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Hi Charles,<br>
<br>
you are right: setting very low esd is not good, and setting it to
zero will disable the restraint completely.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 6/17/15 07:45, CPMAS Chen wrote:<br>
</div>
<blockquote
cite="mid:CAAU4GKbP1wFSyaiPZix2W6qJGJD6E33RcKnTiaWvVUUSeja6rA@mail.gmail.com"
type="cite">
<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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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>
</div>
</div>
</div>
<br>
</div>
</div>
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<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div class="gmail_signature">
<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>
</div>
</div>
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