-family:Verdana,Helvetica,Arial,sans-serif;font-size:14px"><br></p><p style="color:rgb(0,0,0);font-family:Verdana,Helvetica,Arial,sans-serif;font-size:14px">Charles</p></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jun 16, 2015 at 1:12 PM, Oleg Sobolev <span dir="ltr"><<a href="mailto:osobolev@lbl.gov" target="_blank">osobolev@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear Charles,<div><br></div><div>First of all, I would recommend to change <span style="font-size:12.8000001907349px">value_angle_esd from 0 to something like 1 or 2 degrees if you want it to be tight.</span></div><div>Next, make sure that your restraint is actually applied by inspecting the resulting .geo file and locating respective "dihedral" restraint.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On Tue, Jun 16, 2015 at 6:28 AM, CPMAS Chen <span dir="ltr"><<a href="mailto:cpmasmit@gmail.com" target="_blank">cpmasmit@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr"><div>Hi, All Phenix Users,</div><div><br></div><div>I am fitting 2-bromoethanol to the density map. I want to keep its gauche conformation, so I edited the cif for this ligand to restrain the torsion angle,</div><div><br></div><div>loop_</div><div>_chem_comp_tor.comp_id</div><div>_<a href="http://chem_comp_tor.id" target="_blank">chem_comp_tor.id</a></div><div>_chem_comp_tor.atom_id_1</div><div>_chem_comp_tor.atom_id_2</div><div>_chem_comp_tor.atom_id_3</div><div>_chem_comp_tor.atom_id_4</div><div>_chem_comp_tor.value_angle</div><div>_chem_comp_tor.value_angle_esd</div><div>_chem_comp_tor.period</div><div>BRJ Var_01 BR1 CB CB1 OB1 -60.00 0.0 3</div><div><br></div><div><br></div><div>But, after refinement, this angle can be close to 90 or even 120. Even worse is that the fitting at such angles are not better than at -60/60 angle.</div><div><br></div><div>How could I fix/restrain the angle during refinement?</div><div><br></div><div>Thanks!</div><div><br></div><div>Charles</div><div><br></div>***************************************************<br><div class="gmail_extra"><div><p>Charles Chen</p><p>Research Associate</p><p>University of Pittsburgh School of Medicine</p><p>Department of Anesthesiology</p><p>******************************************************</p><p></p></div>
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<p></p><p>***************************************************</p><p>Charles Chen</p><p>Research Associate</p><p>University of Pittsburgh School of Medicine</p><p>Department of Anesthesiology</p><p>******************************************************</p><p></p></div>
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